gebhart/patrepeval huggingface dataset:
Dual expression of mouse and rat VRL‐1 in the dorsal root ganglion derived cell line F‐11 and biochemical analysis of VRL‐1 after heterologous expression (2003)

The vanilloid‐like TRP‐channel VRL‐1 (TRPV2) is a nonselective cation channel expressed by primary sensory neurons and non‐neuronal tissues [Caterina, M.J., Rosen, T.A., Tominaga, M., Brake, A.J and Julius, D. (1999) Nature 398 , 436–441]. It is one of the six members of the vanilloid‐like TRP‐channel family which is now termed the TRPV family [Montell, G., Birnbaumer, L., Flockerzi, V., Bindels, R.J., Brutford, E.A., Caterina, M.J., Clapham, D.E., Harteneck, C., Heller, S., Julius, D., Kojima, I., Mori, Y., Penner, R., Prawitt, D., Scharenberg, A.M., Schultz, G., Shimizu, N. and Zhu, M.X. (2002) Mol. Cell 2 , 229–231]. As it is a temperature‐gated channel, VRL‐1 appears to be functionally related to VR1. In contrast to VR1, VRL‐1 is activated at a higher temperature threshold and it does not respond to capsaicin or protons. Here we describe the expression of VRL‐1 in the rat dorsal root ganglion‐derived cell line F‐11, a hybridoma of mouse neuroblastoma (N18TG2) and rat dorsal root ganglion cells. We found by RT‐PCR that F‐11 cells express not only the rat VRL‐1, but also its mouse orthologue in a single cell. The F‐11 parental cell line N18TG2 also expressed murine VRL‐1. Due to its neuronal character, the DRG‐derived F‐11 cell line provides an experimental system for the study of VRL‐1 biochemistry. However, one has to be aware that both the mouse and the rat protein are expressed simultaneously. Furthermore we cloned VRL‐1 from rat brain and analyzed its glycosylation and localization in comparison to the endogenously expressed protein in F‐11 cells. In contrast to the endogenous VRL‐1 the overexpressed protein is glycosylated. Similar to VR1 the glycosylation is N‐linked as shown by an deglycosylation assay. Immunofluorescence analysis of the endogenous VRL‐1 in F‐11 cells gives only weak signals in the cytoplasm whereas the overexpressed rat VRL‐1 appears mainly at the plasma membrane.
The human v-abl cellular homologue. (1983)

A contiguous region of cellular DNA sequence, 64 kb in length and representing overlapping cellular inserts from three independent cosmid clones, has been isolated from a representative library of human lung carcinoma DNA partially digested with MboI. Within this region of the cellular genome, v-abl homologous sequences are dispersed over a total region of around 32 kb. These sequences represent the entire v-abl human cellular homologue, are colinear with the viral v-abl transforming gene, and contain a minimum of seven intervening sequences. At least eight regions of highly repetitive DNA sequences have been shown to map in close proximity to c-abl coding sequences. In addition to the major c-abl human locus, three regions of human DNA sequence, corresponding to only portions of the v-abl gene, have been identified. Two of these have been molecularly cloned and shown to be distinct from the primary human c-abl locus. Upon transfection to rat embryo fibroblasts in culture, none of the cosmid DNAs containing v-abl homologous sequences exhibited transforming activity. These findings identify and map a single genetic locus of human DNA, c-abl, representing the complete v-abl homologue, and demonstrate the existence of additional human DNA sequences corresponding to more limited, subgenomic regions of v-abl.
Visualizing power system operations in an open market (1997)

All players in the US electricity industry must understand how specific generation decisions, wheeling arrangements, and legislative initiatives affect system operations. This article features PowerWorld, a comprehensive power system simulation package developed to help meet this need. The package is designed for the many new players in the power industry who will never operate an actual system but who must have a basic understanding of its operations. The package, which runs in the Microsoft Windows environment, is user friendly, interactive, and menu driven. It effectively uses visualization techniques to present the basics of power system operations and control simply, yet also with a level of detail to accurately model large-scale systems realistically and with the appropriate level of fidelity. The package has been demonstrated to policy makers, legislative analysts, small and large utilities, and regulatory decision makers both nationally and internationally. It has been found to be a very effective tool for communicating the many technical and economic impacts of third-party access.
Tamsulosin, a selective α 1c ‐adrenoceptor* antagonist: a randomized, controlled trial in patients with benign prostatic ‘obstruction’ (symptomatic BPH) (1995)

