gebhart/patrepeval huggingface dataset:
Aristolochic acid-associated urothelial cancer in Taiwan (2012)

Aristolochic acid, a potent human carcinogen produced by Aristolochia plants, is associated with urothelial carcinoma of the upper urinary tract (UUC). Following metabolic activation, aristolochic acid reacts with DNA to form aristolactam (AL)-DNA adducts. These lesions concentrate in the renal cortex, where they serve as a sensitive and specific biomarker of exposure, and are found also in the urothelium, where they give rise to a unique mutational signature in the TP53 tumor-suppressor gene. Using AL-DNA adducts and TP53 mutation spectra as biomarkers, we conducted a molecular epidemiologic study of UUC in Taiwan, where the incidence of UUC is the highest reported anywhere in the world and where Aristolochia herbal remedies have been used extensively for many years. Our study involves 151 UUC patients, with 25 patients with renal cell carcinomas serving as a control group. The TP53 mutational signature in patients with UUC, dominated by otherwise rare A:T to T:A transversions, is identical to that observed in UUC associated with Balkan endemic nephropathy, an environmental disease. Prominent TP53 mutational hotspots include the adenine bases of (5')AG (acceptor) splice sites located almost exclusively on the nontranscribed strand. A:T to T:A mutations also were detected at activating positions in the FGFR3 and HRAS oncogenes. AL-DNA adducts were present in the renal cortex of 83% of patients with A:T to T:A mutations in TP53, FGFR3, or HRAS. We conclude that exposure to aristolochic acid contributes significantly to the incidence of UUC in Taiwan, a finding with significant implications for global public health.
Quantitative enzymatic production of 6-O -acylglucose esters (1998)

Selective production of emulsifiers from glucose and fatty acids has been achieved using an immobilized Candida antarctica lipase. Optimization of process selectivity considers the solubilities of the sugar and its monoesters in acetone at different temperatures, the percentage of this organic solvent in the reaction mixture, and the reaction temperature. The solvent (acetone) is both easily eliminated and accepted by the European Community for use in the manufacture of foods and/or food additives. Different fatty acids with a longer length chain than that of caprylic acid may be employed. For saturated fatty acids longer than lauric acid, continuous precipitation of the monoester as it is formed at 40 degrees C permits nearly complete conversion (98%) of glucose to the monoester within 2-3 days. The procedure does not require total dissolution of the sugar, and precipitation of the monoester permits selective conversion of charges of glucose higher than 100 mg/mL solvent. A scaleup of the process under the optimum conditions gives high yields of 6-O-lauroyl glucose, which may be readily prepared on a gram scale. Copyright 1998 John Wiley & Sons, Inc.
DFNA5 (ICERE‐1) contributes to acquired etoposide resistance in melanoma cells (2001)

Resistance to drug treatment is a common observation in malignant melanoma. In order to analyze alterations in mRNA expression profiles associated with drug resistance in melanoma cells we previously established a panel of various drug-resistant cell variants derived from the human melanoma line MeWo and compared the mRNA expression profiles by a differential display technique. By that approach it could be demonstrated that the expression level of a mRNA encoded by a gene found to be mutated in non-syndromic hearing impairment, DFNA5 (ICERE-1), was distinctly decreased in the 33-fold etoposide-resistant melanoma cell line MeWo ETO 1. To evaluate the hypothesis that a decrease in DFNA5 mRNA expression level contributes to the acquired etoposide resistance phenotype exhibited by MeWo ETO 1 cells, this drug-resistant line was stably transfected with the DFNA5-encoding cDNA. Transfected clones showed a 30-35% reduced etoposide susceptibility by comparing the IC(25), IC(50) and IC(75) values of these clones with those displayed by the non-transfected, etoposide-resistant melanoma cell line MeWo ETO 1 and controls. Furthermore, etoposide exposure of stable DFNA5 transfectants resulted in an increase of caspase-3-mediated apoptotic events in DFNA5-transfected clones in comparison to MeWo ETO 1 cells and controls. The data therefore demonstrate that a decrease in DNFA5 mRNA expression level is associated with an increased etoposide resistance in melanoma cells due to an elevated cellular susceptibility to trigger a caspase-3-depending signal pathway leading to programmed cell death.
Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples (2019)

Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential for a diagnostic test for influenza virus which also provides insights on transmission, evolution, and drug resistance and simultaneously detects other viruses. We therefore set out to apply the Oxford Nanopore Technologies sequencing method to metagenomic sequencing of respiratory samples. We generated influenza virus reads down to a limit of detection of 10<sup>2</sup> to 10<sup>3</sup> genome copies/ml in pooled samples, observing a strong relationship between the viral titer and the proportion of influenza virus reads (<i>P</i> = 4.7 × 10<sup>-5</sup>). Applying our methods to clinical throat swabs, we generated influenza virus reads for 27/27 samples with mid-to-high viral titers (cycle threshold [<i>C<sub>T</sub></i> ] values, <30) and 6/13 samples with low viral titers (<i>C<sub>T</sub></i> values, 30 to 40). No false-positive reads were generated from 10 influenza virus-negative samples. Thus, Nanopore sequencing operated with 83% sensitivity (95% confidence interval [CI], 67 to 93%) and 100% specificity (95% CI, 69 to 100%) compared to the current diagnostic standard. Coverage of full-length virus was dependent on sample composition, being negatively influenced by increased host and bacterial reads. However, at high influenza virus titers, we were able to reconstruct >99% complete sequences for all eight gene segments. We also detected a human coronavirus coinfection in one clinical sample. While further optimization is required to improve sensitivity, this approach shows promise for the Nanopore platform to be used in the diagnosis and genetic analysis of influenza virus and other respiratory viruses.
Mapping the Lung Proteome in Cystic Fibrosis (2009)

The pathophysiology of cystic fibrosis (CF) lung disease remains incompletely understood. Novel mechanisms in the pathogenesis of CF lung disease may be discovered by studying the patterns of protein expression in bronchoalveolar lavage fluid (BALF). We used shotgun proteomics to analyze BALF samples from 8 CF and 4 control subjects. Differential protein expression between CF and control subjects was determined using spectral counting and statistical analysis. Using Gene Ontology analysis, we identified enriched biological modules and then applied network analysis to construct a protein interaction map in CF lung disease. Shotgun proteomics analysis of BALF identified hundreds of proteins whose differential enrichment or depletion robustly distinguished the CF phenotype from normal controls. Functional categorization and network analysis identified key processes, including the immune response and proteolytic activity that are known contributors to CF lung disease. Importantly, this approach also implicated abnormalities in previously unsuspected pathways, such as dysregulation of the complement system that may have critical roles in the pathogenesis of CF lung disease. By integrating shotgun proteomics with statistical and computational analyses, we have developed a promising approach to understand the pathophysiology of CF lung disease. Our approach should be applicable to a wide range of proteomics-based clinical research.
Effects of Palm Oil Diet on 4, 7, 10, 13,16-Docosapentaenoic Acid Content of Blood Plasma, Red Cells, and Liver and Muscle Lipids in Rats (1994)

The effects of palm oil diets on tissue lipids of rats were studied. Four groups of male Sprague-Dawley rats (4wk old) were maintained on diets containing (10% by weight) physically refined palm oil (PRPO), chemically refined palm oil (CRPO), soybean oil (SO), or canola oil (CO) for two months. Both PRPO and CRPO diets resulted in the appearance of 4, 7, 10, 13,16-docosapentaenoic acid (22:5n-6) in blood plasma, red cells, and liver and muscle lipids, while SO and CO diets did not. This fatty acid was principally found in the phospholipid fraction, such as phosphatidylcholine and phosphatidylethanolamine. The increase of 22:5(n-6) compensated for the decrease of docosahexaenoic acid (DHA; 22:6n-3). The results suggest that diet containing only palm oil as a fat source has a high potential of causing α-linolenic acid deficiency in rats.
Synergistic effect of lactic acid with a chemosterilant metepa to the sound-attracted male mosquitoes (1987)

Autochemosterilization of mosquitoes by a sound trap necessitated designing an improved formulation of chemosterilant for treatment at inside of the trap. When 18 chemicals including some putative mosquito attractants were screened in mixtures of hempa by contact test, lactic acid mixture gave significantly higher sterility than hempa to Culex pipiens molestus. Metepa was more effective and residual than hempa up to 5 days after treatment both in lactic acid mixture and metepa per se. Topical application of the mixture proved the synergistic activity of lactic acid with metepa. Gas chromatographic analysis of metepa showed that males took up 0.4 times less amount of metepa from the mixture-treated sound trap than the metepa-treated sound trap, because lactic acid was somewhat repellent to males. Nevertheless, the sterility of males was slightly higher with the mixturetreated trap than the metepa-treated trap.
Interaction of Lipocalin 2, Transferrin, and Siderophores Determines the Replicative Niche of Klebsiella pneumoniae during Pneumonia (2012)

