gebhart/patrepeval huggingface dataset:
<title>Hybrid Subtraction In Digital Fluorography</title> (1982)

Digital fluorography using temporal subtraction techniques has achieved excellent visualization of the vascular anatomy with intravenous injections of contrast medium. However, clinical studies have demonstrated that a major limitation to this method is patient motion. Movements such as swallowing, breathing, peristalsis, cardiac motion, and arterial pulsations cause artifacts in difference images which can reduce the diagnostic accuracy of the procedure. Many of these artifacts can be eliminated by the use of hybrid subtraction, a second-order technique which combines temporal and dual-energy subtraction. This procedure is described and compared to both temporal and dual energy subtraction methods in terms of data acquisition, iodine signal-to-noise ratios, dose, and x-ray tube loading. Images are shown to demonstrate the viability of this new technique.
Efficient multi-view maintenance in the social semantic web (2012)

The Social Semantic Web (SSW) refers to the mix of RDF data in web content, and social network data associated with those who posted that content. Applications to monitor the SSW are becoming increasingly popular. For instance, marketers want to look for semantic patterns relating to the content of tweets and Facebook posts relating to their products. Such applications allow multiple users to specify patterns of interest, and monitor them in real-time as new data gets added to the web or to a social network. In this paper, we develop the concept of SSW view servers in which all of these types of applications can be simultaneously monitored from such servers. The patterns of interest are views. We show that a given set of views can be compiled in multiple possible ways to take advantage of common substructures, and define the concept of an optimal merge. We develop a very fast MultiView algorithm that scalably and efficiently maintains multiple subgraph views. We show that our algorithm is correct, study its complexity, and experimentally demonstrate that our algorithm can scalably handle updates to hundreds of views on real-world SSW databases with up to 540M edges.
GATA-1 and erythropoietin receptor genes are highly expressed in erythroleukemia. (1998)

We examined expression of the erythroid-associated genes GATA-1 and erythropoietin receptor (EPOR) in primary leukemia using the reverse transcriptase-polymerase chain reaction (RT-PCR). GATA-1 and EPOR mRNAs were detectable in all cases of erythroleukemia (French-American-British classification: M6) or early erythroblastic leukemia. In all other leukemia cases, including M2 through M5, stem cell leukemia, and adult T-cell leukemia, these gene transcripts were undetectable. GATA-2 was detectable in all the cases of primary leukemias examined in this study, except one case of M5. In one case, the phenotype switched from myeloid (M2) to erythroid (M6) and then back to myeloid. Northern blotting and RT-PCR revealed that GATA-1 and EPOR mRNAs were significantly upregulated at the M6 stage compared with the M2 stage. GATA-1 may be involved in the expression of an erythroid phenotype in acute leukemia. We generated HL-60 transfectants exogenously expressing GATA-1. The majority of HL-60 cells expressing GATA-1 lacked azurophilic granules, and electron microscopic analysis revealed that myeloperoxidase activity was negative. Platelet peroxidase activity, which was detectable in both megakaryoblasts and erythroid progenitors, was positive. However, EPOR and glycophorin A mRNAs were undetectable by RT-PCR. These findings suggest that besides GATA-1, a third factor may be required for the expression of mature erythroid phenotypes. In addition, our results indicate that GATA-1 is involved in inactivation of myeloperoxidase and activation of the platelet peroxidase.
Thrombospondin‐1 is an inhibitor of pharmacological activation of soluble guanylate cyclase (2010)

This work demonstrates that TSP-1 is a universal inhibitor of sGC, blocking both haeme-dependent and haeme-independent activation. These data coupled with the reported increases in TSP-1 with age, diabetes, ischaemia/reperfusion, and atherosclerosis implies that the therapeutic potential of all drugs that activate sGC could be compromised in disease states where TSP-1/CD47 signalling is elevated.
RRAD Promotes EGFR-Mediated STAT3 Activation and Induces Temozolomide Resistance of Malignant Glioblastoma (2014)

