gebhart/patrepeval huggingface dataset:
Autocrine Human Growth Hormone Enhancement of Human Mammary Carcinoma Cell Spreading Is Jak2 Dependent* (2000)

We investigated the role of autocrine production of human (h) GH in the attachment and spreading of mammary carcinoma cells in vitro. We used a previously described model system for the study of the autocrine/paracrine role of GH in which the hGH gene (MCF-hGH) or a translation-deficient hGH gene (MCF-MUT) was stably transfected into MCF-7 cells. No differences in attachment to a collagen matrix between MCF-hGH and MCF-MUT cells were observed in either serum-free medium (SFM) or medium containing exogenous hGH, 5% serum, or 10% serum. In contrast, MCF-hGH cells spread more rapidly on a collagen matrix than did MCF-MUT cells. Exogenous hGH and 10% serum interacted with autocrine production of hGH in an additive manner to increase cell spreading. MCF-hGH cells formed filipodia and stress fibers earlier than MCF-MUT cells during the process of cell spreading and possessed marked differences in morphology after spreading. MCF-MUT cells displayed uniform and symmetrical formation of stress fibers, whereas MCF-hGH cells displayed irregular and elongated stress fiber formation. The level of cytoplasmic phosphotyrosine was increased in MCF-hGH compared with MCF-MUT cells during spreading and displayed colocalization with Janus kinase 2 (JAK2). Basal JAK2 tyrosine phosphorylation was increased, and it increased further on spreading in MCF-hGH cells compared with MCF-MUT cells. Transient transfection of JAK2 complementary DNA resulted in interaction with autocrine hGH to increase the rate of cell spreading in MCF-hGH cells compared with MCF-MUT cells. Treatment with a selective JAK2 tyrosine kinase inhibitor (AG 490) reduced the rate of MCF-hGH cell spreading to the rate of MCF-MUT cell spreading. Thus, we conclude that autocrine production of hGH enhances the rate of mammary carcinoma cell spreading in a JAK2-dependent manner.
Measurement of the second-order nonlinear susceptibility of proton-exchanged LiNbO_3 (1992)

We have measured the d(33) nonlinear coefficient in proton-exchanged LiNbO(3) by using angle-dependent reflected second-harmonic generation and observed a reduction to </=1% of the bulk LiNbO(3) value.
Excited State Proton-Transfer Reactions of Coumarin 4 in Protic Solvents (2001)

Excited state 7-hydroxy-4-methyl coumarin (4CUOH) has dual photochemical properties. In water, its neutral form (ROH*) is a strong photoacid and transfers a proton to the solvent with pK* ∼ 0. It is also a strong photobase capable of accepting a proton from some protic solvents or reacting with excess protons in solution. In this study, we measured the rate and dynamics of the reaction of excited state 4CUOH with excess protons in neat monols and water−glycerol solutions. The reaction shows diffusion-controlled reactivity and fits the Smoluchowski model. The reaction can be formulated by the kinetic scheme ROH* + H+ → RO *, where RO * and ROH* are the protonated and neutral forms of the photobase, respectively. Nonexponential decay of the ROH* fluorescence was observed. We analyzed the experimental data within the framework of the diffusive model. The model predicts that the survival probability depends strongly on both the intrinsic rate constant and the mutual diffusion constant.
Mitochondrial Biogenesis through Activation of Nuclear Signaling Proteins (2013)

The dynamics of mitochondrial biogenesis and function is a complex interplay of cellular and molecular processes that ultimately shape bioenergetics capacity. Mitochondrial mass, by itself, represents the net balance between rates of biogenesis and degradation. Mitochondrial biogenesis is dependent on different signaling cascades and transcriptional complexes that promote the formation and assembly of mitochondria--a process that is heavily dependent on timely and coordinated transcriptional control of genes encoding for mitochondrial proteins. In this article, we discuss the major signals and transcriptional complexes, programming mitochondrial biogenesis, and bioenergetic activity. This regulatory network represents a new therapeutic window into the treatment of the wide spectrum of mitochondrial and neurodegenerative diseases characterized by dysregulation of mitochondrial dynamics and bioenergetic deficiencies.
Ultra-Pure Polymerized Bovine Hemoglobin Blood Substitute: Effects on the Coronary Circulation (1992)