Gram-negative bacteria are a common cause of severe hospital-acquired infections. To cause disease, they must obtain iron and secrete the small molecule enterobactin to do so. Animal models of pneumonia using Klebsiella pneumoniae indicate that enterobactin promotes severe disease. Accordingly, the host defense protein lipocalin 2 exploits this common target by binding enterobactin and disrupting its function. However, pathogenic bacteria often make additional siderophores that lipocalin 2 cannot bind, such as yersiniabactin, which could make this host defense ineffective. This work compares the pattern and severity of pneumonia caused by K. pneumoniae based on which siderophores it produces. The results indicate that enterobactin promotes growth around blood vessels that are rich in the iron-binding protein transferrin, but yersiniabactin does not. Together, transferrin and lipocalin 2 protect this space against all types of K. pneumoniae tested. Therefore, the ability to acquire iron determines where bacteria can grow in the lung.
Improved Oxygen Reduction Activity on Pt 3 Ni(111) via Increased Surface Site Availability (2007)

The slow rate of the oxygen reduction reaction (ORR) in the polymer electrolyte membrane fuel cell (PEMFC) is the main limitation for automotive applications. We demonstrated that the Pt3Ni(111) surface is 10-fold more active for the ORR than the corresponding Pt(111) surface and 90-fold more active than the current state-of-the-art Pt/C catalysts for PEMFC. The Pt3Ni(111) surface has an unusual electronic structure (d-band center position) and arrangement of surface atoms in the near-surface region. Under operating conditions relevant to fuel cells, its near-surface layer exhibits a highly structured compositional oscillation in the outermost and third layers, which are Pt-rich, and in the second atomic layer, which is Ni-rich. The weak interaction between the Pt surface atoms and nonreactive oxygenated species increases the number of active sites for O2 adsorption.
Monitoring of Ubiquitin-proteasome Activity in Living Cells Using a Degron (dgn)-destabilized Green Fluorescent Protein (GFP)-based Reporter Protein (2012)

Proteasome is the main intracellular organelle involved in the proteolytic degradation of abnormal, misfolded, damaged or oxidized proteins (1, 2). Maintenance of proteasome activity was implicated in many key cellular processes, like cell's stress response (3), cell cycle regulation and cellular differentiation (4) or in immune system response (5). The dysfunction of the ubiquitin-proteasome system has been related to the development of tumors and neurodegenerative diseases (4, 6). Additionally, a decrease in proteasome activity was found as a feature of cellular senescence and organismal aging (7, 8, 9, 10). Here, we present a method to measure ubiquitin-proteasome activity in living cells using a GFP-dgn fusion protein. To be able to monitor ubiquitin-proteasome activity in living primary cells, complementary DNA constructs coding for a green fluorescent protein (GFP)-dgn fusion protein (GFP-dgn, unstable) and a variant carrying a frameshift mutation (GFP-dgnFS, stable (11)) are inserted in lentiviral expression vectors. We prefer this technique over traditional transfection techniques because it guarantees a very high transfection efficiency independent of the cell type or the age of the donor. The difference between fluorescence displayed by the GFP-dgnFS (stable) protein and the destabilized protein (GFP-dgn) in the absence or presence of proteasome inhibitor can be used to estimate ubiquitin-proteasome activity in each particular cell strain. These differences can be monitored by epifluorescence microscopy or can be measured by flow cytometry.
Species specificity in the cell-free conversion of prion protein to protease-resistant forms: a model for the scrapie species barrier. (1995)

