gebhart/patrepeval huggingface dataset:
A Simple, Highly Efficient Method for Heterologous Expression in Mammalian Primary Neurons Using Cationic Lipid-mediated mRNA Transfection (2010)

Expression of heterologous proteins in adult mammalian neurons is a valuable technique for the study of neuronal function. The post-mitotic nature of mature neurons prevents effective DNA transfection using simple, cationic lipid-based methods. Adequate heterologous protein expression is often only achievable using complex techniques that, in many cases, are associated with substantial toxicity. Here, a simple method for high efficiency transfection of mammalian primary neurons using in vitro transcribed mRNA and the cationic lipid transfection reagent Lipofectamine™ 2000 is described. Optimal transfection conditions were established in adult mouse dissociated dorsal root ganglion (DRG) neurons using a 96-well based luciferase activity assay. Using these conditions, a transfection efficiency of 25% was achieved in DRG neurons transfected with EGFP mRNA. High transfection efficiencies were also obtained in dissociated rat superior cervical ganglion (SCG) neurons and mouse cortical and hippocampal cultures. Endogenous Ca(2+) currents in EGFP mRNA-transfected SCG neurons were not significantly different from untransfected neurons, which suggested that this technique is well suited for heterologous expression in patch clamp recording experiments. Functional expression of a cannabinoid receptor (CB1R), a G protein inwardly rectifying K(+) channel (GIRK4) and a dominant-negative G protein α-subunit mutant (G(oA) G203T) indicate that the levels of heterologous protein expression attainable using mRNA transfection are suitable for most functional protein studies. This study demonstrates that mRNA transfection is a straightforward and effective method for heterologous expression in neurons and is likely to have many applications in neuroscience research.
Novel Copper (Cu) Loaded Core–Shell Silica Nanoparticles with Improved Cu Bioavailability: Synthesis, Characterization and Study of Antibacterial Properties (2012)

We report synthesis of a novel core-shell silica based antimicrobial nanoparticles where the silica shell has been engineered to accommodate copper (Cu). Synthesis of the core-shell Cu-silica nanoparticle (C-S CuSiO2NP) involves preparation of base-hydrolyzed Stöber silica "seed" particles first, followed by the acid-catalyzed seeded growth of the Cu-silica shell layer around the core. The Scanning Electron Microscopy (SEM) and the Transmission Electron Microscopy (TEM) measured the seed particle size to be -380 nm and the shell thickness to be -35 nm. The SEM particle characterization confirms formation of highly monodispersed particles with smooth surface morphology. Characterization of particle size distribution in solution by Dynamic Light Scattering (DLS) technique was fairly consistent with the electron microscopy results. Loading of Cu to nanoparticles was confirmed by the SEM-Energy Dispersive X-Ray Spectroscopy (EDS) and Atomic Absorption Spectroscopy (AAS). The Cu loading was estimated to be 0.098 microg of metallic copper per mg of C-S CuSiO2NP material by the AAS technique. Antibacterial efficacy of C-S CuSiO2NP was evaluated against E. coli and B. subtilis using Cu hydroxide ("Insoluble" Cu compound, sub-micron size particles) as positive control and silica "seed" particles (without Cu loading) as negative control. Bacterial growth in solution was measured against different concentrations of C-S CuSiO2NP to determine the Minimum Inhibitory Concentration (MIC) value. The estimated MIC values were 2.4 microg metallic Cu/mL for both E. coli and B. subtilis. Bac-light fluorescence microscopy based assay was used to count relative population of the live and dead bacteria cells. Antibacterial study clearly shows that C-S CuSiO2NP is more effective than insoluble Cu hydroxide particles at equivalent metallic Cu concentration, suggesting improvement of Cu bioavailability (i.e., more soluble Cu) in C-SCuSiO2NP material due to its core-shell design.
An improved illumination model for shaded display (1980)

To accurately render a two-dimensional image of a three-dimensional scene, global illumination information that affects the intensity of each pixel of the image must be known at the time the intensity is calculated. In a simplified form, this information is stored in a tree of “rays” extending from the viewer to the first surface encountered and from there to other surfaces and to the light sources. A visible surface algorithm creates this tree for each pixel of the display and passes it to the shader. The shader then traverses the tree to determine the intensity of the light received by the viewer. Consideration of all of these factors allows the shader to accurately simulate true reflection, shadows, and refraction, as well as the effects simulated by conventional shaders. Anti-aliasing is included as an integral part of the visibility calculations. Surfaces displayed include curved as well as polygonal surfaces.
The Incidence and Determinants of Decubitus Ulcers in Hospital Care (2013)

