gebhart/patrepeval huggingface dataset:
Walk-Sum Interpretation and Analysis of Gaussian Belief Propagation (2005)

This paper presents a new framework based on walks in a graph for analysis and inference in Gaussian graphical models. The key idea is to decompose correlations between variables as a sum over all walks between those variables in the graph. The weight of each walk is given by a product of edgewise partial correlations. We provide a walk-sum interpretation of Gaussian belief propagation in trees and of the approximate method of loopy belief propagation in graphs with cycles. This perspective leads to a better understanding of Gaussian belief propagation and of its convergence in loopy graphs.
An expeditious and general aromatic iodination procedure (1992)

J. Barluenga, J. M. González, M. A. Garcia-Martin, P. J. Campos and G. Asensio, J. Chem. Soc., Chem. Commun., 1992, 1016 DOI: 10.1039/C39920001016
A Comprehensive Review of Blockchain Consensus Mechanisms (2021)

Since the advent of distributed ledger technologies, they have provided diverse opportunities in a wide range of application domains. This article brings a comprehensive review of the fundamentals of distributed ledger and its variants. Analyzing 185 publications, ranging from academic journals to industry websites, it provides a comparative analysis of 130 consensus algorithms using a novel architectural classification. The distribution of the reviewed algorithms is analyzed in terms of the proposed classification and different application domains, along with the applicability of each class among the top 10 platforms in the most prominent blockchain application domains. Additional conclusions are drawn from the evolution of consensus mechanisms, and the analysis concludes envisaging future prospects for consensus as an important part of distributed ledger technology.
Subset of DC-SIGN+ dendritic cells in human blood transmits HIV-1 to T lymphocytes (2002)

The dendritic cell (DC)-specific molecule DC-SIGN is a receptor for the HIV-1 envelope glycoprotein gp120 and is essential for the dissemination of HIV-1. DC-SIGN is expressed by DCs, both monocyte-derived DCs and DCs in several tissues, including mucosa and lymph nodes. To identify a DC-SIGN(+) DC in blood that may be involved in HIV-1 infection through blood, we have analyzed the expression of DC-SIGN in human blood cells. Here we describe the characterization of a subset of DCs in human blood, isolated from T-/NK-/B-cell-depleted peripheral blood mononuclear cells (PBMCs) on the basis of expression of DC-SIGN. This subset coexpresses CD14, CD16, and CD33 and is thus of myeloid origin. In contrast to CD14(+) monocytes, DC-SIGN(+) blood cells display a DC-like morphology and express markers of antigen-presenting cells, including CD1c, CD11b, CD11c, CD86, and high levels of major histocompatibility complex (MHC) class I and II molecules. This DC population differs from other described CD14(-) blood DC subsets. Functionally, DC-SIGN(+) blood DCs are able to stimulate proliferation of allogeneic T cells and can produce tumor necrosis factor-alpha (TNF-alpha) and interleukin-6 (IL-6) upon activation with lipopolysaccharide (LPS). When they encounter HIV-1, low amounts of these blood DC-SIGN(+) DCs enhance infection of T lymphocytes in trans, whereas blood monocytes and CD14(-) blood DCs are not capable of transmitting HIV-1. Therefore DC-SIGN(+) blood DCs can be the first target for HIV-1 upon transmission via blood; they can capture minute amounts of HIV-1 through DC-SIGN and transfer HIV-1 to infect target T cells in trans.
A Sketching Algorithm for Spectral Graph Sparsification (2014)

