gebhart/patrepeval huggingface dataset:
Alginate, the Slime Exopolysaccharide of Pseudomonas Aeruginosa, Binds Human Leukocyte Elastase, Retards Inhibition by α1-Proteinase Inhibitor, and Accelerates Inhibition by Secretory Leukoprotease Inhibitor (1996)

The interaction of alginate from Pseudomonas aeruginosa ATCC 39324 with human leukocyte elastase was studied by determining the effects of the polysaccharide on the amidolytic activity of the enzyme toward a range of synthetic peptide substrates of different length. The data support a model in which each elastase molecule interacts with a total of 19 uronic acid units on the alginate, primarily through electrostatic forces. Binding of alginate results in occlusion of distal subsites, most likely S4 and S5, of the enzyme's extended substrate-binding domain. As a result, alginate alone appears to be a weak inhibitor of the hydrolysis of long synthetic peptide substrates and [14C]elastin by elastase. Alginate also has effects on the antielastase function of naturally occurring protease inhibitors in the lung: It reduces the association rate of elastase and alpha 1-proteinase inhibitor, whereas it increases the association rate of elastase and secretory leukoprotease inhibitor. In the presence of 36 micrograms/ml alginate, the median concentration found in sputum from cystic fibrosis patients infected with mucoid strains of P. aeruginosa, the second-order rate constant for inhibition of elastase by secretory leukoprotease inhibitor is 2.6-fold greater than that for alpha 1-proteinase inhibitor. Alginate has only a minor effect on the antielastase activities of elafin and a recombinant form of the isolated C-terminal domain of secretory leukoprotease inhibitor. Based on these findings, alginate may be an important factor in determining the local distribution of leukocyte elastase and perturbing the overall protease-antiprotease balance in the infected lungs of cystic fibrosis patients.
Effect of hypotension preceding death on the function of lungs from donors with nonbeating hearts. (1996)

A period of hypotension before death severely impairs cadaveric lung viability.
Overexpression of LSD1 contributes to human carcinogenesis through chromatin regulation in various cancers (2010)

A number of histone demethylases have been identified and biochemically characterized, but the pathological roles of their dysfunction in human disease like cancer have not been well understood. Here, we demonstrate important roles of lysine-specific demethylase 1 (LSD1) in human carcinogenesis. Expression levels of LSD1 are significantly elevated in human bladder carcinomas compared with nonneoplastic bladder tissues (p < 0.0001). cDNA microarray analysis also revealed its transactivation in lung and colorectal carcinomas. LSD1-specific small interfering RNAs significantly knocked down its expression and resulted in suppression of proliferation of various bladder and lung cancer cell lines. Concordantly, introduction of exogenous LSD1 expression promoted cell cycle progression of human embryonic kidney fibroblast cells. Expression profile analysis showed that LSD1 could affect the expression of genes involved in various chromatin-modifying pathways such as chromatin remodeling at centromere, centromeric heterochromatin formation and chromatin assembly, indicating its essential roles in carcinogenesis through chromatin modification.
Characterization of a novel Neisseria meningitidis Fur and iron‐regulated operon required for protection from oxidative stress: utility of DNA microarray in the assignment of the biological role of hypothetical genes (2004)

We have previously shown that in the human pathogen Neisseria meningitidis group B (MenB) more than 200 genes are regulated in response to growth with iron. Among the Fur-dependent, upregulated genes identified by microarray analysis was a putative operon constituted by three genes, annotated as NMB1436, NMB1437 and NMB1438 and encoding proteins with so far unknown function. The operon was remarkably upregulated in the presence of iron and, on the basis of gel retardation analysis, its regulation was Fur dependent. In this study, we have further characterized the role of iron and Fur in the regulation of the NMB1436-38 operon and we have mapped the promoter and the Fur binding site. We also demonstrate by mutant analysis that the NMB1436-38 operon is required for protection of MenB to hydrogen peroxide-mediated killing. By using both microarray analysis and S1 mapping, we demonstrate that the operon is not regulated by oxidative stress signals. We also show that the deletion of the NMB1436-38 operon results in an impaired capacity of MenB to survive in the blood of mice using an adult mouse model of MenB infection. Finally, we show that the NMB1436-38 deletion mutant exhibits increased susceptibility to the killing activity of polymorphonuclears (PMNs), suggesting that the 'attenuated' phenotype is mediated in part by the increased sensitivity to reactive oxygen species-producing cells. This study represents one of the first examples of the use of DNA microarray to assign a biological role to hypothetical genes in bacteria.
A Method for Detecting 8-Methoxypsoralen in the Ocular Lens (1977)

