gebhart/patrepeval huggingface dataset:
Synthesis and Antisense Properties of Fluoro Cyclohexenyl Nucleic Acid (F-CeNA), a Nuclease Stable Mimic of 2′-Fluoro RNA (2012)

We report the design and synthesis of 2'-fluoro cyclohexenyl nucleic acid (F-CeNA) pyrimidine phosphoramidites and the synthesis and biophysical, structural, and biological evaluation of modified oligonucleotides. The synthesis of the nucleoside phosphoramidites was accomplished in multigram quantities starting from commercially available methyl-D-mannose pyranoside. Installation of the fluorine atom was accomplished using nonafluorobutanesulfonyl fluoride, and the cyclohexenyl ring system was assembled by means of a palladium-catalyzed Ferrier rearrangement. Installation of the nucleobase was carried out under Mitsunobu conditions followed by standard protecting group manipulations to provide the desired pyrimidine phosphoramidites. Biophysical evaluation indicated that F-CeNA shows behavior similar to that of a 2'-modified nucleotide, and duplexes with RNA showed slightly lower duplex thermostability as compared to that of the more rigid 3'-fluoro hexitol nucleic acid (FHNA). However, F-CeNA modified oligonucleotides were significantly more stable against digestion by snake venom phosphodiesterases (SVPD) as compared to unmodified DNA, 2'-fluoro RNA (FRNA), 2'-methoxyethyl RNA (MOE), and FHNA modified oligonucleotides. Examination of crystal structures of a modified DNA heptamer duplex d(GCG)-T*-d(GCG):d(CGCACGC) by X-ray crystallography indicated that the cyclohexenyl ring system exhibits both the (3)H(2) and (2)H(3) conformations, similar to the C3'-endo/C2'-endo conformation equilibrium seen in natural furanose nucleosides. In the (2)H(3) conformation, the equatorial fluorine engages in a relatively close contact with C8 (2.94 Å) of the 3'-adjacent dG nucleotide that may represent a pseudo hydrogen bond. In contrast, the cyclohexenyl ring of F-CeNA was found to exist exclusively in the (3)H(2) (C3'-endo like) conformation in the crystal structure of the modified A-form DNA decamer duplex [d(GCGTA)-T*-d(ACGC)](2.) In an animal experiment, a 16-mer F-CeNA gapmer ASO showed similar RNA affinity but significantly improved activity compared to that of a sequence matched MOE ASO, thus establishing F-CeNA as a useful modification for antisense applications.
Anticonvulsant and proconvulsant actions of 2‐deoxy‐d‐glucose (2010)

Although 2-DG protects against seizures in the 6-Hz seizure test, it promotes seizures in some other models. The proconvulsant action may relate to reduced glucose uptake, whereas the anticonvulsant action may require inhibition of glycolysis and shunting of glucose metabolism through the pentose phosphate pathway.
Ultra Performance Liquid Chromatography Mass Spectrometry (2014)

Due to its high sensitivity and selectivity, liquid chromatography-mass spectrometry (LC-MS) is a powerful technique. It is used for various applications, often involving the detection and identification of chemicals in a complex mixture. Ultra Performance Liquid Chromatography Mass Spectrometry: Evaluation and Applications in Food Analysis present
Small, Water-Soluble, Ligand-Stabilized Gold Nanoparticles Synthesized by Interfacial Ligand Exchange Reactions (2000)

A general synthetic approach leading to well-defined, water-soluble gold nanoparticles is described that involves a simple, interfacial ligand exchange reaction between a 1.4 nm phosphine-passivated precursor and an anionic or cationic thiol-containing ligand. We demonstrate the utility of this route by synthesizing water-soluble gold nanoparticles that are stabilized by either an anionic ligand (2-mercaptoethanesulfonate), a cationic ligand (2-(dimethylamino)ethanethiol hydrochloride), or a mixture of both ionic and phosphine ligands. Although the course of the ligand exchange process depends on the nature of the incoming ligand, each of these nanoparticle products retain the small core size and narrow size distribution of the starting particle (1.4 ± 0.4 nm). The stabilities of these nanoparticles to elevated temperature, extremes of pH, and added salt are reported and found to depend on the nature of the exposed headgroups on the ligand shell. Salt-induced aggregation is not observed in any of the cases investigated. Resistance to aggregation is attributed to the protective nature of the ligand shell.
Specific Diagnosis of Progressive Multifocal Leukoencephalopathy by Polymerase Chain Reaction (1994)