We study the problem of compressing a weighted graph $G$ on $n$ vertices, building a "sketch" $H$ of $G$, so that given any vector $x \in \mathbb{R}^n$, the value $x^T L_G x$ can be approximated up to a multiplicative $1+ε$ factor from only $H$ and $x$, where $L_G$ denotes the Laplacian of $G$. One solution to this problem is to build a spectral sparsifier $H$ of $G$, which, using the result of Batson, Spielman, and Srivastava, consists of $O(n ε^{-2})$ reweighted edges of $G$ and has the property that simultaneously for all $x \in \mathbb{R}^n$, $x^T L_H x = (1 \pm ε) x^T L_G x$. The $O(n ε^{-2})$ bound is optimal for spectral sparsifiers. We show that if one is interested in only preserving the value of $x^T L_G x$ for a {\it fixed} $x \in \mathbb{R}^n$ (specified at query time) with high probability, then there is a sketch $H$ using only $\tilde{O}(n ε^{-1.6})$ bits of space. This is the first data structure achieving a sub-quadratic dependence on $ε$. Our work builds upon recent work of Andoni, Krauthgamer, and Woodruff who showed that $\tilde{O}(n ε^{-1})$ bits of space is possible for preserving a fixed {\it cut query} (i.e., $x\in \{0,1\}^n$) with high probability; here we show that even for a general query vector $x \in \mathbb{R}^n$, a sub-quadratic dependence on $ε$ is possible. Our result for Laplacians is in sharp contrast to sketches for general $n \times n$ positive semidefinite matrices $A$ with $O(\log n)$ bit entries, for which even to preserve the value of $x^T A x$ for a fixed $x \in \mathbb{R}^n$ (specified at query time) up to a $1+ε$ factor with constant probability, we show an $Ω(n ε^{-2})$ lower bound.
Measuring critical dimensions and overlays as prescribed by the National Technology Roadmap for Semiconductors (1997)

Continued demands on shrinking features with tighter tolerance on critical dimensions (CDs) and overlays (OL) are placing stringent requirements on parameters that are essentially the building blocks of the metrologies for CDs and overlays. This paper conducts a reality check on the precision and error budgets assigned to CD and overlay controls by the National Technology Roadmap for Semiconductors (NTRS) in light of constraints on parameters that are fundamental to the above measurements.
A Potent, Selective, and Cell-Active Inhibitor of Human Type I Protein Arginine Methyltransferases (2015)

Protein arginine methyltransferases (PRMTs) play a crucial role in a variety of biological processes. Overexpression of PRMTs has been implicated in various human diseases including cancer. Consequently, selective small-molecule inhibitors of PRMTs have been pursued by both academia and the pharmaceutical industry as chemical tools for testing biological and therapeutic hypotheses. PRMTs are divided into three categories: type I PRMTs which catalyze mono- and asymmetric dimethylation of arginine residues, type II PRMTs which catalyze mono- and symmetric dimethylation of arginine residues, and type III PRMT which catalyzes only monomethylation of arginine residues. Here, we report the discovery of a potent, selective, and cell-active inhibitor of human type I PRMTs, MS023, and characterization of this inhibitor in a battery of biochemical, biophysical, and cellular assays. MS023 displayed high potency for type I PRMTs including PRMT1, -3, -4, -6, and -8 but was completely inactive against type II and type III PRMTs, protein lysine methyltransferases and DNA methyltransferases. A crystal structure of PRMT6 in complex with MS023 revealed that MS023 binds the substrate binding site. MS023 potently decreased cellular levels of histone arginine asymmetric dimethylation. It also reduced global levels of arginine asymmetric dimethylation and concurrently increased levels of arginine monomethylation and symmetric dimethylation in cells. We also developed MS094, a close analog of MS023, which was inactive in biochemical and cellular assays, as a negative control for chemical biology studies. MS023 and MS094 are useful chemical tools for investigating the role of type I PRMTs in health and disease.
Layered Environment-Map Impostors for Arbitrary Scenes (2002)

This paper presents a new impostor-based approach to accelerate the rendering of very complex static scenes. The scene is partitioned into viewing regions, and a layered impostor representation is precalculated for each of them. An optimal placement of impostor layers guarantees that our representation is indistinguishable from the original geometry. Furthermore the algorithm exploits common graphics hardware both during preprocessing and rendering. Moreover the impostor representation is compressed using several strategies to cut down on storage space.
Development of the osteoblast phenotype in primary human osteoblasts in culture: Comparison with rat calvarial cells in osteoblast differentiation (1999)

