gebhart/patrepeval huggingface dataset:
An immunoluminometric assay for N-terminal pro-brain natriuretic peptide: development of a test for left ventricular dysfunction (1999)

Measurement of plasma levels of brain natriuretic peptide (BNP) has been used to assess left ventricular dysfunction and prognosis. Levels of the N-terminus of the precursor of BNP (NT-proBNP) have been reported to be elevated to a greater extent than BNP in left ventricular dysfunction. We have devised a non-radioactive sensitive and specific assay for NT-proBNP based on a competitive ligand binding principle. The chemiluminescent label 4-(2-succinimidyloxycarbonylethyl)phenyl-10-methylacridinium 9-carboxylate fluorosulphonate was used to label peptides representing domains in the middle and C-terminal sections of NT-proBNP. Assay of the C-terminal section of NT-proBNP (amino acids 65-76) in patients with proven left ventricular dysfunction [left ventricular wall motion index median 0.9 (range 0.3-1.4)] revealed elevated values [median 639 (386-911) fmol/ml] compared with normal controls [left ventricular wall motion index of 2 in all, NT-proBNP median 159 (120-245) fmol/ml, P<0.001]. Measurement of the middle section of NT-proBNP (amino acids 37-49) was not a discriminating test. It is thus possible to derivatize small peptides with a methyl acridinium label and preserve immunodetection with specific antibodies. Such methodology may allow non-radioactive immunoluminometric assays to be devised.
Far-Field RF Wireless Power Transfer with Blind Adaptive Beamforming for Internet of Things Devices (2017)

Wireless power transfer (WPT) has long been one of the main goals of Nikola Tesla, the forefather of electromagnetic applications. In this paper, we investigate radio-frequency beamforming in the radiative far field for WPT. First, an analytical model of the channel fading is presented, and a blind adaptive beamforming algorithm is adapted to the WPT context. The algorithm is computationally light, because we need not explicitly estimate the channel state information. Then, a testbed with a multiple-antenna software-defined radio configuration on the transmitting side and a programmable energy harvester on the receiving side is developed in order to validate the algorithm in this specific power application. From the results, it can be seen that the implementation of this version of beamforming indeed improves the harvested power. Specifically, at various distances from 50 cm to 1.5 m, the algorithm converges with two, three, and four antennas with an increasing gain as we increase the number of antennas. These encouraging results could have far-reaching consequences in providing wireless power to Internet of Things devices, our target application.
A Functional Retinoic Acid Receptor Encoded by the Gene on Human Chromosome 12 (1990)

A cDNA clone derived from a human hepatocellular carcinoma has been isolated on the basis of homology to the alpha human retinoic acid receptor (RAR alpha) gene. Expression of this cDNA produces a high affinity nuclear binding protein for retinoic acid. The product of this clone when expressed in transfected cells is able to activate transcription of a reporter plasmid through specific DNA sequences in response to the addition of retinoic acid to the medium. Dose-dependent profiles upon trans-activation of the reporter indicate that apparent sensitivity to retinoic acid of this protein is approximately 10-fold higher than that of human RAR alpha and is comparable to that of the second human RAR, RAR beta. This gene has been mapped to human chromosome 12, which is distinct from those coding for either alpha or beta RAR, and thus encodes a third human RAR.
Heat transfer measurements in hypersonic flow using luminescent coating techniques (2002)

Thedevelopmentandapplicationofhigh-speedimagingandluminescentcoatingtechniquestomeasurefull-e eld surface heat-transfer rates in short-duration hypersonic e ow is presented. Tests were performed on an indented cone model at the 48-in. shock tunnel and the LENS I tunnel facilities at Calspan— University of Buffalo Research Center. Nominal test conditions ranged between Mach numbers of 9.5 and 11.1 and Reynolds numbers of 1:4 £ 10 5 and 3 £ 10 5 m ii 1 with run times of less than 10 ms. Processed submillisecond images show the threedimensional, time-dependent development of the embedded separated e ow and shock/boundary-layer interaction into a steady axisymmetric structure bounded by regions of laminar e ow. Conversion from processed image data to full-e eld heat-transfer measurements were performed using both an in situ calibration with thin-e lm platinum heat-transfer gauges as well as an a priori temperature calibration and transient heat-transfer theory. In situ calibrations displayed excellent correlation with surface-mounted gauges, whereas a priori calibrations showed a larger susceptibility to bias errors.
Differential Effects of Oral and Intravenous Lipid Administration on Key Molecules Related to Energy Homeostasis (2016)

