gebhart/patrepeval huggingface dataset:
A Dual Label Oligonucleotide Ligation Assay for Detection of theCYP2C19*1, CYP2C19*2, and CYP2C19*3 Alleles Involving Time-Resolved Fluorometry (1998)

CYP2C19 (S-mephenytoin hydroxylase) is a polymorphically expressed enzyme. Currently, two defective alleles are known--CYP2C19*2 and CYP2C19*3. The authors have developed an oligonucleotide ligation assay to detect these two alleles. This assay combines the hybridization of one common, biotinylated capture probe and two allele-specific probes to the target DNA, with the ability of a DNA ligase to distinguish mismatched nucleotides. The probes are only ligated if they are base paired correctly to the target strand. The biotin is bound to streptavidin, and all DNA not covalently bound to the biotin-labeled capture probe, is removed in a washing procedure. The allele-specific probes are labeled with either europium or samarium, and their emission can be measured simultaneously. The ratio between the emission separates the genotypes. This method was applied on DNA from 19 whites and 21 Vietnamese living in Denmark. All genotypes determined by the assay were consistent with the results from restriction enzyme cleavage. There were 12 poor metabolizers; 10 homozygous CYP2C19*2/CYP2C19*2, one heterozygous CYP2C19*2/CYP2C19*3, and one heterozygous CYP2C19*1/CYP2C19*2. The authors conclude that this assay is well-suited for a high throughput of samples in a routine laboratory. The finding of an apparently heterozygous CYP2C19*1/CYP2C19*2 poor metabolizer, confirms that there are still unknown mutations in CYP2C19.
Application of a color-appearance model to vision through atmospheric haze (1999)

Environmental laws mandate the protection of visibility conditions in national parks and wilderness areas from atmospheric haze, which occurs due to the emissions of anthropogenic air pollutants. To calculate the improvement in visibility that results from the reduction of these air pollutants, it is necessary to quantify the relationship of haze to the color appearance of objects being viewed through it. To this end, a field study was conducted in the Great Smoky Mountains National Park in eastern Tennessee. Color appearance of objects was quantified by color matching with a special visual colorimeter. The Hunt94 color-appearance model was used to compare these matches with simultaneous spectral measurements. In addition to the chromaticity coordinates and luminance of the object, the Hunt94 model requires a number of parameters such as the chromaticity of the adapting light and chromatic and brightness surround induction factors, which need to be determined for the outdoor viewing conditions. This article describes how this was accomplished. Although it accounts for differences in viewing conditions between the colorimeter and daylight conditions, the Hunt94 model does not account for the perceptual transparency effect of haze on outdoor color appearance. These results challenge the manner in which current air quality–visibility models are being utilized. © 1999 John Wiley & Sons, Inc. Col Res Appl, 24, 112–120, 1999
Antiepileptic drug resistance and tolerance in epilepsy. (2007)

Drug-resistant epilepsy is a prevalent problem despite the multiple antiepileptic drug (AED) options available. Despite variations in the definition of drug resistance, clinicians can identify risk factors for AED resistance. Drug-resistant partial epilepsy should be referred early to an epilepsy surgery center. Mimics of drug-resistant epilepsy abound and cause diagnostic confusion. Rapid advances in epilepsy research and pharmacogenomics are providing new insight into the mechanisms of drug resistance and tolerance. Rational AED strategies and promising interventions to treat or prevent drug resistance will reduce the impact on the patient.
Occurrence of antibodies reactive with more than one variant of the putative envelope glycoprotein (gp70) hypervariable region 1 in viremic hepatitis C virus-infected patients (1995)

The hepatitis C virus (HCV) is a frequent cause of chronic liver disease. A mechanism proposed as being responsible for virus persistence is evasion of the host immune response through a high mutation rate in crucial regions of the viral genome. We have sequenced the hypervariable region 1 (HVR1) of the virus isolated from three serum samples, collected during 18 months of follow-up, from an asymptomatic HCV-infected patient. A synthetic peptide of 27 amino acids, corresponding to the HVR1 sequence found to be predominant in both the second and third samples, was used as the antigen for detection of antibodies by enzyme-linked immunosorbent assay (ELISA). We observed reactivity against this HVR1 sequence in the first serum sample before the appearance of the viral isolate in the bloodstream; the reactivity increased in the second and third samples while the cognate viral sequence became predominant. Moreover, our results show that antibodies from all three samples recognize a region mapping at the carboxyl-terminal part of the HVR1 and are cross-reactive with the HVR1 sequence previously found in the same patient. The presence of anti-HVR1 antibodies was investigated in a further 142 HCV patients: 121 viremic and 21 nonviremic. Two synthetic peptides were used, the first corresponding to the sequence derived from the patient described above and the second one synthesized according to the sequence of the HCV BK strain. A high frequency of positive reactions against both HVR1 variants was detected in the samples from the viremic individuals. Finally, antibodies cross-reactive with both variants were shown to be present by competitive ELISA in 6 of 10 viremic patients. The potential negative implications of this observation for the host are discussed.
Real-Time Hardware in the Loop Simulation of Aerospace Power Systems (2007)

