gebhart/patrepeval huggingface dataset:
Anthill: a framework for the development of agent-based peer-to-peer systems (2003)

Recent peer-to-peer (P2P) systems are characterized by decentralized control, large scale and extreme dynamism of their operating environment. As such, they can be seen as instances of complex adaptive systems (CAS) typically found in biological and social sciences. We describe Anthill, a framework to support the design, implementation and evaluation of P2P applications based on ideas such as multi-agent and evolutionary programming borrowed from CAS. An Anthill system consists of a dynamic network of peer nodes; societies of adaptive agents travel through this network, interacting with nodes and cooperating with other agents in order to solve complex problems. Anthill can be used to construct different classes of P2P services that exhibit resilience, adaptation and self-organization properties. We also describe preliminary experiences with Anthill in implementing a file sharing application.
Selection studies of zinc finger-DNA recognition (1997)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1997.
Antagonistic Regulation of β-Globin Gene Expression by Helix-Loop-Helix Proteins USF and TFII-I (2006)

The human beta-globin genes are expressed in a developmental stage-specific manner in erythroid cells. Gene-proximal cis-regulatory DNA elements and interacting proteins restrict the expression of the genes to the embryonic, fetal, or adult stage of erythropoiesis. In addition, the relative order of the genes with respect to the locus control region contributes to the temporal regulation of the genes. We have previously shown that transcription factors TFII-I and USF interact with the beta-globin promoter in erythroid cells. Herein we demonstrate that reducing the activity of USF decreased beta-globin gene expression, while diminishing TFII-I activity increased beta-globin gene expression in erythroid cell lines. Furthermore, a reduction of USF activity resulted in a significant decrease in acetylated H3, RNA polymerase II, and cofactor recruitment to the locus control region and to the adult beta-globin gene. The data suggest that TFII-I and USF regulate chromatin structure accessibility and recruitment of transcription complexes in the beta-globin gene locus and play important roles in restricting beta-globin gene expression to the adult stage of erythropoiesis.
Single-molecule orientation measurements with a quadrated pupil (2013)

This Letter presents a means of measuring the dipole orientation of a fluorescent, orientationally fixed single molecule, which uses a specially designed phase mask, termed a "quadrated pupil," conjugate to the back focal plane of a conventional wide-field microscope. The method leverages the spatial anisotropy of the far-field emission pattern of a dipole emitter and makes this anisotropy amenable to quantitative analysis at the image plane. In comparison to older image-fitting techniques that infer orientation by matching simulations to defocused or excessively magnified images, the quadrated pupil approach is more robust to minor modeling discrepancies and optical aberrations. Precision of 1°-5° is achieved in proof-of-concept experiments for both azimuthal (φ) and polar (θ) angles without defocusing. Since the phase mask is implemented on a liquid-crystal spatial light modulator that may be deactivated without any mechanical perturbation of the sample or imaging system, the technique may be readily integrated into clear aperture imaging studies.
Proceedings 1997 Image Understanding Workshop 11-14 May Hyatt Regency, New Orleans, LA. Volume I, (1997)

Abstract : This proceedings contains the assembled reports of the various research projects that comprise the DARPA Image Understanding (IU) Program. Submissions from forty academic and industrial computer vision research laboratories document progress and lessons learned in research performed for applications in image registration, target recognition, image exploitation, cartography, 3D model reconstruction, video surveillance, activity recognition and content-based image retrieval. This is the 25th proceedings in the series, which has become known as a comprehensive source for the latest research results in image understanding from the nation's leading ID laboratories. Like its predecessors, this proceedings is not peer-reviewed in the traditional sense of a refereed conference or journal. Instead, the principal investigator of each laboratory is responsible for selecting the papers that will represent the work carried out in his lab. Because the reputation of each lab is at stake, the quality of submissions has remained consistently high.
Quantification of Cellular Proliferation in Tumor and Normal Tissues of Patients with Breast Cancer by [18F]Fluorothymidine-Positron Emission Tomography Imaging: Evaluation of Analytical Methods (2005)