Abstract Glioblastoma multiforme (GBM) is an extremely aggressive brain cancer with a median survival of less than 2 years. GBM is characterized by abnormal activation of receptor tyrosine kinase and constitutively activated STAT3. Although EGFR phosphorylation and STAT3 activation are essential for the maintenance of GBM cancer stem cells, the molecular mechanism underlying endosome-mediated STAT3 activation is not fully understood. In the current study, we showed that GTP-binding protein RRAD (RAS associated with diabetes, RAD) physically associates with EGFR, and EEA1, enhancing the stability and endosome-associated nuclear translocation of EGFR. Functionally, RRAD contributes to the activation of STAT3 and expression of the stem cell factors OCT4, NANOG, and SOX2, thereby enhancing self-renewing ability, tumor sphere formation, EMT, and in vivo tumorigenesis. Most importantly, RRAD contributes to poor survival in patients with GBM. RRAD expression is correlated with temozolomide resistance, and, conversely, depletion of RRAD leads to sensitization of highly temozolomide-resistant GBM cells. Our data collectively support a novel function of RRAD in STAT3 activation and provide evidence that RRAD acts as a positive regulator in the EGFR signaling pathway. These results demonstrate a critical role for RRAD in GBM tumorigenesis and provide a rationale for the development of pharmacologic inhibitors of RRAD in GBM. Mol Cancer Ther; 13(12); 3049–61. ©2014 AACR.
Soluble OX40L is associated with presence of autoantibodies in early rheumatoid arthritis (2014)

Clincaltrials.gov NCT00660647, 10 April 2008.
Therapy-Induced Alterations in Host Defense in Children Receiving Therapy for Cancer (1997)

Lehrnbecher, Thomas M.D; Foster, Charles M.D; Vázquez, Nancy Ph.D; Mackall, Crystal L. M.D; Chanock, Stephen J. M.D. Author Information
Gene Composition of High-Yielding Influenza Vaccine Strains Obtained by Recombination (1980)

The genetic composition of 11 high-yielding recombinants of influenza virus was determined by polyacrylamide gel electrophoresis of the 32P-labeled RNAs obtained from the recombinants and their parental viruses. The high-yield recombinants that were selected for potential use as vaccine strains contained the surface hemagglutinin and neuraminidase antigens of the low-yielding parental viruses. The increased growth capacity of the recombinants is associated with the presence of genes derived from the high-yielding laboratory strain A/Puerto Rico/8/34. Although increased growth capacity in these recombinants could not be attributed to specific genes or gene combinations, all of the high-yielding recombinants examined derived the M gene from the A/Puerto Rico/8/34 parent.
Lentiviral Transduction of Dendritic Cells Confers Protective Antiviral Immunity In Vivo (2004)

ABSTRACT Control of a viral infection in vivo requires a rapid and efficient cytotoxic-T-lymphocyte response. We demonstrate that lentivirus-mediated introduction of antigen in dendritic cells confers a protective antiviral immunity in vivo in a lymphocytic choriomeningitis virus model. Therefore, lentiviral vectors may be excellent vaccine candidates for viral infections.
Detection of Epstein-Barr virus messenger RNA in Reed-Sternberg cells of Hodgkin's disease by in situ hybridization with biotinylated probes on specially processed modified acetone methyl benzoate xylene (ModAMeX) sections [see comments] (1991)

Microscopic intracellular detection of Epstein-Barr virus (EBV) messenger RNA in Reed-Sternberg cells of Hodgkin's disease (HD) was possible by in situ hybridization, in tissue sections prepared by a method termed modified acetone methyl benzoate xylene (ModAMeX). The ModAMeX method was initially developed for simultaneous optimal preservation of leucocyte differentiation antigens and morphology. Two biotinylated DNA probes, corresponding to the same BamHI-W (internal repeat) of the EBV genome were used. EBV mRNA was detected in neoplastic cells in 16 of 54 (30%) lymph node biopsy specimens from usual subtypes of HD (lymphocyte predominance, 0/5; nodular sclerosis, 4/22; mixed cellularity, 12/26; unclassified, 0/1). EBV mRNA was also detected in the lymph node biopsy of 1 additional human immunodeficiency virus (HIV)-related case of HD (mixed cellularity) and in 2 of 4 cases of B-cell lymphomas occurring in patients with acquired immunodeficiency syndrome (AIDS). In other non-Hodgkin's lymphomas, EBV mRNA was detected in only 1 of 41 cases. Cases of HD positive for EBV mRNA were immunostained by CD30 and CD15 antibodies. The hybridization signals were exclusively restricted to Reed-Sternberg cells and variants. When analyzed retrospectively, no statistically significant correlation emerged between hybridization findings, EBV serology, or disease outcome over the 3 years of the availability of ModAMeX technique. The findings support the contention of a direct role of EBV in the pathogenesis of HD, at least in some cases.
Assessment of cardiomyocyte DNA synthesis in normal and injured adult mouse hearts (1997)

