gebhart/patrepeval huggingface dataset:
Decoupling Sparsity and Smoothness in the Discrete Hierarchical Dirichlet Process (2009)

We present a nonparametric hierarchical Bayesian model of document collections that decouples sparsity and smoothness in the component distributions (i.e., the “topics”). In the sparse topic model (sparseTM), each topic is represented by a bank of selector variables that determine which terms appear in the topic. Thus each topic is associated with a subset of the vocabulary, and topic smoothness is modeled on this subset. We develop an efficient Gibbs sampler for the sparseTM that includes a general-purpose method for sampling from a Dirichlet mixture with a combinatorial number of components. We demonstrate the sparseTM on four real-world datasets. Compared to traditional approaches, the empirical results will show that sparseTMs give better predictive performance with simpler inferred models. 1
Design, Synthesis, and <i>in Vitro</i> Evaluation of Cyclic Nitrones as Free Radical Traps for the Treatment of Stroke (1996)

Analogs of the cyclic nitrone free radical trap 1 (3,3-dimethyl-3,4-dihydroisoquinoline N-oxide, a cyclic analog of phenyl-tert-butylnitrone (PBN)) were prepared in which (1) the fused phenyl ring was replaced with a naphthalene ring, an electron rich heterocycle, or a dimethylphenol, (2) the nitrone-containing ring comprised five, six, or seven atoms, and (3) the gem-dimethyl group was replaced with spirocyclic groups. The most active antioxidant, which bears a dimethylphenol fused to a 7-membered ring nitrone (compound 6h), inhibited lipid peroxidation in vitro with an IC50 of 22 microM, a 75-fold improvement over that of 1. The previously observed correlation between lipophilicity and activity vs lipid peroxidation in vitro has been further substantiated and refined by this study. Moreover, certain classes of compounds (namely, dimethylphenols 6g,h and furan 6j) have now been found which are considerably more active in vitro than expected on the basis of their log k'(w) values.
Cloning of plasmid genes encoding resistance to cadmium, zinc, and cobalt in Alcaligenes eutrophus CH34 (1987)

A 238-kilobase-pair plasmid, pMOL30, confers resistance to cadmium, zinc, and cobalt salts in Alcaligenes eutrophus CH34. After Tn5 mutagenesis, restriction nuclease analysis, and Southern DNA-DNA hybridization, a 9.1-kilobase-pair EcoRI fragment was found to harbor all of these resistance properties and was cloned into the broad-host-range hybrid plasmid pRK290. When transferred to a plasmid-free derivative of CH34, the hybrid plasmid conferred the same degree of resistance as the parent plasmid pMOL30. In two other Alcaligenes strains, the hybrid plasmid was expressed, but to a lower degree than in CH34 derivatives.
The Microstructure of Wheat: Its Development and Conversion Into Bread (1985)

Wheat endosperm development has been studied in numerous laboratories. The genera 1 i zed scheme of protein body formation assembled from these data indicates that storage proteins are initially formed in the rough endoplasmic reticulum (RER). The storage proteins in RER may be processed via the Golgi apparatus into vesicles that enlarge by several mechanisms into membrane-bounded protein bodies. The prote in bodies are transported through the cytoplasm to the vacuole where they fuse with the tonoplast and deposit the protein granules into the vacuoles. The protein granules fuse with one another, lose water, and eventually become transformed into the matrix. The starchy endosperm is reduced to small particles of starch and protein during milling. These flour particles are dynamically rehydrated during dough formation. The protein forms the major structural network surrounding starch granules in doughs. The framework of bread crumb, however, is of dual composition; the protein network and a newly formed network of gelatinized starch.
RESTest: automated black-box testing of RESTful web APIs (2021)

