gebhart/patrepeval huggingface dataset:
Novel insights into proteolytic cleavage of influenza virus hemagglutinin (2010)

The influenza virus hemagglutinin (HA) mediates the first essential step in the viral life cycle, virus entry into target cells. Influenza virus HA is synthesised as a precursor protein in infected cells and requires cleavage by host cell proteases to transit into an active form. Cleavage is essential for influenza virus infectivity and the HA-processing proteases are attractive targets for therapeutic intervention. It is well established that cleavage by ubiquitously expressed subtilisin-like proteases is a hallmark of highly pathogenic avian influenza viruses (HPAIV). In contrast, the nature of the proteases responsible for cleavage of HA of human influenza viruses and low pathogenic avian influenza viruses (LPAIV) is not well understood. Recent studies suggest that cleavage of HA of human influenza viruses might be a cell-associated event and might be facilitated by the type II transmembrane serine proteases (TTSPs) TMPRSS2, TMPRSS4 and human airway trypsin-like protease (HAT). Here, we will introduce the different concepts established for proteolytic activation of influenza virus HA, with a particular focus on the role of TTSPs, and we will discuss their implications for viral tropism, pathogenicity and antiviral intervention.
Oxidation of graphene with variable defects: alternately symmetrical escape and self-restructuring of carbon rings (2020)

Variable defects such as vacancies and grain boundaries are unavoidable in the synthesis of graphene, but play a central role in the activation of oxidation. Here, we apply reactive molecular dynamics simulations to reveal the underpinning mechanisms of oxidation in graphene with or without defects at the atomic scale. There exist four oxidation modes generating CO2 or CO in different stages, beginning from a single-atom vacancy, and proceeding until the ordered structure broken down into carbon oxide chains. The oxidation process of the graphene sheets experiences four typical stages, in which alternately symmetrical escape phenomenon is observed. Importantly, disordered rings can self-restructure during the oxidation of grain boundaries. Of all defects, the oxidation of vacancy has the lowest energy barrier and is therefore the easiest point of nucleation. This study demonstrates the crucial role of defects in determining the oxidation kinetics, and provides theoretical guidance for the oxidation prevention of graphene and the production of functionalized graphene.
3-Hydroxypyrroles. I. A general synthetic route to 4,5-unsubstituted alkyl 3-hydroxpyrrole-2-carboxylates. (1978)

The synthesis of 4, 5-unsubstituted alkyl 3-hydroxypyrrole-2-carboxylates was described. An equimolar mixture of glycine esters (6) and diethyl ethoxymethylenemalonate (7) gave the condensation products (8) with liberation of ethanol. 3-Hydroxypyrrole-2, 4-dicarboxylates (9) were obtained by the Dieckmann condensation of 8 using alkoxide as condensing agent. Selective partial hydrolysis of pyrrole-diesters (9) using a large excess of alkali hydroxide afforded the 4-carboxylic acids (10), which readily gave alkyl 3-hydroxypyrrole-2-carboxylates (5) on decarboxylation in boiling β-picoline or pyridineacetic acid in good yields.
Genome Sequence of Rhizobium etli CNPAF512, a Nitrogen-Fixing Symbiont Isolated from Bean Root Nodules in Brazil (2011)

Rhizobium etli is a Gram-negative soil-dwelling alphaproteobacterium that carries out symbiotic biological nitrogen fixation in close association with legume hosts. R. etli strains exhibit high sequence divergence and are geographically structured, with a potentially dramatic influence on the outcome of symbiosis. Here, we present the genome sequence of R. etli CNPAF512, a Brazilian isolate from bean nodules. We anticipate that the availability of genome sequences of R. etli strains from distinctly different areas will provide valuable new insights into the geographic mosaic of the R. etli pangenome and the evolutionary dynamics that shape it.
Oxidized LDL–Induced NF-κB Activation and Subsequent Expression of Proinflammatory Genes Are Defective in Monocyte-Derived Macrophages From CD36-Deficient Patients (2000)

