gebhart/patrepeval huggingface dataset:
Atherosclerosis and apoprotein E. An enigmatic relationship. (1988)

In this article, we consider the role of apoprotein E in lipoprotein metabolism and especially in the metabolism of potentially atherogenic lipoproteins. Particular consideration has been given to three features of apoprotein E involvement in lipid cell interactions. Evidence implicating free cholesterol as a mediator of apoprotein E biosynthesis in cholesterol-loaded macrophages is presented. Experiments pointing to apoprotein E as the ligand promoting the interaction of beta-very-low-density lipoprotein (beta-VLDL) with macrophages are summarized. Finally, we describe the influence of fat and cholesterol fed to rhesus monkeys and baboons on the generation of hepatogenous (from isolated liver perfusates) VLDL enriched in cholesterol ester and apoprotein E. These hepatic VLDLs, none of which exhibits beta-electrophoretic mobility, promote cholesterol esterification in macrophages in proportion to their apoprotein E content. The complex role of apoprotein E in the genesis and reversal of atherosclerosis is briefly discussed.
Expression of human glandular kallikrein, hK2, in mammalian cells. (1996)

The human kallikrein family consists of three members, hK1, hK2, and hK3 [prostate-specific antigen (PSA)]. PSA is a widely accepted marker for prostate cancer. The mRNAs for both hK2 and PSA are localized predominantly to prostate epithelium and are regulated by androgens. In addition, hK2 has 78% amino acid homology to PSA. Although similarities to PSA make hK2 a potential prostate cancer marker, they also impede biochemical characterization of hK2 in those human tissues and body fluids where PSA is abundant. To study the expression, biosynthesis, and processing of hK2, recombinant hK2 was expressed in the adenovirus-induced Syrian hamster tumor cell line AV12-664 (AV12-hK2). Expression of hK2 was analyzed by Western blots and ELISA using monoclonal antibodies HK1G 464.3 [specific for prohK2 (phK2)] and HK1D 106.4 [specific for phK2 and mature hK2 (hK2)1. Western blot and ELISA analyses showed that phK2 was secreted into the media by AV12-hK2 cells on day 1 and was gradually converted to the mature form of hK2 by day 7. N-terminal amino acid sequencing verified the Western blot and ELISA data. This demonstrates for the first time that hK2 is secreted as phK2 and converted to hK2 extracellularly. In addition, hK2 detected in day 4-7 AV12-hK2-spent media was enzymatically active. Recombinant hK2 was also expressed in human prostate carcinoma cell lines, PC3 (PC3-hK2) and DU145 (DU145-hK2), that do not express endogenous hK2 or PSA. Similar to AV12-hK2 cells, both cell lines secreted phK2 that was converted to hK2 extracellularly. phK2 was the major form detected in the spent media of PC3-hK2 cells, even after 7 days, indicating a slow conversion of phK2 to hK2. hK2 was the predominant form detected in the spent media of DU145-hK2 starting on day 1, indicating the rapid conversion of phK2 to hK2. In this study, we demonstrate that hK2 exists in different forms and is secreted as phK2. phK2 is then converted to enzymatically active hK2 extracellularly.
Expression of Apoptosis-associated Speck-like Protein Containing a Caspase Recruitment Domain, a Pyrin N-terminal Homology Domain-containing Protein, in Normal Human Tissues (2001)

Apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) is a pyrin N-terminal homology domain (PYD)- and caspase recruitment domain (CARD)-containing a proapoptotic molecule. This molecule has also been identified as a target of methylation-induced silencing (TMS)-1. We cloned the ASC cDNA by immunoscreening using an anti-ASC monoclonal antibody. In this study, we determined the binding site of the anti-ASC monoclonal antibody on ASC and analyzed the expression of ASC in normal human tissues. ASC expression was observed in anterior horn cells of the spinal cord, trophoblasts of the placental villi, tubule epithelium of the kidney, seminiferous tubules and Leydig cells of the testis, hepatocytes and interlobular bile ducts of the liver, squamous epithelial cells of the tonsil and skin, hair follicle, sebaceous and eccrine glands of the skin, and peripheral blood leukocytes. In the colon, ASC was detected in mature epithelial cells facing the luminal side rather than immature cells located deeper in the crypts. These observations indicate that high levels of ASC are abundantly expressed in epithelial cells and leukocytes, which are involved in host defense against external pathogens and in well-differentiated cells, the proliferation of which is regulated.
A geometrically adjustable 16‐channel transmit/receive transmission line array for improved RF efficiency and parallel imaging performance at 7 Tesla (2008)