Testing RESTful APIs thoroughly is critical due to their key role in software integration. Existing tools for the automated generation of test cases in this domain have shown great promise, but their applicability is limited as they mostly rely on random inputs, i.e., fuzzing. In this paper, we present RESTest, an open source black-box testing framework for RESTful web APIs. Based on the API specification, RESTest supports the generation of test cases using different testing techniques such as fuzzing and constraint-based testing, among others. RESTest is developed as a framework and can be easily extended with new test case generators and test writers for different programming languages. We evaluate the tool in two scenarios: offline and online testing. In the former, we show how RESTest can efficiently generate realistic test cases (test inputs and test oracles) that uncover bugs in real-world APIs. In the latter, we show RESTest's capabilities as a continuous testing and monitoring framework. Demo video: https://youtu.be/1f_tjdkaCKo.
Editorial: Revisiting the Effectiveness of Transcranial Direct Current Brain Stimulation for Cognition: Evidence, Challenges, and Open Questions (2017)

EDITORIAL article Front. Hum. Neurosci., 08 September 2017Sec. Brain Imaging and Stimulation Volume 11 - 2017 | https://doi.org/10.3389/fnhum.2017.00448
An on-line ICA-mixture-model-based self-constructing fuzzy neural network (2005)

This paper proposes a new fuzzy neural network (FNN) capable of parameter self-adapting and structure self-constructing to acquire a small number of fuzzy rules for interpreting the embedded knowledge of a system from the given training data set. The proposed FNN is inherently a modified Takagi-Sugeno-Kang (TSK)-type fuzzy-rule-based model with neural network's learning ability. There are no rules initiated at the beginning and they are created and adapted through an on-line learning processing that performs simultaneous structure and parameter identification. In the structure identification of the precondition part, the input space is partitioned in a flexible way according to the newly proposed on-line independent component analysis (ICA) mixture model. The input space is thus represented by linear combinations of independent, non-Gaussian densities. The first input training pattern is assigned to the first rule initially by the on-line ICA mixture model. Afterwards, some additional significant terms (input variables) selected by the on-line ICA mixture model will be added to the consequent part (forming a liner equation of input variables) incrementally or create a new rule in the learning processing. The combined precondition and consequent structure identification scheme can make the network grow dynamically and efficiently. In the parameter identification, the consequent parameters are tuned by the backpropagation rule and the precondition parameters are turned by the on-line ICA mixture model. Both the structure and parameter identifications are done simultaneously to form a fast learning scheme. The derived on-line ICA mixture model also provide a natural linear transformation for each input variable to enhance the knowledge representation ability of the proposed FNN and reduce the required rules and achieve higher accuracy efficiently. In order to demonstrate the performance of the proposed FNN, several experiments covering the areas of system identification, classification, and image segmentation are carried out. Our experiments show that the proposed FNN can achieve significant improvements in the convergence speed and prediction accuracy with simpler network structure.
A concurrent implementation of the prime factor algorithm on hypercube (1991)

The prime factor algorithm (PFA) is an efficient discrete Fourier transform (DFT) computation algorithm in which a one-dimensional DFT is tuned into a multidimensional DFT, consisting of a few short DFTs whose lengths are mutually prime, and then an efficient algorithm is used for the short DFTs. The PFA was implemented on a hypercube using CrOS III communication routines, taking 120 ms to compute the DFT of 5040 complex points using 32 nodes of the Caltech-JPL MARK III Hypercube. It took 105 ms to do a DFT of 4096 complex points using the Cooley-Tukey algorithm with the same hardware configuration. The performance of hypercubes MARK III, NCUBE, and iPSC and the relative importance of communication and calculation are analyzed. With the current communication speed the Cooley-Tukey algorithm performs fast on a massively concurrent processor and the PFA is advantageous when the number of processors is less than 64 or so. The experience with using the PFA also serves as a useful guide to a multidimensional fast Fourier transform implementation using any algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Heat conductivity of oxide coatings by photothermal radiometry between 293 and 1173 K (1988)

Optical generation and optical detection of thermal waves are used to determine the thermal properties of three different oxide coatings on stainless steel substrates at temperatures up to 1173 K. The thermal diffusivities alpha and thermal conductivities k strongly depend on the method of preparation as well as on the environmental conditions during deposition. Our experimental values for alpha and k are generally lower than handbook data for bulk specimens of the same materials.
Tuning Radiative Recombination in Cu-Doped Nanocrystals via Electrochemical Control of Surface Trapping (2012)