-CD36 is 1 of the class B scavenger receptor expressed on monocytes, monocyte-derived macrophages (Mphi), platelets, and adipocytes. In our previous studies, we reported that the uptake of oxidized low density lipoproteins (OxLDLs) is reduced by approximately 50% in Mphi from CD36-deficient patients compared with that in control subjects. Recently, we have shown that CD36 is highly expressed in human atherosclerotic aorta. Possibilities have been raised that besides the wide distribution and multifunctional characteristics of CD36, this molecule may also be involved in the mediation of intracellular signaling. The aim of the present study was to elucidate the role of CD36 in cytokine secretion and to investigate the CD36-mediated intracellular signaling stimulated by OxLDL. On addition of OxLDL or thrombospondin-1, the Mphi from CD36-deficient patients secreted significantly less amounts of tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 beta (IL-1 beta) compared with those from controls. RNase protection assay with multiprobe template sets demonstrated that after incubation with OxLDL, the mRNAs of a variety of cytokines, including genes encoding IL-1Ra, IL-1beta, IL-6, TNF-alpha and -beta, and interferon (IFN)-gamma and -beta, were significantly lower in the Mphi of patients. The addition of antibody against CD36 attenuated this OxLDL-induced response in controls. We also observed a reduced response in nuclear factor-kappa B (NF-kappa B) activity in OxLDL-stimulated Mphi from CD36-deficient patients. Unlike OxLDL, stimulation by lipopolysaccharide induced an increase in NF-kappa B activity in Mphi from CD36-deficient patients, suggesting that lipopolysaccharide-mediated signaling was conserved. These results demonstrate that in addition to the reduced OxLDL uptake that we reported previously, CD36-deficient patients may also have an impaired response of OxLDL-induced NF-kappa B activation and subsequent cytokine expression.
Gene Transfer and Expression Protocols (1991)

Biology is the study of living things. The classical approach might be described as holistic and descriptive, whereas the modern molecular - proach aims to be investigative, reductionist, and mechanistic . Genes contain all the information for the structure of all living things ; thus, the understanding of how genes are regulated is an important step toward understanding the nature of living things. The study of gene regulation has been made more tractable by the design of simple expe- mental models in which a single gene can be isolated from the milieu of the organism. The new science of molecular biology has introduced techniques that permit the design of such experimental models. In - sence, the genome of the organism is dissected in such a manner that specific genes may now be introduced into an appropriate cell line . Subsequent analysis of the proteins expressed from the genes under study results in the identification of the regulatory DNA sequences
Insertion Mutagenesis of wca Reduces Acid and Heat Tolerance of Enterohemorrhagic Escherichia coli O157:H7 (2001)

Strains of enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 produce under stress copious amounts of exopolysaccharide (EPS) composed of colanic acid (CA). Studies were performed to evaluate the association of production of CA with survival of EHEC under adverse environmental conditions. A CA-deficient mutant, M4020, was obtained from a CA-proficient parental strain, E. coli O157:H7 W6-13, by inserting a kanamycin resistance gene cassette (kan) into wcaD and wcaE, 2 of the 21 genes required for CA biosynthesis. M4020 was defective in CA production as determined from the ratio of uronic acid to protein (UA/P) of cells grown from 1 to 4 days at 25 degrees C on minimal glucose agar (MGA), MacConkey agar, and sorbitol-MacConkey agar, and by colony morphology on MGA. The results of stress treatment revealed that M4020 was substantially less tolerant to acid (pH 4.5 and 5.5) and heat (55 and 60 degrees C) in comparison to W6-13, indicating that CA confers on E. coli O157:H7 a protective effect from the environmental stresses of acid and heat.
Purification and Characterization of 2,6-β- d -Fructan 6-Levanbiohydrolase from Streptomyces exfoliatus F3-2 (2000)

Streptomyces exfoliatus F3-2 produced an extracellular enzyme that converted levan, a beta-2,6-linked fructan, into levanbiose. The enzyme was purified 50-fold from culture supernatant to give a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The molecular weights of this enzyme were 54,000 by SDS-PAGE and 60,000 by gel filtration, suggesting the monomeric structure of the enzyme. The isoelectric point of the enzyme was determined to be 4.7. The optimal pH and temperature of the enzyme for levan degradation were pH 5.5 and 60 degrees C, respectively. The enzyme was stable in the pH range 3.5 to 8.0 and also up to 50 degrees C. The enzyme gave levanbiose as a major degradation product from levan in an exo-acting manner. It was also found that this enzyme catalyzed hydrolysis of such fructooligosaccharides as 1-kestose, nystose, and 1-fructosylnystose by liberating fructose. Thus, this enzyme appeared to hydrolyze not only beta-2,6-linkage of levan, but also beta-2,1-linkage of fructooligosaccharides. From these data, the enzyme from S. exfoliatus F3-2 was identified as a novel 2,6-beta-D-fructan 6-levanbiohydrolase (EC 3.2.1.64).
Environmental Control to Reduce Transmission ofClostridium difficile (2000)