In rat osteoblast-like cells, a time-dependent sequence of growth and differentiation-dependent genes has been identified and a model of osteoblast differentiation in culture suggested. We investigated the expression of the bone matrix-associated proteins osteonectin and procollagen I and of the bone cell phenotype-related proteins alkaline phosphatase and osteocalcin during cell culture in primary human osteoblast like cells. Primary human explant cultures from nine young healthy donors were established under highly standardized conditions. Cells in the second passage were analyzed on different days from day 1 to 32, comparing cells growing under the influence of ascorbate with controls. Gene expression was determined by Northern blot analysis or polymerase chain reaction. Osteocalcin expression was also investigated after 1,25-(OH)2D3 stimulation. On the protein level, newly synthesized collagen I, alkaline phosphatase activity, and secretion of osteocalcin were analyzed at all time points. On comparing our findings to the pattern of gene expression suggested for the rat calvarial osteoblast system, we found a similar developmental sequence for the so-called “proliferation” as well as a similar, but lengthened, sequence for the “matrix maturation stage.” During “matrix maturation,” we found an ongoing proliferation despite increased alkaline phosphatase and decreased procollagen I gene expression. Our study, therefore, shows that in pHOB the gene expression profile proceeded to the “matrix maturation stage,” as defined by Owen and colleagues, independent of ongoing proliferation. We were unable to observe the mineralization period as demonstrated by the missing increase of osteocalcin expression and lack of nodule formation in our human osteoblast model. In contrast to the rat system, we found a proliferation stimulating influence of ascorbate, suggesting species-specific differences in response to differentiation factors. From these data, we conclude that general considerations on physiology and pathophysiology of bone cell differentiation have to be confirmed in the human osteoblastic cell system. J. Cell Biochem. 75:22–35, 1999. © 1999 Wiley-Liss, Inc.
Look‐ahead walkaways using effective VTI models (2000)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2000Look‐ahead walkaways using effective VTI modelsAuthors: W. Scott LeaneyW. Scott LeaneySchlumbergerhttps://doi.org/10.1190/1.1815758 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InReddit Permalink: https://doi.org/10.1190/1.1815758FiguresReferencesRelatedDetailsCited byCompressional and shear wave attenuations from walkway VSP and sonic data in an offshore Abu Dhabi oilfield29 September 2021 | Comptes Rendus. Géoscience, Vol. 353, No. 1Interval anisotropic parameter estimation from walkaway vertical seismic profiling data28 September 2012 | Geophysical Prospecting, Vol. 60, No. 6Velocity profile prediction using walkaway VSP dataNobuyasu Hirabayashi and W. Scott Leaney6 October 2006Monte‐Carlo Bayesian look‐ahead inversion of walkaway vertical seismic profiles15 August 2005 | Geophysical Prospecting, Vol. 53, No. 5Sub‐salt velocity prediction with a look‐ahead AVO walkawayW. Scott Leaney, Brian E. Hornby, Allan J. Campbell, Shazia Viceer, Marty Albertin, and Alberto Malinverno3 January 2005 SEG Technical Program Expanded Abstracts 2000 ISSN (print):1052-3812 ISSN (online):1949-4645 Copyright: 2000 Pages: 2484 publication data© 2000 Copyright © 2000 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished Online: 04 Jan 2005 CITATION INFORMATION W. Scott Leaney, (2000), "Look‐ahead walkaways using effective VTI models," SEG Technical Program Expanded Abstracts : 1743-1747. https://doi.org/10.1190/1.1815758 Plain-Language Summary PDF DownloadLoading ...
The design flood problem in changing climates (2012)

While previous editions of ARR have served the engineering profession well, a number of issues have necessitated the production of a new edition. These issues include the many recent developments in knowledge regarding rainfall-runoff processes, the increased computational capacity available to engineering hydrologists, and the rapidly expanding body of information about climate change. As part of the development of the new edition, it has been necessary to review methods used and the implications of assumptions necessary for implementation of these methods. Arising from this review, a way forward for design flood estimation in Australia has been proposed that addresses many of the simplifying assumptions inherent in past methods and enables the inclusion of the hydrological impacts of changing climates which include changing rainfall characteristics, changing catchment vegetation, and changing catchment geomorphology. This new vision for design flood estimation will be incorporated in the new edition of ARR.
Time Series Analysis Of Cancer Metastasis Gene Expression Data Using Predictive Clustering Trees (PCT) (2011)

