gebhart/patrepeval huggingface dataset:
A massively parallel adaptive fast multipole method on heterogeneous architectures (2012)

We describe a parallel fast multipole method (FMM) for highly nonuniform distributions of particles. We employ both distributed memory parallelism (via MPI) and shared memory parallelism (via OpenMP and GPU acceleration) to rapidly evaluate two-body nonoscillatory potentials in three dimensions on heterogeneous high performance computing architectures. We have performed scalability tests with up to 30 billion particles on 196,608 cores on the AMD/CRAY-based Jaguar system at ORNL. On a GPU-enabled system (NSF's Keeneland at Georgia Tech/ORNL), we observed 30× speedup over a single core CPU and 7× speedup over a multicore CPU implementation. By combining GPUs with MPI, we achieve less than 10 ns/particle and six digits of accuracy for a run with 48 million nonuniformly distributed particles on 192 GPUs.
Generation of Tumor Immunity by Bone Marrow-Derived Dendritic Cells Correlates with Dendritic Cell Maturation Stage (1999)

Bone marrow-derived dendritic cells (BmDC) are potent APC and can promote antitumor immunity in mice when pulsed with tumor Ag. This study aimed to define the culture conditions and maturation stages of BmDC that enable them to optimally function as APC in vivo. BmDC cultured under various conditions (granulocyte-macrophage CSF (GM-CSF) or GM-CSF plus IL-4 alone or in combination with Flt3 ligand, TNF-alpha, LPS, or CD40 ligand (CD40L)) were analyzed morphologically, phenotypically, and functionally and were tested for their ability to promote prophylactic and/or therapeutic antitumor immunity. Each of the culture conditions generated typical BmDC. Whereas cells cultured in GM-CSF alone were functionally immature, cells incubated with CD40L or LPS were mature BmDC, as evident by morphology, capacity to internalize Ag, migration into regional lymph nodes, IL-12 secretion, and alloantigen or peptide Ag presentation in vitro. The remaining cultures exhibited intermediate dendritic cell maturation. The in vivo Ag-presenting capacity of BmDC was compared with respect to induction of both protective tumor immunity and immunotherapy of established tumors, using the poorly immunogenic squamous cell carcinoma, KLN205. In correspondence to their maturation stage, BmDC cultured in the presence of CD40L exhibited the most potent immunostimulatory effects. In general, although not entirely, the capacity of BmDC to induce an antitumor immune response in vivo correlated to their degree of maturation. The present data support the clinical use of mature, rather than immature, tumor Ag-pulsed dendritic cells as cancer vaccines and identifies CD40L as a potent stimulus to enhance their in vivo Ag-presenting capacity.
Toll-like receptor 4 activation increases Akt phosphorylation in colon cancer cells. (2009)

Our results identify TLR4 expression in human CRCs and activation of PI3K with LPS treatment. These findings suggest possible treatment strategies targeting TLR4 in CRC.
Biomarkers of hepatic fibrosis, fibrogenesis and genetic pre‐disposition pending between fiction and reality (2007)

Fibrosis is a frequent, life-threatening complication of most chronic liver diseases. Despite major achievements in the understanding of its pathogenesis, the translation of this knowledge into clinical practice is still limited. In particular, non-invasive and reliable (serum-) biomarkers indicating the activity of fibrogenesis are scarce. Class I biomarkers are defined as serum components having a direct relation to the mechanism of fibrogenesis, either as secreted matrix-related components of activated hepatic stellate cells and fibroblasts or as mediators of extracellular matrix (ECM) synthesis or turnover. They reflect primarily the activity of the fibrogenic process. Many of them, however, proved to be disappointing with regard to sensitivity and specificity. Up to now hyaluronan turned out to be the relative best type I serum marker. Class II biomarkers comprise in general rather simple standard laboratory tests, which are grouped into panels. They fulfil most criteria for detection and staging of fibrosis and to a lesser extent grading of fibrogenic activity. More than 20 scores are currently available, among which Fibrotest is the most popular one. However, the diagnostic use of many of these scores is still limited and standardization of the assays is only partially realized. Combining of panel markers in sequential algorithms might increase their diagnostic validity. The translation of genetic pre-disposition biomarkers into clinical practice has not yet started, but some polymorphisms indicate a link to progression and outcome of fibrogenesis. Parallel to serum markers non-invasive physical techniques, for example, transient elastography, are developed, which can be combined with serum tests and profiling of serum proteins and glycans.
A Phase 1 Study of PAmAb, a Fully Human Monoclonal Antibody against Bacillus anthracis Protective Antigen, in Healthy Volunteers (2005)

