gebhart/patrepeval huggingface dataset:
Low simvastatin concentrations reduce oleic acid-induced steatosis in HepG2 cells: An in vitro model of non-alcoholic fatty liver disease (2016)

Non-alcoholic fatty liver disease (NAFLD) is an inflammatory condition caused by hepatic lipid accumulation that is associated with insulin resistance, diabetes and metabolic syndrome. Although statins should be used with caution in liver diseases, they are increasingly investigated as a possible treatment for NAFLD. The present study recreated an <i>in vitro</i> model of NAFLD using HepG<sub>2</sub> cells exposed to oleic acid (OA), which was used to quantify OA-induced lipid accumulation in HepG<sub>2</sub> cells treated with various concentrations of simvastatin. In addition, the effect of simvastatin on HepG<sub>2</sub> cell morphology and microparticle generation as a marker of cell apoptosis was assessed. OA-induced lipid accumulation was quantified by Oil Red O staining and extraction for optical density determination. Stained lipid droplets were visualized using phase contrast microscopy. Furthermore, HepG<sub>2</sub> cell-derived microparticles were counted by flow cytometry subsequent to staining for Annexin V. HepG<sub>2</sub> cells treated with 0-1 mM OA showed dose-dependent lipid accumulation. Treatment of HepG<sub>2</sub> cells with increasing concentrations of simvastatin followed by treatment with 1 mM OA showed that low simvastatin concentrations (4-10 µM) were able to reduce lipid accumulation by ~40%, whereas high simvastatin concentrations (20 and 30 µM) induced apoptotic changes in cell morphology and increased the production of Annexin V<sup>+</sup> microparticles. This suggests that low simvastatin doses may have a role in preventing NAFLD. However, further investigations are required to confirm this action <i>in vivo</i> and to determine the underlying mechanism by which simvastatin reduces hepatic steatosis.
Immunoglobulin G3 from Polyclonal Human Immunodeficiency Virus (HIV) Immune Globulin Is More Potent than Other Subclasses in Neutralizing HIV Type 1 (2001)

Passive antibody prophylaxis against human immunodeficiency virus type 1 (HIV-1) has been accomplished in primates, suggesting that this strategy may prove useful in humans. While antibody specificity is crucial for neutralization, other antibody characteristics, such as subclass, have not been explored. Our objective was to compare the efficiencies of immunoglobulin G (IgG) subclasses from polyclonal human HIV immune globulin (HIVIG) in the neutralization of HIV-1 strains differing in coreceptor tropism. IgG1, IgG2, and IgG3 were enriched from HIVIG by using protein A-Sepharose. All three subclasses bound major HIV-1 proteins, as shown by Western blot assay and enzyme-linked immunosorbent assay. In HIV-1 fusion assays using X4, R5, or X4R5 envelope-expressing effector cells, IgG3 more efficiently blocked fusion. In neutralization assays with cell-free viruses using X4 (LAI, IIIB), R5 (BaL), and X4R5 (DH123), a similar hierarchy of neutralization was found: IgG3 > IgG1 > IgG2. IgG3 has a longer, more flexible hinge region than the other subclasses. To test whether this is important, IgG1 and IgG3 were digested with pepsin to generate F(ab')(2) fragments or with papain to generate Fab fragments. IgG3 F(ab')(2) fragments were still more efficient in neutralization than F(ab')(2) of IgG1. However, Fab fragments of IgG3 and IgG1 demonstrated equivalent neutralization capacities and the IgG3 advantage was lost. These results suggest that the IgG3 hinge region confers enhanced HIV-neutralizing ability. Enrichment and stabilization of IgG3 may therefore lead to improved HIVIG preparations. The results of this study have implications for the improvement of passive immunization with polyclonal or monoclonal antibodies and suggest that HIV-1 vaccines which induce high-titer IgG3 responses could be advantageous.
The "millipede" - nanotechnology entering data storage (2002)

