gebhart/patrepeval huggingface dataset:
Direct Nitric Oxide Detection in Aqueous Solution by Copper(II) Fluorescein Complexes (2006)

A series of FL(n) (n = 1-5) ligands, where FL(n) is a fluorescein modified with a functionalized 8-aminoquinoline group as a copper-binding moiety, were synthesized, and the chemical and photophysical properties of the free ligands and their copper complexes were investigated. UV-visible spectroscopy revealed a 1:1 binding stoichiometry for the Cu(II) complexes of FL(1), FL(3), and FL(5) in pH 7.0 buffered aqueous solutions. The reactions of FL(2) or FL(4) with CuCl(2), however, appear to produce a mixture of 1:1 and 1:2 complexes, as suggested by Job's plots. These binding modes were modeled by the synthesis and X-ray crystal structure determination of Cu(II) complexes of 2-[(quinolin-8-ylamino)methyl]phenol (modL), employed as a surrogate of the FL(n) ligand family. Two kinds of crystals, [Cu(modL)(2)](BF(4))(2) and [Cu(2)(modL')(2)(CH(3)OH)](BF(4))(2) (modL' = 2-[(quinolin-8-ylamino)methyl]phenolate), were obtained. The structures suggest that one oxygen and two nitrogen atoms of the FL(n) ligands most likely bind to Cu(II). Introduction of nitric oxide (NO) to pH 7.0 buffered aqueous solutions of Cu(FL(n)) (1 microM CuCl(2) and 1 microM FL(n)) at 37 degrees C induces an increase in fluorescence. The fluorescence response of Cu(FL(n)) to NO is direct and specific, which is a significant improvement over commercially available small molecule-based probes that are capable of detecting NO only indirectly. The NO-triggered fluorescence increase of Cu(FL(5)) occurs by reduction of Cu(II) to Cu(I) with concomitant dissociation of the N-nitrosated fluorophore ligand from copper. Spectroscopic and product analyses of the reaction of the FL(5) copper complex with NO indicated that the N-nitrosated fluorescein ligand (FL(5)-NO) is the species responsible for fluorescence turn-on. Density functional theory (DFT) calculations of FL(5) versus FL(5)-NO reveal how N-nitrosation of the fluorophore ligand brings about the fluorescence increase. The copper-based probes described in the present work form the basis for real-time detection of nitric oxide production in living cells.
Alternating copolyfluorenevinyles with polynuclear aromatic moieties: Synthesis, photophysics, and electroluminescence (2007)

Abstract Three new copolymers, namely poly(fluorenevinylene‐ alt ‐naphthalenevinylene) ( N ), poly(fluorenevinylene‐ alt ‐anthracenevinylene) ( A ) and poly(fluorenevinylene‐ alt ‐pyrenevinylene) ( P ), were synthesized by Heck coupling of 9,9‐dihexyl‐2, 7‐divinylfluorene with a polynuclear aromatic dibromide. The 9,10‐disubstituted anthracene was obtained exclusively for A while N and P were obtained as a mixture of two isomers with predominant the 1,4‐disubstituted naphthalene and 1,8‐disubstituted pyrene, respectively. The polymers were soluble in common organic solvents and decomposed above 370 °C. Their glass transition temperature increased from 58 to 110 °C by increasing the number of the phenyl rings of the polynuclear aromatic moiety. Rather high‐efficiency blue and blue‐greenish photoluminescence (PL) of these copolymers in solution was largely decreased in their films, indicating the presence of concentration quenching in the solid state. The OLED using these polymers demonstrated green EL in the case of copolymers N and A , and red EL in the P derivative with η EL = 0.26–0.31%. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4661–4670, 2007
A TURNKEY 1.5 µm PICOSECOND Er/Yb FIBER LASER (1993)

We report a "turn-key" picosecond Er/Yb fiber laser for 1.5 µm telecommunications applications. Mode-locking of Er fiber lasers1-3 has been demonstrated using active modulators, saturable absorbers, polarization switching, and non-linear amplifying loop mirrors. Here we report a "turn-key" passively mode-locked 1.5 µm fiber laser employing Er/Yb co-doped fiber pumped by a Nd:YLF (1.053 um) microlaser that was pumped by a diode laser. The mode-locking was achieved using a InGaAsP saturable absorber deposited on a InP substrate. The laser generates stable pulses of 0.5 to 2ps duration and instantly becomes operational every time the power switch is turned-on. Currently available picosecond and sub-picosecond duration lasers require highly skilled personnel to operate the lasers because of too many optical alignments.
PhoA gene fusions in Legionella pneumophila generated in vivo using a new transposon, MudphoA (1992)