PAmAb is safe, well tolerated, and bioavailable after a single intramuscular or intravenous dose, which supports further clinical development of PAmAb as a novel therapeutic agent for inhalational anthrax.
Polymeric in-line fiber modulator using novel processing techniques (1996)

Summary form only given. We have designed and fabricated a polymeric in-line fiber modulator using novel fabrication techniques. This device is based on evanescent coupling from a fiber half-coupler to a nonlinear polymer waveguide and takes advantage of a unique polymer deposition process.
Induction of Allograft Tolerance in the Absence of Fas-Mediated Apoptosis (1999)

Using certain immunosuppressive regimens, IL-2 knockout (KO) mice, in contrast to wild-type (wt) controls, are resistant to the induction of allograft tolerance. The mechanism by which IL-2 regulates allograft tolerance is uncertain. As IL-2 KO mice have a profound defect in Fas-mediated apoptosis, we hypothesized that Fas-mediated apoptosis of alloreactive T cells may be critical in the acquisition of allograft tolerance. To definitively study the role of Fas in the induction of transplantation tolerance, we used Fas mutant B6.MRL-lpr mice as allograft recipients of islet and vascularized cardiac transplants. Alloantigen-stimulated proliferation and apoptosis of Fas-deficient cells were also studied in vivo. Fas mutant B6.MRL-lpr (H-2b) mice rapidly rejected fully MHC-mismatched DBA/2 (H-2d) islet allografts and vascularized cardiac allografts with a tempo that is comparable to wt control mice. Both wt and B6.MRL-lpr mice transplanted with fully MHC-mismatched islet allografts or cardiac allografts can be readily tolerized by either rapamycin or combined costimulation blockade (CTLA-4Ig plus anti-CD40L mAb). Despite the profound defect of Fas-mediated apoptosis, Fas-deficient T cells can still undergo apoptotic cell death in vivo in response to alloantigen stimulation. Our study suggests that: 1) Fas is not necessarily essential for allograft tolerance, and 2) Fas-mediated apoptosis is not central to the IL-2-dependent mechanism governing the acquisition of allograft tolerance.
Fungal Infections in Patients with AIDS and AIDS-related Complex (1986)

Persons with AIDS are predisposed to a variety of previously rare bacterial and fungal infections. Improvement in the quality and duration of survival of AIDS patients depends on the efficacy of treatment for these infections. Between 58-81% of AIDS patients contract fungal infections at some time, and 10-20% of AIDS patients die as a direct consequence of such infections. Oral candidiasis, commonly known as thrush, is the most common fungal infection among AIDS and AIDS Related Complex patients, occurring in 80-90% of cases. In a recent U.S. study, 59% of persons with oral candidiasis who were at high risk of contracting AIDS went on to develop Kaposi's sarcoma and other life- threatening infections. The most common life-threatening fungal infection experienced by AIDS patients is cryptococcosis, a disease occurring among 6% of American AIDS patients and having a mortality rate of 17% during initial infections and 75-100% on relapse. Other opportunistic infections associated with AIDS and AIDS Related Complex are bronchial candidiasis, invasive aspergillosis, disseminated histoplasmosis, and disseminated coccidioidomycosis. All are treatable but eradication i s difficult and relapse common.
Cloning and characterization of the cDNA encoding the human neuromedin U (NmU) precursor: NmU expression in the human gastrointestinal tract (1995)

Many peptide precursors encode more than one bioactive peptide. Recent cloning of the rat neuromedin U (NmU) precursor revealed potential proteolytic processing sites which may generate three associated peptides in addition to the NmU peptide, which is known to have potent uterine contractile effects. To assess the degree of evolutionary conservation, which often suggests conserved biological function and hence physiological importance, we have cloned and sequenced the cDNA encoding the human NmU precursor. Sequence analysis revealed a 174 amino acid human precursor containing the 25 residue NmU peptide near the C terminus of the precursor. The human message sequence was 74% homologous with that of the rat, indicating evolutionary conservation of the precursor between these two species. Four out of five of the putative proteolytic processing sites, first revealed in the rat precursor, were conserved in the human precursor, indicating a similar processing mechanism in both species. Two such processing sites flank a 33 residue peptide sequence which differed in only two amino acids compared with the rat homologue. This conservation suggests a possible biological role for this putative peptide. Northern blot analysis of human gastrointestinal tissues revealed a similar level of mRNA throughout the gastrointestinal tract. RIA using a porcine specific assay showed the highest levels of peptide in the jejunum samples.
HapticFlow: PDE‐based mesh editing with haptics (2004)