Time series microarray data analysis provides an invaluable insight into the genetic progression of metastasis. In this paper we analyzed time series microarray data of cancer metastasis. Predictive clustering using decision trees on time series data integrates clustering and prediction. We present an implementation of PCT on cancer metastasis gene expression data to obtain high level descriptions of clusters of gene expression samples in terms of clinical variables in an unparalleled serendipitous manner. We evaluate time series data from microarray experiments. Each data set records the change over time in the expression level of epithelial cells to facilitate dispersion by induction of Epithelial Mesenchymal Transition (EMT). Implementation of PCT with CLUS-TS on the cancer metastasis gene expression data enables us to understand the early event during tumor metastasis. Summing up, we applied predictive clustering trees to the cancer metastasis gene expression data, where the goal was to obtain integrated high-level descriptions of clusters of gene expression samples in terms of clinical variables. Our preliminary results hint at the potential to understand the molecular pathogenesis of tumor metastasis through predictive clustering using decision trees approach.
Evaluating p97 Inhibitor Analogues for Their Domain Selectivity and Potency against the p97–p47 Complex (2014)

We previously found that p97 ATPase inhibitors 2-(2-amino-1H-benzo[d]imidazol-1-yl)-N-benzyl-8-methoxyquinazolin-4-amine (ML240) and 2-(2H-benzo[b][1,4]oxazin-4(3H)-yl)-N-benzyl-5,6,7,8-tetrahydroquinazolin-4-amine (ML241) specifically target the D2 domain of wild-type p97. In addition, one of the major p97 cofactors, p47, decreases their potencies by ∼50-fold. In contrast, N(2) ,N(4) -dibenzylquinazoline-2,4-diamine (DBeQ) targets both the D1 and D2 domains and shows only a four- to sixfold decrease in potency against the p97-p47 complex. To elucidate structure-activity relationships for the inhibitors, we screened 200 p97 inhibitor analogues for their ability to inhibit the ATPase activity of either or both of the D1 or D2 domains, as well for their effects on p47 potency. The selectivity of 29 of these compounds was further examined by eight-dose titrations. Four compounds showed modest selectivity for inhibiting the ATPase activity of D1. Eleven compounds inhibited D2 with greater potencies, and four showed similar potencies against D1 and D2. p47 decreased the potencies of the majority of the compounds and increased the potencies of five compounds. These results highlight the possibility of developing domain-selective and complex-specific p97 inhibitors in order to further elucidate the physiological roles of p97 and its cofactors.
Karhunen-Loeve multispectral image restoration, part I: Theory (1984)

The theory of optimal image restoration is well established for monochrome imagery. However, a variety of sensors acquire multi-spectral or polychrome imagery. The restoration of multispectral imagery by optimal (Wiener) methods is developed in this paper. It is shown that optimal restoration must take place in the Karhunen-Loeve domain. It is further shown that high quality approximate multispectral restorations must be achieved at less computational cost than exact restoration. This latter point is applied to the development of a fast approximate procedure for restoration of conventional color photography.
Capacity and Conductivity of Body Tissues at Ultrahigh Frequencies (1953)

Dielectric constant and specific resistance are reported for a variety of body tissues throughout the frequency range from 200 to 1,000 mc. The results are analyzed and explained by the cellular structure of tissue, the electrical properties of tissue electrolytes, and tissue protein content. Other results specify the temperature dependence of the electrical constants of tissue material. The temperature coefficients vary with frequency and are in agreement with theoretical expectation. A short description of measuring technique and of tissue sample thermostat is given.
Characterization of Poly-γ-Glutamate Hydrolase Encoded by a Bacteriophage Genome: Possible Role in Phage Infection of <i>Bacillus subtilis</i> Encapsulated with Poly-γ-Glutamate (2003)

Some Bacillus subtilis strains, including natto (fermented soybeans) starter strains, produce a capsular polypeptide of glutamate with a gamma-linkage, called poly-gamma-glutamate (gamma-PGA). We identified and purified a monomeric 25-kDa degradation enzyme for gamma-PGA (designated gamma-PGA hydrolase, PghP) from bacteriophage PhiNIT1 in B. subtilis host cells. The monomeric PghP internally hydrolyzed gamma-PGA to oligopeptides, which were then specifically converted to tri-, tetra-, and penta-gamma-glutamates. Monoiodoacetate and EDTA both inhibited the PghP activity, but Zn(2+) or Mn(2+) ions fully restored the enzyme activity inhibited by the chelator, suggesting that a cysteine residue(s) and these metal ions participate in the catalytic mechanism of the enzyme. The corresponding pghP gene was cloned and sequenced from the phage genome. The deduced PghP sequence (208 amino acids) with a calculated M(r) of 22,939 was not significantly similar to any known enzyme. Thus, PghP is a novel gamma-glutamyl hydrolase. Whereas phage PhiNIT1 proliferated in B. subtilis cells encapsulated with gamma-PGA, phage BS5 lacking PghP did not survive well on such cells. Moreover, all nine phages that contaminated natto during fermentation produced PghP, supporting the notion that PghP is important in the infection of natto starters that produce gamma-PGA. Analogous to polysaccharide capsules, gamma-PGA appears to serve as a physical barrier to phage absorption. Phages break down the gamma-PGA barrier via PghP so that phage progenies can easily establish infection in encapsulated cells.
Adhesives for bead fusion of recycled expandable polystyrene (2002)