To enable effective use of phoA gene fusions in Legionella pneumophila, we constructed MudphoA, a derivative of the mini-Mu phage Mu dII4041, which is capable of generating gene fusions to the Escherichia coli alkaline phosphatase gene (EC 3.1.3.1). Although an existing fusion-generating transposon, TnphoA, has been a useful tool for studying secreted proteins in other bacteria, this transposon and other Tn5 derivatives transpose inefficiently in Legionella pneumophila, necessitating the construction of a more effective vector for use in this pathogen. Using MudphoA we generated fusions to an E. coli gene encoding a periplasmic protein and to an L. pneumophila gene encoding an outer membrane protein; both sets of fusions resulted in alkaline phosphatase activity. We have begun to use MudphoA to mutate secreted proteins of L. pneumophila specifically, since this subset of bacterial proteins is most likely to be involved in host-bacterial interactions. This modified transposon may be useful for studies of other bacteria that support transposition of Mu, but not Tn5, derivatives.
Altered Stoichiometry of FKBP12.6 Versus Ryanodine Receptor as a Cause of Abnormal Ca 2+ Leak Through Ryanodine Receptor in Heart Failure (2000)

An abnormal Ca(2+) leak through the RyR is present in heart failure, and this leak is presumably caused by a partial loss of RyR-bound FKBP12.6 and the resultant conformational change in RyR. This abnormal Ca(2+) leak might possibly cause Ca(2+) overload and consequent diastolic dysfunction, as well as systolic dysfunction.
ODYSSEY FH I and FH II: 78 week results with alirocumab treatment in 735 patients with heterozygous familial hypercholesterolaemia (2015)

Cinicaltrials.gov (identifiers: NCT01623115; NCT01709500).
A theoretical analysis of the role of defects in the adsorption of hydrogen sulfide on graphene (2013)

Density functional theory studies are reported to analyze the interaction between hydrogen sulfide (H2S) and graphene. The electron-ion interactions have been modeled using ultrasoft pseudopotentials and the exchange-correlation energies have been approximated by the method of the generalized gradient approximation in the parameterization of Perdew-Burke-Ernzerhof. Three graphene structures, one intrinsic and two with defects (vacancy and sustitution), and four H2S concentrations have been studied. The optimal geometries, binding energies, density of states (DOS) and charge density were obtained. In order to study the adsorption process three high symmetry sites were considered, namely, top, bridge, and center. The preferential adsorption structure corresponds to the center site in a physical way. The DOS of graphene-H2S systems shows a metallic behavior which coincides with the behavior of the isolated graphene. The geometrical structure of the graphene and the hydrogen sulfide remains unchanged.
Inhibition of autoproteolytic activation of interstitial procollagenase by recombinant metalloproteinase inhibitor MI/TIMP-2 (1991)

The purification and cloning of a novel metalloproteinase inhibitor (MI or TIMP-2) related to tissue inhibitor of metalloproteinases (TIMP) has been recently described by our laboratory (DeClerck, Y.A., Yean, T. D., Ratzkin, B.J., Lu, H.S., and Langley, K.E. (1989) J. Biol. Chem. 264, 17445-17453; Boone, T.C., Johnson, M.J., DeClerck, Y.A., and Langley, K.E. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 2800-2804). We have transfected Chinese hamster ovary cells with a vector containing human MI/TIMP-2 cDNA and purified recombinant-derived MI/TIMP-2 (rMI/rTIMP-2) from the conditioned medium of such cells. We have investigated the inhibitory activity of rMI/rTIMP-2 toward rabbit fibroblast interstitial collagenase. The inhibition of activated collagenase by rMI/rTIMP-2 is stoichiometric and consistent with the formation of a 1:1 molar ratio complex. In addition to blocking the activated enzyme, rMI/rTIMP-2 inhibits the conversion of 52-kDa procollagenase to the 42-kDa active enzyme initiated by organomercurials. When plasmin is used as activator, rMI/rTIMP-2 does not inhibit the plasmin-mediated conversion of the 52-kDa proenzyme to the 46-kDa inactive intermediate but blocks further conversion of the 46-kDa intermediate to the 42-kDa active enzyme. The data indicate that rMI/rTIMP-2 blocks the autoproteolytic activation of procollagenase. Also, rMI/rTIMP-2 forms complexes with the 52-kDa procollagenase, the 46-kDa intermediate, and with the 42-kDa activated enzyme which are stable to sodium dodecyl sulfate (SDS), such that the complexes can be visualized by SDS-polyacrylamide gel electrophoresis. It appears that the formation of a SDS-stable complex with procollagenase requires an initial conformational change of the procollagenase brought about by organomercurials or by plasmin cleavage. The data suggest that MI/TIMP-2 may be able to control the extracellular action of certain metalloproteinases not only at the level of the activated enzyme but also at the level of proenzyme activation.
Experience with collaborative conferencing applications in Named-Data Networks (2013)

