gebhart/patrepeval huggingface dataset:
Coupled Geomechanical and Reservoir Modeling on Parallel Computers (2003)

Abstract In coupled geomechanics and reservoir modeling, the finite element discretization of the force balance equation leads to very large linear systems, whose solution is both time and memory consuming. ICCG (Incomplete Cholesky Factorized Conjugate Gradient) is a popular technique for solving for displacements, but the technique is limited to about 60,000 nodal points on desktop machines. Most large 3D field scale problems will have to be run on parallel machines. In this paper, we present a reduced-communication, super coarsening multigrid method that can be combined with other domain decomposition-based preconditioner to achieve faster convergence with high parallel scalability. A preliminary test case of 1.5 million grid blocks with up to 59 processors shows a parallel efficiency of above 90%.
Nuclear Hormone Receptors, Metabolism, and Aging: What Goes Around Comes Around (2004)

Previous studies have linked the mysterious and inevitable process of aging to essential processes such as metabolism, maturation, and fecundity. Each of these processes is controlled to a large extent by nuclear hormone receptors (NHRs). NHRs also play important roles in the control of periodical processes, the most recently implicated being circadian rhythm. This Review stresses the mounting evidence for tight relationships between each of these NHR-regulated processes and the processes of aging.
The power of procrastination (2011)

Malware continues to remain one of the most important security problems on the Internet today. Whenever an anti-malware solution becomes popular, malware authors typically react promptly and modify their programs to evade defense mechanisms. For example, recently, malware authors have increasingly started to create malicious code that can evade dynamic analysis.
Cross‐Coupling of Aryl Grignard Reagents with Aryl Iodides and Bromides through S<sub>RN</sub>1 Pathway (2011)

Game, SET, and match: Aryl Grignard reagents undergo coupling with aryl halides when toluene is used as a solvent in combination with a small amount of tetrahydrofuran (see scheme). The reaction proceeds through an SRN1 mechanism, and does not require any transition metal catalysts. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Selective expression of an acetylcholine receptor–lacZ transgene in synaptic nuclei of adult muscle fibers (1991)

Acetylcholine receptors (AChRs) are highly concentrated in the postsynaptic membrane at the neuromuscular junction. To investigate mechanisms that lead to the formation or maintenance of this synaptic specialization, we generated transgenic mice in which regulatory elements from the AChR alpha or epsilon-subunit genes are linked to a gene for a reporter protein that is targeted to the nucleus (nlacZ). Both transgenes were selectively expressed and developmentally regulated in muscle; nuclei in both extrafusal (ordinary) and intrafusal (spindle) muscle fibers were labeled. Within individual muscle fibers from epsilon-nlacZ mice, nuclei near synaptic sites were nlacZ-positive, whereas extrasynaptic nuclei were nlacZ-negative. In contrast, nlacZ was expressed in both synaptic and extrasynaptic nuclei when under the control of regulatory elements from the AChR alpha-subunit gene; however, synaptic nuclei were somewhat more intensely stained than extrasynaptic nuclei in a minority of muscle fibers from these mice. Together, our results provide direct evidence for molecular differences between synaptic and extrasynaptic nuclei within a single cytoplasm, and suggest that the motor nerve regulates synapse formation by selectively affecting transcription in synaptic nuclei.
Study of the nematode putative GABA type‐A receptor subunits: evidence for modulation by ivermectin (2002)