The use of 8-methoxypsoralen for treating psoriasis could prove hazardous if this photosensitizing agent enters the ocular lens. Phosphorescence spectra of intact rat lenses reveal concentrations of 8-methoxypsoralen on the order 10(-5)M after intraperitoneal injection of 8-methoxypsoralen. There is evidence that this drug can function as a photosensitizing agent, enhancing ultraviolet-induced changes within the lens.
Arterial Decellularized Scaffolds Produced Using an Innovative Automatic System (2014)

There is still an unmet clinical need for small-caliber artery substitution. Decellularized scaffolds in tissue engineering represent a promising solution. We have developed an innovative system for the automatic decellularization of blood vessels, used to process pig arteries. The system is able to automatically drive a decellularization process in a safe and reliable environment, with complex time patterns, using up to three different decellularization solutions, and providing at the same time a physical stress to improve the decellularization. The decellularization of pig arteries was evaluated by means of histology, DNA quantification and mechanical testing. Outcomes showed scaffolds with no cellular or nuclear remnants and a well-preserved tissue structure, corroborated by mechanical properties similar to native tissue. Decellularized scaffolds were seeded on the inner layer with human endothelial cells and implanted as iliac artery replacement in 4 pharmacologically immune-compromised pigs. This chimeric model was performed as a very preliminary evaluation to investigate the performances of these scaffolds in vivo, and to investigate the fate of seeded cells. Recipients were sacrificed on day 14 and day 70 after surgery, and vessels were found to be patent and with no evidence of thrombi formation. The inner layer was covered by endothelial cells, and the migration of cells positive for α-smooth-muscle actin was observed from the outer layer towards the tunica media. Intriguingly, the endothelial cells on explanted vessels were entirely derived from the host while the seeded cells were lost. In conclusion, this work presents a novel tool for a safe and controlled production of arterial scaffolds, with good decellularization outcomes and a good performance in a short-term, large-animal implantation.
TNFR-Associated Factor Family Protein Expression in Normal Tissues and Lymphoid Malignancies (2000)

TNFR-associated factors (TRAFs) constitute a family of adapter proteins that associate with particular TNF family receptors. Humans and mice contain six TRAF genes, but little is known about their in vivo expression at the single cell level. The in vivo locations of TRAF1, TRAF2, TRAF5, and TRAF6 were determined in human and mouse tissues by immunohistochemistry. Striking diversity was observed in the patterns of immunostaining obtained for each TRAF family protein, suggesting their expression is independently regulated in a cell type-specific manner. Dynamic regulation of TRAFs was observed in cultured PBLs, where anti-CD3 Abs, mitogenic lectins, and ILs induced marked increases in the steady-state levels of TRAF1, TRAF2, TRAF5, and TRAF6. TRAF1 was also highly inducible by CD40 ligand in cultured germinal center B cells, whereas TRAF2, TRAF3, TRAF5, and TRAF6 were relatively unchanged. Analysis of 83 established human tumor cell lines by semiquantitative immunoblotting methods revealed tendencies of certain cancer types to express particular TRAFs. For example, expression of TRAF1 was highly restricted, with B cell lymphomas consistently expressing this TRAF family member. Consistent with results from tumor cell lines, immunohistochemical analysis of 232 non-Hodgkin lymphomas revealed TRAF1 overexpression in 112 (48%) cases. TRAF1 protein levels were also elevated in circulating B cell chronic lymphocytic leukemia specimens (n = 49) compared with normal peripheral blood B cells (p = 0.01), as determined by immunoblotting. These findings contribute to an improved understanding of the cell-specific roles of TRAFs in normal tissues and provide evidence of altered TRAF1 expression in lymphoid malignancies.
A new highly specific monoclonal antibody against placental alkaline phosphatase: a potential marker for the early detection of testis tumour (2000)