Present a new scanning-probe-based data-storage concept called the "millipede" that combines ultrahigh density, terabit capacity, small form factor, and high data rate. Ultrahigh storage density has been demonstrated by a new thermomechanical local-probe technique to store, read back, and erase data in very thin polymer films. With this new technique, nanometer-sized bit indentations and pitch sizes have been made by a single cantilever/tip into thin polymer layers, resulting in a data storage densities of up to 1 Tb/in/sup 2/. High data rates are achieved by parallel operation of large two-dimensional (2-D) atomic force microscope (AFM) arrays that have been batch-fabricated by silicon surface-micromachining techniques. The very large-scale integration (VLSI) of micro/nanomechanical devices (cantilevers/tips) on a single chip leads to the largest and densest 2-D array of 32/spl times/32 (1024) AFM cantilevers with integrated write/read/erase storage functionality ever built. Time-multiplexed electronics control the functional storage cycles for parallel operation of the millipede array chip. Initial areal densities of 100-200 Gb/in/sup 2/ have been achieved with the 32/spl times/32 array chip.
[Construction of an expression vector with a bicistron of green fluorescent protein and HCV 5'NCR controlled luciferase gene and its expression in hepatocytes]. (2003)

An expression vector with a bicistron of GFP and HCV 5'NCR controlled luciferase gene was successfully constructed. GFP and luciferase could express independently. This study can promote the establishment of an anti-HCV drug screen system.
Immunization with a multiple antigen peptide containing defined B- and T-cell epitopes: production of bactericidal antibodies against group B Neisseria meningitidis (1994)

Previous analysis of the class 1 outer-membrane (OM) protein of Neisseria meningitidis has identified discrete epitopes to be potential targets for immune attack. The conformation of these epitopes is important for inducing antibodies which can react with the native protein and promote complement-mediated lysis of the meningococcus. The multiple antigen peptide (MAP) system, which consists of an oligomeric branching lysine core to which are attached dendritic arms of defined peptide antigens, confers some conformational stability and also allows for the preparation of immunogens containing both B-cell and T helper (Th)-cell epitopes. In this study, MAPs were synthesized to contain (i) the subtype P1.16b meningococcal class 1 protein B-cell epitope (B-MAP), and (ii) the P1.16b epitope in tandem with a defined Th-cell epitope, chosen from tetanus toxin (BT-MAP). The B-MAP was nonimmunogenic in animals. In contrast, incorporation of the Th-cell epitope into BT-MAP induced a strong humoral response towards the class 1 protein B-cell epitope. Antisera from immunized mice and rabbits reacted in ELISA with synthetic peptides containing the B-cell epitope, and also cross-reacted with meningococcal OMs from strains of subtype P1.16b and P1.16a. Murine and rabbit antisera showed similar reactivity and epitope specificity, but did not react with denatured class 1 protein in Western blotting, indicating the predominance of antibodies directed towards conformational epitopes. The antisera from rabbits immunized with BT-MAP promoted complement-mediated bactericidal killing not only of the homologous meningococcal subtype P1.16b strain but also of subtype P1.16a.
DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging (2017)

Recent advances in super-resolution fluorescence imaging allow researchers to overcome the classical diffraction limit of light, and are already starting to make an impact in biology. However, a key challenge for traditional super-resolution methods is their limited multiplexing capability, which prevents a systematic understanding of multi-protein interactions on the nanoscale. Exchange-PAINT, a recently developed DNA-based multiplexing approach, in theory facilitates spectrally-unlimited multiplexing by sequentially imaging target molecules using orthogonal dye-labeled 'imager' strands. While this approach holds great promise for the bioimaging community, its widespread application has been hampered by the availability of DNA-conjugated ligands for protein labeling. Herein, we report a universal approach for the creation of DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging, using a variety of affinity reagents such as primary and secondary antibodies, nanobodies, and small molecule binders. Furthermore, we extend the availability of orthogonal imager strands for Exchange-PAINT to over 50 and assay their orthogonality in a novel DNA origami-based crosstalk assay. Using our optimized conjugation and labeling strategies, we demonstrate nine-color super-resolution imaging <i>in situ</i> in fixed cells.
Digital payment systems with passive anonymity-revoking trustees* (1997)

Anonymity of the participants is an important requirement for some applications in electronic commerce, in particular for payment systems. Because anonymity could be in conflict with law enforcement, for instance in cases of blackmailing or money laundering, it has been proposed to design systems i n which a trustee or a set of trustees can selectively revoke the anonymity of the participants involved in a suspicious transaction. From an operational point of view, it can be an important requirement that such trustees are neither involved in payment transactions nor in the opening of an account, but only in case of a justified suspicion. In this paper we present an efficient anonymous digital payment systems satisfying this requirement. The described basic protocol for anonymity revocation can be used in on-line or off-line payment systems.
Osteopontin is produced by rat cardiac fibroblasts and mediates A(II)-induced DNA synthesis and collagen gel contraction. (1996)

