gebhart/patrepeval huggingface dataset:
Basic Science Review: Current Insights on the Biology and Clinical Aspects of VEGF Regulation (2008)

Vascular endothelial growth factor (VEGF) is a key molecule that orchestrates the formation and function of vascular networks. Impaired regulation of angiogenesis is implicated in a number of pathologic states. For instance, neoplasias exhibit uncontrolled angiogenesis, whereas ischemia and states of vascular insufficiency involve reduced VEGF activity. As the role of VEGF has been elucidated in these disease processes, its therapeutic role has been developed. The Food and Drug Administration has approved several anti-VEGF agents for treating colorectal, lung, and kidney cancer. VEGF-inducing agents have also been used experimentally to induce angiogenesis in patients with critical limb ischemia. As more knowledge is gathered about the biology of VEGF and its receptors, there is greater promise for therapeutic modulation of VEGF expression. The purpose of this review is to describe the various therapeutic and biologic factors that regulate the expression of VEGF.
Low-voltage operation of a pentacene field-effect transistor with a polymer electrolyte gate dielectric (2005)

Large operating voltages are often required to switch organic field-effect transistors (OFETs) on and off because commonly used gate dielectric layers provide low capacitive coupling between the gate electrode and the semiconductor. We present here a pentacene OFET gated by a solution-deposited polymer electrolyte film in which the current was modulated over four orders of magnitude using gate voltages less than 2V. A subthreshold slope of 180mV per decade of current was observed during transistor turn on at a source-drain bias of −1V; the estimated dielectric layer specific capacitance was 5μF∕cm2. Sweep rate-dependent hysteresis may be attributed to a combination of ion migration and charge carrier trapping effects. Strategies to improve switching speeds for polymer electrolyte-gated OFETs are also discussed.
Synthesis and redox chemistry of octaethylporphyrin complexes of ruthenium(II) and ruthenium(III) (1983)

The syntheses and characterization of some new octaethylporphyrin complexes of ruthenium(II) and ruthenium(III) are described; the complexes are Ru(OEP)(P″Bu 3 ) 2 , Ru(OEP)(CO)L (L = PPh 3 , P″Bu 3 ), [Ru(OEP)(P″Bu 3 ) 2 ]Br, and Ru(OEP)(P″Bu 3 )Br, where OEP is the dianion of octaethylporphyrin. The Ru(OEP)(CO)EtOH complex, 1, which reversibly loses the ethanol ligand in CH 2 Cl 2 solution, undergoes a one-equivalent oxidation at the porphyrin ligand to generate the cation-radical [Ru(OEP) •+ (CO)] + ; a purple species of 2 A 2u ground state, produced electrochemically in perchlorate media, can coordinate bromide to generate a green 2 A 1u ground state species that also results from oxidation of 1 using bromine. Coordination of pyridine to [Ru(OEP) •+ (CO)] + yields the Ru(OEP) •+ (CO)py species that can also be formed by electrochemical oxidation of Ru(OEP)(CO)py. Addition of tertiary phosphines (PR 3 ) to the cation-radical carbonyl species can lead to formation of [Ru(OEP)(PR 3 ) 2 ] + , via an internal electron transfer process from Ru(II) to the OEP •+ that appears to be triggered by loss of the CO ligand. A reversible one-electron electrochemical oxidation of Ru(OEP)(P″Bu 3 ) 2 at 0.03 V (vs. Ag/AgCl) in CH 2 Cl 2 also gives the ruthenium(III) biphosphine cation, while a further one-electron oxidation at 1.2 V generates [Ru(OEP) •+ (P″Bu 3 ) 2 ] 2+ , a ruthenium(III) π-cation radical characterized by esr. The [Ru(OEP)(P″Bu 3 ) 2 ]Br complex decomposes in the solid state to a mixture of Ru(OEP)(P″Bu 3 )Br, formed together with free phosphine via an intramolecular ligand exchange, and Ru(OEP)(P″Bu 3 ) 2 , formed by reduction of the initial ionic ruthenium(III) cation with the phosphine that appears as [P″Bu 3 Br]Br.
New Thiophene-Linked Conjugated Poly(azomethine)s:  Theoretical Electronic Structure, Synthesis, and Properties (2005)

