gebhart/patrepeval huggingface dataset:
Regulation of monocyte migration by amphoterin (HMGB1) (2004)

Amphoterin (HMGB1) is a 30-kD heparin-binding protein involved in process extension and migration of cells by a mechanism involving the receptor for advanced glycation end products (RAGE). High levels of amphoterin are released to serum during septic shock. We have studied the expression of amphoterin in monocytes and the role of amphoterin and RAGE in monocyte transendothelial migration. Un-activated monocytes in suspension did not reveal amphoterin on their surface, but adherent monocytes exported amphoterin to the cell surface. Immunohistochemical staining of arterial thrombi in vivo revealed amphoterin in mononuclear cells and in surrounding extracellular matrix. Amphoterin was secreted from phorbol ester and interferon-gamma (IFN-gamma)-activated macrophages, and the secretion was inhibited by blocking the adenosine 5'-triphosphate (ATP)-binding cassette transporter-1, a member of the multidrug resistance protein family. Amphoterin was specifically adhesive for monocytes in peripheral blood leukocyte adhesion assay. Adhesion caused an extensive spreading of cells, which was inhibited by the dominant-negative RAGE receptor (soluble ectodomain of RAGE), and adhesion up-regulated chromogranin expression in monocytes, also suggesting a RAGE-dependent interaction. Monocyte transendothelial migration was efficiently inhibited by anti-amphoterin and anti-RAGE antibodies and by the soluble RAGE. We suggest that amphoterin is an autocrine/paracrine regulator of monocyte invasion through the endothelium.
Databases in Protein Crystallography (1998)

Applications of structural databases in the protein crystallographic structure determination process are reviewed, using mostly examples from work carried out by the authors. Four application areas are discussed: model building, model refinement, model validation and model analysis.
Sensitivity and Specificity of Ankle-Brachial Index for Detecting Angiographic Stenosis of Peripheral Arteries (2007)

The ABI value shows a decreasing tendency with increasing severity of stenosis in patients with PAD. ABI measurement is an accurate and reliable noninvasive alternative to conventional DSA in the assessment of lower extremity arteries and the cut-off of 0.95 is the threshold ABI value for detecting PAD in Chinese patients.
[Inhibitory effect of interfering RNA targeting HIF-1alpha and VEGF on retinal neovascularization in the mouse]. (2008)

HIF-1alpha siRNA and VEGF165 siRNA can inhibit retinal neovascularization in the mouse effectively. Co-transfection of these two siRNAs shows the greatest inhibitory effect.
Colocalized Delivery of Adjuvant and Antigen Using Nanolipoprotein Particles Enhances the Immune Response to Recombinant Antigens (2013)

Subunit antigen-based vaccines can provide a number of important benefits over traditional vaccine candidates, such as overall safety. However, because of the inherently low immunogenicity of these antigens, methods for colocalized delivery of antigen and immunostimulatory molecules (i.e., adjuvants) are needed. Here we report a robust nanolipoprotein particle (NLP)-based vaccine delivery platform that facilitates the codelivery of both subunit antigens and adjuvants. Ni-chelating NLPs (NiNLPs) were assembled to incorporate the amphipathic adjuvants monophosphoryl lipid A and cholesterol-modified CpG oligodeoxynucleotides, which can bind His-tagged protein antigens. Colocalization of antigen and adjuvant delivery using the NiNLP platform resulted in elevated antibody production against His-tagged influenza hemagglutinin 5 and Yersinia pestis LcrV antigens. Antibody titers in mice immunized with the adjuvanted NLPs were 5-10 times higher than those observed with coadministration formulations and nonadjuvanted NiNLPs. Colocalized delivery of adjuvant and antigen provides significantly greater immune stimulation in mice than coadministered formulations.
Interleukin-6 is a potent myeloma-cell growth factor in patients with aggressive multiple myeloma (1989)