The effects of stroma-free hemoglobin (SFHgb) on the coronary circulation remain unclear. An intact canine model utilizing intracoronary adenosine to abolish the confounding effect of autoregulation was used to study maximal myocardial oxygen delivery during progressive hemodilution with polymerized bovine SFHgb. The circumflex coronary artery was instrumented with a flow probe, hydraulic constrictor, and proximal and distal catheters for adenosine infusion and distal pressure measurement, respectively. This preparation was used to generate diastolic coronary pressure-flow relations during maximal vasodilation. Maximal coronary conductance and maximal myocardial oxygen delivery were determined in two groups of 7 dogs each following hemodilution, first with 6% hetastarch (Control), followed by further hemodilution with ultra-pure, polymerized, bovine SFHgb. After hemodilution with SFHgb, maximal coronary flow increased slightly without evidence of coronary vasoconstriction. Since hemodilution with this material increases oxygen carrying capacity, maximal oxygen delivery is greater than Control, despite the very low canine hematocrit. These findings suggest: 1) SFHgb can provide adequate oxygen delivery to the myocardium despite extreme degrees of hemodilution, and 2) in this intact model, there is no evidence of adverse coronary vasomotion.
Cytosolic calcium oscillations and insulin release in pancreatic islets of Langerhans. (1998)

Stimulation of insulin release by glucose and other nutrients has been attributed to a rise of cytoplasmic Ca2+([Ca2+]i). In intact pancreatic islets, this rise is organized in oscillations. Two types of [Ca2+]i oscillations are mainly detected. Fast oscillations (frequency of approximately equal to 3 min-1) are consistently observed, and their duration depends on glucose concentration. They are due to a bursting of electrical activity and occur synchronously throughout the islet. Slow oscillations (frequency of 0.2 min-1) also appear in response to other nutrient secretagogues (ketoisocaproate, leucine, isoleucine). They most probably constitute the physiological oscillatory pattern because islets perifused with a solution containing a mixture of amino acids and glucose at concentrations found in the plasma of fed animals showed the same oscillatory pattern. Slow [Ca2+]i oscillations may constitute the framework for pulsatile insulin release observed in vivo.
Giant Retinal Tears (1989)

Three low-viscosity perfluorocarbon liquids provided an intraoperative tool during vitrectomy to manage giant retinal tears. These clear fluids have a high specific gravity (1.8 to 1.9) and are immiscible with water. In six eyes, the giant tear was less than 180 degrees; in 11 eyes, it was 180 degrees or greater. In all eyes, the tear was unfolded and the retina was flattened while the patient was supine. The perfluorocarbon liquid was aspirated and replaced by air-perfluorocarbon gas mixtures (16 eyes) or silicone oil (one eye) at the end of the operation. The retina was reattached in 16 eyes (94%), with a minimum follow-up period of 6 months. In five eyes (29%), the retina was reattached without scleral buckling. Residual droplets of perfluorocarbon liquid were observed in four patients. These new materials complement present surgical techniques for managing giant retinal tears.
An entire functional mammary gland may comprise the progeny from a single cell (1998)

Any epithelial portion of a normal mouse mammary gland can reproduce an entire functional gland when transplanted into an epithelium-free mammary fat pad. Mouse mammary hyperplasias and tumors are clonal dominant populations and probably represent the progeny of a single transformed cell. Our study provides evidence that single multipotent stem cells positioned throughout the mature fully developed mammary gland have the capacity to produce sufficient differentiated progeny to recapitulate an entire functional gland. Our evidence also demonstrates that these stem cells are self-renewing and are found with undiminished capacities in the newly regenerated gland. We have taken advantage of an experimental model where mouse mammary tumor virus infects mammary epithelial cells and inserts a deoxyribonucleic acid copy(ies) of its genome during replication. The insertions occur randomly within the somatic genome. CzechII mice have no endogenous nucleic acid sequence homology with mouse mammary tumor virus; therefore all viral insertions may be detected by Southern analysis provided a sufficient number of cells contain a specific insertional event. Transplantation of random fragments of infected CzechII mammary gland produced clonal-dominant epithelial populations in epithelium-free mammary fat pads. Serial transplantation of pieces of the clonally derived outgrowths produced second generation glands possessing the same viral insertion sites providing evidence for self-renewal of the original stem cell. Limiting dilution studies with cell cultures derived from third generation clonal outgrowths demonstrated that three multipotent but distinct mammary epithelial progenitors were present in clonally derived mammary epithelial populations. Estimation of the potential number of multipotent epithelial cells that may be evolved from an individual mammary-specific stem cell by self-renewal is in the order of 10(12)-10(13). Therefore, one stem cell might easily account for the renewal of mammary epithelium over several transplant generations.
A bacterial two-hybrid system based on a reconstituted signal transduction pathway (1998)