A novel geometrically adjustable transceiver array system is presented. A key feature of the geometrically adjustable array was the introduction of decoupling capacitors that allow for automatic change in capacitance dependent on neighboring resonant element distance. The 16-element head array version of such an adjustable coil based on transmission line technology was compared to fixed geometry transmission line arrays (TLAs) of various sizes at 7T. The focus of this comparison was on parallel imaging performance, RF transmit efficiency, and signal-to-noise ratio (SNR). Significant gains in parallel imaging performance and SNR were observed for the new coil and attributed to its adjustability and to the design of the individual elements with a three-sided ground plane.
Precise Correction of the Dystrophin Gene in Duchenne Muscular Dystrophy Patient Induced Pluripotent Stem Cells by TALEN and CRISPR-Cas9 (2014)

Duchenne muscular dystrophy (DMD) is a severe muscle-degenerative disease caused by a mutation in the dystrophin gene. Genetic correction of patient-derived induced pluripotent stem cells (iPSCs) by TALENs or CRISPR-Cas9 holds promise for DMD gene therapy; however, the safety of such nuclease treatment must be determined. Using a unique k-mer database, we systematically identified a unique target region that reduces off-target sites. To restore the dystrophin protein, we performed three correction methods (exon skipping, frameshifting, and exon knockin) in DMD-patient-derived iPSCs, and found that exon knockin was the most effective approach. We further investigated the genomic integrity by karyotyping, copy number variation array, and exome sequencing to identify clones with a minimal mutation load. Finally, we differentiated the corrected iPSCs toward skeletal muscle cells and successfully detected the expression of full-length dystrophin protein. These results provide an important framework for developing iPSC-based gene therapy for genetic disorders using programmable nucleases.
Transparent, stretchable, carbon-nanotube-inlaid conductors enabled by standard replication technology for capacitive pressure, strain and touch sensors (2013)

This paper describes a standard replication approach for preparing transparent elastomeric conductors with single-walled carbon nanotubes (SWCNTs) inlaid just below the surface. The elastic conductors were fabricated by spray coating a SWCNT suspension in chloroform on a fluorinated substrate, followed by the standard replication, casting liquid elastomers like polydimethylsiloxane on the SWCNT film, curing and peeling off the substrate. The replication strategy can produce elastic conductors with a flat or a desirable patterned surface. The resultant elastic conductors had excellent stability under repeated mechanical loading and stretchability up to 300%. It retained conductance even after 10 tape tests. Using the SWCNT-inlaid stretchable conductors as electrodes, elastic capacitors were fabricated using a mask-assisted method. The results showed that these capacitors are good candidates for multi-functional capacitive pressure, strain, and touch sensors.
Effects of Local Administration of Propolis and Its Polyphenolic Compounds on Tumor Formation and Growth (2005)

Many dietary constituents are chemopreventive in animal models, and experiments with cultured cells are revealing various potential mechanisms of action. Compounds classified as blocking agents can prevent, or greatly reduce, initiation of carcinogenesis, or suppressing agents can act on cell proliferation. Caffeic acid (CA) and caffeic acid phenethyl ester (CAPE), members of the polyphenolic compounds, are present in high concentrations in medicinal plants and propolis, a natural beehive product. A water-soluble extract of propolis (WSDP) and two components of propolis, CA and CAPE were investigated for direct antitumor activity in vivo and in vitro. The local presence of CA and CAPE in the tissue caused a significant delay in tumor formation and increased life span 29.30 to 51.73%, respectively. CA and CAPE, but not WSDP, significantly suppressed human HeLa cervical carcinoma cell proliferation in vitro. Based on these results, we postulate that the antitumor activity of polyphenolic compounds includes direct cytotoxic effects on tumor cells.
Resonance Raman Scattering of Rhodamine 6G as Calculated Using Time-Dependent Density Functional Theory (2006)