It has recently been demonstrated that interleukin-6 (IL-6) is a potent myeloma-cell growth factor in the majority of patients with multiple myeloma (MM). Using an anti-bromodeoxyuridine monoclonal antibody (MoAb) to specifically count myeloma cells in the S-phase (ie, labeling index, LI), we demonstrate that the IL-6 responsiveness of myeloma cells in vitro is directly correlated with their LI in vivo. Myeloma cells from all 13 patients with high LIs in vivo (greater than or equal to 1%) responded in vitro to IL-6, the strongest response occurring in cells from five patients with plasma-cell leukemia. In contrast, the cells of only two of eight patients with low myeloma-cell LIs in vivo (less than 1%) responded to IL-6 in vitro. After seven days of culturing with 1,000 U/mL recombinant IL-6 (rIL-6), the median LI value in the first group of patients (in vivo LI greater than or equal to 1%) was 11%, ie 11 times higher (P less than .01) than the median LI value (1%) in the second group of patients (in vivo LI less than 1%). Thus, the in vitro IL-6 responsiveness of myeloma cells is directly related to their in vivo proliferative status, and hence to the severity of the disease.
Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine. (1975)

High-molecular-weight DNA is known to collapse into very compact particles in a salt solution containing polymers like poly(ethylene oxide) [(EO)n] or polyacrylate. The biological relevance of this phenomenon is suggested by our recent finding that high concentrations of the highly acidic internal peptides found in the mature T4 bacteriophage head, as well as poly(glutamic acid) and poly(aspartic acid), can collapse DNA in a similar manner. The structure of DNAs collapsed by various methods has been studied with electron microscope. We find (EO)n collapses T4 or T7 bacteriophage DNA into compact particles only slightly larger than the size of the T4 and T7 head, respectively. In contrast, polylysine collapses DNA into different types of structures. Double-stranded DNA collapsed with (EO)n is cut by the single-strand specific Neurospora crassa endonuclease (EC 3.1.4.21) into small fragments. Extensive digestion only occurs above the critical concentration of polymer required for DNA collapse, demonstrating the (EO)n-collapsed DNA contains enzyme-vulnerable regions (probably at each fold), which are preferentially attacked. The size of the DNA fragments produced by limit-digestion with the nuclease ranges between 200 and 400 base pairs when DNA is collapsed by (EO)n. Only fragments of DNA which are larger than 600 base pairs are cut by the endonuclease in (EO)n-containing solution.
6Li-loaded liquid scintillators with pulse shape discrimination (1979)

Excellent pulse height and pulse shape discrimination performance has been obtained for liquid scintillators containing as much as 10 wt.% (6)Li-salicylate dissolved in a toluene-methanol solvent system using naphthalene and 9,10 diphenylanthracene as intermediate and secondary solutes. This solution has improved performance at higher (6)Li-loading than solutions in dioxane-water solvent systems, and remains stable at temperatures as low as -10 degrees C. Cells as large as 5 cm in diameter and 15.2 deep have been prepared which have a higher light output for slow neutron detection than (10)B-loaded liquids. Neutron efficiency calculations are also presented.
Soil microbial ecology : applications in agricultural and environmental management (1992)

Provides discussions for the major groups of soil micro-organisms, including rhizobacteria, symbiotic nitrogen-fixing bacteria, pathogenic fungi, mycorrhizal fungi and microalgae. The book describes applications of soil microbial technologies in agriculture, forestry and environmental management.
miR-198 inhibits migration and invasion of hepatocellular carcinoma cells by targeting the HGF/c-MET pathway (2011)

