gebhart/patrepeval huggingface dataset:
Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions. (1996)

Our review of the metabolic pathways of pyridines and aza-arenes showed that biodegradation of heterocyclic aromatic compounds occurs under both aerobic and anaerobic conditions. Depending upon the environmental conditions, different types of bacteria, fungi, and enzymes are involved in the degradation process of these compounds. Our review indicated that different organisms are using different pathways to biotransform a substrate. Our review also showed that the transformation rate of the pyridine derivatives is dependent on the substituents. For example, pyridine carboxylic acids have the highest transformation rate followed by mono-hydroxypyridines, methylpyridines, aminopyridines, and halogenated pyridines. Through the isolation of metabolites, it was possible to demonstrate the mineralization pathway of various heterocyclic aromatic compounds. By using 14C-labeled substrates, it was possible to show that ring fission of a specific heterocyclic compound occurs at a specific position of the ring. Furthermore, many researchers have been able to isolate and characterize the microorganisms or even the enzymes involved in the transformation of these compounds or their derivatives. In studies involving 18O labeling as well as the use of cofactors and coenzymes, it was possible to prove that specific enzymes (e.g., mono- or dioxygenases) are involved in a particular degradation step. By using H2 18O, it could be shown that in certain transformation reactions, the oxygen was derived from water and that therefore these reactions might also occur under anaerobic conditions.
Rhizomucor miehei triglyceride lipase is processed and secreted from transformedAspergillus oryzae (1989)

The cDNA encoding the precursor of the Rhizomucor miehei triglyceride lipase was inserted in an Aspergillus oryzae expression vector. In this vector the expression of the lipase cDNA is under control of the Aspergillus oryzae alpha-amylase gene promoter and the Aspergillus niger glucoamylase gene terminator. The recombinant plasmid was introduced into Aspergillus oryzae, and transformed colonies were selected and screened for lipase expression. Lipase-positive transformants were grown in a small fermentor, and recombinant triglyceride lipase was purified from the culture broth. The purified enzymatically active recombinant lipase (rRML) secreted from A. oryzae was shown to have the same characteristics with respect to mobility on reducing SDS-gels and amino acid composition as the native enzyme. N-terminal amino acid sequencing indicated that approximately 70% of the secreted rRML had the same N-terminal sequence as the native Rhizomucor miehei enzyme, whereas 30% of the secreted rRML was one amino acid residue shorter in the N-terminal. The recombinant lipase precursor, which has a 70 amino acid propeptide, is thus processed in and secreted from Aspergillus oryzae. We have hereby demonstrated the utility of this organism as a host for the production of recombinant triglyceride lipases.
Isolation of mutants in M13 coat protein that affect its synthesis, processing, and assembly into phage. (1985)

The major coat protein (gene 8 protein) of bacteriophage M13 has been studied intensively as a model of membrane assembly, protein packing, and protein-DNA interactions. Because this protein is essential for assembly of the phage, very few mutants have been isolated. We have therefore cloned the gene 8 into a plasmid under control of the araB promoter. In the presence of arabinose, the cloned gene is expressed at a rate comparable to that in an M13-infected cell. Plasmid-derived procoat is inserted across the plasma membrane and processed to coat at a normal rate. The coat can support plaque formation by a defective M13 virus (M13am8) with an amber mutation in its procoat gene. This complementation assay was used to screen the mutagenized, cloned gene 8 for mutants which fail to make fully functional coat. Mutants were obtained which fail to synthesize procoat, which do not convert procoat to mature coat protein, or in which the coat protein is incapable of assembling into infectious virions.
Calpain is the target antigen of a Th1 clone that transfers protective immunity against Schistosoma mansoni (1996)