We report a joint theoretical and experimental study of several new thiophene-based poly(azomethine)s. Hybrid density functional theory (DFT) method was used to calculate the optimized geometry and electronic structure of poly(azomethine)s. Theoretical band gaps of the new thiophene-based poly(azomethine)s were in the range 2.33−2.67 eV, which are smaller than that of the phenylene-based polymer. The variation of the backbone ring (fluorene, carbazole, or naphthalene) or donor/acceptor side group on the phenylene ring significantly affected the dihedral angles and resulted in the variation of electronic properties (ionization potential, electron affinity, and band gap) of the poly(azomethine)s. Five soluble new conjugated poly(azomethine)s derived from the polymerization of 2,5-diformyl-3-hexylthiophene (DFHT) with various diamines were prepared and characterized. The optical and electrochemical band gaps of the polymer films were in the ranges 2.21−2.28 and 2.13−2.24 eV, respectively. The trend of the effect of the backbone ring or side chain on the experimental electronic properties is in good agreement with the theoretical results. Our study demonstrates how the electronic properties of conjugated poly(azomethine)s can be tuned by the backbone ring or side group, which could be important for electronic or optoelectronic applications of the materials.
Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology (2013)

A bottleneck in our capacity to rationally and predictably engineer biological systems is the limited number of well-characterized genetic elements from which to build. Current characterization methods are tied to measurements in living systems, the transformation and culturing of which are inherently time-consuming. To address this, we have validated a completely in vitro approach for the characterization of DNA regulatory elements using Escherichia coli extract cell-free systems. Importantly, we demonstrate that characterization in cell-free systems correlates and is reflective of performance in vivo for the most frequently used DNA regulatory elements. Moreover, we devise a rapid and completely in vitro method to generate DNA templates for cell-free systems, bypassing the need for DNA template generation and amplification from living cells. This in vitro approach is significantly quicker than current characterization methods and is amenable to high-throughput techniques, providing a valuable tool for rapidly prototyping libraries of DNA regulatory elements for synthetic biology.
A real-time control framework for smart power networks with star topology (2013)

Real-time price-based control is expected to play a key role in the operation of the future power network. Recently developed price-based control schemes, despite the fact that they are real-time, pay little attention to their interaction with the dynamics of the power network, focusing mainly on the solution of an appropriately formulated optimization problem. However, the coupling between the solution of the optimization problem and the dynamics of the network should not be ignored as this could result in instability with disastrous consequences. In this paper, we present a decentralized feedback architecture that considers the interaction between the dynamics of the power market and network, and implements real-time control for power networks with star topology. Motivated by optimization decomposition methods, we design a possible control scheme: we first formulate a constrained Optimal Power Flow (OPF) problem, then use a primal-dual decomposition approach to design a dynamic feedback controller for the power network and prove the asymptotic stability of the overall system in a scalable fashion. With the proposed controller, the operation of the network is completely decentralized that all decisions are made locally. Numerical investigations illustrate the performance of the controller.
Olefin synthesis with organic phosphonate carbanions (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOlefin synthesis with organic phosphonate carbanionsJohn Boutagy and Richard ThomasCite this: Chem. Rev. 1974, 74, 1, 87–99Publication Date (Print):February 1, 1974Publication History Published online1 May 2002Published inissue 1 February 1974https://pubs.acs.org/doi/10.1021/cr60287a005https://doi.org/10.1021/cr60287a005research-articleACS PublicationsRequest reuse permissionsArticle Views5132Altmetric-Citations537LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Topotecan Versus Cyclophosphamide, Doxorubicin, and Vincristine for the Treatment of Recurrent Small-Cell Lung Cancer (1999)

Topotecan was at least as effective as CAV in the treatment of patients with recurrent SCLC and resulted in improved control of several symptoms.
Imaging of the Bowel Wall Computed Tomography and Fat Density Oral-Contrast Agent in an Animal Model (1986)