Restrictive antibiotic policies and infection control measures have been shown to reduce the incidence of Clostridium difficile-associated diarrhea (CDAD) among hospitalized patients. To date, the role of environmental disinfectants in reducing nosocomial CDAD rates has not been well studied. In a before-and-after intervention study, patients in 3 units were evaluated to determine if unbuffered 1:10 hypochlorite solution is effective as an environmental disinfectant in reducing the incidence of CDAD. Among 4252 patients, the incidence rate of CDAD for bone marrow transplant patients decreased significantly, from 8.6 to 3.3 cases per 1000 patient-days (hazard ratio, 0.37; 95% confidence interval, 0.19-0.74), after the environmental disinfectant was switched from quaternary ammonium to 1:10 hypochlorite solution in the rooms of patients with CDAD. Reverting later to quaternary ammonium solution increased the CDAD rate to 8.1 cases per 1000 patient-days. No reduction in CDAD rates was seen among neurosurgical intensive care unit and general medicine patients, for whom baseline rates were 3.0 and 1.3 cases per 1000 patient-days, respectively. Unbuffered 1:10 hypochlorite solution is effective in decreasing patients' risk of developing CDAD in areas where CDAD is highly endemic. Presumed mechanisms include reducing the environmental burden and the potential for C. difficile transmission among susceptible patients.
Efficient generation of respiratory syncytial virus (RSV)-neutralizing human MoAbs via human peripheral blood lymphocyte (hu-PBL)-SCID mice and scFv phage display libraries (2000)

SUMMARY RSV is one of the major causes of pneumonia and bronchiolitis in infants and young children and is associated with high mortality. RSV neutralizing human antibody (hu-Ab) is known to mediate resistance to viral infection as well as to be an effective treatment for severe lower respiratory tract RSV infection. We have previously demonstrated that human primary and secondary immune responses can be established in severe combined immunodeficient mice engrafted with human peripheral blood lymphocytes (hu-PBL-SCID). By combining this animal model with the single-chain Fv antibody (scFv) phage display library technique, we were able to investigate further its clinical potential by generating a panel of human scFvs that exhibit both high F glycoprotein (RSV-F) binding affinities (∼108 M−1) and strong neutralizing activities against RSV infection in vitro. Sequencing analysis of the randomly isolated anti-RSV-F scFv clones revealed that they were derived from different VH families with mutations in the complementarity-determining region 1 (CDR1). The results suggest that: (i) RSV-F-specific human immune responses and affinity maturation can be induced in hu-PBL-SCID mice; and (ii) this approach can be applied to generate large numbers of human scFvs with therapeutic potential. Despite the fact that hu-PBL-SCID mouse and human scFv phage display library have individually been established, our approach contributes a simple and significant step toward the generalization of antigen-specific human monoclonal antibody (hu-MoAb) production and their clinical applications.
Environmental guidance of normal and tumor cell plasticity: epithelial mesenchymal transitions as a paradigm (2004)

Epithelial mesenchymal transitions are a remarkable example of cellular plasticity. These transitions are the hallmark of embryo development, are pivotal in cancer progression, and seem to occur infrequently in adult organisms. The reduced incidence of transitions in the adult could result from restrictive functions of the microenvironment that stabilizes adult cell phenotypes and prevents plastic behavior. Multipotential progenitor cells exhibiting a mesenchymal phenotype have been derived from various adult tissues. The ability of these cells to differentiate into all germ layer cell types, raises the question as to whether mesenchymal epithelial transitions occur in the adult organism more frequently than presently appreciated. A series of cytokines are known to promote the transitions between epithelium and mesenchyme. Moreover, several transcription factors and other intracellular regulator molecules have been conclusively shown to mediate these transitions. However, the exact molecular basis of these transitions is yet to be resolved. The identification of the restrictive mechanisms that prevent cellular transitions in adult organisms, which seem to be unleashed in cancerous tissues, may lead to the development of tools for therapeutic tissue repair and effective tumor suppression.
Construction of a diphtheria toxin A fragment-C180 peptide fusion protein which elicits a neutralizing antibody response against diphtheria toxin and pertussis toxin (1992)