A CD4+ clone (clone B), characterized as Th1 based on its selective production of IFN-gamma and IL-2, was established from C57Bl/6 mice protectively immunized against Schistosoma mansoni by intradermal vaccination with soluble worm Ags, plus bacillus Calmette Guerin. In agreement with previous results demonstrating an IFN-gamma-dependent cell-mediated protective mechanism in this vaccination model, Ag-elicited peritoneal macrophages from syngeneic recipients of this clone were activated to kill schistosome larvae (schistosomula) in vitro. Moreover, recipients of clone B displayed significant resistance against cercarial challenge. By screening a battery of lambda(gt11) clones from an adult worm cDNA library, one recombinant (25B) was identified that stimulated clone B specifically. Analysis of the 25B cDNA insert revealed a nucleotide sequence identical with that of the large subunit of schistosome calpain, a Ca2+-activated neutral proteinase. By expressing the products of PCR subcloning, we identified a 146-amino acid region of the 25B gene containing immunologic activity equivalent to the whole polypeptide. Overlapping peptides spanning this region were synthesized, and a core epitope was identified with the sequence EWKGAWCDGS. Since clone B responds to supernatants from cultured schistosomula, we postulate that the recognition of calpain released by invading larvae and resulting induction of Th1 cytokines accounts for the protection mediated by the adoptively transferred clone. Our findings thus implicate calpain as a target of protective immunity in schistosomes and provide the first example of a candidate vaccine Ag for this parasite identified on the basis of T cell reactivity.
Signal Peptide for Protein Secretion Directing Glycophospholipid Membrane Anchor Attachment (1989)

Decay accelerating factor (DAF) is anchored to the plasma membrane by a glycophospholipid (GPI) membrane anchor covalently attached to the COOH-terminus of the protein. A hydrophobic domain located at the COOH-terminus is required for anchor attachment; DAF molecules lacking this domain are secreted. Replacement of the COOH-terminal hydrophobic domain with a signal peptide that normally functions in membrane translocation, or with a random hydrophobic sequence, results in efficient and correct processing, producing GPI-anchored DAF on the cell surface. The structural requirements for GPI anchor attachment and for membrane translocation are therefore similar, presumably depending on overall hydrophobicity rather than specific sequences.
Association of the B-Cell Alloantigen DRw4 with Rheumatoid Arthritis (1978)

Previous testing of patients with rheumatoid arthritis showed that one HLA-D type, Dw4, occurred more frequently than in normal controls. B-cell alloantigens closely related to HLA-D can now be identified by a simple serologic procedure. Using this test, I studied 80 white patients with erosive, rheumatoid-factor-positive rheumatoid arthritis. The B-cell alloantigen HLA-DRw4 occurred in 70 per cent of 54 patients, as compared to 28 per cent of the 68 normal controls (P less than 10(-5)). Both groups were also tested for the HLA-A, B and C antigens and for HLA-D. HLA-Dw4 occurred in 54 per cent of the patients and 16 per cent of the controls (P less than 10(-5)). Small differences observed in several of the HLA-A and B antigens were not statistically significant. The results indicate that rheumatoid arthritis in whites is associated with genes of the HLA-D region and that immunogenetic factors linked to HLA have a role in its pathogenesis.
Evaluating dialog systems used in the real world (2002)

An important aspect of creating high performance natural language dialog systems is the question of how they are evaluated. While a universally accepted method for doing so for pure speech recognition exists, this is not clear for speech understanding or dialog systems. We describe the methods we typically use for our systems and argue that it is not sufficient to evaluate their constituents separately. Instead, a measure for a system in its entity is needed.
Nuclear Receptor Response Elements Mediate Induction of Intestinal MDR1 by Rifampin (2001)

Intestinal P-glycoprotein, which is encoded by the MDR1 gene, plays an important role in the absorption and presystemic elimination of many xenobiotics. Hence, an understanding of the factors regulating its expression and function is of substantial interest. In addition to genetic factors, exposure to drugs such as rifampin can profoundly affect its expression. So far, the mechanisms by which rifampin induces MDR1 expression are poorly understood. Recent studies demonstrate that the nuclear receptor PXR (pregnane X receptor) is involved in xenobiotic induction of CYP3A4. Because CYP3A4 and MDR1 are often co-induced, we investigated whether a similar mechanism is also involved in MDR1 induction. The human colon carcinoma cell line LS174T was used as an intestinal model to study induction because in these cells the endogenous MDR1 gene is highly inducible by rifampin. The 5'-upstream region of human MDR1 was examined for the presence of potential PXR response elements. Several binding sites were identified that form a complex regulatory cluster at about -8 kilobase pairs. Only one DR4 motif within this cluster is necessary for induction by rifampin. We conclude that induction of MDR1 is mediated by a DR4 motif in the upstream enhancer at about -8 kilobase pairs, to which PXR binds.
Chitosan-based delivery systems for mucosal vaccines (2012)