There are major differences between clinical care units in the risk of decubitus ulcers. Epidemiological analysis of routine quality management data is useful to assess the benefit of measures taken in medical care. Continuing evaluation is essential.
Challenges for the development of female-controlled vaginal microbicides (1994)

The development and testing of safe, effective, and affordable microbicidal products for women at risk of human immunodeficiency virus (HIV) raise complex scientific, ethical, and political issues. Ideal would by range of products (gels, foams, suppositories) that protect against HIV and other sexually transmitted diseases without impairing conception. This, in turn, requires the development of vaginal compounds that prevent the attachment of HIV-infected lymphocytes to epithelial surfaces, the secretion of virus from these cells, or the uptake of the virus by the mucosal epithelium with minimal cell membrane disruption. Problematic would be the design of a Phase III effectiveness trail that distributes the burdens and benefits of research equitably and provides controls with an alternate means of protection against HIV while maintaining scientific rigor. Since clinical trials call for a study population with a high seroincidence rate attributable primarily to the sexual transmission of HIV, prostitutes are the logical choice of subjects; sex workers are, however, the women most vulnerable to physical and economic exploitation. Women's input will be essential at each stage of development and testing, and such consultation can provide valuable feedback on method of application and timing of insertion. Finally, public-sector organizations must assume a leadership role in the coordination of the development of HIV prevention technologies.
Degradation of oxidized proteins in mammalian cells (1997)

Protein oxidation in vivo is a natural consequence of aerobic life. Oxygen radicals and other activated oxygen species generated as by-products of cellular metabolism or from environmental sources cause modifications to the amino acids of proteins that generally result in loss of protein function/enzymatic activity. Oxidatively modified proteins can undergo direct chemical fragmentation or can form large aggregates due to covalent cross-linking reactions and increased surface hydrophobicity. Mammalian cells exhibit only limited direct repair mechanisms and most oxidized proteins undergo selective proteolysis. The proteasome appears to be largely responsible for the degradation of soluble intracellular proteins. In most cells, oxidized proteins are cleaved in an ATP-and ubiquitin-independent pathway by the 20 S "core" proteasome. The proteasome complex recognizes hydrophobic amino acid residues, aromatic residues, and bulky aliphatic residues that are exposed during the oxidative rearrangement of secondary and tertiary protein structure: increased surface hydrophobicity is a feature common to all oxidized proteins so far tested. The recognition of such (normally shielded) hydrophobic residues is the suggested mechanism by which proteasome catalyzes the selective removal of oxidatively modified cell proteins. By minimizing protein aggregation and cross-linking and by removing potentially toxic protein fragments, proteasome plays a key role in the overall antioxidant defenses that minimize the ravages of aging and disease.
HMGB1 Mediates Anemia of Inflammation in Murine Sepsis Survivors (2015)

Patients surviving sepsis develop anemia, but the molecular mechanism is unknown. Here we observed that mice surviving polymicrobial gram-negative sepsis develop hypochromic, microcytic anemia with reticulocytosis. The bone marrow of sepsis survivors accumulates polychromatophilic and orthochromatic erythroblasts. Compensatory extramedullary erythropoiesis in the spleen is defective during terminal differentiation. Circulating tumor necrosis factor (TNF) and interleukin (IL)-6 are elevated for 5 d after the onset of sepsis, and serum high-mobility group box 1 (HMGB1) levels are increased from d 7 until at least d 28. Administration of recombinant HMGB1 to healthy mice mediates anemia with extramedullary erythropoiesis and significantly elevated reticulocyte counts. Moreover, administration of anti-HMGB1 monoclonal antibodies after sepsis significantly ameliorates the development of anemia (hematocrit 48.5 ± 9.0% versus 37.4 ± 6.1%, p < 0.01; hemoglobin 14.0 ± 1.7 versus 11.7 ± 1.2 g/dL, p < 0.01). Together, these results indicate that HMGB1 mediates anemia by interfering with erythropoiesis, suggesting a potential therapeutic strategy for anemia in sepsis.
Acrylic-based resin with favorable properties for three-dimensional two-photon polymerization (2004)

