gebhart/patrepeval huggingface dataset:
Measuring Well Injection Profiles of Polymer-Containing Fluids (1982)

Abstract Determining injection flow profiles for various injected fluids was part of the surveillance program for monitoring the performance of Exxon's surfactant flood pilot test recently conducted in the Loudon Field, Fayette County, Illinois. Injection profiles for brine, microemulsion, and polymer drive water were measured using a radioactive tracer flow log. Profiles measured for brine injected prior to the microemulsion flood were in reasonable agreement with absolute permeability profiles determined by core analysis. However, for microemulsion injected in these same intervals, the profiles were found to be erroneous and completely misleading. For the viscous microemulsion, the profiles consistently indicated that all injected fluid was entering the upper one foot of the 13-foot-thick open-hole sandstone interval, thus suggesting the existence of horizontal fractures. Poor dispersion of the radioactive tracer in the viscous microemulsion was believed to be responsible for the anomalous responses. To study the performance of the tracer flow log tool in water and in viscous solutions containing polymer, tests were performed in a visual flow loop using colored dye as a substitute for the radioactive tracer. Results confirmed that the tracer ejection system of the conventional tool usually ejected the tracer directly onto the casing wall where the velocity was substantially less than the average fluid velocity in the casing-tool annulus. When the flowing fluid was water, the turbulent jet of ejected tracer rebounded from the casing wall and was dispersed. However, when the fluid contained polymer, viscous laminar flow dampened dispersion of the tracer and retained it near the pipe wall, thus causing the interpreted flow rate to be essentially near zero. To mitigate this problem, the ejection system of the tool was modified to allow tracer to be ejected closer to the center of the casing-tool annulus where the tracer velocity would be in better agreement with the average fluid velocity. A modified tracer flow log was subsequently used to redetermine injection profiles for microemulsion and polymer drive fluid in the Loudon pilot wells. Profiles measured by this modified tool were in reasonable agreement with profiles measured earlier for brine injection and with profiles of absolute permeability from core data. Results of these experiments therefore show that injection profiles for viscous fluids measured by a conventional radioactive tracer flow log are likely to be unreliable. However, the log tool can be modified to provide reasonable results.
Cytokine expression in intestinal mucosal biopsies. In situ hybridisation of the mRNA for interleukin-1 beta, interleukin-6 and tumour necrosis factor-alpha in inflammatory bowel disease. (1995)

Etiology and pathogenesis of inflammatory bowel disease (IBD) remain obscure. There is substantial evidence that proinflammatory cytokines such as Interleukin-1 beta (IL-1 beta), Interleukin-6 (IL-6) and Tumour Necrosis Factor-alpha (TNF-alpha) exhibit a key role in the the inflammatory process. In situ hybridisation can depict individual cells producing cytokine mRNA. We performed hybridisation with antisense probes specific for IL-1 beta, IL-6 and TNF-alpha on sections of paraffine-embedded biopsies. Specimens obtained from three control persons and six cases of Crohn's disease (CD) were investigated. Only few positive cells were found in tissue sections of control persons, clusters of lamina propria cells or epithelial cells containing cytokine mRNA were not observed. Inflammatory bowel disease tissue contained large numbers of cells producing mRNA specific for the three proinflammatory cytokines assayed. IL-1 beta, IL-6 and TNF-alpha mRNA were predominantly detected corresponding to cells of the lamina propria. Single cells containing mRNA specific for IL-6 were also found among the epithelial lining of intestinal crypts. Epithelial cells containing IL-1 beta and IL-6 mRNA were found in specimens derived from one patient with Crohn's disease. Notably, large amounts of cells containing cytokine mRNA were not only found in inflamed, but also in macroscopically normal mucosa. In conclusion, using proinflammatory cytokines as a model, we established in situ hybridisation on sections of mucosal biopsies permitting further insight into immune activation at individual cell level.
A 40-Year Journey in Search of Selective Antiviral Chemotherapy* (2011)