It is concluded that chitosan derivatives offer advantageous opportunities such as nanoparticle and surface charge manipulation that facilitate vaccine targeting. Nevertheless, these technologies represent a longer-term goal. By contrast, chitosan (unmodified form) with or without a co-adjuvant has significant toxicology and human data to support safe mucosal administration, and thus has the potential for earlier product introduction into the market.
Vitamin D deficiency in obese rats exacerbates nonalcoholic fatty liver disease and increases hepatic resistin and toll-like receptor activation (2011)

VDD exacerbates NAFLD through TLR-activation, possibly by way of endotoxin exposure in a WD rat model. In addition it causes IR, higher hepatic resistin gene expression, and up-regulation of hepatic inflammatory and oxidative stress genes.
Glass Fragility and the Stability of Pharmaceutical Preparations—Excipient Selection (1997)

The objectives of this study were, first, to calculate the zero mobility temperatures, T0, of trehalose and sucrose by the Pikal method from the width of the glass transition and compare these to the literature, obtained by enthalpy relaxation measurement, and second, to compare the T0 values and physicochemical properties of trehalose to those of sucrose in terms of potential to stabilize labile actives in the glassy state. Differential scanning calorimetry and coulometric Karl-Fischer analysis were used. The glass transition temperatures, Tg, for the two carbohydrates at circa 0.7% moisture were 101 degrees C and 64 degrees C for trehalose and sucrose, respectively. Anhydrous amorphous trehalose had a Tg of 116 degrees C. The T0 values were found to be 44 and 3.5 degrees C for trehalose and sucrose, respectively. The Tg-T0 value for sucrose was compared, and found to be in good agreement with that found by enthalpy relaxation measurements. Trehalose was found to be resistant to crystallization above the glass temperature. The study supports the validity of the calculation method proposed by Pikal for T0. It has been proposed in the literature that T0 is a better measure of stability than Tg. Trehalose has a significantly higher T0 than sucrose and thus would work more effectively in stabilizing a labile active.
Effect of N-terminal and Met23 Mutations on the Structure and Dynamics of Onconase (2004)

Onconase (rONC), otherwise known as ranpirnase or P-30 protein, which was initially purified from extracts of Rana pipiens oocytes and early embryos, exhibits anticancer activity both in vitro and in vivo and is in phase III clinical trials for tumor therapy. We have determined the solution NMR structure of a recombinant onconase with Met(-1), Gln1, and Leu23 residues (M-1, Q1, M23L)rONC. The 20 best solution structures had a backbone root mean square deviation of 0.41 +/- 0.09 A with respect to the average structure. The energy-minimized average NMR structure had a backbone root mean square deviation of 0.72 A from the x-ray crystallographic structure of native onconase; however, the orientation of the N-terminal residue in the two structures was very different. Comparison of the 15N HSQC spectrum of (M-1, Q1, M23L)rONC with that of a mutant E1S-rONC, which is identical to the nONC except with the N-terminal pyroglutamyl residue replaced by Ser, showed that N-terminal and residue 23 mutations induced structural changes in regions beyond the mutation sites. Model-free analysis of the backbone amide 15N-T1, 15N-T2, and 15N-1H NOE relaxation data for (M-1, Q1, M23L)rONC and E1S-rONC revealed that the E1S-rONC molecule showed very little flexibility, whereas (M-1, Q1, M23L)rONC exhibited substantial flexibility, which may account for the previously observed reduced stability and increased protease susceptibility. The alpha1 helix and beta-sheets of (M-1, Q1, M23L)rONC displayed bending motions. These data provided strong evidence for the presence of an N-terminal hydrogen bond network in E1S-rONC, but not in (M-1, Q1, M23L)rONC.
Tight Junction Proteins Claudin-1 and Occludin Control Hepatitis C Virus Entry and Are Downregulated during Infection To Prevent Superinfection (2008)