Using polymerase chain reaction (PCR), 34 cerebrospinal fluid (CSF) samples from 28 patients with progressive multifocal leukoencephalopathy (PML) were analyzed. As controls, 116 samples were evaluated from 82 human immunodeficiency virus type 1 (HIV-1)-infected patients and 1 HIV-1-negative patient. Of the HIV-1-positive patients, 23 had cerebral toxoplasmosis, 10 had HIV leukoencephalopathy, and 49 had other neurologic complications. Detection of JC virus (JCV) DNA in CSF was increased 10-fold by the addition of carrier DNA before phenol-chloroform-isoamyl alcohol extraction. The primer pair JC 26/29, from the VP1/large T region, had a limit of detection of 10(5) JCV DNA molecules/100 microL. The primer pair JC 36/39, located in the large T gene region, had a 100-fold lower limit of detection. With JC 26/29, the sensitivity was 43% (12/28) and specificity was 100%. Using JC 36/39, sensitivity increased to 82% (23/28), and false-positive results were not observed. Diagnosis of PML is greatly aided by PCR analysis of CSF.
Generation and Characterization of an IGFBP-7 Antibody: Identification of 31kD IGFBP-7 in Human Biological Fluids and Hs578T Human Breast Cancer Conditioned Media (1997)

The cDNA encoding mac25 (IGFBP-7) was first derived from mRNA isolated from leptomeningial and senescent human mammary epithelial cells (1, 2). The open reading frame was shown to predict a protein with homology to the amino terminus of the IGF binding proteins, (IGFBP)1-6. Studies in our laboratory have shown that baculovirus generated mac25 binds IGF-I and-II in a specific manner, leading to the renaming of mac25 as IGFBP-7 (3). Further studies at the cellular level, to identify the involvement of IGFBP-7 in IGF regulation and cell growth, require a specific antibody against the protein, which has yet to be identified in either culture cells or in vivo. We have now generated three polyclonal antibodies against the purified baculovirus peptide, and, by western immunoblots and immunoprecipitation, demonstrated the existence of a specific 31,000 dalton protein. It is a secreted protein and can be identified in the conditioned media of Hs578T breast cancer cells, as well as in normal human urine, cerebrospinal fluid, and amniotic fluid. Subsequent studies with these antibodies should help elucidate the physiological role(s) of this protein.
Design for suppression of gate-induced drain leakage in LDD MOSFETs using a quasi-two-dimensional analytical model (1992)

A systematic study of gate-induced drain leakage (GIDL) in single-diffusion drain (SD), lightly doped drain (LDD), and fully gate-overlapped LDD (GOLD) NMOSFETs is described. Design curves quantifying the GIDL dependence on gate oxide thickness, phosphorus dose, and spacer length are presented. In addition, a new, quasi-2-D analytical model is developed for the electric field in the gate-to-drain overlap region. This model successfully explains the observed GIDL dependence on the lateral doping profile of the drain. Also, a technique is proposed for extracting this lateral doping profile using the measured dependence of GIDL current on the applied substrate bias. Finally, the GIDL current is found to be much smaller in lightly doped LDD devices than in SD or fully overlapped LDD devices, due to smaller vertical and lateral electric fields. However, as the phosphorus dose approaches 10/sup 14//cm/sup 2/, the LDD and fully overlapped LDD devices exhibit similar GIDL current.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure-Based Design, Synthesis, and Biological Evaluation of Novel Pyrrolyl Aryl Sulfones:  HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors Active at Nanomolar Concentrations (2000)