The incorporation of copper dopants into II-VI colloidal nanocrystals (NCs) leads to the introduction of intragap electronic states and the development of a new emission feature due to an optical transition which couples the NC conduction band to the Cu-ion state. The mechanism underlying Cu-related emission and specifically the factors that control the branching between the intrinsic and impurity-related emission channels remain unclear. Here, we address this problem by conducting spectro-electrochemical measurements on Cu-doped core/shell ZnSe/CdSe NCs. These measurements indicate that the distribution of photoluminescence (PL) intensity between the intrinsic and the impurity bands as well as the overall PL efficiency can be controlled by varying the occupancy of surface defect sites. Specifically, by activating hole traps under negative electrochemical potential (the Fermi level is raised), we can enhance the Cu band at the expense of band-edge emission, which is consistent with the predominant Cu(2+) character of the dopant ions. Furthermore, we observe an overall PL "brightening" under negative potential and "dimming" under positive potential, which we attribute to changes in the occupancy of the electron trap sites (that is, the degree of their electronic passivation) that control nonradiative losses due to electron surface trapping.
The Micro-RNA172c-APETALA2-1 Node as a Key Regulator of the Common Bean-<i>Rhizobium etli</i> Nitrogen Fixation Symbiosis (2015)

Micro-RNAs are recognized as important posttranscriptional regulators in plants. The relevance of micro-RNAs as regulators of the legume-rhizobia nitrogen-fixing symbiosis is emerging. The objective of this work was to functionally characterize the role of micro-RNA172 (miR172) and its conserved target APETALA2 (AP2) transcription factor in the common bean (Phaseolus vulgaris)-Rhizobium etli symbiosis. Our expression analysis revealed that mature miR172c increased upon rhizobial infection and continued increasing during nodule development, reaching its maximum in mature nodules and decaying in senescent nodules. The expression of AP2-1 target showed a negative correlation with miR172c expression. A drastic decrease in miR172c and high AP2-1 mRNA levels were observed in ineffective nodules. Phenotypic analysis of composite bean plants with transgenic roots overexpressing miR172c or a mutated AP2-1 insensitive to miR172c cleavage demonstrated the pivotal regulatory role of the miR172 node in the common bean-rhizobia symbiosis. Increased miR172 resulted in improved root growth, increased rhizobial infection, increased expression of early nodulation and autoregulation of nodulation genes, and improved nodulation and nitrogen fixation. In addition, these plants showed decreased sensitivity to nitrate inhibition of nodulation. Through transcriptome analysis, we identified 114 common bean genes that coexpressed with AP2-1 and proposed these as being targets for transcriptional activation by AP2-1. Several of these genes are related to nodule senescence, and we propose that they have to be silenced, through miR172c-induced AP2-1 cleavage, in active mature nodules. Our work sets the basis for exploring the miR172-mediated improvement of symbiotic nitrogen fixation in common bean, the most important grain legume for human consumption.
Carcinogenesis: a comprehensive survey. Volume I. Polynuclear aromatic hydrocarbons: chemistry, metabolism, and carcinogenesis (1976)

Polynuclear aromatic hydrocarbons are widespread contaminants of the environment, primarily occurring as a result of combustion and pyrolysis of organic materials. Concern over their prevalence stems from the evidence that a significant number are known to be carcinogenic. This volume surveys the chemistry of these compounds, including analytical procedures for environmental and biological samples as well as their metabolism, activation, and mechanism of carcinogenicity. Separate abstracts were prepared for the 31 papers included in the volume.
Thermoelectricity: an Introduction to the Principles (1962)

This book discusses thermoelectricity in metals and semiconductors, with emphasis on the former. The behaviour at low temperatures is of special interest throughout but the book is not confined to this.
Terahertz Response of a Microfabricated Rod–Split-Ring-Resonator Electromagnetic Metamaterial (2005)

