gebhart/patrepeval huggingface dataset:
Collecting and Analyzing Provenance on Interactive Notebooks: when IPython meets noWorkflow (2015)

Interactive notebooks help users explore code, run simulations, visualize results, and share them with other people. While these notebooks have been widely adopted in teaching as well as by scientists and data scientists that perform exploratory analyses, their provenance support is limited to the visualization of some intermediate results and code sharing. Once a user arrives at a result, it is hard, and sometimes impossible, to retrace the steps that led to the result, since they do not collect the provenance for intermediate resuls or of the environment. As a result, users must fulfill this gap using external tools such as workflow management systems. To overcome this limitation, we propose a new approach to capture provenance from notebooks. We build upon no Workflow, a system that systematically collects provenance for Python scripts. By integrating no Workflow and notebooks, provenance is automatically and transparently captured, allowing users to focus on their exploratory tasks within the notebook. In addition, they are able to analyze provenance information within the notebook, to both reason about and debug their work, using visualizations, SQL queries, Prolog queries, and Python code.
iTV handbook: technologies &amp; standards (2004)

Interactive television (iTV) is an evolutionary merging of digital TV and the internet. iTV technology offers new powerful ways for consumers to interact with content and service providers. In Europe, iTV has gained significant traction during the turn of the century. For example, about 500,000 viewers signed up for SkyDigital's email service during 2000. In another example, Nickelodeon's "Watch Your Own Week" voting application was available to SkyDigital viewers during Oct 22-27 2001. While only 100,000 votes were anticipated for the whole week, this goal was reached within two days; a total of 578,000 votes were recorded for the week. Today, Europe counts tens of millions of iTV consumers.The iTV Handbook is a broad overview of the business and technical issues, and could be used as a textbook for an introductory technical course: it lays out the current thinking on commercially viable uses of iTV, surveys the related technical standards, and describes a broad range of technologies and the relationships among them. A whole chapter is devoted to the big picture of the iTV food chain, and another key chapter is devoted to a survey of media streaming methods. A "file system in the sky" is described which is the broadcasting equivalent of the network file system, and can be used to eliminate the notorious "hot spot" encountered when millions of receivers are trying to access a small set of pages. The book provides many rare insights into the nuts and bolts of the technologies being used. For example, the book presents part of the theoretical foundation for MP3 compression, and describes in detail many popular file formats used to deliver iTV content, including GIF, QuickTime, AVI, and ZIP.
CD1 expression defines subsets of follicular and marginal zone B cells in the spleen: beta 2-microglobulin-dependent and independent forms. (1998)

We have used multicolor FACS analysis, immunohistology, and functional assays to study the expression of CD1 on B cell subsets from normal and beta 2m-/- mice. Two B cell subpopulations were identified that express high levels of CD1 in normal mice: splenic marginal zone B cells (IgMhigh IgDlow CD21high CD24intermediate CD23- CD43-) and a newly identified subpopulation of follicular B cells. The latter cells are unusual, because they are IgDhigh CD23+, like follicular B cells, but express high levels of CD21 and IgM, an expression pattern that is associated with marginal zone B cells. Therefore, the high-level expression of CD1 and CD21 was found to be closely associated on splenic B cells. Immunohistology confirmed the expression of CD1 on marginal zone B cells and on clusters of B cells in splenic follicles. Both the high-level CD1 expression by these cells and the low-level CD1 expression by subpopulations of B cells in the spleen, lymph node, peritoneal cavity, and bone marrow were markedly reduced in beta 2m-/- mice. Despite this, a CD1-restricted T cell clone proliferated vigorously in response to LPS-activated spleen cells that had been obtained from both beta 2m-/- and wild-type mice. This response was inhibited by the 3C11 anti-CD1 mAb. These results show the heterogeneity of B cell subsets in their expression of the beta 2m-dependent form of CD1. They further suggest that a beta 2m-independent form of CD1 is expressed on B cells that can stimulate T cells; however, this form is not easily visualized with the anti-CD1 mAb used here.
MACS: a predictable architecture for real time systems (2002)