Pyrrolyl aryl sulfones (PASs) have been recently reported as a new class of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) inhibitors acting at the non-nucleoside binding site of this enzyme (Artico, M.; et al. J. Med. Chem. 1996, 39, 522-530). Compound 3, the most potent inhibitor within the series (EC(50) = 0.14 microM, IC(50) = 0.4 microM, and SI > 1429), was then selected as a lead compound for a synthetic project based on molecular modeling studies. Using the three-dimensional structure of RT cocrystallized with the alpha-APA derivative R95845, we derived a model of the RT/3 complex by taking into account previously developed structure-activity relationships. Inspection of this model and docking calculations on virtual compounds prompted the design of novel PAS derivatives and related analogues. Our computational approach proved to be effective in making qualitative predictions, that is in discriminating active versus inactive compounds. Among the compounds synthesized and tested, 20 was the most active one, with EC(50) = 0.045 microM, IC(50) = 0.05 microM, and SI = 5333. Compared with the lead 3, these values represent a 3- and 8-fold improvement in the cell-based and enzyme assays, respectively, together with the highest selectivity achieved so far in the PAS series.
Testosterone and Other Anabolic Steroids as Cardiovascular Drugs (1999)

There has been much interest in the effect of sex hormones on cardiovascular risk factors and as a therapeutic modality in both men and women. In this article, testosterone is considered as a possible therapy for cardiovascular disease. It has been shown that the level of serum testosterone decreases in men as they age. Healthy men with low testosterone levels have increased cardiovascular risk factors, including high fasting and 2-hour plasma glucose, serum triglycerides, total cholesterol and low-density lipoprotein (LDL) cholesterol, and apo A-I lipoprotein. Injections of testosterone to raise the levels to midnormal range have been shown to decrease total cholesterol and LDL cholesterol, while increasing high-density lipoprotein (HDL) cholesterol. Testosterone affects the clotting system by increasing thromboxane A (2) receptor activity and platelet aggregability. Testosterone has also been shown to augment the fibrinolytic system and antithrombin III activity. In men, testosterone has been shown to have antianginal effects, and endogenous levels have an inverse relationship to systolic blood pressure. Testosterone can be given in oral, injectable, pellet, and transdermal patch forms. There may be a role in administering testosterone to return men to normal physiologic range who have low serum levels. This treatment increases the risk of prostatic cancer, benign prostatism, erythrocytosis, and edema. No long-term studies of the effects of long-term testosterone replacement have been undertaken, so it is difficult to recommend this treatment as yet, but it is being considered as a therapy for augmenting skeletal muscle strength in patients with congestive heart failure.
Packing C 60 in Boron Nitride Nanotubes (2003)

We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride nanotubes (BNNTs). For small-diameter BNNTs, the wire consists of a linear chain of C60 molecules.With increasing BNNT inner diameter, unusual C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) that are unknown for bulk or thin-film forms of C60.C60 in BNNTs thus presents a model system for studying the properties of dimensionally constrained "silo" crystal structures. For the linear-chain case, we have fused the C60 molecules to form a single-walled carbon nanotube inside the insulating BNNT.
Fast polymer integrated circuits (2002)

Using soluble polymers for the active layer and insulating layer, we report on a concept for the fabrication of fast integrated circuits based on p-type organic transistors only. Ring oscillators with frequencies above 100 kHz and propagation stage delays below 0.7 μs are presented. They show a very stable performance over time even without encapsulation, when stored and measured under ambient conditions. Regioregular poly(3-alkylthiophen) is used as the active semiconducting layer, a polymer blend as the insulator, a flexible polyester film as the substrate and metal electrodes. To enable vertical interconnects, the insulating layer is patterned.
Functional role of interleukin 1 beta (IL-1 beta) in IL-1 beta-converting enzyme-mediated apoptosis. (1996)

Prointerleukin-1 beta (pro-IL-1 beta) is the only known physiologic substrate of the interleukin-1 beta (IL-1 beta)-converting enzyme (ICE), the founding member of the ICE/ced-3 cell death gene family. Since secreted mature IL-1 beta has been detected after apoptosis, we investigated whether this cytokine, when produced endogenously, plays a role in cell death. We found that hypoxia-induced apoptosis can be inhibited by either the IL-1 receptor antagonist (IL-1Ra) or by neutralizing antibodies to IL-1 or to its type 1 receptor. IL-1Ra also inhibits apoptosis induced by trophic factor deprivation in primary neurons, as well as by tumor necrosis factor alpha in fibroblasts. In addition, during the G1/S phase arrest, mature IL-1 beta induces apoptosis through a pathway independent of CrmA-sensitive gene activity. We also demonstrate that Ice, when expressed in COS cells, requires the coexpression of pro-IL-1 beta for the induction of apoptosis, which is inhibited by IL-1Ra. Interestingly, we found that mature IL-1 beta has antiapoptotic activity when added exogenously before the onset of hypoxia, which we found is caused in part by its ability to downregulate the IL-1 receptor. Our findings demonstrate that pro-IL-1 beta is a substrate of ICE relevant to cell death, and depending on the temporal cellular commitment to apoptosis, mature IL-1 beta may function as a positive or negative mediator of cell death.
Cystic Pancreatic Lesions: A Simple Imaging-based Classification System for Guiding Management (2005)