We describe a bacterial two-hybrid system that allows an easy in vivo screening and selection of functional interactions between two proteins. This genetic test is based on the reconstitution, in an Escherichia coli cya strain, of a signal transduction pathway that takes advantage of the positive control exerted by cAMP. Two putative interacting proteins are genetically fused to two complementary fragments, T25 and T18, that constitute the catalytic domain of Bordetella pertussis adenylate cyclase. Association of the two-hybrid proteins results in functional complementation between T25 and T18 fragments and leads to cAMP synthesis. Cyclic AMP then triggers transcriptional activation of catabolic operons, such as lactose or maltose, that yield a characteristic phenotype. In this genetic test, the involvement of a signaling cascade offers the unique property that association between the hybrid proteins can be spatially separated from the transcriptional activation readout. This permits a versatile design of screening procedures either for ligands that bind to a given "bait," as in the classical yeast two-hybrid system, or for molecules or mutations that block a given interaction between two proteins of interest.
Dual microwave and optical oscillator (1997)

We describe and demonstrate a novel device in which a microwave oscillation and an optical oscillation are generated and directly coupled with each other. With the mutual influence between the microwave and the optical oscillations, we project that this device is capable of simultaneously generating stable optical pulses down to the subpicosecond level and spectrally pure microwave signals at frequencies greater than 70 GHz.
Prevalence of antibodies to Norwalk virus in England: detection by enzyme-linked immunosorbent assay using baculovirus-expressed Norwalk virus capsid antigen (1993)

A total of 3,250 serum specimens collected in England in 1991 and 1992 were tested by an indirect enzyme-linked immunosorbent assay for antibody to Norwalk virus using baculovirus-expressed capsid antigen, and 2,382 (73.3%) were positive. The prevalence of Norwalk virus antibody differed regionally. It was lowest (24.6%) in 6- to 11-month-old infants and increased to 89.7% in persons over 60 years old.
Segmented Pt/Ru, Pt/Ni, and Pt/RuNi Nanorods as Model Bifunctional Catalysts for Methanol Oxidation (2005)

Five-segment (Pt-Ru-Pt-Ru-Pt, Pt-Ni-Pt-Ni-Pt, and Pt-RuNi-Pt-RuNi-Pt) nanorods with the same overall rod length and the same total Pt segment length were prepared by sequential electrodeposition of the metals into the pores of commercially available anodic aluminum oxide (AAO) membranes. Field-emission scanning electron microscopy (FESEM) showed that the nanorods were about 210 nm in diameter and about 1.5 microm in length. The alternating Pt and oxophilic metal(s) segments could be easily differentiated in backscattered-electron images. X-ray diffraction (XRD) analysis of the nanorods indicated that Pt and Ni were polycrystalline with fcc structures, Ru was hcp, and the co-deposited RuNi adopted the nickel fcc structure with some negative shifts in the Bragg angles. The chemical states of Pt, Ru, and Ni on the nanorod surface were assayed by X-ray photoelectron spectroscopy (XPS), and the presence of Pt(0), Pt(II), Pt(IV), Ru(0), Ru(VI), Ni(0), and Ni(II) was observed. The nanorods were catalytically active for the room-temperature electrooxidation of methanol in acidic solutions. The relative rates of reaction showed the Pt-RuNi pair sites as having the lowest overpotential to dissociate water, the highest catalytic activity in methanol oxidation, and the strongest CO-tolerance in the potential window employed. The use of segmented nanorods with identifiable Pt-oxophilic metal(s) interfaces removes many of the ambiguities in the interpretation of experimental data from conventional alloy catalysts, thereby enabling a direct comparison of the activities of various types of pair sites in methanol oxidation.
UniProt: a worldwide hub of protein knowledge (2018)

The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these proteins. These annotations are supplemented by annotations provided by rule based automated systems, and those imported from other resources. In this article we describe significant updates that we have made over the last 2 years to the resource. We have greatly expanded the number of Reference Proteomes that we provide and in particular we have focussed on improving the number of viral Reference Proteomes. The UniProt website has been augmented with new data visualizations for the subcellular localization of proteins as well as their structure and interactions. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
Regulation of Endothelial Junctional Permeability (2008)