Abstract Expandable polystyrene (EPS) is a plastic cellular material that is commonly used in the packaging industry. Its growing uses have led to environmental concerns over resource sustainability and the dwindling availability of landfill spaces. Although existing approaches to control and manage EPS wastes are available, much effort is still needed to recycle as much of the used materials via developing new processes or applications. This article looks into a new approach using adhesives to promote EPS bead fusion. Two sets of test specimens made of 100% recycled EPS using spray adhesive and powder adhesive were investigated. Their mechanical behaviors of these two adhesive EPS samples were studied. These specimens were compared with the commercially available ones produced using steam injection molding and direct microwave molding. From the findings, the powder adhesive specimens were found to be quite comparable to the steam‐injected ones in terms of better cushioning property, shape definitions, smaller dimensional and density variations than those of sprayed adhesive and microwave ones. The results highlight that powder adhesive mixed with 100% recycled EPS offer a new “green” approach in EPS production with low initial capital outlay and shorter production lead time. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 456–462, 2002
Selective induction of phospholipase D1 in pathogen-activated human monocytes (2001)

Phospholipase D (PLD) activation is part of the complex signalling cascade induced during phagocyte activation. Two PLD isoforms have been cloned, but their role in phagocyte functions is still poorly defined. We report that resting fresh circulating human monocytes expressed PLD1. PLD1 protein expression was rapidly down-regulated during cell culture. Lipopolysaccharide and pathogen-derived agonists (Candida albicans, arabinoside-terminated lipoarabinomannan and Gram-positive bacteria, but not mannose-capped lipoarabinomannan or double-stranded RNA) strongly induced PLD1 expression at both the mRNA and protein levels. Pro-inflammatory cytokines [interleukin (IL)-1β and tumour necrosis factor α] had only a weak effect, whereas immune cytokines (IL-6 and interferon γ), anti-inflammatory cytokines (IL-13 and IL-10) and chemoattractants (fMet-Leu-Phe and macrophage chemoattractant protein 1) were inactive. None of the agonists tested induced significant changes in the basal expression of PLD2 mRNA. Consistent with PLD1 up-regulation was the observation that PLD enzymic activity was higher in monocytes treated with active-pathogen-derived agonists than in control cells, when stimulated with PMA or with chemotactic agonists (fMet-Leu-Phe and C5a). Thus PLD2 seems to be a constitutive enzyme in circulating monocytes. Conversely, PLD1 is an inducible protein, rapidly regulated during culture conditions and selectively induced during cell activation. Therefore PLD1 might have a relevant role in immune responses against pathogens and in chronic inflammation.
Fluid Effects in Temperature Observation Wells (1989)

ABSTRACT Temperature profile data are important in the evaluation of steamflood performance. Observation well temperature profiles are used to determine areal sweep, rate of advance of the heat front, vertical coverage of the steamflood, and heat losses to overlying and underlying strata. In such cases, it is commonly assumed that temperature profiles obtained from observation wells closely represent the true temperature distribution in the surrounding formation. In reality, however, natural convection of the wellbore fluids, heat conduction along the tubing, and probe response time are factors that can alter these profiles. Therefore, these factors must be considered when collecting and evaluating temperature profiles. This paper presents the results of laboratory and field studies of wellbore fluid effects on temperature profiles. The emphasis of this work is on profile smearing caused by natural convection of the wellbore fluid and by slow probe response. Laboratory tests were conducted in a 20-ft vertical well model to initially compare temperature profiles in water- and air-filled wellbores. Field tests were also conducted to further study smearing effects under actual field conditions. Response times of two electrical temperature probe designs, wall-contact, and hanging were also evaluated in the laboratory and the field.