Two alleles of the HG1 gene, which encodes a putative GABA receptor alpha/gamma subunit, were isolated from Haemonchus contortus. These two alleles were shown previously to be associated with ivermectin susceptibility (HG1A) and resistance (HG1E), respectively. Sequence analysis indicates that they differ in four amino acids. To explore the functional properties of the two alleles, a full-length cDNA encoding the beta subunit, a key functional component of the GABA receptor, was isolated from Caenorhabditis elegans (gab-1, corresponding to the GenBank locus ZC482.1) and coexpressed in Xenopus oocytes with the HG1 alleles. When gab-1 was coexpressed with either the HG1A allele or the HG1E allele in Xenopus oocytes, gamma-aminobutyric acid (GABA)-responsive channels with different sensitivity to the agonist were formed. The effects of ivermectin on the hetero-oligomeric receptors were determined. Application of ivermectin alone had no effect on the receptors. However, when coapplied with 10 micro m GABA, ivermectin potentiated the GABA-evoked current of the GAB-1/HG1A receptor, but attenuated the GABA response of the GAB-1/HG1E receptor. We demonstrated that the coexpressed HG1 and GAB-1 receptors are GABA-responsive, and provide evidence for the possible involvement of GABA receptors in the mechanism of ivermectin resistance.
Preparation and Properties of Double-Chain Surfactants Bearing Two Sulfonate Groups (1991)

Novel surfactants with two long-chain alkyl groups and two sulfonate groups were synthesized by reactions of oligo (ethyleneglycol) diglycidyl ethers or bis (2, 3-epoxypropyl) ether with long-chain fatty alcohols, followed by reaction with propanesultone. The double-chain compounds showed good water solubility, excellent micelle forming properties and the higher ability to lower surface tension than general sulfonate type of single-chain surfactants. The effects of structural factors of these surfactants on surface active properties are discussed. These compounds were soluble and showed surface active properties in hard water above 5555 ppm of total hardness as CaCO3. They had better lime-soap dispersing ability than sodium 1-dodecene sulfate or sodium 1-dodecane sulfonate.
Epidemiology and One-Year Outcomes in Patients With Chronic Heart Failure and Preserved, Mid-Range and Reduced Ejection Fraction: An Analysis of The ESC Heart Failure Long-Term Registry (2017)

Heart failure patients stratified according to different categories of LVEF represent diverse phenotypes of demography, clinical presentation, aetiology and outcomes at 1 year. Differences in predictors for mortality might improve risk stratification and management goals.
Initiation and Growth of Transverse Cracks and Edge Delamination in Composite Laminates Part 1. An Energy Method (1980)

This paper is concerned with the basic fracture mechanisms involved in matrix-dominated failures in fibrous composite laminates, Specifically, interlaminar fracture in the form of free-edge ply delamination and intra- laminar fracture in the form of multiple transverse cracks are investigated. In each case, a theory is formulated based on the classical linear fracture mechanics concept of strain energy release rate as a criterion for crack growth. A finite element technique incorporating the virtual crack-closure procedure is developed to generate numerical results. Simultaneously, an experimental study is conducted using a series of graphite epoxy laminates in the form of (±25/90 n ) s , n = 1,2,3. Part 1 of this paper presents the development of the method from the conceptual, physical and numerical considerations, while Part 2 provides for a comparison between the analyti cal and experimental results.
Agonists of proteinase‐activated receptor 1 induce plasma extravasation by a neurogenic mechanism (2001)

Thrombin, generated in the circulation during injury, cleaves proteinase-activated receptor 1 (PAR1) to stimulate plasma extravasation and granulocyte infiltration. However, the mechanism of thrombin-induced inflammation in intact tissues is unknown. We hypothesized that thrombin cleaves PAR1 on sensory nerves to release substance P (SP), which interacts with the neurokinin 1 receptor (NK1R) on endothelial cells to cause plasma extravasation. PAR1 was detected in small diameter neurons known to contain SP in rat dorsal root ganglia by immunohistochemistry and in situ hybridization. Thrombin and the PAR1 agonist TFLLR-NH(2) (TF-NH(2)) increased [Ca(2+)](i) >50% of cultured neurons (EC(50)s 24 mu ml(-1) and 1.9 microM, respectively), assessed using Fura-2 AM. The PAR1 agonist completely desensitized responses to thrombin, indicating that thrombin stimulates neurons through PAR1. Injection of TF-NH(2) into the rat paw stimulated a marked and sustained oedema. An NK1R antagonist and ablation of sensory nerves with capsaicin inhibited oedema by 44% at 1 h and completely by 5 h. In wild-type but not PAR1(-/-) mice, TF-NH(2) stimulated Evans blue extravasation in the bladder, oesophagus, stomach, intestine and pancreas by 2 - 8 fold. Extravasation in the bladder, oesophagus and stomach was abolished by an NK1R antagonist. Thus, thrombin cleaves PAR1 on primary spinal afferent neurons to release SP, which activates the NK1R on endothelial cells to stimulate gap formation, extravasation of plasma proteins, and oedema. In intact tissues, neurogenic mechanisms are predominantly responsible for PAR1-induced oedema.
Method to generate highly stable D-amino acid analogs of bioactive helical peptides using a mirror image of the entire PDB (2018)