In this study, we reassessed the problems encountered in computed tomographic (CT) examinations performed with conventional bowel preparations, and developed a fat density oral contrast in dogs. Conventional high-density agents, water, fat (negative) density, and air were administered using a nasogastric tube to eight dogs (25 separate CT scans). Optimal and consistent identification of the gastrointestinal (GI) tract and mural visualization were achieved with 400 ml of 12.5% to 50% corn oil emulsions administered in four hourly divided doses. Mild diarrhea was observed with the 50% concentration only, but no untoward effect was noted clinically with 25% and 12.5% emulsions. Mixing the negative (fat) density oral contrast with the GI contents produced conditions optimal for high-CT contrast resolution of the GI wall. Standard intravenous administration of iodinated contrast agent enhanced mural visualization and, in conjunction with dynamic scanning, time density curves. This suggests that vascular perfusion could be portrayed. This animal model may be used for the experimental evaluation of a number of GI abnormalities, including ischemic, neoplastic, and inflammatory conditions.
Essential Role for the C5a Receptor in Regulating the Effector Phase of Synovial Infiltration and Joint Destruction in Experimental Arthritis (2002)

A characteristic feature of rheumatoid arthritis is the abundance of inflammatory cells in the diseased joint. Two major components of this infiltrate are neutrophils in the synovial fluid and macrophages in the synovial tissue. These cells produce cytokines including tumor necrosis factor alpha and other proinflammatory mediators that likely drive the disease through its effector phases. To investigate what mechanisms underlie the recruitment of these cells into the synovial fluid and tissue, we performed expression analyses of chemoattractant receptors in a related family that includes the anaphylatoxin receptors and the formyl-MetLeuPhe receptor. We then examined the effect of targeted disruption of two abundantly expressed chemoattractant receptors, the receptors for C3a and C5a, on arthritogenesis in a mouse model of disease. We report that genetic ablation of C5a receptor expression completely protects mice from arthritis.
A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes (2002)

A general approach is described for controlling the RNA-cleaving activity of nucleic acid enzymes (ribozymes and DNAzymes) via the use of oligonucleotide effectors (regulators). In contrast to the previously developed approaches of allosteric and facilitator-mediated regulation of such enzymes, this approach, called 'expansive' regulation, requires that the regulator bind simultaneously to both enzyme and substrate to form a branched three-way complex. Such three-way enzyme-substrate-regulator complexes are catalytically competent relative to the structurally unstable enzyme-substrate complexes. Using the 8-17 and bipartite DNAzymes and the hammerhead ribozyme as model systems, 20- to 30-fold rate enhancements were achieved in the presence of regulators of engineered variants of the above three enzymes, even under unoptimized conditions. Broadly, using this approach ribozyme and DNAzyme variants that are amenable to regulation by oligonucleotide effectors can be designed even in the absence of any knowledge of the folded structure of the relevant ribozyme or DNAzyme. Expansive regulation therefore represents a new and potentially useful technology for both the regulation of nucleic acid enzymes and the detection of specific RNA transcripts.
Absence of asparagine-linked oligosaccharides from glycoprotein D of herpes simplex virus type 1 results in a structurally altered but biologically active protein (1991)