Metastasis is the leading cause of death in patients with hepatocellular carcinoma (HCC) and microRNAs have been implicated to influence this process. Emerging evidence indicates that miR-198 is down-regulated in HCC compared to normal liver parenchyma, but the functional roles of miR-198 in HCC cells remains unexplored. Herein, we show that miR-198 directly targets c-MET via its 3′UTR. Forced expression of miR-198 decreased c-MET expression at both mRNA and protein levels and consequently diminished HGF induced phosphorylation of p44/42 MAPK in HCC cells. Forced expression of miR-198 inhibited HGF promotion of HCC cell migration and invasion in a c-MET dependent manner. In conclusion, we have identified miR-198 as a novel suppressor of HCC cell invasion by negative regulation of the HGF/c-MET pathway.
De Novo Design, Synthesis, and X-ray Crystal Structures of Pyrrolinone-Based .beta.-Strand Peptidomimetics (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDe Novo Design, Synthesis, and X-ray Crystal Structures of Pyrrolinone-Based .beta.-Strand PeptidomimeticsAmos B. Smith III, Mark C. Guzman, Paul A. Sprengeler, Terence P. Keenan, Ryan C. Holcomb, John L. Wood, Patrick J. Carroll, and Ralph HirschmannCite this: J. Am. Chem. Soc. 1994, 116, 22, 9947–9962Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://doi.org/10.1021/ja00101a017RIGHTS & PERMISSIONSArticle Views743Altmetric-Citations96LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (3 MB) Get e-Alerts Get e-Alerts
Size Reduction of Galactosylated PEI/DNA Complexes Improves Lectin-Mediated Gene Transfer into Hepatocytes (1999)

Hepatocytes are interesting targets for gene therapy applications. Several hepatocyte-directed gene delivery vectors have been described. For example, simple galactosyl residues coupled to polyethylenimine (PEI) gave an efficient vector which selectively transfected hepatocytes via the asialoglycoprotein receptor-mediated endocytosis [Zanta, M. A., et al. (1997) Bioconjugate Chem. 8, 839-844]. However, the large size of these galactosylated PEI/DNA complexes prevented their use in vivo. We have investigated the role of the saccharide length on the size of glycosylated-PEI/DNA particles. When 5% of the PEI nitrogens were grafted with a linear tetragalactose structure (lGal4), small and stable particles were formed upon complexation with plasmid DNA. These particles were essentially toroids having a size of 50-80 nm and a zeta-potential close to neutrality. Moreover, these slightly charged PEI-lGal4/DNA complexes were as selective as the previously described galactosylated-PEI vector to transfect hepatocytes, but in addition, they were more efficient. It is expected that the properties of the PEI-lGal4/DNA complexes may increase their diffusion into the liver and their efficiency to transfect hepatocytes.
Regulation of class II MHC gene expression by interferons: insights into the mechanism of action of interferon (review). (1989)

Modulation of class I and II MHC antigen expression by interferons has been the focus of considerable attention because the regulation of these molecules serves as a useful model system to study factors exerting transcriptional control of gene expression and because of the relevance of these molecules to expression of the neoplastic phenotype. While our knowledge of the molecular mechanisms regulating the ability of interferon to mediate enhancement of MHC genes has increased, this information is primarily based on studies employing established cell lines, and it remains to be determined whether similar controls are also exerted in short term cultured cell lines. In this short review, we have discussed the structural organization of the 5' flanking regions of the MHC genes, with special emphasis on class II genes, and the implications of these data for the transcriptional regulation of these and of other interferon inducible genes. Present evidence indicates the existence of at least four conserved upstream sequences which are shared by interferon responsive genes and which appear to be involved in the transcriptional control of these genes. The pattern of metabolic requirements for IFN-alpha and IFN-beta versus IFN-gamma upregulation of the class I and II MHC genes suggests that the regulation of gene expression by IFN-gamma requires unique regulatory molecules, i.e. newly synthesized proteins, which are not required by IFN-alpha and IFN-beta treated cells. These putative mediators of gene expression are likely to be shared by many of the biochemical induction pathways involved in the regulation of genes which exhibit interferon responsive sequences. However, in addition to common regulatory signals, other specific pathways and possibly additional regulatory sequences, are also required to account for locus--or subunit-specific patterns of antigenic modulation. Future studies are required, including those employing short term tumor cell cultures, to precisely define the molecular details of gene regulation of class I and II MHC genes, as well as other interferon--responsive--genes, by interferons. These investigations will not only prove valuable on a fundamental scientific level, but they will also be crucial for the more effective application of interferons in clinical oncology.
Distinct potassium channels on pain-sensing neurons (2001)