In this work, we present the first calculation of the resonance Raman scattering (RRS) spectrum of rhodamine 6G (R6G) which is a prototype molecule in surface-enhanced Raman scattering (SERS). The calculation is done using a recently developed time-dependent density functional theory (TDDFT) method, which uses a short-time approximation to evaluate the Raman scattering cross section. The normal Raman spectrum calculated with this method is in good agreement with experimental results. The calculated RRS spectrum shows qualitative agreement with SERS results at a wavelength that corresponds to excitation of the S(1) state, but there are significant differences with the measured RRS spectrum at wavelengths that correspond to excitation of the vibronic sideband of S(1). Although the agreement with the experiments is not perfect, the results provide insight into the RRS spectrum of R6G at wavelengths close to the absorption maximum where experiments are hindered due to strong fluorescence. The calculated resonance enhancements are found to be on the order of 10(5). This indicates that a surface enhancement factor of about 10(10) would be required in SERS in order to achieve single-molecule detection of R6G.
Characterization of a Mutant Recombinant S100 Protein Using Electrospray Ionization Mass Spectrometry (1997)

Two recombinant proteins derived by thrombin cleavage of a fusion protein between glutathione-S-transferase and CP10 (Chemotactic protein 10 kDa) were separated by C4 reversed-phase high-performance liquid chromatography (RP-HPLC). Both proteins were recognised by a polyclonal antibody to native CP10 following sodium dodecyl sulphate/polyacryamide gel electrophoresis (SDS/PAGE) and Western blotting. The major form (approximately 90%) had a mass of 10308 Da, by electrospray mass spectrometry (ESI-MS), which compared well with the theoretical mass of rCP10 (10307.6 Da) whereas the minor component (approximately 10%) had a mass of 11333 Da, 1025 mass units greater than expected. One sequence was obtained by N-terminal sequencing, suggesting that the N-terminus was not modified. The mass of peptides isolated after Asp-N digestion and C18 RP-HPLC were determined by ESI-MS and each assigned a probable sequence based on the expected peptide man of rCP10. The mutant protein produced one additional peak at 10.0 min with mass 1639 Da and the sequence DSHKEQQRGIPGNSS by Edman degradation. The first 5 amino acids corresponded to the last 5 C-terminal amino acids of rCP10. Analysis of the cDNA sequence of the expression vector used to produce rCP10 indicated that the 10 additional C-terminal amino acids were translated after the insertion of glutamine at the normal TAG stop codon. Another stop codon (TGA) located 27 base pairs downstream halts translation. The calculated mass of the mutant protein is 11332.7 Da, in good agreement with the experimental mass. Readthrough occurs in strains of E. coli (eg JPA101) with the amber mutation supE, and this allowed substitution of glutamine at TAG codons in approximately 5-10% of transcripts.
The spectrin repeat: a structural platform for cytoskeletal protein assemblies (2002)

Spectrin repeats are three-helix bundle structures which occur in a large number of diverse proteins, either as single copies or in tandem arrangements of multiple repeats. They can serve structural purposes, by coordination of cytoskeletal interactions with high spatial precision, as well as a 'switchboard' for interactions with multiple proteins with a more regulatory role. We describe the structure of the alpha-actinin spectrin repeats as a prototypical example, their assembly in a defined antiparallel dimer, and the interactions of spectrin repeats with multiple other proteins. The alpha-actinin rod domain shares several features common to other spectrin repeats. (1) The rod domain forms a rigid connection between two actin-binding domains positioned at the two ends of the alpha-actinin dimer. The exact distance and rigidity are important, for example, for organizing the muscle Z-line and maintaining its architecture during muscle contraction. (2) The spectrin repeats of alpha-actinin have evolved to make tight antiparallel homodimer contacts. (3) The spectrin repeats are important interaction sites for multiple structural and signalling proteins. The interactions of spectrin repeats are, however, diverse and defy any simple classification of their preferred interaction sites, which is possible for other domains (e.g. src-homology domains 3 or 2). Nevertheless, the binding properties of the repeats perform important roles in the biology of the proteins where they are found, and lead to the assembly of complex, multiprotein structures involved both in cytoskeletal architecture as well as in forming large signal transduction complexes.
Studies on Hemorrhagic and Endotoxin Shock in Relation to Vasomotor Changes and Endogenous Circulating Epinephrine, Norepinephrine and Serotonin (1961)