Tamsulosin 0.4 mg once daily is safe, well tolerated and clinically effective in improving symptoms and urinary flow rate in patients with symptomatic BPH.
The ABCs of BMPs (2005)

Bone morphogenetic proteins (BMP) are being increasingly used in orthopaedic surgery. These small molecules are capable of inducing bone formation when delivered in the appropriate concentration and on the appropriate scaffold. Not all BMPs are equally effective, and there are currently only two Food and Drug Administration (FDA)-approved "on-label" applications. There are potential complications related to off-label use of BMPs that need to be understood. When used properly, these molecules have the potential to eliminate the need for iliac crest bone graft harvest and improve the speed and success of bone healing.
How Does Interleukin 15 Contribute to the Pathogenesis of HTLV Type 1-Associated Myelopathy/Tropical Spastic Paraparesis? (2000)

HTLV-1 is the etiological agent of a neurological disease named HAM/TSP that has clinical characteristics similar to those of multiple sclerosis (MS). The PBMC obtained from HAM/TSP patients undergo spontaneous proliferation in the absence of addition of any exogenous cytokines in an ex vivo culture. This spontaneous proliferation has been thought to be due to the proliferation of T cells. It was demonstrated that this proliferation is, in part, due to the production of IL-2 and its receptor (IL-2Ralpha) by HTLV-1-infected T cells. In this review, we demonstrate that IL-15 production also contributes to the spontaneous proliferation of T cells obtained from HAM/TSP PBMC. We provide data indicating that IL-15 expression is elevated in HAM/TSP PBMC when compared to that of the normal donors. Furthermore, we demonstrate that IL-15 overexpression by HTLV-1 is due to Tax trans-activation of its promoter and induction of NF-kappaB transcription factors. On the basis of these studies, we propose a model in which HTLV-1 infection of T cells results in the production of both IL-2 and IL-15 cytokines, growth factors that support the proliferation of T cells.
Poliovirus translation: A paradigm for a novel initiation mechanism (1989)

All eukaryotic cellular mRNAs, and most viral mRNAs, are blocked at their 5' ends with a cap structure (m7GpppX, where X is any nucleotide). Poliovirus, along with a small number of other animal and plant viral mRNAs, does not contain a 5' cap structure. Since the cap structure functions to facilitate ribosome binding to mRNA, translation of polio-virus must proceed by a cap-independent mechanism. Consistent with this, recent studies have shown that ribosomes can bind to an internal region within the long 5' noncoding sequence of poliovirus RNA. Possible mechanisms for cap-independent translation are discussed. Cap-independent translation of poliovirus RNA is of major importance to the mechanism of shut-off of host protein synthesis after infection. Moreover, it is likely to play a role in determining poliovirus neurovirulence and attenuation.
Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase (2008)

Peptide:N-glycanase (PNGase) is an important component of the endoplasmic reticulum-associated protein degradation pathway in which it de-glycosylates misfolded glycoproteins, thus facilitating their proteasomal degradation. PNGase belongs to the transglutaminase superfamily and features a Cys, His, and Asp catalytic triad, which is essential for its enzymatic activity. An elongated substrate-binding groove centered on the active site Cys191 was visualized in the crystal structure of apo-PNGase, whereas its complex with Z-VAD-fmk, a peptide-based inhibitor of PNGase, revealed that the inhibitor occupied one end of the substrate-binding groove while being covalently linked to the active site Cys. Recently, haloacetamidyl-containing carbohydrate-based inhibitors of PNGase were developed and shown to specifically label the active site Cys. In this study, we describe the crystal structure of yeast PNGase in complex with N,N'-diacetylchitobiose (chitobiose). We found that the chitobiose binds on the side opposite to the peptide binding site with the active site Cys191 being located approximately midway between the carbohydrate and peptide binding sites. Mutagenesis studies confirm the critical role of the chitobiose-interacting residues in substrate binding and suggest that efficient oligosaccharide binding is required for PNGase activity. In addition, the N-terminus of a symmetry-related PNGase was found to bind to the proposed peptide-binding site of PNGase. Together with the bound chitobiose, this enables us to propose a model for glycoprotein binding to PNGase. Finally, deleting the C-terminal residues of yeast PNGase, which are disordered in all structures of this enzyme, results in a significant reduction in enzyme activity, indicating that these residues might be involved in binding of the mannose residues of the glycan chain.
Terahertz Spectroscopy : Principles and Applications (2007)