We describe an acrylic-based prepolymer resin that is ideally suited for the fabrication of three-dimensional structures with two-photon polymerization. We characterize the photochemical and photophysical properties of the photoinitiator and present representative structures that demonstrate the favorable mechanical and optical properties of the polymer.
Two bacterial pathogens of Helicoverpa armigera (Hubner) (Lepidoptera : Noctuidae) (2005)

Bacterial pathogens of Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae) were investigated. Two different pathogenic bacteria were isolated from unhealthy and dead larvae. They were identified as Pantoea agglomerans (Ewing and Fife) and Alcaligenes piechaudii Kiredjian et al. on the basis of fatty acid methyl ester (FAMEs) analysis and carbon utilization profiles by using Microbial Identification and Biolog Microplate Systems. Laboratory experiments carried out to determine insecticidal activities of these isolates showed that Pantoea agglomerans and Alcaligenes piechaudii have 95.0% and 98.75% mortality on third-instar larvae of H. armigera, respectively, after 14 days. This is the first study to demonstrate that Pantoea agglomerans and Alcaligenes piechaudii are pathogenic bacterial flora of H. armigera. These bacteria may have great potential for use in biological control of H. armigera.
JUMP-C: A Randomized Trial of Mericitabine Plus Pegylated Interferon Alpha-2a/Ribavirin for 24 Weeks in Treatment-NaÏVe HCV Genotype 1/4 Patients (2013)

A 24-week response-guided combination regimen of mericitabine 1,000 mg BID plus Peg-IFNα-2a/RBV is well tolerated and more effective than a standard 48-week course of Peg-IFNα-2a/RBV.
Preferential expression of novel MUC1 tumor antigen isoforms in human epithelial tumors and their tumor‐potentiating function (1997)

The human MUC1 gene expresses at least 2 type 1 membrane proteins: MUC1/REP, a polymorphic high m.w. MUC1 glycoprotein often highly expressed in breast cancer tissues and containing a variable number of tandem 20 amino acid repeat units, and the MUC1/Y protein, which lacks this repeat array and, therefore, is not polymorphic. Despite their documented importance in signal transduction processes, the relative expression of the 2 isoforms in epithelial tumors is unknown. Using antibody reagents which recognize different MUC1 domains, the expression of these isoforms in malignant epithelial cells has been evaluated. A comparison of the amounts of the 2 isoforms revealed preferential expression of the novel MUC1/Y protein in breast cancer tissue samples. Furthermore, although the MUC1/REP protein is almost undetectable in HeLa cervical adenocarcinoma epithelial cells, the MUC1/Y isoform is extensively expressed in these cells. The presence of the MUC1/Y sequence as well as that of an additional tandem-repeat-array-lacking isoform, designated MUC1/X, were demonstrated by reverse transcriptase PCR amplification of RNA extracted from HeLa and ovarian carcinoma cells. It has been shown previously that the MUC1 cytoplasmic domain interacts with the SH2 domain containing GRB2 protein, which transduces signals to ras, a protein which in its activated form can lead to cell transformation. We present here data demonstrating that MUC1/Y isoform expression increases the tumorigenic potential of DA3 mouse mammary epithelial cells; in contrast, potentiation of tumorigenicity is not observed with MUC1/REP expression. Our studies thus demonstrate that expression of the MUC1 gene in epithelial tumors can give rise to substantial levels of MUC1 proteins devoid of the tandem repeat array, which are generated by alternative splicing mechanisms. Int. J. Cancer 71:741-749, 1997. © 1997 Wiley-Liss Inc.
Transition Metal-Based Polymers with Controlled Architectures:  Well-Defined Poly(ferrocenylsilane) Homopolymers and Multiblock Copolymers via the Living Anionic Ring-Opening Polymerization of Silicon-Bridged [1]Ferrocenophanes (1996)