Glycoprotein D (gD) of herpes simplex virus contains three utilized sites (Asn-X-Ser/Thr) for addition of asparagine-linked carbohydrates (N-CHO). Previously, we used oligonucleotide-directed mutagenesis to alter serine or threonine residues to alanine at each N-CHO addition site. Studies with monoclonal antibodies showed that a mutant protein lacking all three sites (now designated AAA) was structurally altered because of the amino acid change at residue 96 as well as the absence of the N-CHO. In this study, we constructed additional single mutations at site 1 (residues 94 and 96) and found that in most cases, the amino acid change itself adversely affected the conformation of gD. However, changing asparagine 94 to glutamine (Q) at site 1 had the least effect on gD. We constructed a second triple mutant, QAA, which lacked all three N-CHO signals. The antigenic conformation of QAA was similar to that of gD produced in the presence of tunicamycin (TM-gD). However, binding of MAbs to the AAA protein or to single mutants altered at site 1 was reduced compared with TM-gD. Wild-type gD and QAA proteins were equally susceptible to digestion by trypsin or Staphylococcus aureus V8 protease. In contrast, the AAA protein was more sensitive to trypsin but less sensitive to V8, again suggesting conformational alterations of the AAA protein. Despite what appeared to be large changes in structure, each mutant complemented the infectivity of a virus lacking gD (F-gD beta). We conclude that the N-CHO and amino acids at N-CHO site 1 play an important role in forming and/or maintaining gD structure, but none of the N-CHO are required for gD to function in the complementation assay.
Site‐Specific Protein Bioconjugation via a Pyridoxal 5′‐Phosphate‐Mediated N‐Terminal Transamination Reaction (2010)

The covalent attachment of chemical groups to proteins is a critically important tool for the study of protein function and the creation of protein-based materials. Methods of site-specific protein modification are necessary for the generation of well defined bioconjugates possessing a new functional group in a single position in the amino acid sequence. This article describes a pyridoxal 5'-phosphate (PLP)-mediated transamination reaction that is specific for the N-terminus of a protein. The reaction oxidizes the N-terminal amine to a ketone or an aldehyde, which can form a stable oxime linkage with an alkoxyamine reagent of choice. Screening studies have identified the most reactive N-terminal residues, facilitating the use of site-directed mutagenesis to achieve high levels of conversion. Additionally, this reaction has been shown to be effective for a number of targets that are not easily accessed through heterologous expression, such as monoclonal antibodies. Curr. Protoc. Chem. Biol. 2:125-134 © 2010 by John Wiley & Sons, Inc.
Characteristics of Cation Binding to the I Domains of LFA-1 and MAC-1 (1998)

The crystal structures of the I domains of integrins MAC-1 (alphaM beta2; CD11b/CD18) and LFA-1 (alphaL beta2; CD11a/CD18) show that a single conserved cation-binding site is present in each protein. Purified recombinant I domains have intrinsic ligand binding activity, and in several systems this interaction has been demonstrated to be cation-dependent. It has been proposed that the I domain cation-binding site represents a general metal ion-dependent adhesion motif utilized for binding protein ligands. Here we show that the purified recombinant I domain of LFA-1 (alphaLI) binds cations, but with significantly different characteristics compared with the I domain of MAC-1 (alphaMI). Both alphaLI and alphaMI bind 54Mn2+ in a conformation-dependent manner, and in general, cations with charge and size characteristics similar to Mn2+ most effectively inhibit 54Mn2+ binding. Surprisingly, however, physiological levels of Ca2+ (1-2 mM) inhibited 54Mn2+ binding to purified alphaLI, but not to alphaMI. Using 45Ca2+ and 54Mn2+ in direct binding studies, the dissociation constants (KD) for the interactions between these cations and alphaLI were estimated to be 5-6 x 10(-5) and 1-2 x 10(-5) M, respectively. Together with the available structural information, the data suggest differential affinities for Mn2+ and Ca2+ binding to the single conserved site within alphaLI. Antagonism of LFA-1, but not MAC-1, -mediated cell adhesion by Ca2+ may be related to the Ca2+ binding activity of the LFA-1 I domain.
In Vitro and In Vivo Evaluations of Sodium Lauryl Sulfate and Dextran Sulfate as Microbicides against Herpes Simplex and Human Immunodeficiency Viruses (2000)