Scrapie is a transmissible neurodegenerative disease that appears to result from an accumulation in the brain of an abnormal protease-resistant isoform of prion protein (PrP) called PrPsc. Conversion of the normal, protease-sensitive form of PrP (PrPc) to protease-resistant forms like PrPsc has been demonstrated in a cell-free reaction composed largely of hamster PrPc and PrPsc. We now report studies of the species specificity of this cell-free reaction using mouse, hamster, and chimeric PrP molecules. Combinations of hamster PrPc with hamster PrPsc and mouse PrPc with mouse PrPsc resulted in the conversion of PrPc to protease-resistant forms. Protease-resistant PrP species were also generated in the nonhomologous reaction of hamster PrPc with mouse PrPsc, but little conversion was observed in the reciprocal reaction. Glycosylation of the PrPc precursors was not required for species specificity in the conversion reaction. The relative conversion efficiencies correlated with the relative transmissibilities of these strains of scrapie between mice and hamsters. Conversion experiments performed with chimeric mouse/hamster PrPc precursors indicated that differences between PrPc and PrPsc at residues 139, 155, and 170 affected the conversion efficiency and the size of the resultant protease-resistant PrP species. We conclude that there is species specificity in the cell-free interactions that lead to the conversion of PrPc to protease-resistant forms. This specificity may be the molecular basis for the barriers to interspecies transmission of scrapie and other transmissible spongiform encephalopathies in vivo.
Pleural diseases (2003)

Director Pulmonary Disease Program, Saint Thomas Hospital, and Professor of Medicine Vanderbilt University, Nashville, Tennessee, USA. Correspondence to Richard W. Light, MD, Director of Pulmonary Disease Program, Saint Thomas Hospital, 4220 Harding Road, Nashville, TN 37205, USA; e-mail: [email protected]
Activation of mouse macrophages by muramyl dipeptide coupled with an anti-macrophage monoclonal antibody (1992)

A rat IgG2a monoclonal antibody (mAb3A33) directed against the mouse Mac-1 antigen was conjugated with muramyl dipeptide (MDP) by using an intermediate polymer; under such conditions 75 MDP molecules were bound to one antibody molecule. A poly(L-lysine) polymer substituted with muramyl dipeptide and 3-(2-pyridyldithio)propionyl residues were prepared, the remaining lysine epsilon-amino groups were acylated with D-gluconolactone, leading to a neutral polymer; then a few polymer conjugates were coupled to mAb3A33 via a disulfide bridge. The binding capacity of the monoclonal antibody was preserved after conjugation with MDP-polymer molecules. Mouse peritoneal macrophages, incubated for 24 h with MDP-mAb3A33 conjugate became cytostatic against P815 mastocytoma cells, whereas unconjugated mAb3A33 and MDP-bound to a nonspecific rat IgG2a were ineffective. An enhancement of the cytostatic activity induced by MDP-mAb3A33 conjugate was obtained in the presence of gamma-IFN. These results show that several tens of MDP molecules can be linked to a macrophage-specific monoclonal antibody by using a neutral intermediate polymer without impairing the binding antibody capacity and that this type of MDP conjugate can efficiently activate macrophages and therefore could be the basis of the development of new antitumor therapy.
Apelin peptides block the entry of human immunodeficiency virus (HIV) (2000)

The orphan G protein-coupled receptor APJ has been shown to be a coreceptor for human and simian immunodeficiency virus (HIV and SIV) strains. We have determined that some HIV and SIV strains use APJ as a coreceptor to infect the brain-derived NP-2/CD4 cells. Because apelin is an endogenous ligand for the APJ receptor, we examined the inhibitory effects of apelin peptides on HIV infection, and found that the apelin peptides inhibit the entry of some HIV-1 and HIV-2 into the NP-2/CD4 cells expressing APJ. The inhibitory efficiency has been found to be in the order of apelin-36>apelin-17>apelin-13>apelin-12.
Characterization and Evaluation of Silk Protein Hydrogels for Drug Delivery (2006)

The objective of this study was to characterize and evaluate the physicochemical properties and drug release profiles of hydrogels composed of silk protein (SP) polymers. SPs with a low MW (SPL, ca. 18 kDa) and a high MW (SPH, ca. 76 kDa) were used for preparing hydrogels. Both the random coil form and beta-sheet conformation simultaneously existed in the hydrogels according to Fourier-transformed IR determination. Morphologically, the hydrogels showed a sponge-like cross-linked structure produced by physical entanglement as well as chemical hydrogen and covalent bindings. The in vitro buprenorphine delivery from SPH hydrogels showed a slow-release effect, and a zero-order rate was obtained for all preparations. Drug release could be controlled by varying the SPH concentrations or incorporation of SPL into the systems. SP hydrogels showed a stronger barrier property for hydrophilic solutes than for hydrophobic solutes. The incorporation of SPH into Pluronic F-127 (PF-127) hydrogels changed the gel structure from amorphous micelles to a regularly interconnected texture with pores. Furthermore, SPH as an adjuvant polymer in PF-127 and chitosan hydrogels lowered and controlled the amount of drug released from those systems.
Circuit Realization of Impedance Loading for Cross Section Reduction (1970)