My search for a selective antiviral chemotherapy started more than 40 years ago with interferon inducers, then shifted to nucleoside analogs with the discovery of BVDU (brivudin), a highly selective anti-HSV-1 and anti-VZV agent, and to dideoxynucleoside analogs such as d4T (stavudine), anti-HIV agents. The search culminated in the discovery of acyclic nucleoside phosphonates (ANPs) (in collaboration with Antonin Holý), a key class of compounds active against HIV, hepatitis B virus, and DNA viruses at large; the best known of these compounds is tenofovir. Along the way, the principle of the non-nucleoside reverse transcriptase inhibitors (NNRTIs) was established. This work, initiated in collaboration with the late Paul A.J. Janssen, eventually led to the identification of rilpivirine as perhaps an "ideal" NNRTI.
Laser-driven fusion (1974)

The use of intense laser light to bring about thermonuclear reactions in a plasma is of considerable current interest. We present detailed analytical and computational studies which show the feasibility of laser-driven fusion. The required laser technology and the presently anticipated practical difficulties are discussed in outline.
ANCCA, an estrogen-regulated AAA+ ATPase coactivator for ERα, is required for coregulator occupancy and chromatin modification (2007)

AAA+ proteins play crucial roles in diverse biological processes via their ATPase-driven remodeling of macromolecular complexes. Here we report our identification of an evolutionarily conserved AAA+ protein, ANCCA/pro2000, endowed with a bromodomain that is strongly induced by estrogen in human breast cancer cells and is a direct target of protooncogene ACTR/AIB1/SRC-3. We found that ANCCA associates directly with estrogen-bound estrogen receptor (ER) alpha and ACTR. It is selectively recruited, upon estrogen stimulation, to a subset of ERalpha target genes including cyclin D1, c-myc, and E2F1 and is required for their estrogen-induced expression as well as breast cancer cell proliferation. Further studies indicate that ANCCA binds and hydrolyzes ATP and is critical for recruitment of coregulator CBP and histone hyperacetylation at the ER target chromatin. Moreover, mutations at the ATP binding motifs rendered ANCCA defective as a coactivator in mediating estrogen induction of gene expression. Together, our findings reveal an unexpected layer of regulatory mechanism in hormone signaling mediated by ANCCA and suggest that hormone-induced assembly of transcriptional coregulator complexes at chromatin is a process facilitated by AAA+ ATPase proteins.
Advances in Mammalian Cell Line Development Technologies for Recombinant Protein Production (2013)

From 2006 to 2011, an average of 15 novel recombinant protein therapeutics have been approved by US Food and Drug Administration (FDA) annually. In addition, the expiration of blockbuster biologics has also spurred the emergence of biosimilars. The increasing numbers of innovator biologic products and biosimilars have thus fuelled the demand of production cell lines with high productivity. Currently, mammalian cell line development technologies used by most biopharmaceutical companies are based on either the methotrexate (MTX) amplification technology or the glutamine synthetase (GS) system. With both systems, the cell clones obtained are highly heterogeneous, as a result of random genome integration by the gene of interest and the gene amplification process. Consequently, large numbers of cell clones have to be screened to identify rare stable high producer cell clones. As such, the cell line development process typically requires 6 to 12 months and is a time, capital and labour intensive process. This article reviews established advances in protein expression and clone screening which are the core technologies in mammalian cell line development. Advancements in these component technologies are vital to improve the speed and efficiency of generating robust and highly productive cell line for large scale production of protein therapeutics.
Caspase activation and neuroprotection in caspase-3- deficient mice after in vivo cerebral ischemia and in vitro oxygen glucose deprivation (2002)