The first electromagnetic metamaterials (EM3) produced by microfabrication are reported. They are based on the rod-split-ring-resonator design as proposed by Pendry et al. [IEEE Trans. Microwave Theory Tech. 47, 2075 (1999)] and experimentally confirmed by Smith et al. [Phys. Rev. Lett. 84, 4184 (2000)] in the GHz frequency range. Numerical simulation and experimental results from far infrared (FIR) transmission spectroscopy support the conclusion that the microfabricated composite material is EM3 in the range 1-2.7 THz. This extends the frequency range in which EM3 are available by about 3 orders of magnitude well into the FIR, thereby widely opening up opportunities to verify the unusual physical implications on electromagnetic theory as well as to build novel electromagnetic and optical devices.
Abnormal morphology of melanosomes in the autoimmune vitiligo-prone Smyth line chicken does not appear to be due to alteration in lipid composition (83.16) (2010)

Abstract The Smyth line (SL) chicken is an important animal model for autoimmune vitiligo. SL vitiligo is multifactorial in nature including genetic susceptibility, immune system components and environmental triggers. Genetic susceptibility to SL vitiligo appears to be manifested in part by an inherent melanocyte defect. SL melanosomes (pigment-carrying organelles) have irregular-shaped membranes with pigmented extensions that may be due to abnormal lipid composition. Lipids can affect protein topology and trafficking (and hence protein degradation and presentation), membrane stability and oxidative stress resistance. To compare melanosomal lipids from SL and control lines of chickens, melanosomes were isolated from growing feathers of 4-week-old SL, Brown line (parental control) and Light Brown Leghorn (vitiligo-resistant) chickens and lipids were extracted. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) combined with thin-layer chromatography (TLC) was used to determine expression differences in different classes of lipids by using TLC-MALDI imaging technique. Total fatty acid composition was examined by gas chromatography-mass spectrometry (GC-MS) of fatty acid methyl esters. Statistical analysis of preliminary data shows no significant differences in total fatty acid and phospholipid composition in melanosomes from SL and control chickens. Hence, lipid composition may not explain the melanosomal abnormalities observed in SL melanocytes.
Low-loss titanium dioxide waveguides and resonators using a dielectric lift-off fabrication process (2015)

We present a bi-layer lift-off fabrication approach to create low-loss amorphous titanium dioxide (TiO2) integrated optical waveguides and resonators for visible and near-infrared applications. This approach achieves single-mode waveguide losses as low as 7.5 dB/cm around 633 nm and 1.2 dB/cm around 1550 nm, a factor of 4 improvement over previous reports, without the need to optimize etching conditions. Depositing a secondary 260-nm TiO2 layer can reduce losses further, with the optimized process yielding micro-ring resonators with loaded quality factors as high as 1.5 × 10(5) around 1550 nm and 1.6×10(5) around 780 nm. These losses render our TiO2 devices suitable for visible and telecommunications applications; in addition, the simplicity of this lift-off approach is broadly applicable to other novel material platforms, particularly using near-visible wavelengths.
Hand-eye and radial distortion calibration for rigid endoscopes (2013)

Our experimental results show the effectiveness of simultaneously estimating hand-eye and distortion parameters for 3D reconstruction.
IL-10 selectively induces HLA-G expression in human trophoblasts and monocytes (1999)

HLA-G plays an essential role in feto-maternal tolerance by inhibiting lysis by maternal NK cells. The factors that allow tissue-specific activation of HLA-G gene expression in trophoblasts remain to be characterized. We investigated the potential effect of IL-10, a cytokine which is secreted in placenta, on HLA-G gene transcription in trophoblasts. Using Northern blot, RNase protection assay and RT-PCR analysis, we demonstrated that IL-10 enhances steady-state levels of HLA-G transcription in cultured trophoblast cells. We further tested the effect of IL-10 on HLA-G gene transcription and protein expression in peripheral blood monocytes, showing that IL-10 can up-regulate HLA-G cell surface expression in this cell type. This effect of IL-10 is selective, since classical MHC class I products and MHC class II are down-regulated in monocytes following IL-10 treatment. Induction of HLA-G expression by IL-10 on monocytes may thus play a role in down-regulation of the immune response. We propose that IL-10 secretion by trophoblasts during pregnancy may also influence the HLA class I expression pattern at the feto-maternal barrier, thus protecting the fetus from rejection. This should be taken into consideration in the design of treatment for pathologies of pregnancy.
Chemically Integrated Inorganic‐Graphene Two‐Dimensional Hybrid Materials for Flexible Energy Storage Devices (2016)