Techniques for realizing a reactance which is a decreasing function of frequency are discussed. A Negative Impedance Converter (NIC) circuit is analyzed and techniques given for compensating for imperfections and frequency dependence. An RC realization of the desired impedance is given, and it is demonstrated that this realization can be modified to compensate for phase shift in the NIC. An analytical and numerical analysis of a NIC based on amplifiers with 50 ohm input and output impedances is presented.
Discovery of a PCAF Bromodomain Chemical Probe (2016)

The p300/CBP-associated factor (PCAF) and related GCN5 bromodomain-containing lysine acetyl transferases are members of subfamily I of the bromodomain phylogenetic tree. Iterative cycles of rational inhibitor design and biophysical characterization led to the discovery of the triazolopthalazine-based L-45 (dubbed L-Moses) as the first potent, selective, and cell-active PCAF bromodomain (Brd) inhibitor. Synthesis from readily available (1R,2S)-(-)-norephedrine furnished L-45 in enantiopure form. L-45 was shown to disrupt PCAF-Brd histone H3.3 interaction in cells using a nanoBRET assay, and a co-crystal structure of L-45 with the homologous Brd PfGCN5 from Plasmodium falciparum rationalizes the high selectivity for PCAF and GCN5 bromodomains. Compound L-45 shows no observable cytotoxicity in peripheral blood mononuclear cells (PBMC), good cell-permeability, and metabolic stability in human and mouse liver microsomes, supporting its potential for in vivo use.
Design of Peptides That Form Amyloid‐Like Fibrils Capturing Amyloid β1–42 Peptides (2007)

Amyloid beta-peptide (Abeta) plays a critical role in Alzheimer's disease (AD). The monomeric state of Abeta can self-assemble into oligomers, protofibrils, and amyloid fibrils. Since the fibrils and soluble oligomers are believed to be responsible for AD, the construction of molecules capable of capturing these species could prove valuable as a means of detecting these potentially toxic species and of providing information pertinent for designing drugs effective against AD. To this aim, we have designed short peptides with various hydrophobicities based on the sequence of Abeta14-23, which is a critical region for amyloid fibril formation. The binding of the designed peptides to Abeta and the amplification of the formation of peptide amyloid-like fibrils coassembled with Abeta are elucidated. A fluorescence assay utilizing thioflavin T, known to bind specifically to amyloid fibrils, revealed that two designed peptides (LF and VF, with the leucine and valine residues, respectively, in the hydrophobic core region) could form amyloid-like fibrils effectively by using mature Abeta1-42 fibrils as nuclei. Peptide LF also coassembled with soluble Abeta oligomers into peptide fibrils. Various analyses, including immunostaining with gold nanoparticles, enzyme-linked immunosorbent assays, and size-exclusion chromatography, confirmed that the LF and VF peptides formed amyloid-like fibrils by capturing and incorporating Abeta1-42 aggregates into their peptide fibrils. In this system, small amounts of mature Abeta1-42 fibrils or soluble oligomers could be transformed into peptide fibrils and detected by amplifying the amyloid-like fibrils with the designed peptides.
Systematic substitution of individual bases in two important single‐stranded regions of the HDV ribozyme for evaluation of the role of specific bases (1993)

To elucidate the role of specific bases in the self-cleavage activity of the human hepatitis delta virus (HDV) ribozyme, systematic substitutions of individual bases in two important single-stranded regions [between nucleotides 726-731 (SSrA region) and 762-766 (SSrB region)] were carried out by oligonucleotide-directed point mutagenesis. Among the mutants obtained, 12 mutants (G726 variants, G727A, G727C, G728C, G762A, G762C, C763 variants and A766C) could not tolerate the respective base-substitutions and self-cleavage activities were reduced to very low levels (10%), suggesting a requirement of the respective bases. In particular, G726 in the SSrA region and C763 in the SSrB region were found to be essential for the ribozyme activity. We could determine the preferred sequences, 5'-G-G-(G/A/U)-N-(A/U/G)-Pu-3' for SSrA and 5'-(G/U)-C-N-(A/G/U)-A-3' for SSrB regions, respectively.