We propose a hybrid approach for conference applications for Named-Date Networks (NDN). This hybrid approach combines a participant-driven, distributed server-based approach for conference control and management with a server-less approach for media forwarding. The participant-driven, distributed server-based approach provides robust and efficient conference control and management that is resilient to single point of failure and can scale dynamically with any conference size. The server-less media forwarding eliminates traffic concentration and congestion in the network. We have carried out experiments using XMPP-based conference tools over CCNx and have successfully built the media forwarding for two conference tools (audio and whiteboard) on Android platform. This hybrid approach leverages NDN to support robust and efficient conference applications.
Protein function: a practical approach (1990)

Minizing protein in activation ligand-protein binding affinities ligand blotting affinity labelling cross-linking of protein subunits and ligands by the introduction of disulphide bonds determining the roles of subunits in protein function analysis of sequence-specific DNA-binding proteins identification and purification of sequence-specific DNA-binding proteins chemical characterization of functional groups in proteins by competitive labelling chemical modification site-directed mutagenesis, based on the phosphorothioate approach.
High-throughput kinase assays with protein substrates using fluorescent polymer superquenching (2005)

The QTL Lightspeed protein detection system provides a simple mix and measure "turn on" assay for the detection of kinase activity using natural protein substrates. The platform is robust and allows for identification of inhibitors of kinase activity.
AURORA: a vision-based roadway departure warning system (2002)

AURORA is a vision-based system designed to warn a vehicle driver of possible impending roadway departure accidents. It employs a downward looking color video camera with a wide angle lens, a digitizer, and a portable Sun Sparc workstation. Using a binormalized adjustable template correlation algorithm, it reliably detects lane markers on structured roads at 60 Hz. A time-to-lane-crossing (TLC) measurement is calculated for each image based on the estimation of vehicle's lateral position and velocity. This measurement is used to trigger an alarm when the TLC falls below a preset threshold. Promising results have been achieved under a variety of weather and lighting conditions, on many road types.
Controlling the Morphology of Nanocrystal–Polymer Composites for Solar Cells (2003)

Abstract We have shown recently that the use of high‐aspect‐ratio inorganic nanorods in conjunction with conjugated polymers is a route to obtaining efficient solar cells processed from solution. Here, we demonstrate that the use of binary solvent mixtures in which one of the components is a ligand for the nanocrystals is effective in controlling the dispersion of nanocrystals in a polymer. By varying the concentration of the solvent mixture, phase separation between the nanocrystal and polymer could be tuned from micrometer scale to nanometer scale. In addition, we can achieve nanocrystal surfaces that are free of surfactant through the use of weak binding ligands that can be removed through heating. When combined, the control of film morphology together with surfactant removal result in nanorod–polymer blend photovoltaic cells with a high external quantum efficiency of 59 % under 0.1 mW cm –2 illumination at 450 nm.
A review of californium-252 neutron brachytherapy for cervical cancer (1991)