Abstract This paper presents HapticFlow , a haptics‐based direct mesh editing system founded upon the concept of PDE‐based geometric surface flow. The proposed flow‐based approach for direct geometric manipulation offers a unified design paradigm that can seamlessly integrate implicit, distance‐field based shape modeling with dynamic, physics‐based shape design. HapticFlow provides an intuitive haptic interface and allows users to directly manipulate 3D polygonal objects with ease. To demonstrate the effectiveness of our new approach, we developed a variety of haptics‐based mesh editing operations such as embossing, engraving, sketching as well as force‐based shape manipulation operations. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Activity of the Bcl-2 Family Inhibitor ABT-263 in a Panel of Small Cell Lung Cancer Xenograft Models (2008)

ABT-263 is a potent, orally bioavailable inhibitor of Bcl-2 family proteins that has recently entered clinical trials. The efficacy data reported here suggest that SCLC is a promising area of clinical investigation with this agent.
Lung surfactants. II. Effects of fatty acids, triacylglycerols and protein on the activity of lung surfactant. (1983)

The relations between the kinds of fatty acids and triacylglycerols present and the properties of lung surfactants were examined with modified lung surfactants. Palmitic acid-tripalmitoylglycerol, stearic acid-tristearoylglycerol and mixtures of fatty acids-triacylglycerols gave good surface activities with the lung surfactant, but oleic acid-trioleoylglycerol did not give good surface activity in vitro. Lung surfactants modified with palmitic acid-tripalmitoylglycerol, stearic acid-tristearoylglycerols and the mixtures restored the initial lung pressure-volume characteristics to the excised lung after these characteristics had been lost as a result of lavage in situ. Fatty acids gave better surface activities with the lung surfactant than triacylgycerols. The lung surfactants modified with palmitic acid, stearic acid and a mixture of fatty acids showed better surface activities in vitro and gave better lung pressure-volume characteristics in situ than those with oleic acid and triacylglycerols. The protein contained in the bovine lung surfactant was a lipoprotein in which the molar ratio of phopsholipids to protein was about 100 : 1. The molecular weight of the protein was 35000 and was reduced to 10000 by pretreatment with 2-mercaptoethanol after the removal of the phospholipids from the lipoprotein. This protein contained a large proportion of nonpolar amino acids. The lipoprotein showed spontaneous spreading with 1, 2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), and with mixtures of DPPC and palmitic acid or tripalmitoylglycerol. The lipoprotein also enlarged the areas of the hysteresis loops of DPPC and the mixtures.
Genome organization and DNA accessibility control antigenic variation in trypanosomes (2018)

Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host<sup>1</sup>. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility<sup>2,3</sup>. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding<sup>4</sup>. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses-Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing-that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation.
Designed Self-Doped Titanium Oxide Thin Films for Efficient Visible-Light Photocatalysis (2002)

Efficient photocatalytic activity in the visible range has been achieved with titanium oxide thin films. Doping, induced by oxygen deficiencies, is the key to the increased photodegradation properties of the film as both experimental and theoretical studies of the thin films demonstrate. The Figure shows an AFM image of the surface morphology of a TiO2 layer.
High-performance flexible zinc tin oxide field-effect transistors (2005)

Flexible transistors were fabricated by sputter deposition of zinc tin oxide (ZTO) onto plasma-enhanced chemical vapor deposition gate dielectrics formed on flexible polyimide substrates with a blanket aluminum gate electrode. The flexible transistors exhibited high on-currents of 1mA, on/off ratios of 106, subthreshold voltage slopes of 1.6V/decade, turn-on voltages of −17V, and mobilities of 14cm2V−1s−1. Capacitance measurements indicate that the threshold voltage and subthreshold slope are primarily influenced by residual doping in the ZTO rather than by defects at the semiconductor/dielectric interface, and are useful for assessing contact resistance.
Electrical conduction models for isotropically conductive adhesive joints (1997)

An electrical conduction model for silver filled isotropically conductive adhesives (ICA) was developed. The model combines the microscopic resistance of the bulk silver particles and the contact between silver flakes with the macroscale resistor network calculation by percolation theory. The resistivities of the composites were calculated by resistor network simulations considering both contact effects and particle size effects. Three different types of film typically exist on the silver surface: residual organic films; tarnish films; and a thin epoxy layer. The contact resistance between silver flakes can be due to a constriction resistance, to the tunneling resistance through insulating films, or to the resistance of more conductive layers. The constriction resistance is produced by the restriction of the current flow by small contact spots and is controlled by the actual contact spot area (metallic contact), which is dependent on the contact force between flakes. The tunneling resistance is caused by the very thin layer which may reside on the silver flakes between the metallic contact spots, and is dependent on a barrier film thickness and potential. Oxide and sulfide tarnish films are typically degenerate semiconductors. Two- and three-dimensional (2-D and 3-D) computer simulations were performed to predict the effects of particle sizes, shapes, and distribution on the percolation conduction thresholds and cluster sizes. The model predicts that the percolation threshold decreases with broad particle size distributions and high aspect ratio particles. The effective resistivity of the adhesive depends on the thickness dimension of the adhesive pad geometry, with very thin layers resulting in high percolation thresholds and high resistivities. Resistivity does not change with the pad thicknesses greater than a certain thickness level. Silver flake orientation on the surface increases the resistivity of the conductive adhesive pads, but in the same magnitude range. The resistivities of the materials are controlled by silver flake sizes and the nature of the contacts.
Caspase-2 Is Localized at the Golgi Complex and Cleaves Golgin-160 during Apoptosis (2000)

