gebhart/patrepeval huggingface dataset:
THE INHIBITORY EFFECT OF GALLAMINE ON MUSCARINIC RECEPTORS (1976)

1 The inhibitory effect of gallamine (1.1 muM-1.1 mM) on negative inotropic responses to acetylcholine (ACh) or carbachol (CCh) was investigated in isolated electrically stimulated atria of the guinea-pig. Gallamine caused parallel rightward shifts of the dose-response curves to the agonists, with no depression of the maximal response. 2 Gallamine (0.11 - 1.1 mM) produced a greater degree of antagnism towards CCh than towards ACh. With either agonist, the degree of antagonism produced by gallamine in high concentrations was less than that expected for a competitive antagonist.. 3 Similar findings were made when either negative inotropic or chronotropic responses were recorded in spontaneously beating guinea-pig atria. The inhibitory effect of gallamine against the negative inotropic response to cholinomimetics in electrically stimulated atria was not altered either in the presence of propranol (17 muM) or in atria obtained from guinea-pigs pretreated with diisopropylphosphorofluoridate (DEP) 12.5 mumol/kg, in divided doses over 3 days). 4 When ACh was used as the agonist, combination of gallamine with atropine (0.05-0.4 muM) produced dose-ratios which were less than expected for combination of two competitive antagonists. The same phenomenon was observed in atria obtained from guinea-pigs pretreated with DFP. 5 It is suggested that the antagonism produced by gallamine is a type of non-competitive inhibition, which has been termed "metaffinoid antagonism". An antagonist of this type allosterically alters the affinity of the agonist for its binding site, rather than changing the effectiveness of the agonist-receptor interaction.
Experience Transfer for the Configuration Tuning in Large-Scale Computing Systems (2010)

This paper proposes a new strategy, the experience transfer, to facilitate the management of large-scale computing systems. It deals with the utilization of management experiences in one system (or previous systems) to benefit the same management task in other systems (or current systems). We use the system configuration tuning as a case application to demonstrate all procedures involved in the experience transfer including the experience representation, experience extraction, and experience embedding. The dependencies between system configuration parameters are treated as transferable experiences in the configuration tuning for two reasons: 1) because such knowledge is helpful to the efficiency of the optimal configuration search, and 2) because the parameter dependencies are typically unchanged between two similar systems. We use the Bayesian network to model configuration dependencies and present a configuration tuning algorithm based on the Bayesian network construction and sampling. As a result, after the configuration tuning is completed in the original system, we can obtain a Bayesian network as the by-product which records the dependencies between system configuration parameters. Such a network is then embedded into the tuning process in other similar systems as transferred experiences to improve the configuration search efficiency. Experimental results in a web-based system show that with the help of transferred experiences, the configuration tuning process can be significantly accelerated.
Laser Acupuncture for Treating Musculoskeletal Pain: A Systematic Review with Meta-analysis (2014)

Laser acupuncture has been studied extensively over several decades to establish evidence-based clinical practice. This systematic review aims to evaluate the effects of laser acupuncture on pain and functional outcomes when it is used to treat musculoskeletal disorders and to update existing evidence with data from recent randomized controlled trials (RCTs). A computer-based literature search of the databases MEDLINE, AMED, EMBASE, CINAHL, SPORTSDiscus, Cochrane Library, PubMed, Current Contents Connect, Web of Science, and SCOPUS was used to identify RCTs comparing between laser acupuncture and control interventions. A meta-analysis was performed by calculating the standardized mean differences and 95% confidence intervals, to evaluate the effect of laser acupuncture on pain and functional outcomes. Included studies were assessed in terms of their methodological quality and appropriateness of laser parameters. Forty-nine RCTs met the inclusion criteria. Two-thirds (31/49) of these studies reported positive effects, were of high methodological quality, and reported the dosage adequately. Negative or inconclusive studies commonly failed to demonstrate these features. For all diagnostic subgroups, positive effects for both pain and functional outcomes were more consistently seen at long-term follow-up rather than immediately after treatment. Moderate-quality evidence supports the effectiveness of laser acupuncture in managing musculoskeletal pain when applied in an appropriate treatment dosage; however, the positive effects are seen only at long-term follow-up and not immediately after the cessation of treatment.
Soluble 3′,6-Substituted Indirubins with Enhanced Selectivity toward Glycogen Synthase Kinase -3 Alter Circadian Period (2008)