Since 1976 a clinical trial has been conducted to test the feasibility, the potential, and to develop methods for using the neutron-emitting radioactive isotope, californium-252 (Cf-252), for the treatment of cervical cancer. A total of 218 patients were treated in the initial study period from 1976 until 1983. The trials initially treated advanced (Stages III and IV) cervical cancer patients using different doses and schedules; they were extended to include unfavorable presentations of Stages I and II because of favorable results in the initial trials. The authors began to treat patients with Stage IB bulky or barrel-shaped tumors and the majority were treated with both radiation and hysterectomy. Actuarial survival was determined for Stage IB disease and was 87% at 5 years and 82% at 10 years. For those tested with preoperative radiation it was 92% at 5 and 87% at 10 years. For Stage II, it was 62% 5 years and 61% at 10. Survival 5 years after combined radiation and surgical therapy for Stage II disease was 68%. For Stage III, it was 33% at 5 years and 25% at 10. However, 5-year survival using the early neutron implant was 46% versus approximately 19% for delayed Cf-252 or cesium 137. Different schedules and sequences of neutrons and photons greatly altered outcome. Neutron treatment before external photon therapy was better for all stages of disease. Only about 5% of all patients developed complications after neutron therapy. No hematologic or mesenchymal second tumors were observed. Neutron brachytherapy was found to be very effective for producing rapid response and greatly improved local control of bulky, barrel, or advanced cervical cancers. The clinical trial identified and evolved schedules, doses, doses per session, and developed methods different from standard photon therapy but highly effective for local control and cure of cervical cancers of all stages. Clinical and radiobiologic understanding for the use of neutron therapy was greatly advanced by this trial. Future trials will focus on patients with advanced disease and will require evaluation of adjuvant chemotherapy studies and neutron-enhancing chemicals.
Ironing out the wrinkles in the rare biosphere through improved OTU clustering (2010)

Deep sequencing of PCR amplicon libraries facilitates the detection of low-abundance populations in environmental DNA surveys of complex microbial communities. At the same time, deep sequencing can lead to overestimates of microbial diversity through the generation of low-frequency, error-prone reads. Even with sequencing error rates below 0.005 per nucleotide position, the common method of generating operational taxonomic units (OTUs) by multiple sequence alignment and complete-linkage clustering significantly increases the number of predicted OTUs and inflates richness estimates. We show that a 2% single-linkage preclustering methodology followed by an average-linkage clustering based on pairwise alignments more accurately predicts expected OTUs in both single and pooled template preparations of known taxonomic composition. This new clustering method can reduce the OTU richness in environmental samples by as much as 30-60% but does not reduce the fraction of OTUs in long-tailed rank abundance curves that defines the rare biosphere.
Emission at 1.3 µmfrom dysprosium-doped Ga:La:S glass (1994)

The potential for optical amplification at 1.3 µm is demonstrated in a dysprosium-doped gallium-lanthanum-sulphide based glass. Lifetimes of 59 µs are observed for the 6H9/2 - 6H15/2 transition for which the emission peaks at 1.32 µm. A radiative lifetime of 203 µs is calculated by a Judd-Ofelt analysis, indicating a total radiative quantum efficiency of 29%. A pump absorption cross-section 20 times greater than Pr3+ suggests that shorter fibre devices may be possible.
Transurethral ultrasound applicators with directional heating patterns for prostate thermal therapy:In vivoevaluation using magnetic resonance thermometry (2004)

A catheter-based transurethral ultrasound applicator with angularly directional heating patterns has been designed for prostate thermal therapy and evaluated in canine prostate in vivo using MRI to monitor and assess performance. The ultrasound transducer array (3.5 mm diameter tubular transducers, active sectors, was integrated to a flexible delivery catheter (4 mm OD), and encapsulated within an expandable balloon (35 mm×10 mm OD, ambient water) for coupling and cooling of the prostatic urethra. These devices were used to thermally coagulate targeted portions of the canine prostate while using MR thermal imaging (MRTI) to monitor the therapy. MRI was also used for target definition, positioning of the applicator, and evaluation of target viability post-therapy. MRTI was based upon the complex phase-difference mapping technique using an interleaved gradient echo-planar imaging sequence with lipid suppression. MRTI derived temperature distributions, thermal dose exposures, T1–contrast enhanced MR images, and histology of sectioned prostates were used to define destroyed tissue zones and characterize the three-dimensional heating patterns. The ultrasound applicators produced directed zones of thermal coagulation within targeted tissue which extended 15–20 mm radially to the outer boundary of the prostate within 15 min. Transducer activation lengths of 17 mm and 24 mm produced contiguous zones of coagulation extending axially and from base to apex, respectively. Peak temperatures around were measured, with corresponding to outer boundary at treatment time. These devices are MRI compatible, and when coupled with multiplanar MRTI provide a means for selectively controlling the length and sector angle of therapeutic thermal treatment in the prostate.
Organization of Acenes with a Cruciform Assembly Motif (2006)