The selected mAb ATC2 has high specificity for human germ cell tumours, the target antigen for ATC2 being PLAP, although the antigenic epitope(s) differ from those recognized by H17E2. Thus ATC2 may be useful for monitoring serum levels of PLAP in patients with testis cancer and may be relevant for detecting cancer cells in the semen of individuals with suspected testis cancer, particularly in those with equivocal findings on ultrasonography.
Macrophage progenitors from mouse bone marrow and spleen differ in their expression of the Ly-6C differentiation antigen. (1993)

Using mAb and magnetic and fluorescence-activated cell sorting, together with culturing in semisolid culture medium, we show that essentially all splenic macrophage progenitors are Ly-6ChiMac-1-. By contrast, bone marrow macrophage progenitors were more heterogeneous in Ly-6C expression, the majority being restricted to the Ly-6CdimMac-1- and the Ly-6C-Mac-1- subsets. These findings provide immunophenotype evidence that macrophages in the spleen and bone marrow arise from different progenitors.
Role of mRNA translational efficiency in bovine growth hormone expression in Escherichia coli. (1984)

The conditions necessary for high-level expression of methionyl bovine growth hormone (Met-bGH) in Escherichia coli were investigated. Plasmids were constructed that contain a thermoinducible runaway replicon and either the E. coli tryptophan or lipoprotein promoter and ribosome binding sites, which served as transcriptional and translational initiation sites for the expression of the bGH gene. The expression of Met-bGH was low with either system. However, expression levels of up to 30% of total cell protein were obtained after the introduction of additional codons 3' to the initiating AUG codon, thus altering the NH2-terminal amino acid sequence of bGH. To obtain high-level expression of Met-bGH a two-cistron system was constructed in which the codons that enhanced the expression of bGH were incorporated into the first cistron, and the coding region for Met-bGH was incorporated into the second cistron. This approach may be generally applicable to achieving high-level expression of a gene that contains NH2-terminal sequences that do not allow for its efficient expression. Analyses of the stabilities of the bGH derivatives and their transcripts in vivo suggested that the variations in the level of expression were due to variations in the efficiency of mRNA translation.
Protease-cleaved iron-transferrin augments oxidant-mediated endothelial cell injury via hydroxyl radical formation. (1995)

Previous work has shown that the Pseudomonas-derived protease, pseudomonas elastase (PAE), can modify transferrin to form iron complexes capable of catalyzing the formation of hydroxyl radical (.OH) from neutrophil (PMN)-derived superoxide (.O2-) and hydrogen peroxide (H2O2). As the lung is a major site of Pseudomonas infection, the ability of these iron chelates to augment oxidant-mediated pulmonary artery endothelial cell injury via release of 51Cr from prelabeled cells was examined. Diferrictransferrin previously cleaved with PAE significantly enhanced porcine pulmonary artery endothelial cell monolayer injury from 2.3-6.3 to 15.8-17.0% of maximum, resulting from exposure to H2O2, products of the xanthine/xanthine oxidase reaction, or PMA-stimulated PMNs. Iron associated with transferrin appeared to be responsible for cell injury. Spin trapping and the formation of thiobarbituric acid-reactive 2-deoxyribose oxidation products demonstrated the production of .OH in this system. The addition of catalase, dimethyl thiourea, and the hydrophobic spin trap, alpha-phenyl-n-terbutyl-nitrone, offered significant protection from injury (27.8-58.2%). Since sites of Pseudomonas infection contain other proteases, the ability of porcine pancreatic elastase and trypsin to substitute for PAE was examined. Results were similar to those observed with PAE. We conclude .OH formation resulting from protease alteration of transferrin may serve as a mechanism of tissue injury at sites of bacterial infection and other processes characterized by increased proteolytic activity.
Progress toward the determination of Sr2+ in highly basic solutions using imaging optical fiber sensor arrays (2005)