Glycogen synthase kinase -3 (GSK-3) is a key enzyme involved in numerous physiological events and in major diseases, such as Alzheimer's disease, diabetes, and cardiac hypertrophy. Indirubins are bis-indoles that can be generated from various natural sources or chemically synthesized. While rather potent and selective as GSK-3 inhibitors, most indirubins exhibit low water solubility. To address the issue of solubility, we have designed novel analogues of 6-bromo-indirubin-3'-oxime with increased hydrophilicity based on the GSK-3/indirubins cocrystal structures. The new derivatives with an extended amino side chain attached at position 3' showed potent GSK-3 inhibitory activity, enhanced selectivity, and dramatically increased water solubility. Furthermore, some of them displayed little or no cytotoxicity. The new indirubins inhibit GSK-3 in a cellular reporter model. They alter the circadian period measured in rhythmically expressing cell cultures, suggesting that they might constitute tools to investigate circadian rhythm regulation.
Effects of epinephrine and hypotaurine on in-vitro fertilization in the golden hamster (1982)

Using an experimental design in which the addition of hypotaurine or epinephrine was staggered through time, evidence was found that suggests these two compounds are working independently and sequentially to stimulate the fertilizing capacity of hamster spermatozoa in vitro. Prior exposure of spermatozoa to hypotaurine is a prerequisite for the action of epinephrine in causing activation and penetration of hamster ova. A definite role for hypotaurine in inducing capacitation of hamster spermatozoa is also demonstrated. The alpha-adrenergic antagonist, phentolamine, was more effective in blocking fertilization of hamster ova in vitro than was propranolol, a beta-antagonist. This indicates tha catecholamines may be working by way of alpha-adrenergic receptors in causing capacitation of hamster spermatozoa. The failure to block fertilization with phentolamine after epinephrine has exerted its effect implies that epinephrine acts in a hormone-like fashion.
Extraction of regulatory gene/protein networks from Medline (2005)

The revised GENIA corpus, the POS tagger, the extraction rules and the full sets of extracted relations are available from http://www.bork.embl.de/Docu/STRING-IE
A Subregion of Reelin Suppresses Lipoprotein-Induced Cholesterol Accumulation in Macrophages (2015)

Activation of apolipoprotein E receptor-2 (apoER2) and very low density lipoprotein receptor (VLDLR) inhibits foam cell formation. Reelin is a ligand of these receptors. Here we generated two reelin subregions containing the receptor binding domain with or without its C-terminal region (R5-6C and R5-6, respectively) and studied the impact of these peptides on macrophage cholesterol metabolism. We found that both R5-6C and R5-6 can be secreted by cells. Purified R5-6 protein can bind apoER2 and VLDLR. Overexpression of apoER2 in macrophages increased the amount of R5-6 bound to the cell surface. Treatment of macrophages with 0.2 μg/ml R5-6 elevated ATP binding cassette A1 (ABCA1) protein level by ~72% and apoAI-mediated cholesterol efflux by ~39%. In addition, the medium harvested from cells overexpressing R5-6 or R5-6C (R5-6- and R5-6C-conditioned media, respectively) also up-regulated ABCA1 protein expression, which was associated with accelerated cholesterol efflux and enhanced phosphorylation of phosphatidylinositol 3 kinase (PI3K) and specificity protein-1 (Sp1) in macrophages. The increased ABCA1 expression and cholesterol efflux by R5-6- and R5-6C-conditioned media were diminished by Sp1 or PI3K inhibitors mithramycin A and LY294002. Further, the cholesterol accumulation induced by apoB-containing, apoE-free lipoproteins was significantly less in macrophages incubated with R5-6- or R5-6C-conditioned medium than in those incubated with control conditioned medium. Knockdown of apoER2 or VLDLR attenuated the inhibitory role of R5-6-conditioned medium against lipoprotein-induced cholesterol accumulation. These results suggest that the reelin subregion R5-6 can serve as a tool for studying the role of apoER2 and VLDLR in atherogenesis.
Reverse transcription multiplex PCR for differentiation between polio- and enteroviruses from clinical and environmental samples (1995)

For the rapid detection of polioviruses and their differentiation from nonpoliovirus enteroviruses, we developed a protocol in which clinical or environmental specimens are first inoculated onto cell cultures in tubes. After overnight incubation, the cultures are subjected to reverse transcription multiplex PCR with a primer pair which detects all enteroviruses (T. Hyypiä, P. Auvinen, and M. Maaronen, J. Gen. Virol. 70:3261-3268 1989) and two newly designed primer pairs specific for all 36 poliovirus strains tested. The PCR products can unequivocally be identified by their lengths in agarose gels, whereas the genetic heterogeneity of the poliovirus strains precludes identification by back-hybridization with internal probes. The proposed protocol is highly insensitive to the inhibitory effects of substances in the sample (stool, sewage). It allows for the detection of polioviruses and for polioviruses to be distinguished from nonpoliovirus enteroviruses within 24 h, and it allows for the concomitant isolation of a viable strain suitable for further typing.
Diode-pumped cw bulk Er:Yb:glass laser (1991)