(Abstract) This paper presents new results obtained with a real-time simulator for aerospace power systems capable of hardware in the loop simulation. This means that the model under test runs in real-time in the simulator and it can drive and receive signals from a real system through its analog and digital interfaces. The simulator uses low cost reconfigurable computing infrastructure (e.g. embedded processors and FPGAs) and it is capable of having simulation steps on the order of 0.4 microseconds, that is suitable to represent typical modern aerospace power systems. As an example, we realize the simulation of a sequential switching shunt series regulator (S4R) system using Matlab/Simulink and compare it to the results produced by the FPGA based simulator.
Highly Crystalline Cubic Mesoporous TiO<sub>2</sub> with 10-nm Pore Diameter Made with a New Block Copolymer Template (2004)

A strategy is shown to fabricate highly organized mesoporous anatase films exhibiting favorable properties for photocatalysis and photovoltaic applications by the hydrolysis/condensation of TiCl4 in the presence of PHB−PEO block copolymer templates. Dipcoating for evaporation-induced-self-assembly followed by a straight thermal treatment was employed. The evaporation/structuration process and the thermal treatment were mechanistically followed by in situ GISAXS/WAXS measurements, and the final product was carefully analyzed by spectroscopic ellipsometry and transmission electron microscopy to reveal the consequences of crystallization onto the micro-, the meso-, and the macroscale.
A cognitive theory of consciousness (1988)

List of figures and tables Preface Part I. Introduction: 1. What is to be explained? some preliminaries Part II. The Basic Model: 2. Model 1: conscious representations are internally consistent and globally distributed 3. The neural basis of conscious experience Part III. The Fundamental Role of Context: 4. Model 2: unconscious contexts shape conscious experience 5. Model 3: conscious experience is informative - it always demands some degree of adaptation Part IV. Goals and Voluntary Control: 6. Model 4: Goal contexts, spontaneous problem solving, and the stream of consciousness 7. Model 5: volition as ideomotor control of thought and action Part V. Attention, self, and conscious self-monitoring: 8. Model 6: attention as control of access to consciousness 9. Model 7. Self as the dominant context of experience and action Part VI. Consciousness is Functional: 10. The functions of consciousness Part VII. Conclusion: 11. A summary and some future directions Glossary and guide to theoretical claims References Name index, Subject index.
Guanidine Hydrochloride Inhibits the Generation of Prion “Seeds” but Not Prion Protein Aggregation in Yeast (2002)

[PSI(+)] strains of the yeast Saccharomyces cerevisiae replicate and transmit the prion form of the Sup35p protein but can be permanently cured of this property when grown in millimolar concentrations of guanidine hydrochloride (GdnHCl). GdnHCl treatment leads to the inhibition of the replication of the [PSI(+)] seeds necessary for continued [PSI(+)] propagation. Here we demonstrate that the rate of incorporation of newly synthesized Sup35p into the high-molecular-weight aggregates, diagnostic of [PSI(+)] strains, is proportional to the number of seeds in the cell, with seed number declining (and the levels of soluble Sup35p increasing) in the presence of GdnHCl. GdnHCl does not cause breakdown of preexisting Sup35p aggregates in [PSI(+)] cells. Transfer of GdnHCl-treated cells to GdnHCl-free medium reverses GdnHCl inhibition of [PSI(+)] seed replication and allows new prion seeds to be generated exponentially in the absence of ongoing protein synthesis. Following such release the [PSI(+)] seed numbers double every 20 to 22 min. Recent evidence (P. C. Ferreira, F. Ness, S. R. Edwards, B. S. Cox, and M. F. Tuite, Mol. Microbiol. 40:1357-1369, 2001; G. Jung and D. C. Masison, Curr. Microbiol. 43:7-10, 2001), together with data presented here, suggests that curing yeast prions by GdnHCl is a consequence of GdnHCl inhibition of the activity of molecular chaperone Hsp104, which in turn is essential for [PSI(+)] propagation. The kinetics of elimination of [PSI(+)] by coexpression of a dominant, ATPase-negative allele of HSP104 were similar to those observed for GdnHCl-induced elimination. Based on these and other data, we propose a two-cycle model for "prionization" of Sup35p in [PSI(+)] cells: cycle A is the GdnHCl-sensitive (Hsp104-dependent) replication of the prion seeds, while cycle B is a GdnHCl-insensitive (Hsp104-independent) process that converts these seeds to pelletable aggregates.
High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers (2009)

Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of <200 bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5% of CpG islands and 91.1% of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10 ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.
Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants (2017)

The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.
A CANKER AND DIE‐BACK OF ROSES CAUSED BY <i>GRIPHOSPHAERIA GORTICOLA</i> (1939)

S ummary A canker and die‐back of roses caused by Griphosphaeria corticola (Fckl.) v. Höhnel is described. Conidial fructifications, which may be acervuli or ill‐defined pycnidia. precede the formation of perithecia. Conidial isolations are of slightly differing types as regards size and shape of spores, cultural behaviour and relative pathogenicity, but at present they are all referred provisionally to Coryneum microstictum B. & Br. Some of the conidial isolations have given rise to perithecia, but others have not. Successful inoculations both with conidia and ascospores are described. In Nature, infection by this parasite may occur through pruning wounds, dead buds, leaf scars, wounds made by thorns, and rust lesions. The following varieties of roses appear to be particularly susceptible to the disease: Duchess of Atholl, Lady Inchiquin and Golden Emblem. The pathological anatomy of the disease is described. Infection may occur at all times of the year except summer, when the rapid formation of “gum barriers” by the host tissues checks invasion. The disease is not likely to become widespread unless neglected. Diseased shoots should be cut out; with some varieties normal pruning operations should sufficiently control the disease.
Anisotropy properties of magnetic colloidal materials (2002)

Magnetic anisotropy of particulate magnetic materials is investigated with respect to the particle shape and compacting geometry. Uniform sized micro-rods and microspheres, coated with nickel, were used. Our results reveal that uniformly aligned rods show the largest magnetic anisotropy, while the field-oriented suspension of coated micro-rods shows somewhat weaker magnetic anisotropy, which is in excellent quantitative agreement with the theoretical calculation. The magnetic anisotropy drops significantly when the micro-rods were replaced by microspheres, even when they were aligned in chain-like formations.
Tellurapyrylium dyes. 3. Oxidative halogen addition and tellurium-halogen exchange (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTellurapyrylium dyes. 3. Oxidative halogen addition and tellurium-halogen exchangeMichael R. Detty and Henry R. LussCite this: Organometallics 1986, 5, 11, 2250–2256Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://pubs.acs.org/doi/10.1021/om00142a013https://doi.org/10.1021/om00142a013research-articleACS PublicationsRequest reuse permissionsArticle Views201Altmetric-Citations29LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
A radius-bucketing approach to fast vector quantization encoding (2003)

The authors present a computationally efficient encoding scheme for vector quantization. Efficiency is achieved by combining techniques: homes are bucketed into the subset of codewords in the same region as the input point; the energy of the input point eliminates codewords not in the same energy range; the smallest hyperrectangle parallel to the coordinate axes that bounds the Voronoi region associated with the codeword acts as a discriminant; and approximations to the actual distortion are used to avoid multiplications. Simulations on Gaussian sources with ranges of codebook sizes and block sizes indicate that the encoding time, measured in multiplications, actually falls with increasing codebook size. It is shown that with no increase in signal/noise ratio the algorithm substantially outperforms tree search and binary hyperplane testing search.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
α-<i>C</i>-Galactosylceramides:  Synthesis and Immunology (2006)