Biologics are a rapidly growing class of therapeutics with many advantages over traditional small molecule drugs. A major obstacle to their development is that proteins and peptides are easily destroyed by proteases and, thus, typically have prohibitively short half-lives in human gut, plasma, and cells. One of the most effective ways to prevent degradation is to engineer analogs from dextrorotary (D)-amino acids, with up to 10<sup>5</sup>-fold improvements in potency reported. We here propose a general peptide-engineering platform that overcomes limitations of previous methods. By creating a mirror image of every structure in the Protein Data Bank (PDB), we generate a database of ∼2.8 million D-peptides. To obtain a D-analog of a given peptide, we search the (D)-PDB for similar configurations of its critical-"hotspot"-residues. As a proof of concept, we apply our method to two peptides that are Food and Drug Administration approved as therapeutics for diabetes and osteoporosis, respectively. We obtain D-analogs that activate the GLP1 and PTH1 receptors with the same efficacy as their natural counterparts and show greatly increased half-life.
Revisiting the Arcade Learning Environment: Evaluation Protocols and Open Problems for General Agents (2018)

The Arcade Learning Environment (ALE) is an evaluation platform that poses the challenge of building AI agents with general competency across dozens of Atari 2600 games. It supports a variety of different problem settings and it has been receiving increasing attention from the scientific community, leading to some high-profile success stories such as the much publicized Deep Q-Networks (DQN). In this article we take a big picture look at how the ALE is being used by the research community. We show how diverse the evaluation methodologies in the ALE have become with time, and highlight some key concerns when evaluating agents in the ALE. We use this discussion to present some methodological best practices and provide new benchmark results using these best practices. To further the progress in the field, we introduce a new version of the ALE that supports multiple game modes and provides a form of stochasticity we call sticky actions. We conclude this big picture look by revisiting challenges posed when the ALE was introduced, summarizing the state-of-the-art in various problems and highlighting problems that remain open.
The Web as a Knowledge-Base for Answering Complex Questions (2018)

Alon Talmor, Jonathan Berant. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers). 2018.
Integrating evolutionary computation and sociotechnical simulation for flushing contaminated water distribution systems (2012)

A water distribution contamination event occurs when a chemical or pathogen is introduced to a pipe network dedicated to the delivery of potable water. During an event, complex interactions among consumers, utility operators, decision makers, and the pipe network can influence the number of exposed consumers, as human actors adapt their water use activities in response to warnings or exposure. An agent-based model is developed to model the water contamination event and provides insight and understanding about the effect of interactions on public health, such as the number of exposed consumers. Utility operators can protect consumers using a wide range of mitigation responses, and opening a set of hydrants is typically an effective strategy for flushing contaminated water before it reaches consumers. The ABM framework is coupled with an Evolutionary Strategy (ES)-based search to identify an optimal strategy for manipulating hydrants to minimize the number of exposed consumers. The application of the simulation-optimization framework is demonstrated for a virtual mid-sized municipality, Mesopolis.
Generalized MQDT representation (2011)

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Research of Text Classification Based on Improved TF-IDF Algorithm (2018)