This manuscript describes initial progress toward the development of an imaging optical fiber microsphere sensor array for real-time monitoring of Sr2+ in process streams from high-level radioactive waste (HLW) remediation. Fura-2, a fluorescent molecular recognition compound, which displays increased fluorescence intensity upon complexation with divalent cations, was employed as a probe to quantify Sr2+. The solution-based detection of Sr2+ using Fura-2 was investigated in the presence of low Ca2+ concentrations and at high pH and ionic strength. A linear range of 6.7 × 10−7 M to 6.7 × 10−4 M was obtained for Sr2+ in neutral solutions containing trace Ca2+ and 6.7 × 10−8 M and 6.7 × 10−4 M for Sr2+ in high pH, high ionic strength solutions. Additionally, the stability of imaging optical fibers to harsh, high pH conditions was examined. These experiments suggest the fiber surface may need to be modified so that they are stable during the anticipated measurement times required for HLW.
Long-term Outcomes of Ranibizumab Therapy for Diabetic Macular Edema: The 36-Month Results from Two Phase III Trials (2013)

Proprietary or commercial disclosure may be found after the references.
CCR2 is required for CD8-induced graft-versus-host disease (2005)

Graft-versus-host disease (GVHD) is a major complication of allogeneic hematopoietic stem cell transplantation (HSCT). Migration of donor-derived T cells into GVHD target organs plays a critical role in the development of GVHD and chemokines and their receptors are important molecules involved in this process. Here, we demonstrate in murine bone marrow transplantation models that the expression of the inflammatory CC chemokine receptor 2 (CCR2) on donor-derived CD8+ T cells is relevant for the control of CD8+ T-cell migration and development of GVHD. Recipients of CCR2-deficient (CCR2-/-) CD8+ T cells developed less damage of gut and liver than recipients of wild-type CD8+ T cells, which correlated with a reduction in overall GVHD morbidity and mortality. Assessment of donor CD8+ T-cell target organ infiltration revealed that CCR2-/- CD8+ T cells have an intrinsic migratory defect to the gut and liver. Other causes for the reduction in GVHD could be excluded, as alloreactive proliferation, activation, IFN-gamma production and cytotoxicity of CCR2-/- CD8+ T cells were intact. Interestingly, the graft-versus-tumor effect mediated by CCR2-/- CD8+ T cells was preserved, which suggests that interference with T-cell migration by blockade of CCR2 signaling can separate GVHD from GVT activity.
Simulation of atomic force microscope tip–sample/sample–tip reconstruction (1995)

The image obtained with the atomic force microscope is a convolution of the tip and sample. A numerical algorithm which has been previously reported enables the removal of the tip geometry, hence exposing a more accurate picture of the sample. The efficacy of such a scheme is explored with the use of simulations of the tip–sample interaction using simple geometric considerations. Two examples that illustrate the limitations of image analysis by such procedures are presented.
Identification of Porphyromonas gingivalis Genes Specifically Expressed in Human Gingival Epithelial Cells by Using Differential Display Reverse Transcription-PCR (2004)

Porphyromonas gingivalis, one of the causative agents of adult periodontitis, can invade and survive within host epithelial cells. The molecular mechanisms by which P. gingivalis induces uptake and adapts to an intracellular environment are not fully understood. In this study, we have investigated the genetic responses of P. gingivalis internalized within human gingival epithelial cells (GECs) in order to identify factors involved in invasion and survival. We compared the differential display of arbitrarily PCR-amplified gene transcripts in P. gingivalis recovered from GECs with the display of transcripts in P. gingivalis control cultures. Over 20 potential differentially expressed transcripts were identified. Among these, pepO, encoding an endopeptidase, and genes encoding an ATP-binding cassette (ABC) transporter and a cation-transporting ATPase were upregulated in GECs. To investigate the functionality of these gene products, mutants were generated by insertional inactivation. Compared to the parental strain, mutants of each gene showed a significant reduction in their invasion capabilities. In addition, GEC cytoskeletal responses to the mutants were distinct from those induced by the parent. In contrast, adhesion of the mutant strains to GECs was not affected by lack of expression of the gene products. These results suggest that PepO, a cation-transporting ATPase, and an ABC transporter are required for the intracellular lifestyle of P. gingivalis.
Subpicosecond electrooptic sampling: Principles and applications (1986)