Caspase-3 is a major cell death effector protease in the adult and neonatal nervous system. We found a greater number and higher density of cells in the cortex of caspase-3(-/-) adult mice, consistent with a defect in developmental cell death. Caspase-3(-/-) mice were also more resistant to ischemic stress both in vivo and in vitro. After 2 h of ischemia and 48 h of reperfusion, cortical infarct volume was reduced by 55%, and the density of terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling-positive cells was decreased by 36% compared with wild type. When subjected to oxygen-glucose deprivation (2 h), cortical neurons cultured from mice deficient in caspase-3 expression were also more resistant to cell death by 59%. Mutant brains showed caspase-specific poly(ADP-ribose) polymerase cleavage product (85-kDa fragment) in vivo and in vitro, suggesting redundant mechanisms and persistence of caspase-mediated cell death. In the present study, we found that caspase-8 mediated poly(ADP-ribose) polymerase cleavage in caspase-3(-/-) neurons in vivo and in vitro. In addition, mutant neurons showed no evidence of compensatory activation by caspase-6 or caspase-7 after ischemia. Taken together, these data extend the pharmacological evidence supporting an important role for caspase-3 and caspase-8 as cell death mediators in mammalian cortex and indicate the potential advantages of targeting more than a single caspase family member to treat ischemic cell injury.
Role of plasmalemmal caveolae in signal transduction (1998)

Caveolae are specialized plasmalemmal microdomains originally studied in numerous cell types for their involvement in the transcytosis of macromolecules. They are enriched in glycosphingolipids, cholesterol, sphingomyelin, and lipid-anchored membrane proteins, and they are characterized by a light buoyant density and resistance to solubilization by Triton X-100 at 4 degreesC. Once the identification of the marker protein caveolin made it possible to purify this specialized membrane domain, it was discovered that caveolae also contain a variety of signal transduction molecules. This includes G protein-coupled receptors, G proteins and adenylyl cyclase, molecules involved in the regulation of intracellular calcium homeostasis, and their effectors including the endothelial isoform of nitric oxide synthase, multiple components of the tyrosine kinase-mitogen-activated protein kinase pathway, and numerous lipid signaling molecules. More recent work has indicated that caveolae further serve to compartmentalize, modulate, and integrate signaling events at the cell surface. This specialized plasmalemmal domain warrants direct consideration in future investigations of both normal and pathological signal transduction in pulmonary cell types.
Highly birefringent hollow-core photonic bandgap fiber (2004)

A hollow-core photonic band-gap fiber with very high group birefringence is fabricated and characterized. Two independent methods, wavelength scanning and direct measurement of differential group delay (DGD), are used to obtain the group beatlength and group birefringence. The fiber illustrates a very high group birefringence of 0.025 at 1550 nm. The wavelength dependence of the group beatlength and group birefringence are also analyzed.
Angiopoietin-2 is associated with decreased endothelial nitric oxide and poor clinical outcome in severe falciparum malaria (2008)

Adherence of parasitized erythrocytes to activated endothelium causes microvascular obstruction, tissue ischemia, and clinical complications in severe malaria (SM); however, the mechanisms leading to endothelial activation remain unclear. The angiogenic factors, angiopoietin-2 (Ang-2) and vascular endothelial growth factor (VEGF) are modulators of endothelial activation, with Ang-2 release from Weibel-Palade bodies (WPBs) being regulated by endothelial nitric oxide (NO). We explored the relationships between endothelial NO bioavailability, Ang-2, VEGF, tissue perfusion, and clinical outcomes in SM. We measured plasma Ang-2 and VEGF, together with biomarkers of severity from 146 adults with and without SM, in parallel with longitudinal measures of endothelial function by using reactive hyperemia peripheral arterial tonometry (a measure of endothelial NO bioavailability). Regression was used to relate concentrations of Ang-2/VEGF with malaria disease severity, biomarkers of perfusion, endothelial activation, and parasite biomass. The longitudinal relationship between Ang-2 and endothelial function was assessed by using a mixed-effects model. Ang-2 concentrations were elevated in SM and associated with increased venous lactate, plasma intercellular cell adhesion molecule-1 concentrations, parasite biomass, and mortality. In contrast, VEGF concentrations were inversely associated with these biomarkers. Ang-2 concentrations were significantly better predictors of death than venous lactate (P = 0.03). Recovery of endothelial function was associated with falling concentrations of Ang-2. Ang-2 release from endothelial cells with reduced NO bioavailability is likely to contribute to endothelial activation, sequestered parasite biomass, impaired perfusion, and poor outcome in severe falciparum malaria. Agents that improve endothelial NO, reduce WPB exocytosis, and/or antagonize Ang-2 may have therapeutic roles in SM.
Protein- and Metal-dependent Interactions of a Prominent Protein in Mussel Adhesive Plaques (2010)