Rosenberg, J. C. M.D.; LILLEHEI, RICHARD C. M.D.; LONGERBEAM, JERROLD M.D.; ZIMMERMANN, BERNARD M.D. Author Information
Glycerol Monooleate-Based Nanocarriers for siRNA Delivery in Vitro (2012)

We present studies of the delivery of short interfering ribonucleic acid (siRNA) into a green fluorescent protein (GFP) expressing cell line, using lipid nanocarriers in cubic lyotropic liquid crystal form. These carriers are based on glycerol monooleate (GMO) and employ the use of varying concentrations of cationic siRNA binding lipids. The essential physicochemical parameters of the cationic lipid/GMO/siRNA complexes such as particle size, ζ otential, siRNA uptake stability, lyotropic mesophase behavior, cytotoxicity,and gene silencing efficiency were systematically assessed. We find that the lipid nanocarriers were effectively taken up by mammalian cells and that their siRNA payload was able to induce gene silencing in vitro. More importantly, it was found that the nonlamellar structure of some of the lipid nanocarrier formulations were more effective at gene silencing than their lamellar structured counterparts. The development of cationic lipid functionalized nonlamellar GMO-based nanostructured nanoparticles may lead to improved siRNA delivery vehicles.
Photoarylation of Iodocarboranes with Unactivated (Hetero)Arenes: Facile Synthesis of 1,2‐[(Hetero)Aryl]n‐o‐Carboranes (n=1,2) and o‐Carborane‐Fused Cyclics (2016)

Photoarylation of iodocarboranes with unactivated arenes/heteroarenes at room temperature has been achieved, for the first time, thus leading to the facile synthesis of a large variety of cage carbon mono(hetero)arylated and di(hetero)arylated o-carboranes. This work represents a clean, efficient, transition-metal-free, and cheap synthesis of functionalized carboranes, which has significant advantages over the known methods.
MEX-3 interacting proteins link cell polarity to asymmetric gene expression inCaenorhabditis elegans (2002)

The KH domain protein MEX-3 is central to the temporal and spatial control of PAL-1 expression in the C. elegans early embryo. PAL-1 is a Caudal-like homeodomain protein that is required to specify the fate of posterior blastomeres. While pal-1 mRNA is present throughout the oocyte and early embryo, PAL-1 protein is expressed only in posterior blastomeres, starting at the four-cell stage. To better understand how PAL-1 expression is regulated temporally and spatially, we have identified MEX-3 interacting proteins (MIPs) and characterized in detail two that are required for the patterning of PAL-1 expression. RNA interference of MEX-6, a CCCH zinc-finger protein, or SPN-4, an RNA recognition motif protein, causes PAL-1 to be expressed in all four blastomeres starting at the four-cell stage. Genetic analysis of the interactions between these mip genes and the par genes, which provide polarity information in the early embryo, defines convergent genetic pathways that regulate MEX-3 stability and activity to control the spatial pattern of PAL-1 expression. These experiments suggest that par-1 and par-4 affect distinct processes. par-1 is required for many aspects of embryonic polarity, including the restriction of MEX-3 and MEX-6 activity to the anterior blastomeres. We find that PAL-1 is not expressed in par-1 mutants, because MEX-3 and MEX-6 remain active in the posterior blastomeres. The role of par-4 is less well understood. Our analysis suggests that par-4 is required to inactivate MEX-3 at the four-cell stage. Thus, PAL-1 is not expressed in par-4 mutants because MEX-3 remains active in all blastomeres. We propose that MEX-6 and SPN-4 act with MEX-3 to translate the temporal and spatial information provided by the early acting par genes into the asymmetric expression of the cell fate determinant PAL-1.
Dynamic force microscopy by means of the phase-controlled oscillator method (1997)