Cardiomyocyte DNA synthesis was examined in normal and injured adult mouse hearts. In preliminary studied DNA synthesis was monitored by [3H]thymidine incorporation, followed by autoradiographic analysis of dispersed cell preparations. No synthetic cells were identified when 20,000 ventricular cardiomyocytes from normal adult hearts were examined. A high throughput assay was developed to establish the actual labeling index for the adult mouse heart. The assay utilized [3H]thymidine incorporation in transgenic mice which expressed a nuclear-localized beta-galactosidase (beta-Gal) reporter gene exclusively in cardiac myocytes. Cardiomyocyte DNA synthesis was evidenced by colocalization of beta-Gal activity and silver grains in autoradiograms of histological sections. Examination of 180,000 ventricular cardiomyocyte nuclei from normal adult transgenic mice identified a single synthetic nucleus, suggesting a maximum labeling index of 0.0005%. Cardiomyocyte DNA synthesis was next examined in hearts injured by focal cauterization of the left ventricular free wall. Only three synthetic nuclei were identified when 36,000 cardiomyocyte nuclei in the perinecrotic zone of the injured heart were examined. No additional synthetic nuclei were identified when 180,000 nuclei in regions distal to the necrotic zone were examined. These data confirm that cardiomyocyte DNA synthesis in the adult mouse heart is extremely rare and provide baseline data for analyses in genetically modified animals.
The Local Structure of Amorphous Silicon (2012)

It is widely believed that the continuous random network (CRN) model represents the structural topology of amorphous silicon. The key evidence is that the model can reproduce well experimental reduced density functions (RDFs) obtained by diffraction. By using a combination of electron diffraction and fluctuation electron microscopy (FEM) variance data as experimental constraints in a structural relaxation procedure, we show that the CRN is not unique in matching the experimental RDF. We find that inhomogeneous paracrystalline structures containing local cubic ordering at the 10 to 20 angstrom length scale are also fully consistent with the RDF data. Crucially, they also matched the FEM variance data, unlike the CRN model. The paracrystalline model has implications for understanding phase transformation processes in various materials that extend beyond amorphous silicon.
Infection of a Laboratory Worker with Simian Immunodeficiency Virus (1994)

Simian immunodeficiency viruses (SIVs) are primate lentiviruses that are morphologically similar and biologically related to human immunodeficiency viruses (HIVs)1–4. SIVs naturally infect some nonhuman primate species, such as African green monkeys and sooty mangabey monkeys, without causing immunodeficiency. In contrast, experimental SIV infection of other susceptible primate species, such as macaques, can cause chronic wasting syndromes and a disease similar to the human acquired immunodeficiency syndrome (AIDS)5–10. Because of the similarities between the human and nonhuman lentiviruses, SIV and its susceptible primate host have become the principal model for studying the pathogenesis of AIDS and developing . . .
Biological applications of photochemical switches (1993)

Photochemistry Conjugated to Biological Switches Photoinduced Reorganization of Bilayer Membranes Photodynamic Transport and Release of Ions Photoregulation of Enzymes Photolabile Precursors of Nucleotides and Neurotransmitters.
Cloning, characterization, and expression in Escherichia coli of the Streptomyces clavuligerus gene encoding deacetoxycephalosporin C synthetase (1989)

Biosynthesis of cephalosporin antibiotics involves an expansion of the five-membered thiazolidine ring of penicillin N to the six-membered dihydrothiazine ring of deacetoxycephalosporin C by a deacetoxycephalosporin C synthetase (DAOCS) enzyme activity. Hydroxylation of deacetoxycephalosporin C to form deacetylcephalosporin C by a deacetylcephalosporin C synthetase (DACS) activity is the next step in biosynthesis of cephalosporins. In Cephalosporium acremonium, both of these catalytic activities are exhibited by a bifunctional enzyme, DAOCS-DACS, encoded by a single gene, cefEF. In Streptomyces clavuligerus, separable enzymes, DAOCS (expandase) and DACS (hydroxylase), catalyze these respective reactions. We have cloned, sequenced, and expressed in E. coli an S. clavuligerus gene, designated cefE, which encodes DAOCS but not DACS. The deduced amino acid sequence of DAOCS from S. clavuligerus (calculated Mr of 34,519) shows marked similarity (approximately 57%) to the deduced sequence of DAOCS-DACS from C. acremonium; however, the latter sequence is longer by 21 amino acid residues.
Outbreaks of HumanSalmonellaInfections Associated with Live Poultry, United States, 1990–2014 (2016)