The adhesive plaques of Mytilus byssus are investigated increasingly to determine the molecular requirements for wet adhesion. Mfp-2 is the most abundant protein in the plaques, but little is known about its function. Analysis of Mfp-2 films using the surface forces apparatus detected no interaction between films or between a film and bare mica; however, addition of Ca(2+) and Fe(3+) induced significant reversible bridging (work of adhesion W(ad) approximately 0.3 mJ/m(2) to 2.2 mJ/m(2)) between two films at 0.35 m salinity. The strongest observed Fe(3+)-mediated bridging approaches the adhesion of oriented avidin-biotin complexes. Raman microscopy of plaque sections supports the co-localization of Mfp-2 and iron, which interact by forming bis- or tris-DOPA-iron complexes. Mfp-2 adhered strongly to Mfp-5, a DOPA-rich interfacial adhesive protein, but not to another interfacial protein, Mfp-3, which may in fact displace Mfp-2 from mica. In the presence of metal ions or Mfp-5, Mfp-2 adhesion was fully reversible. These results suggest that plaque cohesiveness depends on Mfp-2 complexation of metal ions, particularly Fe(3+) and also by Mfp-2 interaction with Mfp-5 at the plaque-substratum interface.
Crystallinity and the effect of ionizing radiation in polyethylene. II. Crosslinking in chain‐folded single crystals (1975)

Abstract In order to ascertain whether the crystal core of irradiated polyethylene single crystals is free from crosslinks—as would follow from the results of Part I—the fold surface of irradiated single crystals was shaved off with ozone and the resulting product examined by GPC for molecular weight. It was found that on ozone degradation the entire material, which had been insolubilized by radiation‐induced crosslinking, has become soluble hence became available for the GPC analysis. The chromatograms displayed the same peaked development with degradation as the unirradiated crystals leading eventually to single traverse dicarboxylic acids. This proves the absence of crosslinks within the crystal interior of the material as examined by GPC. The appearance of some additional low molecular weight material, is attributed to scission at the radiation‐induced double bonds due to ozone which eliminates the possibility of the existence of crosslinks within the lattice such as might provide scission sites for ozone. The conclusion could therefore be reached that, to the extent assessable by our GPC test, there are no radiation‐induced crosslinks within the crystal lattice, hence the crosslinks produced must be entirely confined to the fold surface region of the crystals.
Nucleotide sequence comparison between heat-labile toxin B-subunit cistrons from Escherichia coli of human and porcine origin (1985)

The nucleotide sequence of the LT-BH cistron (eltBH) from an enterotoxigenic Escherichia coli strain infectious for humans was determined and compared with the LT-B cistron sequence from a porcine E. coli isolate. Both cistrons were shown to comprise 375 nucleotide base pairs, and discrepancies were detected at eight positions. Of the nonhomologous base pairs, six resulted in codon changes that would lead to amino acid variations. The nucleotide sequence distal to both LT-B cistrons was also determined, and only three differences were detected in 197 base pairs. An HhaI site unique to eltBH was shown to be present in all the heat-labile (LT) genes from 31 human isolates surveyed, whereas the restriction enzyme recognition site was absent in the gene from 46 porcine E. coli isolates. The results suggest that two genetically discernable LT groups are identifiable and that the groups are also distinguishable by the isolation source (human or porcine) of the infecting E. coli strains.
Genetic conservation in applied tree breeding programs. (2001)

Abstract. This paper reviews how population size and structure impacts the maintenance of genetic variation in breeding and gene resource populations. We discuss appropriate population sizes for low frequency alleles and point out some examples of low frequency alleles in the literature. Development of appropriate breeding populations and gene resource populations are discussed.
Connective Tissue Growth Factor in Drug‐Induced Gingival Overgrowth (2001)