Preface Instrumentation and Methods Terahertz Time-Domain Spectroscopy with Photoconductive Antennas R. Alan Cheville Nonlinear Optical Techniques for Terahertz Pulse Generation and Detection-Optical Rectification and Electrooptic Sampling Ingrid Wilke and Suranjana Sengupta Time-Resolved Terahertz Spectroscopy and Terahertz Emission Spectroscopy Jason B. Baxter and Charles A. Schmuttenmaer Applications in Physics and Materials Science Time-Resolved Terahertz Studies of Carrier Dynamics in Semiconductors, Superconductors, and Strongly Correlated Electron Materials Robert A. Kaindl and Richard D. Averitt Time-Resolved Terahertz Studies of Conductivity Processes in Novel Electronic Materials Jie Shan and Susan L. Dexheimer Optical Response of Semiconductor Nanostructures in Terahertz Fields Generated by Electrostatic Free-Electron Lasers Sam Carter, John Cerne, and Mark S. Sherwin Applications in Chemistry and Biomedicine Terahertz Spectroscopy of Biomolecules Edwin J. Heilweil and David F. Plusquellic Pharmaceutical and Security Applications of Terahertz Spectroscopy J. Axel Zeitler, Thomas Rades, and Philip F. Taday Index
Fluorescence-based fibre optic arrays: a universal platform for sensing (2003)

Optical fibres provide a universal sensing platform as they are easily integrated with a multitude of different sensing schemes. Such schemes enable the preparation of a multitude of sensors from relatively straightforward pH sensors, to more complex ones, including artificial olfaction sensors, high-density oligonucleotide arrays, and high-throughput cell-based arrays. Imaging fibre bundles comprised of thousands of fused optical fibres are the basis for an optically connected, individually addressable parallel sensing platform. Fibre optic imaging bundles possess miniature feature sizes (3-10 micron diameter fibres), allowing high-density sensor packing (approximately 2 x 10(7) sensors per cm2). Imaging fibre bundles transmit coherent images enabling combined imaging and sensing, relating the responses monitored by the sensor to observable physical changes. The individual fibre cores can also be selectively etched to form a high-density microwell array capable of housing complementary sized microsensors. The miniature feature sizes facilitate a faster response and more sensitive measurement capabilities. The platform is extremely versatile in its sensing design, allowing the sensing scheme to be tailored to fit the experimental design, whether for monitoring single analytes or more complex multiplexed assays. A number of sensing schemes and applications are described in this review.
SPM-927 (Schwarz Pharma). (2003)

Schwarz Pharma, under license from Harris FRC, is developing SPM-927, synthesized by researchers at the University of Houston, for the potential treatment of epilepsy and neuropathic pain.
Molecular Cloning and Expression of Mammalian Peroxisomaltrans-2-Enoyl-coenzyme A Reductase cDNAs (2000)

Chain elongation of fatty acids is an important cellular process and is believed to occur in the endoplasmic reticulum of all eukaroytic cells. Herein we describe the cloning and characterization of a peroxisomal NADPH-specific trans-2-enoyl-CoA reductase, the key enzyme for a proposed peroxisomal chain elongation pathway. The reductase was solubilized and partially purified from guinea pig liver peroxisomes by affinity chromatography. On SDS-polyacrylamide gel electrophoresis, a 40-kDa band was identified as the enzyme, and its partial amino acid sequence (27 amino acids) was determined. A full-length cDNA for the reductase was cloned from a guinea pig liver cDNA library. The open reading frame of this nucleotide sequence encodes a 302-amino acid polypeptide with a calculated molecular mass of 32.5 kDa. Full-length mouse and human cDNA clones encoding homologous proteins have also been isolated. All of these translated polypeptides have the type I peroxisomal targeting signal, AKL, at the carboxyl terminus. The identity of the cloned enoyl-CoA reductase cDNAs was confirmed by expressing the guinea pig and human cDNAs in Escherichia coli. The His-tagged recombinant enzymes were found to have very high NADPH-specific 2-enoyl-CoA reductase activity with similar properties and specificity as the liver peroxisomal reductase. Both the natural and the recombinant enzyme catalyze the reduction of trans-2-enoyl-CoAs of varying chain lengths from 6:1 to 16:1, having maximum activity with 10:1 CoA. Northern blot analysis demonstrated that a single transcript of 1.3 kilobases is present in most mouse tissues, with particularly high concentrations in liver and kidney.
Not All Polyriboinosinic-polyribocytidylic Acids (Poly I:C) are Equivalent for Inducing Maturation of Dendritic Cells (2009)