The efficacy of sodium lauryl sulfate (SLS), a sulfated anionic chaotropic surfactant, and dextran sulfate (DS), a polysulfated carbohydrate, against herpes simplex virus (HSV) and human immunodeficiency virus (HIV) infections was evaluated in cultured cells and in different murine models of HSV infection. Results showed that both SLS and DS were potent inhibitors of the infectivities of various HSV-1 and HSV-2 strains. Pretreatment of HIV-1 (strain NL4-3) with SLS also reduced its infectivity to 1G5 cells. DS prevented the binding of HSV to cell surface receptors and therefore its entry into cells. Pretreatment of HSV-1 (strain F) with 50 microM SLS resulted in a complete loss of virus infectivity to Vero cells. However, viruses were able to enter into cells and to produce in the nuclei capsid shells devoid of a DNA core. The amount of the glycoprotein D gene produced in these cells remained unchanged compared to controls, suggesting that SLS could interfere with the maturation of the virus. At a higher SLS concentration (100 microM), HSV was highly damaged by SLS pretreatment and only a few viral particles could enter into cells to produce abnormal capsids. Although DS was a more potent inhibitor of HSV infectivity in vitro, it was unable to provide any protection in murine models of HSV infection. However, SLS conferred a complete protection of animals infected cutaneously with pretreated viruses. In addition, skin pretreatment of mice with a polymer formulation containing SLS completely prevented the development of cutaneous lesions. More interestingly, intravaginal pretreatment of mice with SLS in a buffered solution also completely protected against lethal HSV-2 infection. Taken together, our results suggest that SLS could thus represent a candidate of choice as a microbicide to prevent the sexual transmission of HIV, HSV, and possibly other pathogens that cause sexually transmitted diseases.
A source-level dynamic analysis methodology and tool for high-level synthesis (1997)

This paper presents a novel source-level dynamic analysis methodology and tool for High-Level Synthesis (HLS). It not only for the first time enables HLS to offer source-level design debugging on the `synthesized' RTL designs, but also allows the designer to analyze their dynamic characteristics, such as resource utilization, power consumption, etc., at the algorithmic (source) level. This technology has been proven in the industry as the critical element for successfully designing a microcontroller with 300+ instructions with Matisse, an interactive HLS system. Additionally, we demonstrate the use of this technology for architectural power optimization.
Nameprep: A Stringprep Profile for Internationalized Domain Names (IDN) (2003)

This document describes how to prepare internationalized domain name (IDN) labels in order to increase the likelihood that name input and name comparison work in ways that make sense for typical users throughout the world. This profile of the stringprep protocol is used as part of a suite of on-the-wire protocols for internationalizing the Domain Name System (DNS).
Cinchona-derived organocatalysts for asymmetric carbon-carbon bond formation (2007)

Cinchona alkaloids bearing a hydrogen bond donor on the C6’ position have been recently shown to be powerful bifunctional organocatalysts for enantioselective transformations. A brief overview of the field of asymmetric organocatalysis and some general information on Cinchona alkaloids are followed by a review of the literature on this emerging subclass of organocatalysts, highlighting the applications in the synthesis of natural products.
Reconstitution of Cyclin D1-Associated Kinase Activity Drives Terminally Differentiated Cells into the Cell Cycle (2001)

Terminal cell differentiation entails definitive withdrawal from the cell cycle. Although most of the cells of an adult mammal are terminally differentiated, the molecular mechanisms preserving the postmitotic state are insufficiently understood. Terminally differentiated skeletal muscle cells, or myotubes, are a prototypic terminally differentiated system. We previously identified a mid-G(1) block preventing myotubes from progressing beyond this point in the cell cycle. In this work, we set out to define the molecular basis of such a block. It is shown here that overexpression of highly active cyclin E and cdk2 in myotubes induces phosphorylation of pRb but cannot reactivate DNA synthesis, underscoring the tightness of cell cycle control in postmitotic cells. In contrast, forced expression of cyclin D1 and wild-type or dominant-negative cdk4 in myotubes restores physiological levels of cdk4 kinase activity, allowing progression through the cell cycle. Such reactivation occurs in myotubes derived from primary, as well as established, C2C12 myoblasts and is accompanied by impairment of muscle-specific gene expression. Other terminally differentiated systems as diverse as adipocytes and nerve cells are similarly reactivated. Thus, the present results indicate that the suppression of cyclin D1-associated kinase activity is of crucial importance for the maintenance of the postmitotic state in widely divergent terminally differentiated cell types.