ontinuous-wave laser operation of bulk Er:Yb:phosphate glass pumped at 980 nm by an InGaAs index-guided diode laser has been achieved for the first time to our knowledge, with 2 mW of output power obtained at 1.54 microm. To optimize pumping conditions and to investigate the effects of pump wavelength, the Er(3+):Yb(3+) glass disk has also been pumped by a Ti:Al(2)O(3) laser at 960 and 980 nm, and we obtained high output power (70 mW) and the highest slope efficiency (21% for 980-nm pumping) reported to date for a bulk Er:glass laser.
Microstrip antennas covered with dielectric materials (2003)

A dielectric cover is usually added on top of a microstrip antenna to protect the antenna from environmental damage. The effects of a dielectric cover on the characteristics of circular and annular ring patch antennas are investigated. The theoretical results are derived from the conventional Hankel transform analysis. Some experimental data are also obtained to verify the theory. In general, it is found that when the thickness of the cover is increased, the resonant frequency decreases monotonically. It is also observed that the half-power bandwidth only changes slightly with the superstrate thickness.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Illumination for computer generated pictures (1975)

The quality of computer generated images of three-dimensional scenes depends on the shading technique used to paint the objects on the cathode-ray tube screen. The shading algorithm itself depends in part on the method for modeling the object, which also determines the hidden surface algorithm. The various methods of object modeling, shading, and hidden surface removal are thus strongly interconnected. Several shading techniques corresponding to different methods of object modeling and the related hidden surface algorithms are presented here. Human visual perception and the fundamental laws of optics are considered in the development of a shading rule that provides better quality and increased realism in generated images.
Principal component analysis: a review and recent developments (2016)

Large datasets are increasingly common and are often difficult to interpret. Principal component analysis (PCA) is a technique for reducing the dimensionality of such datasets, increasing interpretability but at the same time minimizing information loss. It does so by creating new uncorrelated variables that successively maximize variance. Finding such new variables, the principal components, reduces to solving an eigenvalue/eigenvector problem, and the new variables are defined by the dataset at hand, not a priori, hence making PCA an adaptive data analysis technique. It is adaptive in another sense too, since variants of the technique have been developed that are tailored to various different data types and structures. This article will begin by introducing the basic ideas of PCA, discussing what it can and cannot do. It will then describe some variants of PCA and their application.
Transactional memory with data invariants (2006)

This paper introduces a mechanism for asserting invariants that are maintained by a program that uses atomic memory transactions. The idea is simple: a programmer writes check E where E is an expression that should be preserved by every atomic update for the remainder of the program’s execution. We have extended STM Haskell to dynamically evaluate check statements atomically with the user’s updates: the result is that we can identify precisely which update is the first one to break an invariant.
Population Genetic Analysis of Propionibacterium acnes Identifies a Subpopulation and Epidemic Clones Associated with Acne (2010)

The involvement of Propionibacterium acnes in the pathogenesis of acne is controversial, mainly owing to its dominance as an inhabitant of healthy skin. This study tested the hypothesis that specific evolutionary lineages of the species are associated with acne while others are compatible with health. Phylogenetic reconstruction based on nine housekeeping genes was performed on 210 isolates of P. acnes from well-characterized patients with acne, various opportunistic infections, and from healthy carriers. Although evidence of recombination was observed, the results showed a basically clonal population structure correlated with allelic variation in the virulence genes tly and camp5, with pulsed field gel electrophoresis (PFGE)- and biotype, and with expressed putative virulence factors. An unexpected geographically and temporal widespread dissemination of some clones was demonstrated. The population comprised three major divisions, one of which, including an epidemic clone, was strongly associated with moderate to severe acne while others were associated with health and opportunistic infections. This dichotomy correlated with previously observed differences in in vitro inflammation-inducing properties. Comparison of five genomes representing acne- and health-associated clones revealed multiple both cluster- and strain-specific genes that suggest major differences in ecological preferences and redefines the spectrum of disease-associated virulence factors. The results of the study indicate that particular clones of P. acnes play an etiologic role in acne while others are associated with health.
Molecular Therapy with Recombinant p53 Adenovirus in an Androgen-Independent, Metastatic Human Prostate Cancer Model (1996)