This study compares the behavior of 2 commercially available polyriboinosinic-polyribocytidylic acids (poly I:C1 and poly I:C2) and the structural analog poly I:C12U in regard to dendritic cell (DC) maturation. When the Toll-like receptor 3 (TLR3) agonists are tested in combination with interferon-alpha, tumor necrosis factor-alpha, interleukin (IL)-1beta, and interferon-gamma (the so-called alpha-type-1 DC), the 3 different cocktails generate phenotypically mature DCs, but with different functional properties. Higher migratory capacity is observed with poly I:C1, the only poly I:C allowing spontaneous release of IL-12p70 by DCs. However, upon CD40 triggering, cocktails containing poly I:C2 or poly I:C12U allow a far higher production of IL-12p70 compared with those containing poly I:C1. Using a TLR signaling pathway reverse transcription profiler polymerase chain reaction to analyze changes in gene expression after treatment of DCs with the agonists alone, we show that 39% of the 84 tested genes are differentially regulated between the 3 conditions. Poly I:C12U induces far fewer regulated genes than the 2 other poly I:Cs. These different behaviors could be due to alternative ways of sensing double-stranded RNA, which do not rely solely on TLR3 but also on other types of receptors, depending on the size of poly I:Cs. As the 2 poly I:Cs tested here have very different molecular weights, this could partly explain the observed differences. In conclusion, neither the poly I:Cs nor their structural analog poly I:C12U have an equivalent behavior. This should be taken into an account not only when they are used in cocktails for DC maturation but also when analyzing signaling pathways with synthetic double-stranded RNA analogs.
Integrative Genomic Analysis of Protein Kinase C (PKC) Family Identifies PKCι as a Biomarker and Potential Oncogene in Ovarian Carcinoma (2006)

The protein kinase C (PKC) family plays a key regulatory role in a wide range of cellular functions as well as in various cancer-associated signal transduction pathways. Here, we investigated the genomic alteration and gene expression of most known PKC family members in human ovarian cancer. The DNA copy number of PKC family genes was screened by a high-resolution array-based comparative genomic hybridization in 89 human ovarian cancer specimens. Five PKC genes exhibited significant DNA copy number gains, including PKCiota (43.8%), PKCbeta1 (37.1%), PKCgamma (27.6%), PKCzeta (22.5%), and PKCtheta (21.3%). None of the PKC genes exhibited copy number loss. The mRNA expression level of PKC genes was analyzed by microarray retrieval approach. Two of the amplified PKC genes, PKCiota and PKCtheta, were significantly up-regulated in ovarian cancer compared with normal ovary. Increased PKCiota expression correlated with tumor stage or grade, and PKCiota overexpression was seen mostly in ovarian carcinoma but not in other solid tumors. The above results were further validated by real-time reverse transcription-PCR with 54 ovarian cancer specimens and 24 cell lines; overexpression of PKCiota protein was also confirmed by tissue array and Western blot. Interestingly, overexpressed PKCiota did not affect ovarian cancer cell proliferation or apoptosis in vitro. However, decreased PKCiota expression significantly reduced anchorage-independent growth of ovarian cancer cells, whereas overexpression of PKCiota contributed to murine ovarian surface epithelium transformation in cooperation with mutant Ras. We propose that PKCiota may serve as an oncogene and a biomarker of aggressive disease in human ovarian cancer.
Influence of Prosthetic Groups on Protein Folding and Subunit Assembly (1972)