Metabolic responses to lipids depend on the route of administration. Only iv lipids trigger a dose-dependent fibroblast growth factor 21 secretion, which is nonglucagon mediated. Intravenous lipids also induce hyperinsulinemia without concurrent decreases in glucose, a phenomenon observed in insulin-resistant states. Orally administered lipids mostly affect gastrointestinal tract-secreted molecules important in glucose and energy homeostasis such as glucagon, incretins, and peptide YY.
Inhibition of human endothelial cell proliferation in vitro and neovascularization in vivo by D-penicillamine. (1989)

To investigate the effects of D-penicillamine (D-Pen) on angiogenesis, we have studied the effects of this drug on in vitro proliferation of human endothelial cells (EC) and in vivo corneal neovascularization. D-Pen, in the presence of copper sulfate, suppressed tritiated thymidine ([3H]TdR) incorporation into EC in a dose-dependent manner. Significant inhibition was observed with D-Pen concentrations attainable in the serum and tissues of treated patients. Neither D-Pen nor copper ion alone significantly affected [3H]TdR incorporation into EC. The inhibition by D-Pen and copper was blocked by catalase (CAT) or horseradish peroxidase but not by boiled CAT or SOD. When rabbits were daily injected intravenously with D-Pen at the per kilogram dosage administered to rheumatoid patients, neovascularization as quantitated by the proliferation of corneal new blood vessels was significantly inhibited. These results suggest that hydrogen peroxide generated by D-Pen and copper exerts a pronounced antiangiogenic effect through inhibition of EC proliferation. It is, therefore, considered that D-Pen may suppress rheumatoid synovitis by reducing the number of small blood vessels available for the emigration of chronic inflammatory cells, and the proliferation of the synovial tissue.
Two Stars and a Movie Camera (2013)

Screen Couples Chemistry: The Power of 2, by Martha P. Nochimson, University of Texas Press, 2002.
Novel viral vectors in infectious diseases (2017)

Since the development of vaccinia virus as a vaccine vector in 1984, the utility of numerous viruses in vaccination strategies has been explored. In recent years, key improvements to existing vectors such as those based on adenovirus have led to significant improvements in immunogenicity and efficacy. Furthermore, exciting new vectors that exploit viruses such as cytomegalovirus (CMV) and vesicular stomatitis virus (VSV) have emerged. Herein, we summarize these recent developments in viral vector technologies, focusing on novel vectors based on CMV, VSV, measles and modified adenovirus. We discuss the potential utility of these exciting approaches in eliciting protection against infectious diseases.
Cytotoxicity of 35 dental resin composite monomers/additives in permanent 3T3 and three human primary fibroblast cultures (1998)

It was the purpose of this investigation to determine the cytotoxic effects (ED50 concentrations) of 35 monomers or additives identified in commercial dental resin composites. Monolayers of permanent 3T3 cells and three primary human fibroblast types derived from oral tissues (gingiva, pulp, and periodontal ligament) were used as test systems. All substances were tested in concentrations ranging from 0.01 to 5.0 mM. In general, ED50 values varied from 0.06 to > 5 mM. Within the groups of co(monomers), initiators, and cointiators, severe (e.g., Bis-GMA, UDMA, DMBZ, and DMDTA) or moderate (HEMA, BEMA, CQ, DMPT, and DMAPE) cytotoxic effects could be evaluated. Within the group of reaction/decomposition products, only moderate or slight effects were found (ED50: 0.7 to > 5 mM). The inhibitor BHT, the contaminant TPSb, and the photostabilizer HMBP, however, were highly cytotoxic in all cell cultures. In addition, the ED50 values of DBPO and HMBP significantly varied (0.43-3.8 mM, respectively, and 0.44-3.07 mM) with the applied cell culture. Our comprehensive screening shows that for several of the highly cytotoxic composite components, less cytotoxic alternatives are available. Furthermore, there was no cell type identified which was consistently less or more sensitive to the toxic effects of the tested compounds than the others. Primary human periodontal ligament and pulp fibroblasts, however, were found to be more sensitive than 3T3 and gingival fibroblasts to alterations from most tested substances.
The Role of Rhodopsin Glycosylation in Protein Folding, Trafficking, and Light-Sensitive Retinal Degeneration (2009)