In recent years, with the rapid development of Internet Technology, text data is growing rapidly every day. Users need to filter out the information they need from a large amount of text. Therefore, automatic text classification technology can help users find information. In order to address problems, such as ignoring contextual semantic links and different vocabulary importance in traditional text classification techniques, this paper presents a vector representation of feature words based on the deep learning tool Word2vec, and the weight of the feature words is calculated by the improved TF-IDF algorithm. By multiplying the weight of the word and the word vector, the vector representation of the word is realized. Finally, each text is represented by accumulating all the word vectors. Thus, text classification is carried out.
Feature Based Calibration of a Network of Kinect Sensors (2018)

The availability of affordable depth sensors in conjunction with common RGB cameras, such as the Microsoft Kinect, can provide robots with a complete and instantaneous representation of the current surrounding environment. However, in the problem of calibrating multiple camera systems, traditional methods bear some drawbacks, such as requiring human intervention. In this thesis, we propose an automatic and reliable calibration framework that can easily estimate the extrinsic parameters of a Kinect sensor network. Our framework includes feature extraction, Random Sample Consensus and camera pose estimation from high accuracy correspondences. We also implement a robustness analysis of position estimation algorithms. The result shows that our system could provide precise data under certain amount noise.\nKeywords\nKinect, Multiple Camera Calibration, Feature Points Extraction, Correspondence, RANSAC
A physiological ear model for specific loudness and masking (2002)

In a variety of applications the processing of arbitrary sound signals requires models for loudness perception or auditory masking with improved accuracy, compared to psychoacoustical models known so far. In general, perceptual models can only reach higher accuracy due to special assumptions concerning signal characteristics. The presented human ear model overcomes these restrictions because of the physiological modelling approach of sound processing in the ear, which is valid, independent from the signal characteristics. The results shown indicate that psychoacoustic observations in terms of loudness and masking are closely met. Additionally, the basilar membrane motion in the inner ear is obtained as intermediate quantity in accordance with physiological measurements, supporting the hypotheses about outer hair cell operation in the inner ear.
Perineural Dexmedetomidine Added to Ropivacaine for Sciatic Nerve Block in Rats Prolongs the Duration of Analgesia by Blocking the Hyperpolarization-activated Cation Current (2011)

Dexmedetomidine added to ropivacaine caused approximately a 75% increase in the duration of analgesia, which was reversed by pretreatment with an I(h) current enhancer. The analgesic effect of dexmedetomidine was not reversed by an α(2)-adrenoceptor antagonist.
Quantitative Method for the Profiling of the Endocannabinoid Metabolome by LC-Atmospheric Pressure Chemical Ionization-MS (2007)

The endocannabinoid system's biological significance continues to grow as novel endocannabinoid metabolites are discovered. Accordingly, a myopic view of the system that focuses solely on one or two endocannabinoids, such as anandamide or 2-arachidonoyl glycerol, is insufficient to describe the biological responses to perturbations of the system. Rather, the endocannabinoid metabolome as a whole must be analyzed. The work described here is based on liquid chromatography coupled with atmospheric pressure chemical ionization mass spectrometry. This method has been validated to quantify, in a single chromatographic run, the levels of 15 known or suspected metabolites of the endocannabinoid system in the rat brain and is applicable to other biological matrixes. We have obtained an endocannabinoid profile specifically for the frontal cortex of the rat brain and have determined anandamide level differences following the administration of the fatty acid amide hydrolase inhibitor AM374.
High-numerical-aperture I-line stepper (1990)

I-line stepper technology is described which features a new generation high NA lens and an improved implementation of a phase grating alignment system. Combining the high NA lens with high contrast resist processing enables O.5um processing to be supported with good process latitude and CD control without adverse effects due to lens heating. Alignment technology compatible with advanced processing is described. Overlay data taken from several steppers shows less than lOOnm capability which is sufficient to support O.5um design rules. Further advancements in Iline processing technology to O.41um are described which allows this technology to be used in developing advanced products.
Combining multiple microarrays in the presence of controlling variables (2006)

A set of programs written in R will be electronically sent upon request.
Role of Short Tandem Repeat DNA in Forensic Casework in the UK—Past, Present, and Future Perspectives (2002)