Abstract Separated, heme-free, α- and β-globins have been prepared from the heme-containing α and β subunits of human hemoglobin. It is shown that the α- and β-globins are different in molecular weight, secondary structure, sulfhydryl reactivity, and a number of other properties from the heme-containing α and β subunits to which the isolated globin chains can be reconstituted and from which they derive. Moreover, the following have been demonstrated. (a) The separated globin chains are folded very differently from one another, although the basic folding features of the parent subunits are highly similar. (b) Removal of heme from the isolated β chain results in a β-globin with an s20,w value of 2.7, corresponding to a dimer. The heme-containing chain is tetrameric. The dimeric form of β-globin occurs in 20 mm as well as 0.1 m phosphate (or Tris) and over a range of pH values from 6.7 to 8. (c) Removal of heme from the isolated α chain results in an α-globin of markedly increased sedimentation coefficient. The value of the sedimentation coefficient is dependent on the concentration of buffer in which the initial globin precipitate is dissolved and against which it is dialyzed. When the initial phosphate concentration is 0.1 m, the s20,w value is 2.5 (corresponding to dimer). At 20 mm phosphate, the value is 6.6 (possibly corresponding to octamer). The heme-containing subunit has an s20,w value of 1.9 (corresponding to monomer, predominantly). (d) Sulfhydryl reactivity is sharply reduced in both isolated globin chains, in contrast to complete accessibility of sulfhydryl in the heme-containing separated subunits. In 15% sodium dodecyl sulfate, all sulfhydryl groups in the globin chains react with Ellman's reagent. (e) In the absence of heme, at accessible temperature (4°) and low phosphate concentration, the isolated, soluble α- and β-globin chains do not measurably combine. Under these conditions apohemoglobin (αβ-globin) occurs as a dimer. An analysis of secondary structure in terms of primary sequence reveals that pros thetic group binding has quite different effects on the two globin chains and that this represents a major influence on the attainment of native structure of hemoglobin.
Identification of Proliferating Cells in Human Gliomas Using the Monoclonal Antibody Ki-67 (1988)

Ki-67 is a monoclonal antibody directed against a nuclear antigen present only in proliferating cells in the G1, S, G2, and M phases of the cell cycle. Fifty-one frozen glioma specimens were stained with Ki-67 using the avidin-biotin immunoperoxidase system. For each tumor, six different randomly selected fields were examined. The percentage of Ki-67-positive cells in the total number of cells in the five fields counted with counterstaining has been calculated. The areas of necrosis and the vascular endothelial cells when they were distinguishable were not included in the calculation. The indices determined on this material ranged from 0% to 4.5% (mean, 1.0; SD, 1.5) for 16 low grade astrocytomas; from 0.7% to 7.4% (mean, 3.5; SD, 2.2) for 8 anaplastic astrocytomas; and from 1.7% to 32.2% (mean, 11.1; SD, 8.2) for 27 glioblastomas. The differences among the means of each group are statistically significant. Five patients with malignant gliomas with an index of less than 2.5 had survival times of more than 40 weeks. These results show that the Ki-67 index of proliferating cells in human gliomas correlates with the usual histological classification of these tumors. There is a potential interest in using this technique in routine histopathology because it is simple and more rapid than the classic methods of evaluation of proliferating cells.
CpG methylation of an endogenous retroviral enhancer inhibits transcription factor binding and activity. (1991)

The endogenous retrovirus, intracisternal A-particle (IAP), is expressed at unique stages during murine embryogenesis and is also activated during the in vitro differentiation of F9 cells. We have examined the DNA elements and protein factors that control IAP expression during F9 differentiation. In the present study an IAP upstream enhancer (IUE) is identified by transient transfection assays and found to be active in both undifferentiated and differentiated cells. Further analyses reveal that a ubiquitous 65 kDa protein factor, the IUE binding protein (IUEB), binds with the IUE. Site-specific methylation within the IUEB binding site strongly inhibits both IUEB binding and IUE transcriptional activity, suggesting that methylation may regulate IUE function and IAP expression.
Open outcry and electronic trading in futures exchanges (1999)

Despite the efficiency gains that accompany automation, most large futures exchanges have been reluctant to move away from the traditional trading floor, citing early evidence that open outcry exchanges were more liquid than electronic exchanges. More recent studies, however, suggest that electronic trading is superior to open outcry in many respects, including liquidity. In this article, the author compares the twotrading systems. Although many exchanges are shifting towards electronic trading, there are still several obstacles to this transition. But as technology rapidly reduces the cost of automation and increases the demand for global 24-hour trading, a worldwide transition to electronic order-matching will likely be the next important milestone for futures exchanges. Less-automated exchanges (including the Canadian futures exchanges) will undoubtedly continue to study and promote automation in order to keep pace with technological innovations.