Cystic lesions of the pancreas are increasingly being recognized due to the widespread use of cross-sectional imaging. The initial evaluation of a pancreatic cyst should be directed toward exclusion of a pseudocyst. Patients with pseudocysts generally have a history of acute or chronic pancreatitis, whereas those with cystic tumors most often lack such a history. Several types of cystic lesions are encountered in the pancreas. Because of morphologic overlap at imaging, accurate characterization of these lesions can be difficult. Computed tomography and magnetic resonance imaging are excellent modalities for both initial detection and characterization of cystic pancreatic lesions. An imaging classification system for these lesions has been proposed that is based on the morphologic features of the lesion. This system can be helpful in characterizing lesions, narrowing the differential diagnosis, and making decisions regarding the treatment of affected patients. Endoscopic ultrasonography-guided aspiration and biopsy is useful in cases that are indeterminate at cross-sectional imaging or that require observation.
Seed‐expressed fluorescent proteins as versatile tools for easy (co)transformation and high‐throughput functional genomics in Arabidopsis (2003)

We demonstrate that fluorescent proteins can be used as visual selection markers for the transformation of Arabidopsis thaliana by the floral dip method. Seed-specific expression of green fluorescent protein (GFP) variants, as well as DsRed, permits the identification of mature transformed seeds in a large background of untransformed seeds by fluorescence microscopy. In planta visualization of transformed seeds in siliques shows that susceptibility to floral dip transformation is limited to a small, defined window in flower development. In the competent stage, the random transformation of up to 25% of the seeds within a single silique may occur. The use of fluorescent proteins with different spectral characteristics allows a rapid identification and genetic analysis of seeds that have received multiple genes-of-interest in co-transformation experiments. The data reveal that co-transformation does not occur at random, since the co-transformed genes are integrated at a single genetic locus in approximately 70% of the cases. This genetic linkage of the co-transformed genes greatly simplifies metabolic pathway engineering by reverse genetics in Arabidopsis. Additional advantages of using visual selection instead of antibiotic resistance include a rapid identification of the effect of the T-DNA insertion or the transgene on seed development and/or germination. This technology, of tagging and identifying transformed seeds by fluorescence provides a novel high-throughput screening system with many potential applications in plant biotechnology.
Functionalized Poly(ethylene glycol)-Based Bioassay Surface Chemistry That Facilitates Bio-Immobilization and Inhibits Nonspecific Protein, Bacterial, and Mammalian Cell Adhesion (2007)

This paper describes a new bioassay surface chemistry that effectively inhibits non-specific biomolecular and cell binding interactions, while providing a capacity for specific immobilization of desired biomolecules. Poly(ethylene glycol) (PEG) as the primary component in nonfouling film chemistry is well-established, but the multicomponent formulation described here is unique in that it (1) is applied in a single, reproducible, solution-based coating step; (2) can be applied to diverse substrate materials without the use of special primers; and (3) is readily functionalized to provide specific attachment chemistries. Surface analysis data are presented, detailing surface roughness, polymer film thickness, and film chemistry. Protein non-specific binding assays demonstrate significant inhibition of serum, fibrinogen, and lysozyme adsorption to coated glass, indium tin oxide, and tissue culture polystyrene dishes. Inhibition of S. aureus and K. pneumoniae microbial adhesion in a microfluidic flow cell, and inhibition of fibroblast cell adhesion from serum-based cell culture is shown. Effective functionalization of the coating is demonstrated by directing fibroblast adhesion to polymer surfaces activated with an RGD peptide. Batch-to-batch reproducibility data are included. The in situ cross-linked PEG-based coating chemistry is unique in its formulation, and its surface properties are attractive for a broad range of in vitro bioassay applications.
Epoxy Resins (2004)