Angiotensin II (AII) is a critical factor in cardiac remodeling which involves hypertrophy, fibroblast proliferation, and extracellular matrix production. However, little is known about the mechanism by which AII accelerates these responses. Osteopontin is an acidic phosphoprotein with RGD (arginine-glycine-aspartate) sequences that are involved in the vascular smooth muscle cell remodeling process. We identified the presence of osteopontin mRNA and protein in cultured rat cardiac fibroblasts and its prominent regulation by AII (10(-11) M). Osteopontin message levels were increased fourfold (P < 0.01) and protein fivefold (P < 0.05) at 24 h after addition of AII (10(-7) M). This response was inhibited by the AT1 receptor blocker, losartan. Osteopontin mRNA levels were increased in hypertrophied ventricles from animals with renovascular hypertension (1.6-fold, P < 0.05) and aortic banding (2.9-fold, P < 0.05). To examine the function of osteopontin, we determined its effects on (a) the ability of cardiac fibroblasts to contract three-dimensional collagen gels and (b) cardiac fibroblast growth. A monoclonal antibody against osteopontin partially blocked AII-induced three-dimensional collagen gel contraction by cardiac fibroblasts (64+/-4 vs. 86+/-5% in the presence of antibody, P < 0.05), while osteopontin itself promoted contraction of the gels by fibroblasts (71+/-5%, P < 0.05 compared with control). Either a monoclonal antibody against beta3 integrin which is a ligand for osteopontin or the RGD peptide blocked both AII and osteopontin-induced collagen gel contraction. Thus, the osteopontin RGD sequence binds to beta3 integrins on the fibroblast to promote fibroblast binding to collagen. All induced a threefold increase in DNA synthesis of cardiac fibroblasts, which was completely blocked by antibodies against osteopontin and beta3 integrin, or by RGD peptide, but not by controls. Thus, All-induced growth of cardiac fibroblasts also requires osteopontin engagement of the beta3 integrin. Taken together, these results provide the first evidence that osteopontin is a potentially important mediator of AII regulation of cardiac fibroblast behavior in the cardiac remodeling process.
Proteolytic Processing and Assembly ofgag and gag-pol Proteins of TED, a Baculovirus-Associated Retrotransposon of the Gypsy Family (1998)

TED (transposable element D) is an env-containing member of the gypsy family of retrotransposons that represents a possible retrovirus of invertebrates. This lepidopteran (moth) retroelement contains gag and pol genes that encode proteins capable of forming viruslike particles (VLP) with reverse transcriptase. Since VLP are likely intermediates in TED transposition, we investigated the roles of gag and pol in TED capsid assembly and maturation. By using constructed baculovirus vectors and TED Gag-specific antiserum, we show that the principal translation product of gag (Pr55(gag)) is cleaved to produce a single VLP structural protein, p37(gag). Replacement of Asp436 within the retrovirus-like active site of the pol-encoded protease (PR) abolished Pr55(gag) cleavage and demonstrated the requirement for PR in capsid processing. As shown by expression of an in-frame fusion of TED gag and pol, PR is derived from the Gag-Pol polyprotein Pr195(gag-pol). The PR cleavage site within Pr55(gag) was mapped to a position near the junction of a basic, nucleocapsid-like domain and a C-terminal acidic domain. Once released by cleavage, the C-terminal fragment was not detected. This acidic fragment was dispensable for VLP assembly, as demonstrated by the formation of VLP by C-terminal Pr55(gag) truncation proteins and replacement of the acidic domain with a heterologous protein. In contrast, C-terminal deletions that extended into the adjacent nucleocapsid-like domain of Pr55(gag) abolished VLP recovery and demonstrated that this central region contributes to VLP assembly or stability, or both. Collectively, these data suggest that the single TED protein p37(gag) provides both capsid and nucleocapsid functions. TED may therefore use a simple processing strategy for VLP assembly and genome packaging.
Stilbazulenyl Nitrone (STAZN):  A Nitronyl-Substituted Hydrocarbon with the Potency of Classical Phenolic Chain-Breaking Antioxidants (2002)