Differential expression of ion channels contributes functional diversity to sensory neuron signaling. We find nerve injury induced by the Chung model of neuropathic pain leads to striking reductions in voltage-gated K(+) (Kv) channel subunit expression in dorsal root ganglia (DRG) neurons, suggesting a potential molecular mechanism for hyperexcitability of injured nerves. Moreover, specific classes of DRG neurons express distinct Kv channel subunit combinations. Importantly, Kv1.4 is the sole Kv1 alpha subunit expressed in smaller diameter neurons, suggesting that homomeric Kv1.4 channels predominate in A delta and C fibers arising from these cells. These neurons are presumably nociceptors, because they also express the VR-1 capsaicin receptor, calcitonin gene-related peptide, and/or Na(+) channel SNS/PN3/Nav1.8. In contrast, larger diameter neurons associated with mechanoreception and proprioception express high levels of Kv1.1 and Kv1.2 without Kv1.4 or other Kv1 alpha subunits, suggesting that heteromers of these subunits predominate on large, myelinated afferent axons that extend from these cells.
Familial hypercholesterolemia: current treatment and advances in management (2008)

Heterozygous familial hypercholesterolemia is associated with elevated levels of LDL-cholesterol and the development of premature cardiovascular disease. The condition is considerably under-diagnosed and under-treated. Statins are the first choice treatment for all patients with heterozygous familial hypercholesterolemia. For those patients who do not reach their treatment target or who are unable to use adequate statin dose, several alternative treatment modalities can be used, either as add-on therapy or as monotherapy. In this review the various treatment options are discussed.
Incorporation of methylene blue and nanogold into polyvinyl chloride catheters; a new approach for light-activated disinfection of surfaces (2012)

Methylene blue and 2 nm gold nanoparticles were incorporated into commercial PVC catheters by use of a simple “swell–encapsulation–shrink” method using acetone–water mixtures. Neither the methylene blue nor the nanogold leached into aqueous solution and the assemblage was stable to photodegradation upon laser irradiation. Exposure of the modified catheters to red laser light for 4–8 minutes induced the lethal photosensitisation of Staphylococcus epidermidis and Escherichia coli. Results from time-resolved EPR spectroscopy suggested that enhanced methylene blue triplet state production occurs in the presence of 2 nm gold nanoparticles. The implication being that the levels of reactive oxygen species are higher in these co-doped materials than with methylene blue alone.
Experimental validation of the importance of seed complement frequency to siRNA specificity (2008)

Pairing between the hexamer seed region of a small interfering RNA (siRNA) guide strand (nucleotides 2-7) and complementary sequences in the 3' UTR of mature transcripts has been implicated as an important element in off-target gene regulation and false positive phenotypes. To better understand the association between seed sequences and off-target profiles we performed an analysis of all possible (4096) hexamers and identified a nonuniform distribution of hexamer frequencies across the 3' UTR transcriptome. Subsequent microarray analysis of cells transfected with siRNAs having seeds with low, medium, or high seed complement frequencies (SCFs) revealed that duplexes with low SCFs generally induced fewer off-targets and off-target phenotypes than molecules with more abundant 3' UTR complements. These findings provide the first experimentally validated strategy for designing siRNAs with enhanced specificity and allow for more accurate interpretation of high throughput screening data generated with existing siRNA/shRNA collections.
Stability of Sodium Electrodeposited from a Room Temperature Chloroaluminate Molten Salt (1995)

Room temperature molten salts consisting of 1-methyl-3-ethylimidazo]ium chloride (MEIC) and aluminum chloride (A]C13) have been examined as possible electrolytes for a room temperature design of the sodium/iron(II) chloride battery. This work examines the conditions required to achieve efficient reduction and oxidation of sodium from a sodium chloride buffered, neutral melt. Two substrates were examined, tungsten and 303 stainless steel, using both cyclic voltammetry and chronopotentiometry. Melts were protonated using a closed electrochemical cell to allow quantification of the effect of dissolved HC1 on the efficiency of the sodium couple. A threshold of approximately 6 Torr HC1 partial pressure was observed for sodium plating-stripping. Below this threshold, the sodium couple was not observed. The results show that the sodium plating-stripping efficiency increases with increasing current density; however, the efficiency reaches a maximum and is adversely affected by high overpotentials and extended exposure of the sodium to the melt. It appears that some passivation occurs as even a very thin layer of plated sodium exhibits a steady open-circuit voltage over long periods in the melt.
A Review of the Key Clinical Trials of 2014 (2015)