Dynamic force microscopy, a technique also known as non-contact force microscopy, has proved to be a powerful tool for atomic resolution imaging. A number of schemes have been developed, but recently the oscillator method has become the preferred operating mode. Here, the force sensor acts as resonator in an active feedback circuit. A practical implementation of the method is described and the underlying key concepts are discussed. It is shown that a tracking oscillator excitation scheme is superior to the more standard direct feedback method for cases in which the force sensor exhibits only a weak resonance enhancement. Furthermore, the simultaneous measurement of dissipative interaction channels is an important extension of dynamic force microscopy. It allows one to differentiate between sample materials via their plasto-mechanical response. As an example, a Cr test grating has been imaged in the constant force gradient mode. The dissipation measured on Cr-covered areas is significantly lower than that on the bare quartz glass substrate, which enables one to distinguish between the two materials with a lateral resolution comparable to that of the topographic image.
Tolerance to a dominant T cell epitope in the acetylcholine receptor molecule induces epitope spread and suppresses murine myasthenia gravis (1997)

Myasthenia gravis (MG) is a T cell-dependent, Ab-mediated autoimmune disease. T cells reactive to a dominant peptide alpha 146-162 of acetylcholine receptor (AChR) alpha subunit participate in murine MG pathogenesis. To suppress the autoimmune response to AChR, a high dose of alpha146-162 peptide in IFA was administered parenterally as a tolerogen, after the development of a primary T cell immune response to AChR. This form of AChR T cell peptide tolerance suppressed the in vitro T cell proliferative response to AChR and its dominant alpha146-162 and subdominant alpha182-198 peptides through epitope spread. Administration of alpha146-162 peptide in IFA after the primary immune response to AChR also significantly suppressed the serum anti-AChR Ab of the IgG2b isotype and clinical incidence of MG in C57BL/6 mice. Furthermore, the production of IFN-gamma, IL-2, and IL-10 cytokines by AChR, alpha146-162, and alpha182-198 peptide-reactive cells was suppressed by alpha146-162 peptide tolerance, and the epitope spread observed could be attributed to the reduction in the above cytokine production. Therefore, AChR T cell-dominant peptide tolerance could be adapted in the Ag-specific therapy of MG.
Intratumoral Immunization: A New Paradigm for Cancer Therapy (2014)

Abstract Immune cell infiltration in the tumor microenvironment is of prognostic and therapeutic import. These immune cell subsets can be heterogeneous and are composed of mature antigen-presenting cells, helper and effector cytotoxic T cells, toleragenic dendritic cells, tumor-associated macrophages, and regulatory T cells, among other cell types. With the development of novel drugs that target the immune system rather than the cancer cells, the tumor immune microenvironment is not only prognostic for overall patient outcome, but also predictive for likelihood of response to these immune-targeted therapies. Such therapies aim to reverse the cancer immunotolerance and trigger an effective antitumor immune response. Two major families of immunostimulatory drugs are currently in clinical development: pattern recognition receptor agonists (PRRago) and immunostimulatory monoclonal antibodies (ISmAb). Despite their immune-targeted design, these agents have so far been developed clinically as if they were typical anticancer drugs. Here, we review the limitations of this conventional approach, specifically addressing the shortcomings of the usual schedules of intravenous infusions every 2 or 3 weeks. If the new modalities of immunotherapy target specific immune cells within the tumor microenvironment, it might be preferable to deliver them locally into the tumor rather than systemically. There is preclinical and clinical evidence that a therapeutic systemic antitumor immune response can be generated upon intratumoral immunomodulation. Moreover, preclinical results have shown that therapeutic synergy can be obtained by combining PRRagos and ISmAbs to the local tumor site. Clin Cancer Res; 20(7); 1747–56. ©2014 AACR.
True Blue Inorganic Optoelectronic Devices (2000)

The realization of blue light-emitting optoelectronic devices has attracted much attenion. Here the leading candidates (ZnSe, GaN, SiC, organic polymers) are examined and research towards the improvement of zinc selenide in particular is reviewed. Deposition methods, precursors, and p-type dopants are all discussed. The Figure shows a p–n junction after equilibration.
Nonsurgical Reconstruction of Thoracic Aortic Dissection by Stent–Graft Placement (1999)

These preliminary observations suggest that elective, nonsurgical insertion of an endovascular stent-graft is safe and efficacious in selected patients who have thoracic aortic dissection and for whom surgery is indicated. Endoluminal repair may be useful for interventional reconstruction of thoracic aortic dissection.