Stilbazulenyl nitrone (STAZN), 8, a nitronyl-substituted hydrocarbon, is a novel second-generation azulenyl nitrone with significantly enhanced potency as a chain-breaking antioxidant vs conventional alpha-phenyl nitrones previously investigated as antioxidant therapeutics. A convenient (1)H NMR-based assay for assessing the potency of chain-breaking antioxidants has shown that STAZN is ca. 300 times more potent in inhibiting the free radical-mediated aerobic peroxidation of cumene than is PBN and the experimental stroke drug NXY-059. Such levels of antioxidant efficacy are unprecedented among archetypal alpha-phenyl nitrone spin traps. Furthermore, STAZN outperforms such classical phenolic antioxidants as BHT and probucol and rivals the antioxidant potency of Vitamin E in a polar medium comprised of 80% cumene and 20% methanol. The Volodarskii electron-transfer mechanism involving the intermediacy of the STAZN radical cation has been implicated in attempts to ascertain the basis for the increased potency of STAZN over the three alpha-phenyl nitrones PBN, S-PBN, and NXY-059.
Genetics and genomics in pediatric septic shock (2012)

Pediatric sepsis and septic shock are increasingly being studied by genetic and genomic approaches and the accumulating data hold the promise of enhancing our future approach to this ongoing clinical problem.
Production of tumor necrosis factor/cachectin by human B cell lines and tonsillar B cells. (1988)

The production of TNF/cachectin by human B cell lines and tonsillar B cells was examined. Of the 15 B cell lines examined, 9 cell lines synthesize TNF mRNA constitutively. PMA stimulated most cell lines to accumulate increased amounts of TNF. SeD, 8866P, 32al, RPMI 1788, and four bone marrow-derived EBV-transformed cell lines accumulated high levels of TNF mRNA when stimulated by PMA. TNF production by these cell lines was examined. RPMI 1788 and WIH8 produced little TNF constitutively, but synthesized 5-7 ng/ml TNF when stimulated by PMA. A pre-B cell line, Nalm-6, did not synthesize any detectable amount of TNF mRNA, even with PMA stimulation. Tonsillar B cells could also be stimulated to produce TNF. PMA or Staphylococcus aureus Cowan I strain (SAC) alone stimulated some TNF mRNA accumulation, whereas B cell growth factor (BCGF) or anti-mu did not. This accumulation was synergistically elevated by the combinations of PMA and SAC, or PMA and anti-mu. BCGF increased PMA-, SAC-, PMA plus SAC-, or PMA plus anti-mu-induced TNF mRNA accumulations about twofold. The accumulation of TNF mRNA in tonsillar B cells stimulated by PMA plus SAC was between 32 and 48 h, the same peak interval as the accumulation of TNF and IL-2 mRNA in tonsillar T cells. This is in contrast to PMA or PMA plus A23187-stimulated RPMI 1788 cells in which TNF mRNA accumulation was maximal at 1-2 h. TNF activities found in tonsillar B cell supernatants correlated with the TNF mRNA levels in the cells. However, more TNF activity was found on the second-day than the third-day supernatants, indicating active TNF uptake by the B cells. Cyclosporin A (CsA) inhibited SAC and anti-mu responses in B cells in much the same way as the anti-CD3 responses in T cells. SAC-, PMA plus SAC-, and PMA plus anti-mu-stimulated, but not PMA-stimulated, increases in TNF mRNA accumulations in tonsillar B cells were inhibited by CsA. TNF production seems to increase in parallel with B cell proliferation, but the relationship of these two functions needs to be further examined.
Small doses of recombinant factor Vila in acquired deficiencies of vitamin K dependent factors (1999)

Muleo, G.; Santoro, R.; Iannaccaro, P. G.; Papaleo, P.; Leo, F.; Zappala, D.; Elia, L. Author Information
p53 mutations are not selected for in simian virus 40 T-antigen-induced tumors from transgenic mice (1992)