The endothelium is a semi-permeable barrier that regulates the flux of liquid and solutes, including plasma proteins, between the blood and surrounding tissue. The permeability of the vascular barrier can be modified in response to specific stimuli acting on endothelial cells. Transport across the endothelium can occur via two different pathways: through the endothelial cell (transcellular) or between adjacent cells, through interendothelial junctions (paracellular). This review focuses on the regulation of the paracellular pathway. The paracellular pathway is composed of adhesive junctions between endothelial cells, both tight junctions and adherens junctions. The actin cytoskeleton is bound to each junction and controls the integrity of each through actin remodeling. These interendothelial junctions can be disassembled or assembled to either increase or decrease paracellular permeability. Mediators, such as thrombin, TNF-alpha, and LPS, stimulate their respective receptor on endothelial cells to initiate signaling that increases cytosolic Ca2+ and activates myosin light chain kinase (MLCK), as well as monomeric GTPases RhoA, Rac1, and Cdc42. Ca2+ activation of MLCK and RhoA disrupts junctions, whereas Rac1 and Cdc42 promote junctional assembly. Increased endothelial permeability can be reversed with "barrier stabilizing agents," such as sphingosine-1-phosphate and cyclic adenosine monophosphate (cAMP). This review provides an overview of the mechanisms that regulate paracellular permeability.
Exploitation of Heparanase Inhibitors from Microbial Metabolites Using an Efficient Visual Screening System (2004)

In this paper we describe the establishment of an efficient visual method for screening heparanase inhibitors, and we present the results of screening 10,000 microbial culture broths. Heparanase-overexpressing stable clones of the human hepatocellular carcinoma HepG2 cells were established and used as an enzyme source. Digestion of heparan sulfate (HS) was detected using novel HS-containing tablets or SDS-polyacrylamide gel electrophoresis. This method was able to find suramin, a known heparanase inhibitor, from a library of typical enzyme inhibitors. By screening 10,000 culture broths of microorganisms (actinomycetes, fungi, and bacteria) an actinomycete strain, RK99-A234, was found to have heparanase inhibitory activity. RK-682 was identified in the fermentation broth as a heparanase inhibitor, IC50 = 17 microM.
The isolation of CpG islands from human chromosomal regions 11q13 and Xp22 by segregation of partlymelted molecules (1998)

We isolated fragments containing parts of CpG islands from human chromosomal regions chosen for expected differences in gene density by segregation of partly melted molecules. Restriction fragments of P1 bacteriophage clones covering a region of 11q13 and those of cosmid clones derived from Xp22 were recovered from bands in denaturing gradient gels that were retained following prolonged exposure to electric field. Forty-five independent fragments derived from 11q13 and five from Xp22 were isolated. Nucleotide sequence analysis revealed that 11 of the 45 fragments from 11q13 contained CpG islands including four derived from known genes in 11q13. None of the five fragments derived from Xp22 resembled CpG islands. The number of CpG island fragments obtained was consistent with the expectation based on the number of Not I restriction endonuclease sites present at these regions. Adjustment of parameters in our quasi-theoretical approach to the rate of fragment dissociation improves the discrimination between retention and non-retention. The results support probable identification of CpG island fragments by their reduced rate of strand dissociation when retarded in a denaturing gradient gel.
Excited-State Energy-Transfer Dynamics in Self-Assembled Triads Composed of Two Porphyrins and an Intervening Bis(dipyrrinato)metal Complex (2003)