A tight junction (TJ) protein, claudin-1 (CLDN1), was identified recently as a key factor for hepatitis C virus (HCV) entry. Here, we show that another TJ protein, occludin, is also required for HCV entry. Mutational study of CLDN1 revealed that its tight junctional distribution plays an important role in mediating viral entry. Together, these data support the model in which HCV enters liver cells from the TJ. Interestingly, HCV infection of Huh-7 hepatoma cells downregulated the expression of CLDN1 and occludin, preventing superinfection. The altered TJ protein expression may contribute to the morphological and functional changes observed in HCV-infected hepatocytes.
Bioimmunotherapy for melanoma using fully human antibodies targeting MCAM/MUC18 and IL‐8 (2006)

Metastatic melanoma is associated with high rate of patients' mortality and represents a great challenge for cancer therapies because of its notorious resistance to chemotherapeutic drugs. Considerable efforts have been made over the last 2 decades in pursuit of new treatment modalities and identification of molecular events associated with melanoma progression and development of metastases. The acquisition of the metastatic phenotype is associated with overexpression of the adhesion molecule MCAM/MUC18 and the angiogenic factor IL-8. In this review, we summarize our current knowledge on MCAM/MUC18 and IL-8, their transcriptional regulation, and their role in melanoma growth, angiogenesis and metastasis. Further, we report on the development of new fully human antibodies, anti-MCAM/MUC18 (ABX-MA1) and anti-IL-8 (ABX-IL8), and their effects on tumor growth and metastasis in animal models. Collectively, our studies suggest that ABX-MA1 and ABX-IL8 could serve as new modalities for the treatment of melanoma either alone, or in combination with conventional chemotherapy or other antitumor agents.
Interleukin-11 protects against renal ischemia and reperfusion injury (2012)

Renal ischemia reperfusion (IR) injury causes renal tubular necrosis, apoptosis, and inflammation leading to acute and chronic kidney dysfunction. IL-11 is a multifunctional hematopoietic cytokine clinically approved to treat chemotherapy-induced thrombocytopenia. Recent studies suggest that IL-11 also has potent antiapoptotic and antinecrotic properties. In this study, we tested the hypothesis that exogenous IL-11 protects against renal IR injury and determined the mechanisms involved in renal protection. Pretreatment with human recombinant IL-11 (HR IL-11) or with long-acting site-specific polyethylene glycol (PEG)-conjugated human IL-11 analog (PEGylated IL-11) produced partial but significant protection against renal IR injury in mice. In addition, HR IL-11 or PEGylated IL-11 given 30-60 min after IR also provided renal protection in mice. Significant reductions in renal tubular necrosis and neutrophil infiltration as well as tubular apoptosis were observed in mice treated with HR IL-11 or PEGylated IL-11. Furthermore, HR IL-11 or PEGylated IL-11 decreased both necrosis and apoptosis in human proximal tubule (HK-2) cells in culture. Mechanistically, IL-11 increased nuclear translocation of hypoxia-inducible factor-1α (HIF-1α) and induced sphingosine kinase-1 (SK1) expression and activity in HK-2 cells. Moreover, selective HIF-1α inhibitors blocked IL-11-mediated induction of SK1 in HK-2 cells. Finally, HR IL-11 or PEGylated IL-11 failed to protect against renal IR injury in SK1-deficient mice. Together, our data show powerful renal protective effects of exogenous IL-11 against IR injury by reducing necrosis, inflammation, and apoptosis through induction of SK1 via HIF-1α.
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes (2003)

Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington University's Genome Sequencing Center (GSC), St Louis. A sister project at the University of Edinburgh and the Sanger Institute is also underway. More than 295,000 ESTs have been generated from >30 nematodes other than Caenorhabditis elegans including key parasites of humans, animals and plants. Nematode.net currently provides NemaGene EST cluster consensus sequence, enhanced online BLAST search tools, functional classifications of cluster sequences and comprehensive information concerning the ongoing generation of nematode genome data. The long-term goal of nematode.net is to provide the scientific community with the highest quality sequence information and tools for studying these diverse species.
Numerical Simulation of Microscale Ion-Driven Air Flow (2003)