The MACS (multiple active context system) architecture is a high-performance, multiple context, cacheless processor designed around the goal of predictability. Multiple contexts provide highly predictable memory and pipeline performance, while at the same time allowing multiple threads to execute with independent timing characteristics. The design emphasis is on provable execution speed and independent timing of each context. Task-level parallelism is used to maintain high processor throughput while individual threads execute at a relatively slow, but very predictable, rate. The authors investigate the suitability of such a system to real time and determine how predictability varies as a function of parallelism (performance), memory issue latency and memory size.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Amphiregulin induces tyrosine phosphorylation of the epidermal growth factor receptor and p185erbB2. Evidence that amphiregulin acts exclusively through the epidermal growth factor receptor at the surface of human epithelial cells. (1993)

The COOH-terminal half of the amphiregulin (AR) molecule has sequence homology to epidermal growth factor (EGF). The ability of AR to elicit in vivo phosphorylation of the EGF receptor (EGFR) and p185erbB2 was studied in four human epithelial cell lines which expressed either or both of the receptor tyrosine kinases. AR induced the phosphorylation of the EGFR and p185erbB2, and phosphoamino acid analysis revealed enhanced phosphorylation of tyrosine residues in both receptor proteins. A monoclonal antibody (mAb) which binds to the extracellular domain of the EGFR blocked the phosphorylation of the EGFR and p185erbB2 as well as AR-induced mitogenesis indicating that the EGFR mediated these responses. In MDA-MB-453 cells which lack EGFRs, AR did not induce phosphorylation of p185erbB2, did not affect proliferation, and had no detectable effect on the phosphorylation of cellular proteins isolated using an anti-phosphotyrosine mAb. Qualitatively, in vivo phosphorylations induced by AR and EGF were found to be indistinguishable as demonstrated by analysis of cellular 32P-labeled proteins isolated with the anti-phosphotyrosine mAb. Moreover, in the presence of the anti-EGFR mAb, AR had no effect on the proliferation of cells. These results provide strong evidence that the EGFR is the sole cell surface mediator of the action of AR in human epithelial cells.
Stromelysin/transin and tumor progression. (1990)

Transin is an oncogene-inducible protein which has been shown to be the rat homologue of an extracellular matrix-degrading metalloproteinase known as stromelysin. The activity of transin/stromelysin is regulated at several levels: (1) at the transcriptional level, it is positively regulated by oncogenes, tumor promoters, and certain growth factors, and is negatively regulated by several agents including glucocorticoids and transforming growth factor-beta; (2) the protease activity is produced by processing of an inactive precursor form to an active enzyme; and (3) total protease activity is modulated by activity of tissue inhibitors of metalloproteinases (TIMPs). The association of transin/stromelysin expression with tumor progression suggests that it plays an important role in cancer.
Design and Synthesis of Pyrrolidine-5,5-<i>trans-</i>lactams (5-Oxohexahydropyrrolo[3,2-<i>b</i>]pyrroles) as Novel Mechanism-Based Inhibitors of Human Cytomegalovirus Protease. 2. Potency and Chirality (2001)

The stereospecific synthesis of a series of alpha-methylpyrrolidine-5,5-trans-lactam inhibitors of human cytomegalovirus (HCMV) protease is described. Examination of the SAR in this series has defined the size and chirality of the alpha-substituent, optimized the acyl substituent on the lactam nitrogen, and defined the steric constraint of this functionality. The SAR of the functionality on the pyrrolidine nitrogen of the trans-lactam has been investigated, and this has led to the discovery of potent serine protease inhibitors that are highly selective for the viral enzyme over the mammalian enzymes elastase, thrombin, and acetylcholine esterase. The mechanism of action of our lead compounds has been established by mass spectrometry, and enzymatic degradation of HCMV deltaAla protease acylated with these inhibitors showed that Ser 132 is the active site nucleophile. The crystal structure of HCMV protease was obtained and used to model the conformationally restricted, chiral (S)-proline-alpha-methyl-5,5-trans-lactams into the active site groove of the enzyme, enabling us to direct and rationalize the SAR in this series. The activity against HCMV deltaAla protease is the greatest with inhibitors based on the dansyl-(S)-proline alpha-methyl-5,5-trans-lactam template, which have low nanomolar activity against the viral enzyme.
Deep Feature Consistent Variational Autoencoder (2017)