The synthesis and characterization of various triads composed of a linear array of two zinc porphyrins joined via an intervening bis(dipyrrinato)metal(II) complex are reported. The preparation exploits the facile complexation of dipyrrins with divalent metal ions to give bis(dipyrrinato)metal(II) complexes [abbreviated (dp)(2)M]. Copper(II) and palladium(II) chelates of dipyrrins (available by oxidation of dipyrromethanes) were prepared in 50-80% yield. A one-flask synthesis of bis(dipyrrinato)zinc(II) complexes was developed by oxidation of a dipyrromethane with DDQ or p-chloranil in the presence of Zn(OAc)(2).2H(2)O in THF ( approximately 80% yield). Three routes were developed for preparing porphyrin-dipyrrins: (1). Suzuki coupling of a boronate-substituted zinc porphyrin (ZnP) and bis[5-(4-iodophenyl)dipyrrinato]Pd(II) to give the (ZnP-dp)(2)Pd triad (50% yield), followed by selective demetalation of the (dp)(2)Pd unit by treatment with 1,4-dithiothreitol under neutral conditions (71% yield); (2). oxidation of a porphyrin-dipyrromethane with p-chloranil in the presence of Zn(OAc)(2).2H(2)O followed by chromatography on silica gel (71% yield); and (3). condensation of a dipyrrin-dipyrromethane and a dipyrromethane-dicarbinol under InCl(3) catalysis followed by oxidation with DDQ (10-16% yield). Four triads of form (ZnP-dp)(2)Zn were prepared in 83-97% yield by treatment of a porphyrin-dipyrrin with Zn(OAc)(2).2H(2)O at room temperature. Free base dipyrrins typically absorb at 430-440 nm, while the bis(dipyrrinato)metal complexes absorb at 460-490 nm. The fluorescence spectra/yields and excited-state lifetimes of the (ZnP-dp)(2)Zn triad in toluene show (1). efficient energy transfer from the bis(dipyrrinato)zinc(II) chromophore to the zinc porphyrins (98.5% yield), and (2). little or no quenching of the resulting excited zinc porphyrin relative to the isolated chromophore. Taken together, these results indicate that bis(dipyrrinato)zinc(II) complexes can serve as self-assembling linkers that further function as secondary light-collection elements in porphyrin-based light-harvesting arrays.
Galphas-coupled receptor signaling actively down-regulates α4β1-integrin affinity: A possible mechanism for cell de-adhesion (2008)

We conclude that Galphas-coupled GPCRs can rapidly down modulate the affinity state of VLA-4 binding pocket through a cAMP dependent pathway. This plays an essential role in the regulation of cell adhesion. We discuss several possible implications of this described phenomenon.
The Effect of Neuromuscular Stimulation of the Genioglossus on the Hypopharyngeal Airway (2002)

NS of the genioglossus muscle was effective in increasing the hypopharyngeal airway and may provide a useful alternative to direct stimulation of the hypoglossal nerve with a nerve cuff electrode in the development of neuroprosthetic treatments for obstructive sleep apnea.
Return of the Coronavirus: 2019-nCoV (2020)

The emergence of a novel coronavirus (2019-nCoV) has awakened the echoes of SARS-CoV from nearly two decades ago. Yet, with technological advances and important lessons gained from previous outbreaks, perhaps the world is better equipped to deal with the most recent emergent group 2B coronavirus.
Counterion-Hopping along the Backbone of Single-Stranded DNA in Nanometer Pores: A Mechanism for Current Conduction (2007)

Molecular dynamics calculations are performed to investigate ionic current conduction through nanopores in the presence of single-stranded DNA. We find the counterions to be strongly attracted to the phosphate groups of the DNA, with resident time on the order of nanoseconds, while coions are strongly excluded. The diffusion constant of the counterions is calculated and used to estimate the ionic current through the pore, which gives a similar magnitude as in experiment. The results suggest a counterion-hopping mechanism along the ssDNA backbone in the current conduction through nanopores.
Glycerol Enhancement of Ligand-Polylysine/DNA Transfection (1996)

Primary human fibroblasts and a series of cell lines (A549, BNL CL.2, H225, NIH 3T3 and Rat-1) are efficiently transfected by using positively charged complexes of plasmid DNA and transferrin-polylysine or polylysine in the presence of glycerol (1 molar to 1.8 molar, depending on the cell type). An increase in gene expression of up to several-hundredfold (compared to complexes without glycerol) is obtained if the transfection mixture is incubated with the cells for 3-4 h at 37 degrees C. This simple method has been used for transient expression of luciferase, beta-galactosidase and interleukin-2, and also for the generation of stably transfected cells.
DNMT1–MicroRNA126 Epigenetic Circuit Contributes to Esophageal Squamous Cell Carcinoma Growth via ADAM9–EGFR–AKT Signaling (2014)

Our results indicate that miR-126 is a potential prognostic indicator for ESCC and suggest that a novel "DNMT1-miR-126 epigenetic circuit" is involved in ESCC progression. Consequently, miR-126-based epigenetic modulations may provide a basic rationale for new approaches to antitumor therapeutics.