Caspases are an extended family of cysteine proteases that play critical roles in apoptosis. Animals deficient in caspases-2 or -3, which share very similar tetrapeptide cleavage specificities, exhibit very different phenotypes, suggesting that the unique features of individual caspases may account for distinct regulation and specialized functions. Recent studies demonstrate that unique apoptotic stimuli are transduced by distinct proteolytic pathways, with multiple components of the proteolytic machinery clustering at distinct subcellular sites. We demonstrate here that, in addition to its nuclear distribution, caspase-2 is localized to the Golgi complex, where it cleaves golgin-160 at a unique site not susceptible to cleavage by other caspases with very similar tetrapeptide specificities. Early cleavage at this site precedes cleavage at distal sites by other caspases. Prevention of cleavage at the unique caspase-2 site delays disintegration of the Golgi complex after delivery of a pro-apoptotic signal. We propose that the Golgi complex, like mitochondria, senses and integrates unique local conditions, and transduces pro-apoptotic signals through local caspases, which regulate local effectors.
Total synthesis of (-)-eudistomin L and (-)-debromoeudistomin L (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of (-)-eudistomin L and (-)-debromoeudistomin LMasako Nakagawa, Jin Jun Liu, and Tohru HinoCite this: J. Am. Chem. Soc. 1989, 111, 7, 2721–2722Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/ja00189a060https://doi.org/10.1021/ja00189a060research-articleACS PublicationsRequest reuse permissionsArticle Views437Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Obesity in Young Men after Famine Exposure in Utero and Early Infancy (1976)

In a historical cohort study of 300,000 19-year-old men exposed to the Dutch famine of 1944-45 and examined at military induction, we tested the hypothesis that prenatal and early postnatal nutrition determines subsequent obesity. Outcomes were opposite depending on the time of exposure. During the last trimester of pregnancy and the first months of life, exposure produced significantly lower obesity rates (P less than 0.005). This result is consistent with the inference that nutritional deprivation affected a critical period of development for adipose-tissue cellularity. During the first half of pregnancy, however, exposure resulted in significantly higher obesity rates (P less than 0.0005). This observation is consistent with the inference that nutritional deprivation affected the differentiation of hypothalamic centers regulating food intake and growth, and that subsequent increased food availability produced an accumulation of excess fat in an organism growing to its predetermined maximum size.
Dual Inhibition of PI3K and mTORC1/2 Signaling by NVP-BEZ235 as a New Therapeutic Strategy for Acute Myeloid Leukemia (2010)

Our results clearly show the antileukemic efficiency of the NVP-BEZ235 compound, which therefore represents a promising option for future AML therapies.
Use of Lytic Bacteriophage for Control of Experimental Escherichia coli Septicemia and Meningitis in Chickens and Calves (1998)

A lytic bacteriophage, which was previously isolated from sewage and which attaches to the K1 capsular antigen, has been used to prevent septicemia and a meningitis-like infection in chickens caused by a K1+ bacteremic strain of Escherichia coli. Protection was obtained even when administration of the phage was delayed until signs of disease appeared. The phage was able to multiply in the blood. In newly borne colostrum-deprived calves given the E. coli orally, intramuscular inoculation of phage delayed appearance of the bacterium in the blood and lengthened life span. With some provisos there is considerable potential for this approach to bacterial-disease therapy.
The berkeley restaurant project (1994)

This paper describes the architecture and performance of the Berkeley Restaurant Project (BeRP), a medium-vocabulary, speaker-independent, spontaneous continuous speech understanding system currently under development at ICSI. BeRP serves as a testbed for a number of our speech-related research projects, including robust feature extraction, connectionist phonetic likelihood estimation, automatic induction of multiplepronunciation lexicons, foreign accent detection and modeling, advanced language models, and lip-reading. In addition, it has proved quite usable in its function as a database frontend, even though many of our subjects are non-native speakers of English.