We present a novel method for constructing Variational Autoencoder (VAE). Instead of using pixel-by-pixel loss, we enforce deep feature consistency between the input and the output of a VAE, which ensures the VAE's output to preserve the spatial correlation characteristics of the input, thus leading the output to have a more natural visual appearance and better perceptual quality. Based on recent deep learning works such as style transfer, we employ a pre-trained deep convolutional neural network (CNN) and use its hidden features to define a feature perceptual loss for VAE training. Evaluated on the CelebA face dataset, we show that our model produces better results than other methods in the literature. We also show that our method can produce latent vectors that can capture the semantic information of face expressions and can be used to achieve state-of-the-art performance in facial attribute prediction.
The biology of cholinesterases (1974)

The biology of cholinesterases , The biology of cholinesterases , کتابخانه مرکزی دانشگاه علوم پزشکی ایران
Invasion of Human Coronary Artery Cells by Periodontal Pathogens (1999)

There is an emerging paradigm shift from coronary heart disease having a purely hereditary and nutritional causation to possibly having an infectious etiology. Recent epidemiological studies have shown a correlation between periodontal disease and coronary heart disease. However, to date, there is minimal information as to the possible disease mechanisms of this association. It is our hypothesis that invasion of the coronary artery cells by oral bacteria may start and/or exacerbate the inflammatory response in atherosclerosis. Since a few periodontal pathogens have been reported to invade oral epithelial tissues, we tested the ability of three putative periodontal pathogens-Eikenella corrodens, Porphyromonas gingivalis, and Prevotella intermedia-to invade human coronary artery endothelial cells and coronary artery smooth muscle cells. In this study we demonstrate by an antibiotic protection assay and electron microscopy that specific species and strains invade coronary artery cells at a significant level. Actin polymerization and eukaryotic protein synthesis in metabolically active cells were required since the corresponding inhibitors nearly abrogated invasion. Many intracellular P. gingivalis organisms were seen to be present in multimembranous vacuoles resembling autophagosomes by morphological analysis. This is the first report of oral microorganisms invading human primary cell cultures of the vasculature.
Advanced Non-Soldering Interconnection (1991)

The number of soldered joints per circuit is rapidly increasing, especially on surface mounted boards. As a result, defective solder joints are becoming the dominant cause of board failures. Also, there is a move to closer spacing of connections which leads to solder bridging and difficulty of flux removal and joint inspection. These, coupled with other solder disadvantages, have led the military and industrial companies to look for alternative component connection methods. Because of the high cost of components and the circuit substrates it is mandatory to be able to replace defective parts easily.
Phylogeny of the genus Flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector (2000)

Attempts to define the evolutionary relationships and origins of viruses in the genus Flavivirus are hampered by the lack of genetic information particularly amongst the non-vectored flaviviruses. Using a novel protocol for sequence determination, the first complete coding sequence of St Louis encephalitis virus and those of two representative non-vectored flaviviruses, Rio Bravo (isolated from bat) and Apoi (isolated from rodent), are reported. The encoded polyproteins of Rio Bravo and Apoi virus are the smallest described to date within the genus FLAVIVIRUS: The highest similarities with other flaviviruses were found in the NS3 and NS5 genes. The proteolytic cleavage sites for the viral serine protease were highly conserved among the flaviviruses completely sequenced to date. Comparative genetic amino acid alignments revealed that p-distance cut-off values of 0.330-0.470 distinguished the arthropod-borne viruses according to their recognized serogroups and Rio Bravo and Apoi virus were assigned to two distinct non-vectored virus groups. Within these serogroups, cladogenesis based on the complete ORF sequence was similar to trees based on envelope and NS5 sequences. In contrast, branching patterns at the deeper nodes of the tree were different from those reported in the previous study of NS5 sequences. The significance of these observations is discussed.
Nondestructive Microwave Measurement of Moisture Content and Mass of Single Peanut Kernels (1993)