Ion-driven air flow is a novel method of pumping air at microscale dimensions using the concept of ion drag. The method employs a series of micro-fabricated electrodes to generate strong electric fields that pump unipolar ions through air. Ions collide repeatedly with neutral molecules, thus generating bulk motion of the gas. Meso-scale motion is obtained by changing the voltage of electrodes rapidly over time to create a nearly continuous force on the ions. One application of this technology involves generation of air flow through microchannels or other micro-featured surfaces to create compact, high flux heat sinks for electronics cooling. A numerical model of the fluid-ion-electric field interaction has been developed. The momentum and continuity equations are supplemented with equations for electric charge transport and for electric potential. The momentum equations are coupled through a body-force term to the charge transport and electric field equations, both of which are coupled to the momentum equations and to each other through source and convection terms. The model describes the one-dimensional, time-dependent flow of air and ions between evenly spaced microscale planar electrodes, of which the voltages are switched at frequencies on the order of 1 MHz. The flow is investigated to determine the effect of switching frequency on maximum velocity and pressure head.
Protection of Rhesus Monkeys against Infection with Minimally Pathogenic Simian-Human Immunodeficiency Virus: Correlations with Neutralizing Antibodies and Cytotoxic T Cells (2005)

We studied the capacity of active immunization of rhesus monkeys with HIV-1 envelope protein (Env) to induce primary virus cross-reactive neutralizing antibodies to prevent infection following intravenous challenge with simian-human immunodeficiency virus (SHIV). Monkeys were immunized with the human immunodeficiency type 1 (HIV-1) strain R2 Env. Initially, the Env was expressed in vivo by an alphavirus replicon particle system, and then it was administered as soluble oligomeric gp140. Concurrently, groups of monkeys received expression vectors that encoded either simian immunodeficiency virus (SIV) gag/pol genes or no SIV genes in vivo to test the additional protective benefit of concurrent induction of virus-specific cell-mediated immune (CMI) responses. Groups of control monkeys received either the gag/pol regimen or sham immunizations. The antibodies induced by the Env immunization regimen neutralized diverse primary HIV-1 strains. Similarly, potent CMI responses were induced by the gag/pol regimen, as measured by gamma interferon enzyme-linked immunospot assays. Differences in the responses among groups of monkeys strongly suggested that there was interference between the Env and gag/pol immunization regimens. Complete protection of some of the monkeys against infection after intravenous challenge with the partially pathogenic SHIV(DH12R (Clone 7)) was associated independently with both neutralizing antibody and CMI responses. Protection was associated with SHIV(DH12 (Clone 7)) serum neutralizing antibody titers of > or =1:80 or with cellular immune responses corresponding to >2,000 spot forming cells per 10(6) peripheral blood mononuclear cells. Immunization was also associated with a reduction in the magnitude and duration of virus load. Induction of cross-reactive, primary HIV-1-neutralizing antibodies is feasible and, when potent, may result in complete protection against infection with a heterologous challenge virus strain.
Biocompatibility and biodegradation of a bone composite containing tricalcium phosphate and genipin crosslinked gelatin (2004)

A biodegradable composite (GGT) containing tricalcium phosphate ceramic particles and genipin crosslinked gelatin was developed for use as a bone substitute. The objective of this study was to assess the biocompatibility and the osteoconductivity of the GGT composite on new bone formation in vitro. Additionally, biodegradation and biocompatibility of the GGT composite in animals were investigated. Results of the GGT composites cocultured with osteoblasts showed that the concentration of genipin used as a crosslinking agent should be <0.5 wt % to avoid cytotoxicity. For in vivo degradation studies, we found that when the concentration of genipin in the composite <0.5 wt % was not enough to fully crosslink the gelatin, it results in a rapid degradation of the gelatin-genipin mixture. However, we also found that the foreign body capsule surrounding the GGT composite containing 1.0 wt % of the genipin was much thicker than that in the other three groups, that is, the composites containing 0.05, 0.1, and 0.5 wt % of the genipin. We therefore concluded that the ideal concentration of genipin used in the GGT was 0.5 wt %. Finally, we examined the organ culture units, which were maintained in cultured medium for 5 weeks. Morphology of tissue was observed and the quantitative evaluation of the regenerated bone was determined. We found that the GGT composites containing 0.5 wt % of the genipin had an excellent biocompatibility and could produce osteoconduction for the regenerating bone tissues.