The data from the present study show significantly higher CTGF staining in phenytoin-induced gingival overgrowth tissues compared to controls, cyclosporin A-, or nifedipine-induced gingival overgrowth. Moreover, semiquantitative analyses of histologic samples support the concept that the phenytoin overgrowth tissues are fibrotic. These associations suggest a possible role for CTGF in promoting development of fibrotic lesions in phenytoin-induced gingival overgrowth.
Group 4 catalysts for ethene polymerization containing tetradentate salicylaldiminato ligands (2006)

The structural properties of three new classes of titanium and zirconium complex bearing tetradentate salicylaldiminato proligands are elucidated using X-ray diffraction and NMR spectroscopy. On activation with MAO co-catalyst, their behaviour in ethene polymerization depends strongly on the nature of the structure and the substitution pattern. One titanium complex based on a 2-aminobenzylamine (C3-chain) backbone has a trans arrangement of the co-ligand sites and, unsurprisingly, does not polymerize ethene. The 1,8-diaminonaphthalene (C3-chain) backbone gives a rather ring-strained cis complex, but was also unproductive. A range of cis complexes of zirconium with the 2,2'-diaminobibenzyl (C6-chain) backbone give low to moderate productivities of multimodal poly(ethene), while in contrast the structurally analogous titanium compounds provide highly active, single site catalysts. Thermal degradation of these catalysts is slowed significantly by a substitution pattern on the phenolate unit which sterically protects the imine donor unit; a phenomenon which has been previously observed in much lower activity catalysts based on 2,2'-diaminobiphenyl (C4-chain) but which does not improve the stability of the very highly active unbridged systems.
Review article: Polymer-matrix Nanocomposites, Processing, Manufacturing, and Application: An Overview (2006)

This review is designed to be a comprehensive source for polymer nanocomposite research, including fundamental structure/property relationships, manufacturing techniques, and applications of polymer nanocomposite materials. In addition to presenting the scientific framework for the advances in polymer nanocomposite research, this review focuses on the scientific principles and mechanisms in relation to the methods of processing and manufacturing with a discussion on commercial applications and health/safety concerns (a critical issue for production and scale-up). Hence, this review offers a comprehensive discussion on technology, modeling, characterization, processing, manufacturing, applications, and health/safety concerns for polymer nanocomposites.
Effects of protein hydrolysis on pasting properties of wheat flour (2012)

Abstract Protein hydrolysis is used widely in the food industry for the purpose of improvement of food or industrial quality, and the processing exists concurrently or subsequently with starch pasting. The effects of protein hydrolysis using papain, pepsin, trypsin, and dithiothreitol (DTT) on flour pasting properties were here investigated at five set concentrations. There were notable decreases in the peak, the trough viscosity, and the integral area of the viscosity curve as the concentrations of papain, trypsin, and DTT increased. DDT and pepsin concentration did not have any effect on final viscosity. Both breakdown and setback showed significant downtrends as the concentration of papain increased but no change as DDT concentration varied. Low concentrations of papain and pepsin prolonged peak time slightly, but higher concentrations shortened it significantly. For trypsin and DTT, low concentrations increased peak time notably, but high concentrations decreased it significantly. Pasting time and temperature increased in the presence of papain, pepsin, and trypsin, more so at higher concentrations. These results supply a basis for the utilization of hydrolyzed protein in the food industry and for the further studies on the interactions between protein and starch during processing.
Review Paper: A critical review of the present and future prospects for electronic paper (2011)

Abstract— The commercial success of monochrome electronic paper (e‐Paper) is now propelling the development of next‐generation flexible, video, and color e‐Paper products. Unlike the early battles in the 1980s and 1990s between transmissive and emissive display technologies, there is a extraordinary diversity of technologies vying to become the next generation of e‐Paper. A critical review of all major e‐Paper technologies, including a technical breakdown of the performance limitations based on device physics and commentary on possible future breakthroughs, is presented. In addition, the visual requirements for color e‐Paper are provided and compared to standards used in conventional print. It is concluded that researchers have much work remaining in order to bridge the significant gap between reflective electronic displays and print‐on‐paper.