Abstract Epoxy resins are reactive intermediates used to produce a versatile class of thermosetting polymers. They are characterized by the presence of a three‐membered cyclic ether group commonly referred to as an epoxy group, 1,2‐epoxide, or oxirane. The most widely used epoxy resins are diglycidyl ethers of bisphenol A derived from bisphenol A and epichlorohydrin. The outstanding performance characteristics of the thermosets derived from bisphenol A epoxies are largely conveyed by the bisphenol A moiety (toughness, rigidity, and elevated temperature performance), the ether linkages (chemical resistance), and the hydroxyl and epoxy groups (adhesive agents). In addition to bisphenol A, other starting materials such as aliphatic glycols and both phenol and o ‐cresol novolacs are used to produce specialty resins. Epoxy resins may also include epoxide‐bearing compounds based on aromatic amine, triazine, and cycloaliphatic backbones. A variety of reagents have been described for converting the liquid and solid epoxy resins to the cured state, which is necessary for the development of the ultimate end‐use properties. The curing agents or hardeners are categorized as either catalytic or coreactive. Catalytic curing agents initiate resin homopolymerization, either cationic or anionic, as a consequence of using a Lewis acid or base in the curing process. Coreactive curing agents are polyfunctional compounds typically possessing active hydrogens that are employed up to stoichiometric quantities with epoxy resins. The important classes of coreactive curing agents include multifunctional amines and their amide derivatives, polyphenols, polymeric thiols, polycarboxylic acids, anhydrides, phenol–formaldehyde novolacs and resoles, and amino–formaldehyde resins. The largest single use of epoxy resins is in the protective coatings market where high corrosion resistance and adhesion to substrates are important. Epoxies have gained wide acceptance in protective coatings and in electrical and structural applications because of their exceptional combination of properties such as toughness, adhesion, chemical and thermal resistance, and good electrical properties.
Pseudohexagonal 2D DNA Crystals from Double Crossover Cohesion (2004)

Two-dimensional pseudohexagonal trigonal arrays have been constructed by self-assembly from DNA. The motif used is a bulged-junction DNA triangle whose edges and extensions are DNA double crossover (DX) molecules, rather than conventional DNA double helices. Experiments were performed to establish whether the success of this system results from the added stiffness of DX molecules or the presence of two sticky ends at the terminus of each edge. Removal of one sticky end precludes lattice formation, suggesting that it is the double sticky end that is the primary factor enabling lattice formation.
Pd-Pt Bimetallic Nanodendrites with High Activity for Oxygen Reduction (2009)

Controlling the morphology of Pt nanostructures can provide a great opportunity to improve their catalytic properties and increase their activity on a mass basis. We synthesized Pd-Pt bimetallic nanodendrites consisting of a dense array of Pt branches on a Pd core by reducing K2PtCl4 with L-ascorbic acid in the presence of uniform Pd nanocrystal seeds in an aqueous solution. The Pt branches supported on faceted Pd nanocrystals exhibited relatively large surface areas and particularly active facets toward the oxygen reduction reaction (ORR), the rate-determining step in a proton-exchange membrane fuel cell. The Pd-Pt nanodendrites were two and a half times more active on the basis of equivalent Pt mass for the ORR than the state-of-the-art Pt/C catalyst and five times more active than the first-generation supportless Pt-black catalyst.
Acquiring and pointing (2011)

Research literature has shown that pen tilt is a promising input modality in pen-based interaction. However, the human capability to control pen tilt has not been fully evaluated. This paper systematically investigates the human ability to perform discrete target selection tasks by varying the stylus' tilt angle through two controlled experiments: pen tilt target acquiring (Experiment 1) and tilt pointing (Experiment 2). Results revealed a decreasing power relationship between angular width and selection time in Experiment 1. The results of Experiment 2 confirmed that pen tilt pointing can be modeled by Fitts' law. Based on our quantitative analysis, we discuss the human ability to control pen tilt and the implications of pen tilt use. We also propose a taxonomy of pen tilt based interaction techniques and showcase a series of possible pen tilt technique designs.