This paper summarizes key clinical trials during 2014 and should be of practical interest to clinicians and cardiology researchers.
VASCULAR ENDOTHELIAL GROWTH FACTOR ANTISENSE PRETREATMENT OF BLADDER CANCER CELLS SIGNIFICANTLY ENHANCES THE CYTOTOXICITY OF MITOMYCIN C, GEMCITABINE AND CISPLATIN (2005)

One of the 3 AS-ODNs tested (VEGF857) significantly sensitizes human transitional cell carcinoma cells to CT. We suggest VEGF as an additional putative target to enhance the therapeutic benefit of, for example mitomycin C and gemcitabine instillation treatment schedules.
Abstract 2732: Multiplex immunoanalysis of cytokines in EUS-FNAs and in plasma to detect pancreatic cancer (2010)

Abstract Background: Endoscopic ultrasound fine needle aspirations (EUS-FNAs) are frequently used to diagnose masses of the pancreas. Immunohistochemical analysis aids in the separation by FNAs of chronic inflammatory diseases, benign tumors, and neuroendocrine tumors from adenocarcinomas. Multiplex immunoassay of plasma or EUS-FNAs for cytokines might also be useful diagnostically. Method: An extra EUS-FNA was obtained from consented patients for research; these were stored at −80°C neat or in 100 μl of 10% DMSO in RPMI 1640. EUS-FNAs were randomly selected from the collection to include 61 cases of pancreatic adenocarcinoma, 14 (all) neuroendocrine tumors, and 6 (all) benign pancreatic diseases. These EUS-FNAs were thawed in lysis buffer, diluted to samples with 500 μg/ml total protein and analyzed in duplicate using a 27 plex kit for IL-1b, IL-1ra, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-12, IL-13, IL-15, IL-17, Eotaxin, FGF Basic, G-CSF, GM-CSF, IFN-g, IP-10, MCP-1, MIP-1a, MIP-1b, PDGFbb, RANTES, TNFα, and VEGF. Samples of unprocessed plasma matching the EUS-FNAs were also analyzed for these same 27 cytokines and in non-matching plasma for 8 cytokines. Results: The analysis by Luminex technology of 8 cytokines in the plasma of 100 patients with pancreatic cancer (PANCA) or of 33 patients suspected, but not having PANCA, indicated that il-8 (P&amp;lt;0.006) might be useful in the separation of patients with PANCA. Il-2, il-4, il-6, il-10, IFN-γ, TNF GM-CSF were not useful. Based on EUS-FNA, those cytokines which appear most useful in separating diagnostic groups are interleukin 1 receptor antagonist (il- 1ra), interleukin 6, and interleukin 8 (P=0.012 or less). When these three cytokines were optimally combined, there is a clear separation of PANCA from benign/inflammatory conditions plus neuroendocrine tumors P&amp;lt;2.1E-06. Conclusions: These results suggest that the use of multiplex immunoassays of blood and of EUS-FNAs might be useful in the diagnosis of pancreatic cancer. (1) For plasma levels only, il-8 is more strongly correlated with cancer versus benign conditions or neuroendocrine tumors; thus il-6 and the combination of il-6 with il-8 does not improve the identification of cancer. (2) There is no correlation between plasma levels of il-6 and il-8 with il-6 and il-8 levels from EUS-FNAs. (3) For EUS-FNA, the il-1ra has the strongest correlation with cancer P&amp;lt;8.2E-06 followed by il-8 P&amp;lt;1.7E-05. The il-8 levels but not the il-6 levels add to the separation of cancer by il-1ra. (4) Combining il-8 plasma levels with il-8 levels by FNA only slightly improves the correlation. Sponsored in part by the Early Detection Research Network (EDRN) Reference Laboratory at UAB (5U24CA086359-10) and the Pancreatic SPORE at UAB (5P20CA101955-05). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2732.