This paper reviews the principles and applications of electrooptic sampling for the characterization of repetitive ultrafast electrical transients. Electrooptic sampling is an electric field sensitive technique that utilizes ultrashort optical pulses as "sampling gates" via the Pockels effect in electrooptic media and has demonstrated subpicosecond temporal resolution and microvolt sensitivity. The technique can be adapted to characterize a wide variety of picosecond electronic devices such as field-effect transistors and photodetectors as well as probe complete integrated circuits with high temporal and spatial resolution.
Experimental Evaluation of Carbon Dots Stabilized Foam for Enhanced Oil Recovery (2019)

Foams are used as divergent fluids for conformance control in enhanced oil recovery (EOR) operations. It is created by mixing a surfactant and a gas in situ in high-permeability reservoirs (e.g., surfactant alternating gas or SAG). Foams exhibit instability issues at reservoir conditions with a highly complex pore network, high pressure, high temperature, and high salinity. Here, we examine the stability and efficacy of foams formed with and without the addition of carbon nanoparticles (or nanodots). Carbon particles have demonstrated stability, mobility, and scalability for harsh reservoir environment use and application as a tracer technology. In this study, we investigate the feasibility of using inexpensive carbon dots as “foam boosters.” The experiments involved using different levels of brine salinities (ranging from seawater to formation connate water), different concentrations of the nanodots (ranging from 5 to 500 ppm), different types of surfactants (anionic, cationic, and nonionic) and gases (CO2, N2, and air), and different levels of temperature (ranging from 27 to 100 °C) to target representative conditions of Saudi Arabian reservoirs. In addition, we examined both foam structure, such as the gas–liquid interface, and liquid film lamella to better understand the mechanisms contributing to foamability and foam stability. The study highlights and unravels the complex interrelationship of the different influencing components on the stability of foam with the addition of the carbon particles. The bulk and porous media stabilities of the foams are analyzed using a static foam analyzer and an HP/HT core-flood system, respectively. Foam stability is assessed in terms of type and amount of modified/functionalized carbon particles, surfactant, and gas. We observed that the bulk foam containing only trace amounts (5–10 ppm) of carbon nanodots shows improved stability in a high-salinity medium. The particles improved the foam stability maximum by 70% and more than doubled the foam half-life for some foams. Confocal microscopy images of the foam structure of systems containing an increased concentration of carbon particles reveal an increased thickness of the lamellae and a decreased average bubble size. This is a clear indication of the enhanced foam stability. Carbon dots decreased the drainage rate of the lamellae and delayed the bubble rupture point or coalescence. The particles improved the foam stability by preferentially positioning itself in the lamella and preventing liquid drainage and film thinning.
Cognitive function and health-related quality of life four years after cardiac arrest (2015)

Cognitive impairment four years after cardiac arrest affected more than one quarter of the patients. Short-term memory was predominantly affected.
Evaluation of U.S. Plant Introductions of Watermelon for Resistance to Powdery Mildew (2005)

Two hundred sixty-six Citrullus lanatus (Thumb.) Matsum. &amp; Nakai accessions (Plant Introductions and named cultivars) were tested against a race 2 Sphaerotheca fuliginea (Schlechtend.: Fr.) Pollacci isolate to evaluate for resistance to powdery mildew disease. Growth room-grown seedlings were artificially inoculated with conidia from watermelon host leaves at 2-day intervals from the appearance of the first true leaf until test results data were taken, when the second true leaf was fully expanded. Plants were evaluated on a 1 to 9 scale of increasing disease severity. Disease indices (DIs) were calculated as weighted averages for each entry. All genotypes with resistant plants (powdery mildew rating 1 to 3) were reevaluated in a replicated test of 3 replications of 10 plants each. Disease indices were again calculated. Twenty-two plant introductions (PIs) and one named variety displayed intermediate resistance to powdery mildew in the replicated test with DIs ranging from 5.0 to 6.0.