A genetically engineered gene fusion was constructed which encoded a nontoxic derivative of the A fragment of diphtheria toxin joined to the C180 peptide of the S1 subunit of pertussis toxin. The product of this gene fusion, termed the DTA-C180 protein, was purified from the periplasm of Escherichia coli to approximately 80% purity. The DTA-C180 protein possessed an apparent molecular weight of 43,000 by reduced sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The DTA-C180 protein was cleaved into two tryptic peptides, which migrated with apparent molecular weights of approximately 22,000. One tryptic peptide reacted with diphtheria antitoxin, while the other tryptic peptide reacted with anti-C180 peptide immunoglobulin G. The DTA-C180 protein did not inhibit protein synthesis or stimulate clustering morphology in Chinese hamster ovary cells. The DTA-C180 protein elicited an immune response, in guinea pigs, against both the DTA and C180 peptide components of the fusion protein, with alum being a more efficient adjuvant than Freund's adjuvant for eliciting neutralization titers. Neutralization titers elicited by DTA-C180 protein were weaker than those elicited by diphtheria toxoid and pertussis toxin 9K/129G, a genetically engineered double mutant of pertussis toxin. Three doses of DTA-C180 protein yielded a neutralization titer of 1/750 against pertussis toxin in Chinese hamster ovary cells and a neutralization titer of 1/50 against diphtheria toxin in Vero cells. This is the first report of a protein derived from a recombinant S1 subunit that elicits a neutralizing titer against pertussis toxin.
Genome‐wide profiling of stored mRNA inArabidopsis thalianaseed germination: epigenetic and genetic regulation of transcription in seed (2005)

To reveal the transcriptomes of Arabidopsis seed, comprehensive expression analysis was performed using ATH1 GeneChips (Affymetrix, Santa Clara, CA, USA). In the dry seed, more than 12 000 stored mRNA species were detected, including all ontological categories. Statistical analysis revealed that promoters of highly expressed genes in wild-type dry seeds overrepresented abscisic acid-responsive elements (ABREs) containing the core motif ACGT. Although the coupling element and seed-specific enhancer RY motif alone were not prominently overrepresented in genes with high expression, the presence of these elements in combination with ABRE was associated with particularly high gene expression. The transcriptome of the imbibed seeds differed from that of the dry seed even at 6 h after seed imbibition. After imbibition many upregulated and downregulated genes were co-regulated in clusters of three to five genes. Genes for which expression was affected by the abi5 mutation tended to be located in clusters, suggesting that transactivation by ABI5 is not restricted to a single gene, but affects other proximal genes. Furthermore, cytosine methylation was observed not only in large silent retrotransposon clusters in centromeric regions, but also in non-centromeric silent gene clusters in the seed. These results suggest that such regions might be transcriptionally silenced by methylation or heterochromatin structures. Our analyses reveal that transcriptomes of Arabidopsis seed are characterized by multiple regulatory mechanisms: epigenetic chromatin structures, chromosomal locations (e.g. co-regulated gene clusters) and cis-acting elements.
Chemotherapy of glioblastoma in rats using doxorubicin‐loaded nanoparticles (2004)