There is an unmet need to develop imaging methods for the early and objective assessment of breast tumors to therapy. 3'-Deoxy-3'-[18F]fluorothymidine ([18F]FLT)-positron emission tomography represents a new approach to imaging thymidine kinase activity, and hence, cellular proliferation. We compared graphical, spectral, and semiquantitative analytic methodologies for quantifying [18F]FLT kinetics in tumor and normal tissue of patients with locally advanced and metastatic breast cancer. The resultant kinetic parameters were correlated with the Ki-67 labeling index from tumor biopsies. [18F]FLT accumulation was detected in primary tumor, nodal disease, and lung metastasis. In large tumors, there was substantial heterogeneity in regional radiotracer uptake, reflecting heterogeneity in cellular proliferation; radiotracer uptake in primary tumors also differed from that of metastases. [18F]FLT was metabolized in patients to a single metabolite [18F]FLT-glucuronide. Unmetabolized [18F]FLT accounted for 71.54 +/- 1.50% of plasma radioactivity by 90 minutes. The rate constant for the metabolite-corrected net irreversible uptake of [18F]FLT (Ki) ranged from 0.6 to 10.4 x 10(-4) and from 0 to 0.6 x 10(-4) mL plasma cleared/s/mL tissue in tumor (29 regions, 15 patients) and normal tissues, respectively. Tumor Ki and fractional retention of radiotracer determined by spectral analysis correlated with Ki-67 labeling index (r = 0.92, P < 0.0001 and r = 0.92, P < 0.0001, respectively). These correlations were superior to those determined by semiquantitative methods. We conclude that [18F]FLT-positron emission tomography is a promising clinical tool for imaging cellular proliferation in breast cancer, and is most predictive when analyzed by graphical and spectral methods.
Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy (2009)

An important part of characterizing any protein molecule is to determine its size and shape. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. Instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elongated. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. A combination of hydrodynamics and electron microscopy is especially powerful.
Improvement of Ionic Conductivity of Room Temperature Molten Salt Based on Quaternary Ammonium Cation and Imide Anion (1999)

The improvement of the conductivity of room temperature molten salt (RTMS) based on quaternary aliphatic ammonium cations (QA) and bis(trifluoromethanesulfon)imide was investigated. The conductivity was apparently increased with decreasing molecular weight of cation. The lightest cation was trimethylpropylammonium, which indicate relatively high conductivity of 4.0 mS cm−1 (30°C). Further improvement could be performed by slight modifications such as an addition of a methyl group and a replacement of carbon to oxygen in the alkyl side chain. The effect of such modifications to the conductivity was attributed to the difference of dipole moment of QA estimated by MOPAC. The electrochemical properties of RTMS based on QA were also investigated. The cathodic limits of RTMS based on QA were different according to the cationic structure. Since the most negative cathodic limit obtained was −0.4 V vs. Li/Li+, the plating and stripping behavior of lithium on Ni could be performed in the RTMS based on QA.
Inductively Coupled Plasmas For Highly Efficient and Low Damage Resist Stripping (2005)

A new plasma source using inductively coupled plasma (ICP) excitation has been developed that offers several advantages over more commonly used microwave-based sources, including low generation of damaging species such as charged particles and UV radiation and less heat production by the plasma. The new ICP source is inherently more efficient in producing the neutral reactive (atomic and molecular) oxygen species active in the strip process. A range of damage and contamination tests, including measurements of wafer charging, mobile metal and heavy metal contamination, and minority carrier lifetime degradation, confirm that the ICP source produces less wafer charge damage and contamination than typical microwave systems. This paper discusses the fundamental physics of the ICP source and presents results of computer modeling studies using a Boltzmann code which explain the overall increase in performance. The calculations give the distribution of electron energies in the plasma along with the rate constants for the high energy inelastic collision processes which produce oxygen dissociation, ionization, and UV excitation. These calculations show that in the ICP source, less than 0.3% of the power goes into the production of charged particles and UV radiation, and about 17% goes into the production of heat. The ICP source therefore requires less heavily baffled gas flow and generates a much lower heat load on the plasma chamber walls, making it much more compatible with advanced process chemistries such as those using fluorine.
Differential Host-dependent Expression of -galactosyl Epitopes on Viral Glycoproteins: A Study of Eastern Equine Encephalitis Virus as a Model (1994)

The carbohydrate epitope Gal alpha 1-3Gal beta 1-4GlcNAc-R (alpha-galactosyl) is abundantly expressed on cells of non-primate mammals, prosimians and New World monkeys, where it is synthesized by the enzyme alpha 1,3-galactosyltransferase (alpha 1,3GT). Old World monkeys, apes and humans lack alpha 1,3GT and hence do not synthesize alpha-galactosyl epitopes. Instead, these species produce a natural antibody, anti-Gal, which interacts specifically with alpha-galactosyl epitopes and which constitutes up to 1% of circulating immunoglobulins in humans. We have used eastern equine encephalitis (EEE) virus as a model to examine the differential expression of alpha-galactosyl epitopes on the glycoproteins of virus propagated in cells that either produce or lack alpha 1,3GT. As predicted, virus propagated in Vero cells (derived from the African green monkey, an Old World monkey) did not express alpha-galactosyl epitopes. In contrast, virus propagated in mouse 3T3 cells (EEE3T3) expressed approximately 80 alpha-galactosyl epitopes per virion on both the E1 and the E2 envelope glycoproteins. Thus, expression of the alpha-galactosyl epitope on virions paralleled that on host cells. The binding of anti-Gal antibody to these epitopes on EEE3T3 virions partially neutralized virus infectivity, raising the possibility that anti-Gal production in hosts may influence the initial infectious stage of viruses expressing alpha-galactosyl epitopes.
On rectified linear units for speech processing (2013)