The immunostimulant activity of alpha-galactosylceramides provided the impetus for the research described here. The activity was first discovered via screening of extracts of a marine sponge. The active materials purified from the extracts were alpha-O-galactosylceramides. The work described herein focuses on syntheses of alpha-C-galactosylceramides. Crucial methodologies for the syntheses were (i) Ramberg-Bäcklund reaction, (ii) modified Julia olefination, (iii) olefin cross-metathesis, and (iv) Sharpless asymmetric epoxidation in four independent routes. The immunostimulant activity of the synthetic alpha-C-galactosylceramide far surpasses that of the O-galactosyl material. A discussion of the reasons for the difference in activity is presented.
Chemical Modification of the Mitochondrial Complex I Inhibitor 1-Trichloromethyl-1,2,3,4-tetrahydro-β-carboline: Synthesis and Evaluation of N-Alkanoyl Derivatives (2000)

Abstract Several N-alkanoyl derivatives (4-9 and 13-16) of the potent mitochondrial complex I inhibitor TaClo (1-trichlorom ethyl-1,2,3,4-tetrahydro-β-carboline, 2) have been synthesized in order to elucidate the role of hydrophobic portion in the inhibitory action. Using rat brain homogenates or submitochondrial particles, the inhibitory effects of these compounds towards NADH-ubiquinone reductase (complex I) activity indeed appeared to correlate quite strongly with their lipophilic character. An X-ray structure analysis, exemplarily performed for N-acetyl-TaClo (4), revealed the N-substituent of such chlorinated agents to be dramatically pushed out of the β-carboline ring ‘plane’ due to the high steric demand of the huge trichloromethyl group at C-1.
Evaluation of Chiral Bidentate Ligand—Metal Complexes in Asymmetric 1,3‐Dipolar Cycloaddition Reaction of Nitrones with 3‐Alkenoyl‐2‐oxazolidinones. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
IFNγ enhances IL‐23 production during <i>Francisella</i> infection of human monocytes (2008)

We previously demonstrated that monocytes produce IL-23 during Francisella infection, and that IL-23 induces IFNgamma from NK cells. Here, we demonstrate that IFNgamma-priming of monocytes enhances IL-23 production during Francisella infection. This effect was seen on the IL12/23 p40 subunit. Induction of IL-12/23 p40 is reported to be enhanced by IRF-1 and IRF-8. Consistently, microarray analysis of IFNgamma-treated monocytes revealed a significant induction of the IRFs. Interestingly, IFNgamma-primed monocytes produced IL-12 p70, a more potent inducer of IFNgamma than IL-23. We propose that there exists an amplification loop between monocyte IL-23 and NK/T cell IFNgamma that leads to IL-12 p70 production.
Investigating the emergence of shared attention through an embodied computational modeling approach: a progress report (2004)

Summary form only given. We present a simple computational model of the emergence of gaze following behavior in infant caregiver interactions. We regard gaze following as a skill that infants acquire because they learn that monitoring their caregiver's direction of gaze allows them to predict where interesting objects/events in their environment are (Moore, 1996). In particular, we propose a specific "basic set" of mechanisms that are sufficient for gaze following to emerge (Fasel and Deak, 2002). This basic set comprises perceptual and motivational biases and habituation mechanisms driving the infant to look at and shift attention between "interesting" visual stimuli, a generic learning mechanism that learns behavioral strategies to satisfy these preferences, and a structured environment providing correlations between where caregivers look and where interesting stimuli are. We formalize these ideas in a simple model based on temporal difference learning. We analyze the model and demonstrate that a) the proposed basic set of mechanisms is indeed sufficient for gaze following to emerge and b) alterations of parameters of some of the basic set mechanisms motivated by findings on developmental disorders lead to impairments in the learning of gaze following that are typical of these disorders.
Low-temperature MoO<sub>3</sub>film from a facile synthetic route for an efficient anode interfacial layer in organic optoelectronic devices (2013)

A low temperature solution-processed MoO3 (sMoO3) thin film with a facile method for organic optoelectronic devices is developed. The film is extremely smooth with a root mean square (RMS) roughness of 0.318 nm, which is a significant advance for fabricating devices. An X-ray photoelectron spectroscopy (XPS) measurement shows that the sMoO3 possesses few Mo5+ states with a Mo : O stoichiometry of 2.99, demonstrating a nearly ideal MoO3 stoichiometry at a low annealing temperature. The sMoO3 film exhibits a superior hole injection ability in both an organic light-emitting diode (OLED) and organic photovoltaic cell (OPV), compared to conventional hole injection material poly (3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS). It is proved that the sMoO3 fabricated by the simple and low-cost method is an excellent alternative to a PEDOT:PSS anode buffer layer for solution-processed organic optoelectronic devices.
Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data (2017)

Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322 bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.