Backyard poultry flocks have increased in popularity concurrent with an increase in live poultry-associated salmonellosis (LPAS) outbreaks. Better understanding of practices that contribute to this emerging public health issue is needed. We reviewed outbreak reports to describe the epidemiology of LPAS outbreaks in the United States, examine changes in trends, and inform prevention campaigns. LPAS outbreaks were defined as ≥2 culture-confirmed human Salmonella infections linked to live poultry contact. Outbreak data were obtained through multiple databases and a literature review. During 1990-2014, a total of 53 LPAS outbreaks were documented, involving 2,630 illnesses, 387 hospitalizations, and 5 deaths. Median patient age was 9 years (range <1 to 92 years). Chick and duckling exposure were reported by 85% and 38% of case-patients, respectively. High-risk practices included keeping poultry inside households (46% of case-patients) and kissing birds (13%). Comprehensive One Health strategies are needed to prevent illnesses associated with live poultry.
Characterization of motifs which are critical for activity of the cyclic AMP-responsive transcription factor CREB. (1991)

Cyclic AMP mediates the hormonal stimulation of a number of eukaryotic genes by directing the protein kinase A (PK-A)-dependent phosphorylation of transcription factor CREB. We have previously determined that although phosphorylation at Ser-133 is critical for induction, this site does not appear to participate directly in transactivation. To test the hypothesis that CREB ultimately activates transcription through domains that are distinct from the PK-A site, we constructed a series of CREB mutants and evaluated them by transient assays in F9 teratocarcinoma cells. Remarkably, a glutamine-rich region near the N terminus appeared to be important for PK-A-mediated induction of CREB since removal of this domain caused a marked reduction in CREB activity. A second region consisting of a short acidic motif (DLSSD) C terminal to the PK-A site also appeared to synergize with the phosphorylation motif to permit transcriptional activation. Biochemical experiments with purified recombinant CREB protein further demonstrate that the transactivation domain is more sensitive to trypsin digestion than are the DNA-binding and dimerization domains, suggesting that the activator region may be structured to permit interactions with other proteins in the RNA polymerase II complex.
Delivery of Short Hairpin RNA Sequences by Using a Replication-Competent Avian Retroviral Vector (2004)

While recent studies have demonstrated that retroviral vectors can be used to stably express short hairpin RNA (shRNA) to inhibit gene expression, these studies have utilized replication-defective retroviruses. We describe the creation of a replication-competent, Gateway-compatible retroviral vector capable of expressing shRNA that inhibits the expression of specific genes.
Double-blind clinical evaluation of the relative efficacy of ibuprofen and glucosamine sulphate in the management of osteoarthrosis of the knee in out-patients (1982)

A double-blind trial was carried out in 40 out-patients with unilateral osteoarthrosis of the knee to compare the efficacy and tolerance of oral treatment with 1.5 g glucosamine sulphate or 1.2 g ibuprofen daily over a period of 8 weeks. Pain scores decreased faster during the first 2 weeks in the ibuprofen than in the glucosamine treatment group. Although the rate of decrease was slower, the reduction in pain scores was continued throughout the trial period in patients an glucosamine and the difference between the two groups turned significantly in favour of glucosamine at Week 8. No significant differences were observed in swelling or any of the other parameters monitored. Tolerance was satisfactory with both treatments, with only minor complaints being reported by 2 patients on glucosamine compared with 5 patients on ibuprofen.
Interfaces and the edge percolation map of random directed networks (2007)

The traditional node percolation map of directed networks is reanalyzed in terms of edges. In the percolated phase, edges can mainly organize into five distinct giant connected components, interfaces bridging the communication of nodes in the strongly connected component and those in the in and out components. Formal equations for the relative sizes in the number of edges of these giant structures are derived for arbitrary joint degree distributions in the presence of local and two-point correlations. The uncorrelated null model is fully solved analytically and compared against simulations, finding an excellent agreement. Interfaces, and their particular conformations giving place from "hairy ball" percolation landscapes to bottleneck straits, could bring new light to the discussion of how a structure is interwoven with functionality in flow networks.
Active Control of Surface Plasmon Waveguides with a Phase Change Material (2015)