Deep neural networks have recently become the gold standard for acoustic modeling in speech recognition systems. The key computational unit of a deep network is a linear projection followed by a point-wise non-linearity, which is typically a logistic function. In this work, we show that we can improve generalization and make training of deep networks faster and simpler by substituting the logistic units with rectified linear units. These units are linear when their input is positive and zero otherwise. In a supervised setting, we can successfully train very deep nets from random initialization on a large vocabulary speech recognition task achieving lower word error rates than using a logistic network with the same topology. Similarly in an unsupervised setting, we show how we can learn sparse features that can be useful for discriminative tasks. All our experiments are executed in a distributed environment using several hundred machines and several hundred hours of speech data.
Nucleotide sequence and transcriptional initiation site of two Pseudomonas aeruginosa pilin genes. (1986)

The complete nucleotide sequences of the 1.2-kilobase HindIII fragments which contain the pilin genes of two independently isolated strains of Pseudomonas aeruginosa (PAK and PA103) have been determined and compared to that of strain PA01 (Sastry, P. A., Finlay, B. B., Pasloske, B. L., Paranchych, W., Pearlstone, J. R., and Smollier, L. B. (1985) J. Bacteriol. 164, 571-577). The fragments share extensive regions of homology, including the 5'- and 3'-flanking sequences as well as the 5' end of the pilin gene. The most highly diverged segments of the pilin genes are those which encode the variable carboxyl-terminal region of the pilin polypeptides. The pilin polypeptides each contain a 6-amino acid amino-terminal leader peptide (Met-Lys-Ala-Gln-Lys-Gly) and are nearly identical in the following 60 amino acids. The carboxyl-terminal portion of the pilin polypeptides contain extensive regions of divergence in their amino acid sequences, although hydropathicity analysis of the pilin polypeptides indicated that they are structurally similar. The transcriptional initiation site of the PAK pilin gene has been determined by S1 nuclease mapping. The promoter region at -10 and -35 base pairs from the transcriptional initiation site shows no significant homology to the consensus Escherichia coli promoter, but the -12 and -24 regions show a high degree of homology to promoters which require the ntrA gene product for transcription. Several other Pseudomonas promoters and the promoters of the homologous pilin genes from other bacterial species also share homology to this sequence.
Thermoset-Layered Silicate Nanocomposites. Quaternary Ammonium Montmorillonite with Primary Diamine Cured Epoxies (2000)

The role of various quaternary ammonium-modified montmorillonites in epoxy/diamine nanocomposite formation is examined to further refine the criteria for selection of organic modifiers necessary to enable fabrication of thermoset resins containing nanoscale dispersions of inorganic phases. Utilization of a hydroxyl-substituted quaternary ammonium modifier affords flexibility to combine both catalytic functionality, which increases the intragallery reaction rate, with enhanced miscibility toward both reagents. The rheological implications of these processing techniques are discussed with regards to using thermoset nanocomposites as a matrix in conventional fiber reinforced composites. The use of a low-boiling solvent to enhance mixability and processability of the initial mixtures is shown not to alter the structure or properties of the final nanocomposite. Also, the use of autoclave techniques enabled fabrication of high-quality specimens containing up to 20 wt % organically modified layered silicate (OLS). Finally, exfoliated and partially exfoliated epoxy/diamine nanocomposites were produced with enhanced heat-distortion temperature and increased flammability resistance.
An in situ electrical study on primary hydrogen spillover from nanocatalysts to amorphous carbon support (2008)

Primary hydrogen spillover has been studied using a unique electrical method. We observed that at ambient temperature, when a discontinuous nanogranular Pd film is on the top of an amorphous carbon film, the electrical conductance of the carbon film decreases in pressurized hydrogen. In comparison, in the absence of this Pd layer, the conductance of the carbon film remains unchanged in pressurized hydrogen. The observed decrease in the current in the Pd/carbon structure is ascribed to the hydrogenation of the dangling carbon bonds and sp2-sp3 transition in the amorphous carbon by the primary spillover hydrogen atoms from Pd nanoclusters.
BLUETONGUE IN SHEEP AND GOATS (1975)