This study explores the assembly in the crystalline state of a class of pentacenes that are substituted along their long edges with aromatic rings forming rigid, cruciform molecules. The crystals were grown from the gas phase, and their structures were compared with DFT-optimized geometries. Both crystallographic and computed structures show that a planar acene core is the exception rather than the rule. In the assembly of these molecules, the phenyl groups block the herringbone motif and further guide the arrangement of the acene core into higher order structures. The packing for the phenyl-substituted derivatives is dictated by close contacts between the C-H's of the pendant aromatic rings and the carbons at the fusions in the acene backbone. Using thiophene substituents instead of phenyls creates cofacially stacked acenes. In thin films, the thiophene-substituted derivative forms devices with good electrical properties: relatively high mobility, high ON/OFF ratios, and low threshold voltage for device activation. An unusual result is obtained for the decaphenyl pentacene when devices are fabricated on its crystalline surface. Although its acene cores are well isolated from each other, this material still exhibits good electrical properties.
BAS1 : A gene regulating brassinosteroid levels and light responsiveness in Arabidopsis (1999)

The Arabidopsis bas1-D mutation suppresses the long hypocotyl phenotype caused by mutations in the photoreceptor phytochrome B (phyB). The adult phenotype of bas1-D phyB-4 double mutants mimics that of brassinosteroid biosynthetic and response mutants. bas1-D phyB-4 has reduced levels of brassinosteroids and accumulates 26-hydroxybrassinolide in feeding experiments. The basis for the mutant phenotype is the enhanced expression of a cytochrome P450 (CYP72B1). bas1-D suppresses a phyB-null allele, but not a phyA-null mutation, and partially suppresses a cryptochrome-null mutation. Seedlings with reduced BAS1 expression are hyperresponsive to brassinosteroids in a light-dependent manner and display reduced sensitivity to light under a variety of conditions. Thus, BAS1 represents one of the control points between multiple photoreceptor systems and brassinosteroid signal transduction.
Human IgG Fc Receptors (1997)

Human IgG receptors constitute a family of glycoprotein complexes consisting of ligand-binding, and associated signaling chains. Three leukocyte classes (Fc gamma RI, II, and III) and one separate endothelial Fc gamma R class (FcRB) are defined which are expressed on hematopoietic and endothelial cells. Upon interaction with IgG, Fc gamma R initiate a plethora of signaling cascades involving receptor signaling motifs, and protein tyrosine kinases and phosphatases. These cascades ultimately culminate in activation or deactivation of effector cells, resulting in initiation or down-modulation of cellular processes. Recent evidence points to a crucial in vivo role of Fc gamma R in both initiation and regulation of inflammatory and cytotoxic responses. These Fc gamma R-mediated immune responses can be exploited to develop novel immunotherapies.
Staphylococcus aureus SigB activity promotes a strong fibronectin–bacterium interaction which may sustain host tissue colonization by small‐colony variants isolated from cystic fibrosis patients (2008)

Genes encoding cell-surface proteins regulated by SigB are stably expressed in Staphylococcus aureus small-colony variants (SCVs) isolated from cystic fibrosis (CF) patients. Our hypothesis is that CF-isolated SCVs are locked into a colonization state by sustaining the expression of adhesins such as fibronectin-binding proteins (FnBPs) throughout growth. Force spectroscopy was used to study the fibronectin-FnBPs interaction among strains varying for their SigB activity. The fibronectin-FnBPs interaction was described by a strength of 1000+/-400 pN (pulling rate of 2 microm s(-1)), an energetic barrier width of 0.6+/-0.1 A and an off-rate below 2 x 10(-4) s(-1). A CF-isolated SCV highly expressed fnbA throughout growth and showed a sustained capacity to bind fibronectin, whereas a prototypic strain showed a reduced frequency of fibronectin-binding during the stationary growth phase when its fnbA gene was down-regulated. Reduced expression of fnbA was observed in sigB mutants, which was associated with an overall decrease adhesion to fibronectin. These results suggest that the fibronectin-FnBPs interaction plays a role in the formation of a mechanically resistant adhesion of S. aureus to host tissues and supports the hypothesis that CF-isolated SCVs are locked into a colonization state as a result of a sustained SigB activity.