The ability to manipulate light propagation at the nanoscale is of vital importance for future integrated photonic circuits. In this work we exploit the high contrast in the optical properties of the phase change material Ge2Sb2Te5 to control the propagation of surface plasmon polaritons at a Au/SiO2 interface. Using grating couplers, normally incident light at λ = 1.55 μm is converted into propagating surface plasmons on a Au waveguide. Single laser pulses (λ = 975 nm) are applied to a thin film of Ge2Sb2Te5 placed on top of the device, which, upon transition from its amorphous to crystalline structural phase, dramatically increases both its refractive index and absorption coefficient, thus inhibiting propagation of the plasmonic mode. This effect is investigated for different interaction lengths between the phase change material and the Au waveguide, and contrast values in the transmitted intensity up to several tens of percents are demonstrated.
A Link Between RNA Interference and Nonsense-Mediated Decay in Caenorhabditis elegans (2000)

Double-stranded RNA (dsRNA) inhibits expression of homologous genes by a process involving messenger RNA degradation. To gain insight into the mechanism of degradation, we examined how RNA interference is affected by mutations in the smg genes, which are required for nonsense-mediated decay. For three of six smg genes tested, mutations resulted in animals that were initially silenced by dsRNA but then recovered; wild-type animals remained silenced. The levels of target messenger RNAs were restored during recovery, and RNA editing and degradation of the dsRNA were identical to those of the wild type. We suggest that persistence of RNA interference relies on a subset of smg genes.
Phase Behavior of a Block Copolymer in Solvents of Varying Selectivity (2000)

The effect of the thermodynamic selectivity of a solvent on the self-assembly of a styrene−isoprene (SI) diblock copolymer with block molecular weights of 1.1 × 104 and 2.1 × 104 g/mol is investigated. We explore the phase behavior from the melt state to dilute solution in solvents that are of varying selectivities for the two blocks. Bis(2-ethylhexyl) phthalate (DOP) is a neutral good solvent for SI. Di-n-butyl phthalate (DBP) and diethyl phthalate (DEP) are good solvents for PS but marginal and poor, respectively, for PI. Tetradecane (C14) is utilized as a complementary solvent that is good for PI but poor for PS. Small-angle X-ray scattering (SAXS) and static birefringence are used to locate and identify order−order (OOT) and order−disorder transitions (ODT). Dynamic and static light scattering were used to characterize the dilute solution micellar behavior. The neat polymer forms the gyroid (G1) morphology at low temperature, an OOT to hexagonal-packed cylinders (C1) occurs at 185 °C, and the ODT is located at 238 °C. Dilution with DOP decreases the OOT temperature in agreement with the dilution approximation, i.e., χOOT ∼ φ-1, but the ODT follows a stronger dependence of χODT ∼ φ-1.4. The slightly selective solvent DBP stabilizes the ordered state relative to DOP. Rich lyotropic and thermotropic behavior is observed among regions of lamellae (L), inverted gyroid (G2), inverted hexagonal-packed cylinders (C2), and inverted body-centered-cubic spheres (S2bcc). Solutions in DEP display similar morphological behavior, along with significantly increased ODT temperatures. Because of the asymmetric block copolymer composition, the phase behavior in the isoprene-selective solvent C14 is markedly different, as only G1, C1, and S1bcc phases are observed. The overall sequence of phases with dilution and/or heating is rationalized on the basis of diagonal trajectories across the phase map (temperature vs composition) for undiluted block copolymers: addition of a neutral solvent corresponds to increasing the temperature and thus a “vertical” trajectory, whereas the partitioning between microdomains of a selective solvent amounts to a “horizontal” trajectory to a renormalized block volume composition. However, a variety of novel features are observed in DEP: the formation of face-centered-cubic packed micelles, a reentrant thermotropic ODT, and a large window of L + C2 coexistence. The dependence of the principal length scale, d*, on φ, T, and structure is also considered. The strongly temperature-dependent selectivity produces a crossover in the scaling of d* vs φ for the lamellar phase: the addition of a selective solvent increases d*, but as the solvent becomes neutral, d* decreases. This phenomenon is captured by self-consistent mean-field calculations.