Several mutations in the N terminus of the G-protein-coupled receptor rhodopsin disrupt NXS/T consensus sequences for N-linked glycosylation (located at N2 and N15) and cause sector retinitis pigmentosa in which the inferior retina preferentially degenerates. Here we examined the role of rhodopsin glycosylation in biosynthesis, trafficking, and retinal degeneration (RD) using transgenic Xenopus laevis expressing glycosylation-defective human rhodopsin mutants. Although mutations T4K and T4N caused RD, N2S and T4V did not, demonstrating that glycosylation at N2 was not required for photoreceptor viability. In contrast, similar mutations eliminating glycosylation at N15 (N15S and T17M) caused rod death. Expression of T17M was more toxic than T4K to transgenic photoreceptors, further suggesting that glycosylation at N15 plays a more important physiological role than glycosylation at N2. Together, these results indicate that the structure of the rhodopsin N terminus must be maintained by an appropriate amino acid sequence surrounding N2 and may require a carbohydrate moiety at N15. The mutant rhodopsins were rendered less toxic in their dark inactive states, because RD was abolished or significantly reduced when transgenic tadpoles expressing T4K, T17M, and N2S/N15S were protected from light exposure. Regardless of their effect on rod viability, all of the mutants primarily localized to the outer segment and Golgi and showed little or no endoplasmic reticulum accumulation. Thus, glycosylation was not crucial for rhodopsin biosynthesis or trafficking. Interestingly, expression of similar bovine rhodopsin mutants did not cause rod cell death, possibly attributable to greater stability of bovine rhodopsin.
Desazadesmethyldesferrithiocin Analogues as Orally Effective Iron Chelators (1998)

Further structure-activity studies of desferrithiocin analogues are carried out. (S)-Desazadesmethyldesferrithiocin, 2-(2-hydroxyphenyl)-Delta2-thiazoline-4(S)-carboxylic acid, serves as the principal framework in the current paper. Desazadesmethyldesferrithiocin can be structurally altered with facility, and data are already available on its iron-clearing properties and toxicity parameters. Four different kinds of structural modifications of this framework are undertaken: introduction of hydroxy, carboxy, or methoxy groups on the aromatic ring; alteration of the thiazoline ring; increasing the distance between the ligand donor atoms; and benz-fusion of the aromatic rings. The structural modifications described are shown to have a tremendous impact on both the iron clearance and toxicity profiles of the desazadesmethyldesferrithiocin molecule. All of the compounds are assessed in a bile-duct-cannulated rodent model to determine iron clearance efficiency. Ligands which demonstrate an efficiency of greater than 2% are carried forward to the iron-overloaded primate for iron-clearing measurements. Ligands with efficiencies greater than 3% in the primate are then evaluated in a formal toxicity study in rodents. On the basis of the results of the present work, 2-(2, 4-dihydroxyphenyl)-Delta2-thiazoline-4(S)-carboxylic acid is a promising candidate for clinical evaluation.
Randomized Phase II Comparison of Dose-Intense Gemcitabine: Thirty-Minute Infusion and Fixed Dose Rate Infusion in Patients With Pancreatic Adenocarcinoma (2003)

Pharmacokinetic and clinical data in this trial supports the continued evaluation of the FDR infusion strategy with gemcitabine.
Synthesis of Porphyrin–CdSe Quantum Dot Assemblies: Controlling Ligand Binding by Substituent Effects (2015)

Cadmium selenide quantum dots of 2.2-2.3 nm diameter were prepared by phosphorus-free methods using oleic acid as stabilizing surface ligand. Ligand exchange monitored quantitatively by (1)H NMR spectroscopy gave an estimate of 30-38 monodentate ligands per nanocrystal, with a ligand density of 1.8-2.3 nm(-2). The extent of ligand exchange with macrocycles carrying one or more functional groups was investigated, with the aim of producing nanocrystal-macrocycle conjugates with a limited number of coligands. Metal-free porphyrins are able to sequester the Cd(2+) ions from the Cd(oleate)2 outer layer of the nanocrystals. Zinc porphyrin complexes carrying one carboxylate function displace oleate efficiently to give porphyrin/CdSe composites with porphyrins stacked upright on the crystal surface. Porphyrins with four potential ligating sites are able to bind to the crystal surface only if the donors are at the end of sufficiently long and flexible tethers. High-dilution methods allowed the synthesis and isolation of well-defined composites of composition [CdSe{porphyrin}2], where porphyrin = 5,10,15,20-tetrakis{3-(carboxy-n-alkyloxy)phenyl}porphyrinato zinc (n = 5 or 10) and 5,10,15,20-tetrakis{3-(11-undecenyloxythiol)phenyl}porphyrinato zinc. Comparison of the composition data obtained by (1)H NMR spectroscopy with luminescence quenching behavior suggests a dependence of quenching efficiency on the tether length. Luminescence quenching was also observed for porphyrins that, according to (1)H NMR results, do not undergo surface ligand exchange.
Direct Detection of Bacterial Genomic DNA at Sub-Femtomolar Concentrations Using Single Molecule Arrays (2013)