A description is given of the symptomatology, pathology and pathogenesis of bluetongue in sheep and goats. The economic significance of the disease in South Africa is discussed.
Directed ortho lithiation of isophthalonitrile. New methodology for the synthesis of 1,2,3-trisubstituted benzenes (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirected ortho lithiation of isophthalonitrile. New methodology for the synthesis of 1,2,3-trisubstituted benzenesTimothy D. Krizan and J. C. MartinCite this: J. Org. Chem. 1982, 47, 13, 2681–2682Publication Date (Print):June 1, 1982Publication History Published online1 May 2002Published inissue 1 June 1982https://pubs.acs.org/doi/10.1021/jo00134a038https://doi.org/10.1021/jo00134a038research-articleACS PublicationsRequest reuse permissionsArticle Views1277Altmetric-Citations37LEARN 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-Alertsclose Get e-Alerts
Reactions of Type II Restriction Endonucleases with 8-Base Pair Recognition Sites (1999)

Type II restriction endonucleases usually recognize 4-6-base pair (bp) sites on DNA and cleave each site in a separate reaction. A few type II endonucleases have 8-bp recognition sites, but these seem unsuited for restriction, since their sites are rare on most DNA. Moreover, only one endonuclease that recognizes a target containing 8 bp has been examined to date, and this enzyme, SfiI, needs two copies of this site for its DNA cleavage reaction. In this study, several endonucleases with 8-bp sites were tested on plasmids that have either one or two copies of the relevant sequence to determine if they also need two sites. SgfI, SrfI, FseI, PacI, PmeI, Sse8781I, and SdaI all acted through equal and independent reactions at each site. AscI cleaved the DNA with one site at the same rate as that with two sites but acted processively on the latter. In contrast, SgrAI showed a marked preference for the plasmid with two sites and cleaved both sites on this DNA in a concerted manner, like SfiI. Endonucleases that require two copies of an 8-bp sequence may be widespread in nature, where, despite this seemingly inappropriate requirement, they may function in DNA restriction.
In vivo endoscopic OCT imaging of precancer and cancer states of human mucosa (1997)

First results of endoscopic applications of optical coherence tomography for in vivo studies of human mucosa in respiratory, gastrointestinal, urinary and genital tracts are presented. A novel endoscopic OCT (EOCT) system has been created that is based on the integration of a sampling arm of an all-optical-fiber interferometer into standard endoscopic devices using their biopsy channel to transmit low-coherence radiation to investigated tissue. We have studied mucous membranes of esophagus, larynx, stomach, urinary bladder, uterine cervix and body as typical localization for carcinomatous processes. Images of tumor tissues versus healthy tissues have been recorded and analyzed. Violations of well-defined stratified healthy mucosa structure in cancered tissue are distinctly seen by EOCT, thus making this technique promising for early diagnosis of tumors and precise guiding of excisional biopsy.
Thermal and Photochemical Decomposition of Gaseous Aluminum Trimethyl (1946)

The thermal decomposition of gaseous aluminum trimethyl, in the absence of hydrogen, is nearly 94 percent homogeneous and of kinetic order three-halves over the pressure range 10 to 85 mm measured at room temperature. The reaction products consist largely of methane and to a lesser extent ethane, ethylene, and hydrogen and a solid deposit on the walls of the reaction vessel. A reaction mechanism involving methyl radicals is proposed. The apparent energy of activation, calculated on this basis, is found to be 45 kcal., in agreement with the experimentally determined figure. The high ratio of methane produced to alkyl decomposed suggests that aluminum trimethyl in the vapor state at room temperatures must consist at least of tetrameric molecular complexes. In the presence of hydrogen, both the decomposition rate and the energy of activation are reduced as compared to the decomposition of the pure alkyl, a puzzling effect for which no satisfactory explanation can at present be offered. Photochemically, the presence of hydrogen seems to have little effect on the over-all decomposition but enhances the relative amount of methane slightly. In this, aluminum trimethyl appears to differ from mercury dimethyl which is known to decompose faster thermally and photochemically in the presence of hydrogen than in its absence.
TMAHW etchants for silicon micromachining (1991)

Etching solutions based on tetramethyl ammonium hydroxide and water (TMAHW) are proposed for etching monocrystalline silicon. The nature of TMAHW solutions is discussed with respect to anisotropy, selectivity, and IC-process compatibility. At a solution temperature of 80 degrees C and 2 wt.% TMAH, a maximum
Brief Report: Stimulation of Bone Marrow Colony Growth In Vitro by Human Urine (1969)

Abstract Using a new technic of bone marrow culture in agar, urine samples from 50 humans have been tested for their ability to stimulate the formation of granulocyte—mononuclear cell growth in vitro. Significant colony stimulating activity has been found with 25 out of 50 unconcentrated urine samples from both normal humans and patients with a variety of disease states.