The analysis of short tandem repeat (STR) DNA sequences is of fundamental importance to forensic science because they have become the recognized standard in constructing national public databases. Consequently, considerable effort has been expended in developing multiplexed (one tube) reactions that analyze several loci in combination. The implementation of STRs in casework cannot take place without a full understanding of the systems used. The purpose of validation is to characterize multiplexes when one is challenged with forensic samples. For example, mixtures are often encountered that may be particularly difficult to interpret against a background of allelic artifacts. By increasing the number of PCR amplification cycles, it is possible to dramatically boost the sensitivity of the system so that just a handful of cells may be successfully analyzed. However, interpretation is much more complex because the origin of DNA profiles may be less certain and complicated by issues such as contamination, the potential for innocent transfer and a predominance of mixtures. This review provides a brief historical background of the development of STRs in forensic casework that culminated in the creation of national DNA databases. The development of guidelines to interpret complex DNA profiles, such as mixtures, is outlined. Finally, the recent innovation of low copy number DNA profiling is explained along with the special considerations needed to report in court.
Opsonophagocytic and Bactericidal Activity Mediated by Purified IgG Subclass Antibodies After Vaccination with the Norwegian Group B Meningococcal Vaccine (1998)

To study how the different immunoglobulin (Ig)G subclass antibodies may confer protection against systemic meningococcal disease, we isolated IgG1, IgG2 and IgG3 antibodies from plasma from vaccinees immunized with the Norwegian meningococcal outer membrane vesicle vaccine. Four IgG1, one IgG2 and four IgG3 preparations were purified. The IgG2 and IgG3 subclass preparations were free from contaminating subclasses, whereas the IgG1 preparations contained from 0 to 14% of IgG2 and/or IgG3. Immunoblotting against whole-cell meningococcal antigens showed broad specificities of the various preparations, both within and between subclasses. These subclass preparations were tested for opsonophagocytic and bactericidal activity. As targets we used two different variants of the meningococcal vaccine strain, with low (44/76-SL) and high (44/76-1) expression of the outer membrane protein Opc. Using polymorphonuclear leucocytes as effector cells in the presence of human complement, all three IgG subclass preparations revealed high, and similar, opsonophagocytic activities against 44/76-SL, whereas against 44/76-1 the IgG2 preparation showed a reduced activity and most IgG3 preparations were slightly more active than the IgG1 preparations. Regarding bactericidal activity, all the three subclasses were highly active against 44/76-SL. Against 44/76-1 the bactericidal activities were somewhat more varied: all IgG1 and three IgG3 preparations exhibited higher activities than against 44/76-SL. Due to the low concentration in the IgG2 preparations, only a weak activity was seen against 44/76-1. One IgG3 preparation that was highly opsonophagocytic revealed no bactericidal activity against either of the two bacterial variants examined. In conclusion, we have shown that the IgG subclass effector functions differ from person to person, but that antibodies of IgG1, IgG2 and IgG3 subclasses, judged by their behaviour in the functional tests, may all contribute to protection against meningococcal disease.
Pyogenic Granuloma Stimulates Angiogenesis in the Chick Embryo Chorioallantoic Membrane (1996)

Ten samples of pyogenic granuloma and 10 of normal skin from age- and sex-matched controls were grafted onto the chick embryo chorioallantoic membrane (CAM) to investigate their possible angiogenic activity. The angiogenic response in pathological and control implants was assessed on histologic sections by a planimetric point-count method 4 days after grafting. The CAM mast cells were also quantified. The vascular counts in the area underlying the pyogenic granuloma were four times higher than those of normal skin. A higher number of mucosa-like mast cells was detected in the intermediate mesenchyme of the CAM in pathological samples in comparison to controls. Pyogenic granuloma may promote angiogenesis leading to release of several angiogenic factors. The role played in angiogenic response by the inflammatory cells, mainly mast cells, forming the perilesional infiltrate was supported by this study.