We report a method for the sensitive measurement of genomic DNA based on the direct detection of single molecules of DNA in arrays of femtoliter wells. The method begins by generating short fragments of DNA from large, double-stranded molecules of genomic DNA using either restriction enzymes or sonication. Single-stranded fragments are then generated by melting the duplex, and these fragments are hybridized to complementary biotinylated detection probes and capture probes on paramagnetic beads. The resulting DNA complexes are then labeled with an enzyme (streptavidin-β-galactosidase), and single enzymes associated with these complexes on beads are detected in single molecule arrays (Simoa). DNA concentration is quantified by determining the average number of enzymes per bead via Poisson statistics (digital) or the average bead intensity (analog). The Simoa DNA assay was used to detect genomic DNA purified from S. aureus with an average limit of detection (LOD) of 0.07 fM, or 2100 DNA molecules per 50 μL sample. We used this assay to detect S. aureus spiked into (a) whole blood, with an average LOD of 1100 bacteria per 25 μL sample (0.074 fM), and (b) water from the Charles River, with an LOD of 1300 bacteria per 50 μL sample (0.042 fM). Bacteria were detected in river water without prior purification of DNA. The Simoa DNA assay, which directly detects target DNA molecules without molecular replication, is an attractive alternative to existing sensitive DNA detection technologies that rely on amplification using polymerases, such as the polymerase chain reaction (PCR).
Ontological design (2009)

In this paper, we describe the concept of ontological design. We show how ontologies can be used as cognitive maps of complex, ill-structured, plastic problems. They can be used to concisely encapsulate the core logic of a problem. From it one can also derive a closed set of a very large number of natural language descriptions of a problem. The ontologies can be plastic but at the same time systematic, repeatable, and extensible. They can be used to map the gaps between the states-of-the-art, -practice, and - need. Knowing the gaps strategies can be designed to bridge them. Thus, ontological design is a method of logical analysis, synthesis of research and practical knowledge, its interpretation, and application to the design of solutions to complex, ill-structured, and plastic problems. We illustrate ontological design in the context of eHealth.
Evidence that arginyl-glycyl-aspartate peptides and fibrinogen gamma chain peptides share a common binding site on platelets. (1987)

Synthetic peptides corresponding to the carboxyl terminus of the fibrinogen gamma chain inhibit the binding of fibrinogen, fibronectin, and von Willebrand factor to platelets, yet the active decapeptide sequence has only been found in fibrinogen to date. In contrast, all three proteins contain Arg-Gly-Asp sequences, and peptides containing Arg-Gly-Asp are potent inhibitors of their binding to activated platelets. We have analyzed the relationship between these peptide sets by direct binding assays. H12 (gamma 400-411) inhibited the binding of an Arg-Gly-Asp-containing peptide to platelets with similar dose response to inhibition of fibronectin binding. We have previously reported that GPIIb-IIIa binds to immobilized Arg-Gly-Asp peptides and can be eluted by Arg-Gly-Asp-containing peptides in solution. Both H12 and L10 (gamma 402-411) completely eluted GPIIb-IIIa bound to immobilized Arg-Gly-Asp peptides. Conversely, when GPIIb-IIIa was bound to immobilized L10, either L10 or an Arg-Gly-Asp peptide could elute it. Peptide specificity was established by the failure of Gly-Arg-Gly-Glu-Ser-Pro or acetylated L10 to elute GPIIb-IIIa from the immobilized peptides. These results indicate that the two peptide sets interact with the same receptor which contains GPIIb-IIIa.
Neuritogenic and survival‐promoting effects of the P2 peptide derived from a homophilic binding site in the neural cell adhesion molecule (2003)