The lethal phenotypes of advanced prostate cancer are androgen independent (AI) and metastatic to the axial skeleton. Our laboratory has developed an AI mouse model of metastatic human prostate cancer. In this communication, we report the development of tumor suppressor gene therapy in this AI and metastatic (C4-2) cancer model. By using recombinant adenovirus as a delivery vehicle, we introduced a wild-type p53 tumor suppressor gene into prostate cancer cell lines. Despite a silent mutation at codon 152 of the p53 gene, C4-2 cells express functional, but low, levels of p53 protein. However, the other prostatic cell lines, PC-3 and DU145, have a deletion mutation and two point mutations of the p53 gene, respectively. In vitro studies showed that cell growth, as measured by the thymidine incorporation assay, was inhibited in the C4-2, PC-3, and DU145 cells infected with wild-type p53 adenovirus in comparison to control viruses. Recombinant wild-type p53 adenovirus inhibited prostate tumor growth and its production of prostate-specific antigen (PSA) when injected into C4-2 tumors in nude mice. All p53-treated mice were tumor free as long as 12 weeks after cessation of the 8-week treatment regimen. Two of 8 p53-treated mice developed small tumors growing at distant sites after a prolonged period of follow-up observation. Moreover, other AI prostate cancer cells, PC-3 and DU145, treated with Ad5-CMV-p53 failed to develop into tumors in vivo. This gene therapy strategy may be used against AI prostatic cancer regardless of p53 gene mutation status.
Association and Expression Analyses With Single-Nucleotide Polymorphisms in <emph type="ital">TOMM40</emph> in Alzheimer Disease (2011)

Although we did not replicate the earlier association between the APOE 3-TOMM40 haplotypes and age at onset, we observed that the polyT polymorphism is associated with risk of LOAD in APOE 33 homozygotes in a large case-control series but in the opposite direction as in the previous study.
A Scalable Framework for Modeling Competitive Diffusion in Social Networks (2010)

Multiple phenomena often diffuse through a social network, sometimes in competition with one another. Product adoption and political elections are two examples where network diffusion is inherently competitive in nature. For example, individuals may choose to only select one product from a set of competing products (i.e. most people will need only one cell-phone provider) or can only vote for one person in a slate of political candidate (in most electoral systems). We introduce the weighted generalized annotated program (wGAP) framework for expressing competitive diffusion models. Applications are interested in the eventual results from multiple competing diffusion models (e.g. what is the likely number of sales of a given product, or how many people will support a particular candidate). We define the “most probable interpretation” (MPI) problem which technically formalizes this need. We develop algorithms to efficiently solve MPI and show experimentally that our algorithms work on graphs with millions of vertices.
Video fingerprinting for copy identification: from research to industry applications (2009)

Research that began a decade ago in video copy detection has developed into a technology known as "video fingerprinting". Today, video fingerprinting is an essential and enabling tool adopted by the industry for video content identification and management in online video distribution. This paper provides a comprehensive review of video fingerprinting technology and its applications in identifying, tracking, and managing copyrighted content on the Internet. The review includes a survey on video fingerprinting algorithms and some fundamental design considerations, such as robustness, discriminability, and compactness. It also discusses fingerprint matching algorithms, including complexity analysis, and approximation and optimization for fast fingerprint matching. On the application side, it provides an overview of a number of industry-driven applications that rely on video fingerprinting. Examples are given based on real-world systems and workflows to demonstrate applications in detecting and managing copyrighted content, and in monitoring and tracking video distribution on the Internet.
Hindbrain GRP receptor blockade antagonizes feeding suppression by peripherally administered GRP (1996)

Bombesin (BN)-like peptides injected peripherally or centrally suppress food intake in rats. The relationship between the central and peripheral actions of BN is unknown. However, experimental evidence supports a critical role for the caudal hindbrain in mediating the feeding effects of BN. To investigate this relationship further, we examined the ability of fourth ventricular infusion of a specific gastrin-releasing peptide (GRP) antagonist, [D-F5, Phe6, D-Ala11]BN-(6-13) methyl ester (BN-ME), to block suppression of glucose intake (0.5 kcal/ml) produced by intraperitoneal administration of GRP-(18-27) in 5-h food-deprived male Sprague-Dawley rats (n = 10). We found that fourth ventricular administration of 10, 32, and 100 ng BN-ME blocked the suppression of glucose intake produced by peripherally administered 10 nmol/kg GRP-(18-27). The most effective dose of BN-ME (100 ng) blocked the ability of peripheral injection of GRP-(18-27) to inhibit glucose intake but had no effect on intake when given alone. These results demonstrate that the availability of caudal hindbrain GRP receptors is necessary for peripherally administered GRP-(18-27) to reduce food intake in rats.
Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein (2009)

Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1–3 and 7–8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4–6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.