Glioblastomas belong to the most aggressive human cancers with short survival times. Due to the blood-brain barrier, they are mostly inaccessible to traditional chemotherapy. We have recently shown that doxorubicin bound to polysorbate-coated nanoparticles crossed the intact blood-brain barrier, thus reaching therapeutic concentrations in the brain. Here, we investigated the therapeutic potential of this formulation of doxorubicin in vivo using an animal model created by implantation of 101/8 glioblastoma tumor in rat brains. Groups of 5-8 glioblastoma-bearing rats (total n = 151) were subjected to 3 cycles of 1.5-2.5 mg/kg body weight of doxorubicin in different formulations, including doxorubicin bound to polysorbate-coated nanoparticles. The animals were analyzed for survival (% median increase of survival time, Kaplan-Meier). Preliminary histology including immunocytochemistry (glial fibrillary acidic protein, ezrin, proliferation and apoptosis) was also performed. Rats treated with doxorubicin bound to polysorbate-coated nanoparticles had significantly higher survival times compared with all other groups. Over 20% of the animals in this group showed a long-term remission. Preliminary histology confirmed lower tumor sizes and lower values for proliferation and apoptosis in this group. All groups of animals treated with polysorbate-containing formulations also had a slight inflammatory reaction to the tumor. There was no indication of neurotoxicity. Additionally, binding to nanoparticles may reduce the systemic toxicity of doxorubicin. This study showed that therapy with doxorubicin bound to nanoparticles offers a therapeutic potential for the treatment of human glioblastoma.
A Comparative Study of the Supercontraction of Major Ampullate Silk Fibers of Orb-Web-Building Spiders (Araneae) (1981)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Immune response to orally consumed antigens and probiotic bacteria (2000)

The gut mucosal system must fulfil conflicting roles in suppressing immune responses against orally fed antigens (tolerance) while still retaining the ability to respond to potential enteric pathogens. It must also, to a large degree, not mount an immune response against commensal enteric bacteria and the administration of large numbers of probiotic bacteria formulated as dietary supplements in food products. Contrary to this dogma, it has been found that feeding ovalbumin as a marker antigen, in association with selected probiotic bacteria, appears to prime for an intestinal immune response that is further augmented by skin vaccination. Skin immunization is known to stimulate a strong innate, humoral and cellular immune response. Such dominant immunogenic signals appear to override tolerogenic signals engendered by oral feeding of antigen. High-dose antigen feeding stimulated a strong Th2-dependent antibody response to skin vaccination but completely suppressed cytotoxic T cell responses. This was true even when ovalbumin was administered in conjunction with various selected probiotic bacteria. However, while yeast appeared to be better at priming for an enhanced humoral response, Lactobacillus fermentum and Staphylococcus carnosus were more effective in enhancing the postvaccinal lymphoproliferative response against ovalbumin.
Field Emission and Field Ionization (1961)

Contents: Theory of Field Emission. Field-Emission Microscopy and Related Topics. Field Ionization and Related Phenomena. Some Applications of Field Emission to Adsorption. Some Miscellaneous Applications of Field Emission.
Assembly of Graphene Sheets into 3D Macroscopic Structures (2012)

Integration of graphene sheets, 2D nanoscale building blocks, into 3D macroscopic assemblies and ultimately into a functional system is essential to explore the advanced properties of individual graphene sheets for macroscopic applications. This Concept paper summarizes different ways, such as flow-directed assembly, layer-by-layer deposition, template-directed method, and leavening strategy to assemble graphene sheets into the layered and porous 3D macroscopic structures. The obtained structures show unique properties, such as flexible network, high specific surface area, and outstanding electrical and mechanical properties. Furthermore, the functional systems based on such graphene 3D macroscopic structures have shown enhanced performance in the applications of energy storage, catalysis, environmental remediation, and sensing.
Inhibition of brain histamine synthesis increases food intake and attenuates vasopressin response to salt loading in rats. (1994)

Alpha-fluoromethylhistidine (FMH), a histamine synthesis inhibitor, was infused into the lateral cerebral ventricle of male Long-Evans rats for 7 days at a dose of 60 mcg/day. During this period animals were housed in metabolic cages; water and food consumption were measured and urine samples were collected. FMH-treated rats ate significantly more than controls and had a significantly greater weight increase. Concomitantly, sodium and potassium excretion increased. On the seventh day, rats were injected i.p. with 6.67 ml/kg of either 5.8% NaCl or physiological saline. Animals were decapitated 1 h after injection and plasma vasopressin, corticosterone and posterior pituitary vasopressin levels were determined by radioimmunoassay. NaCl loading significantly increased plasma vasopressin in control rats but not in rats pretreated with FMH. FMH alone had no effect. There were no significant changes in pituitary vasopressin or plasma corticosterone. These results clearly suggest an inhibitory role for the histaminergic system in the regulation of food intake. They also agree with, although not proving, the stimulatory control of vasopressin release by the histaminergic system in rat brain.