State-of-the-art energy storage devices are capable of delivering reasonably high energy density (lithium ion batteries) or high power density (supercapacitors). There is an increasing need for these power sources with not only superior electrochemical performance, but also exceptional flexibility. Graphene has come on to the scene and advancements are being made in integration of various electrochemically active compounds onto graphene or its derivatives so as to utilize their flexibility. Many innovative synthesis techniques have led to novel graphene-based hybrid two-dimensional nanostructures. Here, the chemically integrated inorganic-graphene hybrid two-dimensional materials and their applications for energy storage devices are examined. First, the synthesis and characterization of different kinds of inorganic-graphene hybrid nanostructures are summarized, and then the most relevant applications of inorganic-graphene hybrid materials in flexible energy storage devices are reviewed. The general design rules of using graphene-based hybrid 2D materials for energy storage devices and their current limitations and future potential to advance energy storage technologies are also discussed.
Interactions of the Mcm1 MADS Box Protein with Cofactors That Regulate Mating in Yeast (2002)

The yeast Mcm1 protein is a member of the MADS box family of transcriptional regulatory factors, a class of DNA-binding proteins that control numerous cellular and developmental processes in yeast, Drosophila melanogaster, plants, and mammals. Although these proteins bind DNA on their own, they often combine with different cofactors to bind with increased affinity and specificity to their target sites. To understand how this class of proteins functions, we have made a series of alanine substitutions in the MADS box domain of Mcm1 and examined the effects of these mutations in combination with its cofactors that regulate mating in yeast. Our results indicate which residues of Mcm1 are essential for viability and transcriptional regulation with its cofactors in vivo. Most of the mutations in Mcm1 that are lethal affect DNA-binding affinity. Interestingly, the lethality of many of these mutations can be suppressed if the MCM1 gene is expressed from a high-copy-number plasmid. Although many of the alanine substitutions affect the ability of Mcm1 to activate transcription alone or in combination with the α1 and Ste12 cofactors, most mutations have little or no effect on Mcm1-mediated repression in combination with the α2 cofactor. Even nonconservative amino acid substitutions of residues in Mcm1 that directly contact α2 do not significantly affect repression. These results suggest that within the same region of the Mcm1 MADS box domain, there are different requirements for interaction with α2 than for interaction with either α1 or Ste12. Our results suggest how a small domain, the MADS box, interacts with multiple cofactors to achieve specificity in transcriptional regulation and how subtle differences in the sequences of different MADS box proteins can influence the interactions with specific cofactors while not affecting the interactions with common cofactors.
Physiological consequences of DnaK and DnaJ overproduction in Escherichia coli (1992)

The physiological consequences of molecular chaperone overproduction in Escherichia coli are presented. Constitutive overproduction of DnaK from a multicopy plasmid containing large chromosomal fragments spanning the dnaK region resulted in plasmid instability. Co-overproduction of DnaJ with DnaK stabilized plasmid levels. To examine the effects of altered levels of DnaK and DnaJ in a more specific manner, an inducible expression system for dnaK and dnaJ was constructed and characterized. Differential rates of DnaK synthesis were determined by quantitative Western blot (immunoblot) analysis. Moderate levels of DnaK overproduction resulted in a defect in cell septation and formation of cell filaments, but co-overproduction of DnaJ overcame this effect. Further increases in the level of DnaK terminated culture growth despite increased levels of DnaJ. DnaK overproduction was found to be bacteriocidal, and this effect was also partially suppressed by DnaJ. The bacteriocidal effect was apparent only with cultures which were allowed to enter stationary phase, indicating that DnaK toxicity is growth phase dependent.