Principles for determining moisture content and mass of individual peanut kernels by microwave resonator measurements are discussed, and data are presented showing the application of these principles. By measuring the shift in the resonant frequency and the change in the cavity transmission characteristics when a peanut is inserted into the cavity, it is possible to obtain the moisture content of the kernel independent of its mass and apparently independent of peanut type, as far as Runner and Virginia market types are concerned. It is also possible to determine the kernel mass independent of kernel shape simultaneously with the moisture determination. Moisture contents in the range from 4 to 14%, wet basis, were determined with an uncertainty of 0.9% moisture, and the uncertainty in the mass determination was less than 0.05 g.
Efavirenz plasma levels can predict treatment failure and central nervous system side effects in HIV-1-infected patients (2001)

Treatment failure and CNS side-effects are associated with low and high efavirenz plasma levels, respectively. The important inter-individual variability in efavirenz levels strongly argues for dose adjustment on the basis of therapeutic drug monitoring to optimize treatment.
Tumorigenicity of mouse thymoma is suppressed by soluble type II transforming growth factor beta receptor therapy. (1999)

Many types of tumor cells overexpress transforming growth factor beta (TGF-beta), which is believed to promote tumor progression. We hypothesized that overexpression of the extracellular region of the type II TGF-beta receptor (soluble TbetaRII) would compete for or block TGF-beta binding to TbetaRs on immune cells, preventing TGF-beta-mediated immunosuppression and consequently resulting in the eradication of tumor cells. We tested this in the mouse thymoma cell line EL4, which has been reported to suppress cellular immunity by secreting a large amount of TGF-beta. Transduction of EL4 with recombinant retrovirus encoding soluble TbetaRII resulted in the secretion of heterogeneously glycosylated, 25 to 35 kDa truncated TbetaRII. Inoculation of 1 x 10(4) to 5 x 10(4) soluble TbetaRII-modified EL4 cells (EL4/Ts, EL4 cells transduced with recombinant retrovirus encoding soluble TbetaRII and neomycin resistance gene) s.c. to mice showed reduced tumorigenicity, as indicated by lower overall tumor incidence (7%, 1 of 14; P < 0.001) compared with unmodified EL4 (100%, 9 of 9) or vector-modified EL4 cells (EL4/neo, EL4 cells transduced with recombinant retrovirus encoding neomycin resistance gene; 100%, 4 of 4). Administration of mitomycin C-treated EL4/Ts cells (1 x 10(6)) after EL4 inoculation (1 x 10(4)) reduced tumor incidence from 100% (5 of 5 in mice inoculated with mitomycin C-treated EL4/neo) to 40% (4 of 10, P < 0.05), indicating that supply of soluble TbetaRII could actually block TGF-beta-mediated tumorigenesis. In vitro tumor cytotoxicity assays revealed 3-5-fold higher cytotoxic activity with lymphocytes from EL4/Ts-bearing mice compared with those from EL4- or EL4/neo-bearing mice, indicating that the observed tumor rejection was mediated by restoration of the tumor-specific cellular immunity. These data suggest that expression of soluble TbetaRII is an effective strategy for treating highly progressive tumors secreting TGF-beta.
Adsorption of NO on Cu-SAPO-34 and Co-SAPO-34:  A Periodic DFT Study (2008)

The location of Cu(I), Cu(II), and Co(II) cations at the extraframework sites of metal cation exchanged SAPO-34 as well as their adsorption properties toward NO are studied by periodic DFT calculations with the PW91 functional. The relative stability of configurations with variable positions of the Si → P substitutions and cation sites was examined; structures with the divalent cation located in proximity to closely spaced negative framework charges were of highest stability. The highest adsorption capacities of the divalent Cu and Co cations were determined for an environment with Si → P substitutions separated in the unit cells, but the interaction between the cation and the more distant negative charges is important for the formation of a stable adsorption complex. The Cu(I)−NO configuration in SAPO-34 is bent, with an angle ∠Cu(I)−N−O of 141.0°. This enables an interaction of the dz2 state of the cation with both the σ and π* molecular orbitals. Backdonation to the π* state leads to a red-shift of the NO stretching frequency by ∼100 cm-1, in good agreement with experiment. For divalent metal cations Cu(II) and Co(II), the highest adsorption energies are related to wider ∠M(II)−N−O angles, shorter M(II)−N bonds, and a slightly weakened N−O bond, indicating a significant electrostatic contribution (ion-dipole interactions) to the bonding and a much less pronounced dπ → π* back-donation, as reflected by an almost unchanged NO stretching frequency.
Spinal implants: past, present, and future (2002)