The neural cell adhesion molecule (NCAM) plays a pivotal role in neural development, regeneration, and plasticity. NCAM mediates adhesion and subsequent signal transduction through NCAM-NCAM binding. Recently, a peptide ligand termed P2 corresponding to a 12-amino-acid sequence in the FG loop of the second Ig domain of NCAM was shown to mimic NCAM homophilic binding as reflected by induction of neurite outgrowth in hippocampal neurons. We demonstrate here that in concentrations between 0.1 and 10 microM, P2 also induced neuritogenesis in primary dopaminergic and cerebellar neurons. Furthermore, it enhanced the survival rate of cerebellar neurons although not of mesencephalic dopaminergic neurons. Moreover, our data indicate that the protective effect of P2 in cerebellar neurons was due to an inhibition of the apoptotic process, in that caspase-3 activity and the level of DNA fragmentation were lowered by P2. Finally, treatment of neurons with P2 resulted in phosphorylation of the ser/thr kinase Akt. Thus, a small peptide mimicking homophilic NCAM interaction is capable of inducing differentiation as reflected by neurite outgrowth in several neuronal cell types and inhibiting apoptosis in cerebellar granule neurons.
Histone deacetylase inhibitors as potential anti-skin cancer agents. (1999)

The regulation of squamous differentiation is a tightly regulated process involving transcriptional repression and activation. Previous studies have established that squamous carcinoma cell lines inappropriately regulate the transcription of genes important to the control of squamous differentiation. Histone deactylase inhibitors such as trichostatin A (TSA) and butyrate disrupt normal chromatin structure and cause alterations in gene expression/regulation. For these reasons, we examined the effects of both butyrate and TSA on the growth and differentiation of human keratinocytes or squamous carcinoma cells in tissue culture. We found that treatment of keratinocytes or squamous carcinoma cells with butyrate induced a reversible growth arrest. TSA, on the other hand, induced an irreversible growth arrest in both keratinocytes and squamous carcinoma cells. The growth arrest of keratinocytes induced by TSA or butyrate was accompanied by a reduction in the mRNA levels for proliferation gene cdk1 and an induction of the mRNA for the differentiation-specific transglutaminase type I gene (TG1). In contrast, the squamous carcinoma cells had decreased cdk1 and TG1 mRNA in response to TSA or butyrate. Both of these agents produced transient increases in the acetylation of histone H4 in keratinocytes and squamous carcinoma cells. These data indicated that TSA may have potential as a topical treatment for epidermal malignancies.
Formulations of dietary supplements and herbal extracts for relaxation and anxiolytic action: Relarian. (2009)

Dietary supplements are widely used for desired effects on memory, insomnia, mood and anxiety. This review focuses on supplements which have anxiolytic or mild relaxation properties and enhance mood. For example, Kava (Piper methysticum) is reported to have anaxiolytic actions and to reduce tension through skeletal muscle relaxation. Dried passion flower (genus Passiflora) is reported to reduce insomnia and hysteria. Skullcap (genus Scutellaria), hops (Humulus lupulus), lemon balm (Melissa officinalis) and Valerian (Valeriana officinalis) root are all herbs reported as anaxiolytic calming agents. Further, extracts of Magnolia and Phellondendron bark are mild sedatives. Supplements such as gamma-aminobutyric acid (GABA), theanine, tryptophan and 5-hydroxytryptophan (5-HTP) are reported to promote relaxation. In general, these supplements appear to act as GABA receptor agonists or to boost GABA levels, although Kava inhibits both norephinephrine uptake and sodium and potassium channels and 5-HTP may act through elevation of serotonin. While questions remain in the literature regarding the medicinal value of these supplements in treating mood and anxiety disorders, based on cellular and animal studies as well as human clinical trials the literature supports a role for these preparations as useful alternatives in the management of the stress and anxiety of everyday life.
Image quality assessment using contourlet transform (2009)

We present a novel objective full-reference image quality assessment metric based on multiscale geometric analysis. The multichannel behavior of the human vision system is emulated by contourlet transform, a perceptual subband decomposition. Not only the contrast-masking effect but also the entropy-masking effect is considered to deal with the visual masking issue. In the error pooling stage, the frequency sensitivity of the HVS is investigated. Nonlinear and linear fusion schemes of subband distortion are compared. Extensive validation experiments are performed on two professional image databases, the LIVE database supplied by the University of Texas and the A57 database supplied by Cornell University. Compared with several state-of-the-art image quality metrics, the proposed metric demonstrates improvement on prediction accuracy and robustness.