Many diverse tumors contain cells that select for mutations at the p53 gene locus. This appears to be the case because the p53 gene product can act as a negative regulator of cell division or a tumor suppressor. These mutations then eliminate this activity of the p53 gene product. The simian virus 40 (SV40) large T antigen binds to p53 and acts as an oncogene to promote cellular transformation and initiate tumors. If the binding of T antigen to the p53 protein inactivated its tumor suppressor activity, there would be no selection pressure for p53 mutants to appear in tumors. To test this idea, transgenic mice that carried and expressed the SV40 large T-antigen gene were created. Expression of the T antigen was directed to the liver, using the albumin promoter, and the choroid plexus, using the SV40 enhancer-promoter. A large number of papillomas (indicated in parentheses) of the choroid plexus (14), hepatocellular carcinomas (5), liver adenomas (10), and tumors of clear-cell foci (5) were examined for mutant and wild-type p53 genes and gene products. In all cases, the tumor extracts contained readily detectable T-antigen-p53 protein complexes. A monoclonal antibody specifically recognizing the wild-type p53 protein (PAb246) reacted with p53 in every tumor extract. A monoclonal antibody specifically recognizing mutant forms of the p53 protein (PAb240) failed to detect p53 antigens in these extracts. Finally, p53 partial cDNAs were sequenced across the regions of common mutations in this gene, and in every case only the wild-type sequence was detected. These results strongly support the hypothesis that T antigen inactivates the wild-type p53 tumor-suppressing activity and there is no need to select for mutations at the p53 locus.
Novel differences in renal gene expression in a diet-induced obesity model (2017)

Obesity is a significant risk factor for both chronic kidney disease and end-stage renal disease. To better understand disease development, we sought to identify novel genes differentially expressed early in disease progression. We first confirmed that mice fed a high-fat (HF) diet exhibit early signs of renal injury including hyperfiltration. We then performed RNA-Seq using renal cortex RNA from C57BL6/J male mice fed either HF or control (Ctrl) diet. We identified 1,134 genes differentially expressed in the cortex on HF vs. Ctrl, of which 31 genes were selected for follow-up analysis. This included the 9 most upregulated, the 11 most downregulated, and 11 genes of interest (primarily sensory receptors and G proteins). Quantitative (q)RT-PCR for these 31 genes was performed on additional male renal cortex and medulla samples, and 11 genes (including all 9 upregulated genes) were selected for further study based on qRT-PCR. We then examined expression of these 11 genes in Ctrl and HF male heart and liver samples, which demonstrated that these changes are relatively specific to the renal cortex. These 11 genes were also examined in female renal cortex, where we found that the expression changes seen in males on a HF diet are not replicated in females, even when the females are started on the diet sooner to match weight gain of the males. In sum, these data demonstrate that in a HF-diet model of early disease, novel transcriptional changes occur that are both sex specific and specific to the renal cortex.
TRENDS IN METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS IN UNITED STATES HOSPITALS (1993)

Gaynes, Robert P.; Culver, David H.; Horan, Teresa C.; Henderson, Tonya S.; Tolson, James S.; Martone, William J.; Nichols, Ronald Lee Author Information
The roles of alkyl halide additives in enhancing perovskite solar cell performance (2014)

C–X bond of alky halide additives cleavages during thermal annealing, resulting in frees halide ions to participate in perovskite formation.
Large Scale HPLC Purification of Oligodeoxyribonucleotides for Studies of the Binding of CC-1065 to DNA by NMR Spectroscopy (1989)

Abstract We have investigated four different HPLC columns and several conditions in search of the most efficient procedure for purification of milligram amounts of DNA. We are reporting the optimal conditions for a preparative purification using a Dupont Zorbax Bioseries Oligo column.
Reactions in the Rechargeable Lithium–O2 Battery with Alkyl Carbonate Electrolytes (2011)

The nonaqueous rechargeable lithium-O(2) battery containing an alkyl carbonate electrolyte discharges by formation of C(3)H(6)(OCO(2)Li)(2), Li(2)CO(3), HCO(2)Li, CH(3)CO(2)Li, CO(2), and H(2)O at the cathode, due to electrolyte decomposition. Charging involves oxidation of C(3)H(6)(OCO(2)Li)(2), Li(2)CO(3), HCO(2)Li, CH(3)CO(2)Li accompanied by CO(2) and H(2)O evolution. Mechanisms are proposed for the reactions on discharge and charge. The different pathways for discharge and charge are consistent with the widely observed voltage gap in Li-O(2) cells. Oxidation of C(3)H(6)(OCO(2)Li)(2) involves terminal carbonate groups leaving behind the OC(3)H(6)O moiety that reacts to form a thick gel on the Li anode. Li(2)CO(3), HCO(2)Li, CH(3)CO(2)Li, and C(3)H(6)(OCO(2)Li)(2) accumulate in the cathode on cycling correlating with capacity fading and cell failure. The latter is compounded by continuous consumption of the electrolyte on each discharge.