Spinal fusion has become a widely used technique to treat a variety of spinal instability syndromes including those due to trauma, tumor, infection, degeneration, and deformity. Spinal fusion is always performed using bone graft with or without stabilizing implants. The degree of the associated instability usually determines the necessity of implants. Instrumentation of the spine has undergone revolutionary changes over the past decade. It has evolved from the use of only wire, to wire holding rods, to rods with hooks, to universal systems which include hooks, wires, pedicle screws, and rods or plates. Rods and plates can be contoured to enable segmental maneuvering of the individual vertebrae.
Photocrosslinking of 5-Iodouracil-Substituted RNA and DNA to Proteins (1993)

5-Iodouracil-substituted RNA and DNA were crosslinked regiospecifically to associated proteins in yields of 70 to 94% of bound nucleic acid. Irradiation of the iodouracil chromophore with monochromatic, long-wavelength ultraviolet radiation (325 nanometers) eliminates excitation of other nucleic acid and protein chromophores. The combination of high crosslinking yields, excellent specificity, and elimination of photodamage to other chromophores represents an important advance toward the precise identification of contacts in nucleoprotein complexes.
Fluorescence-Based Screening of Asymmetric Acylation Catalysts through Parallel Enantiomer Analysis. Identification of a Catalyst for Tertiary Alcohol Resolution (2001)

A technique for high-throughput screening of kinetic resolution catalysts is reported. The method relies on carrying simultaneous kinetic resolutions in a multiwell plate format wherein each well contains a unique catalyst and a small amount of a pH-activated fluorescent sensor (3). By conducting experiments such that each catalyst is evaluated in parallel in the presence of each isolated enantiomer, an indication of catalyst activity is obtained on a per enantiomer basis. Catalysts that are highly active for one enantiomer but modestly active for another are then reevaluated in conventional kinetic resolutions. From these screens, a highly selective (k(rel) = 46) pentapeptide (4) was obtained for a model secondary alcohol (1). In addition, peptide 10 was found to afford excellent selectivities (k(rel) > 20) for a number of alcohol substrates (9a-9f) in the traditionally challenging tertiary class.
Gene Therapy of Orthotopic Hepatocellular Carcinoma in Rats Using Adenovirus Coding for Interleukin 12 (2001)

The use of gene therapy to enhance antitumor immunity has emerged as a promising procedure to fight cancer. In this study we have tested the ability of an adenovirus carrying interleukin 12 (IL-12) gene (AdCMVIL-12) to eliminate tumoral lesions in 3 animal models of orthotopic hepatocellular carcinoma (HCC). Intratumoral injection of AdCMVIL-12 in animals with a single big tumor nodule implanted in the liver resulted in significant inhibition of tumor growth in a dose-dependent manner. Fifty percent of animals that received a dose of 5 x 10(9) plaque-forming units, showed complete regression of the tumor 2 weeks after treatment. In animals with 2 independent tumor nodules in the left liver lobe, injection in only one of them of 5 x 10(9) pfu AdCMVIL-12 induced, 15 days after therapy, complete regression of 50% of treated tumors and also of 50% of untreated lesions, with 60% long-term survival. Rats that were tumor free after therapy with AdCMVIL-12 showed protection against tumor rechallenge. A group of rats received the carcinogen diethylnitrosamine and developed multiple hepatic dysplasic nodules of 1 to 5 mm in diameter. These animals were treated by intrahepatic artery injection of either AdCMVIL-12 (5 x 10(9) pfu) or control vector. In this model AdCMVIL-12 induced complete tumor regression in 20% of treated rats and inhibited tumor growth in 60% of cases with an increase in rat survival. Activation of natural killer (NK) cells and inhibition of angiogenesis were found to be antitumor mechanisms set in motion by AdCMVIL-12. Our data indicate that experimental HCC can be efficiently treated by intratumoral or intravascular injection of adenovirus expressing IL-12.