The living anionic ring-opening polymerization (ROP) of the methylated silicon-bridged [1]ferrocenophane Fe(η-C5H4)2SiMe2 1 initiated by n-BuLi, PhLi, FcLi (Fc = Fe(η-C5H4)(η-C5H5)), and 1,1‘-dilithioferrocene, fcLi2· 2/3TMEDA (fc = Fe(η-C5H4)2) in THF at 20 °C has allowed the preparation of well-defined poly(ferrocenyldimethylsilanes) [Fe(η-C5H4)2SiMe2]n 4 with control of molecular weights, narrow polydispersities, and controlled end-group structures. The living anionic ROP of 1 has also been used to prepare a variety of novel, well-defined organometallic/organic/inorganic multiblock copolymers constructed from a combination of poly(ferrocenyldimethylsilane) (PFS), polystyrene (PS), and poly(dimethylsiloxane) (PDMS). The materials prepared included PFS-b-PDMS diblock copolymers (7a and 7b), PDMS-b-PFS-b-PDMS triblock copolymers (8a and 8b), a PS-b-PFS diblock copolymer (10a), a PS-b-PFS-b-PDMS triblock copolymer (11), a PS-b-PFS-b-PDMS-b-PFS-b-PS pentablock copolymer (12), a PFS-b-PS-b-PFS triblock copolymer (15), and a PDMS-b-PFS-b-PS-b-PFS-b-PDMS pentablock copolymer (16). These materials were studied by cyclic voltammetry which afforded two reversible oxidation waves characteristic of redox-coupling arising from interactions between the skeletal iron atoms in the ferrocenylsilane blocks. The multiblock copolymers were also characterized by DSC which showed the presence of individual thermal transitions for each block which indicated that they were incompatible. In addition, the morphology of a film of PS-b-PFS (10a) was investigated by TEM which showed a high degree of phase separation leading to the formation of microdomains of polystyrene and poly(ferrocenyldimethylsilane).
Magnetron sputter coating of microspherical substrates (1979)

The fabrication of laser fusion targets requires the deposition of various metal and dielectric layers on microspherical substrates (100–500 μm diameter). The continuous motion for uniformly coating these spherical substrates has been accomplished for rf sputtering applications. In one approach, the spheres being coated are bounced and laterally swept across a table as the frequency of vibration of the table is changed continously. In another approach, the sputtering gas is also a levitation gas. The argon is fed through a collimated hole structure and keeps the microsphere both levitated and rotating during the sputter deposition. The uniformity and surface quality of the deposited films obtained by these two techniques are compared.
Proteolytic requirements for thrombin activation of anti-hemophilic factor (factor VIII). (1988)

Factor VIII functions in the intrinsic pathway of coagulation as the cofactor for factor IXa proteolytic activation of factor X. Proteolytic cleavage is required for activation and may be responsible for inactivation of cofactor activity. To identify which of the multiple cleavages are required for activation and inactivation of factor VIII, site-directed DNA-mediated mutagenesis of the factor VIII cDNA was performed and the altered forms of factor VIII were expressed in COS-1 monkey cells and characterized. Conversion of arginine residues to isoleucine residues at the aminoterminal side of the cleavage sites at positions 740, 1648, and 1721 resulted in cleavage resistance at the modified site with no alteration in the in vitro procoagulant activity and the susceptibility to thrombin activation. Similar modification of the thrombin cleavage sites at either position 372 or position 1689 resulted in molecules with residual factor VIII activity but resistant to thrombin cleavage at the modified site and not susceptible to thrombin activation. Modification of the arginine to either an isoleucine or a lysine at residue 336, the site postulated for proteolytic inactivation by activated protein C, resulted in a factor VIII molecule with increased procoagulant activity. This increased activity may result from greater resistance to proteolytic inactivation. A model for the activation and inactivation of factor VIII is proposed.
Generation of ozone by pulsed corona discharge over water surface in hybrid gas–liquid electrical discharge reactor (2005)

Ozone formation by a pulse positive corona discharge generated in the gas phase between a planar high voltage electrode made from reticulated vitreous carbon and a water surface with an immersed ground stainless steel plate electrode was investigated under various operating conditions. The effects of gas flow rate (0.5–3 litre min−1), discharge gap spacing (2.5–10 mm), applied input power (2–45 W) and gas composition (oxygen containing argon or nitrogen) on ozone production were determined. Ozone concentration increased with increasing power input and with increasing discharge gap. The production of ozone was significantly affected by the presence of water vapour formed through vaporization of water at the gas–liquid interface by the action of the gas phase discharge. The highest energy efficiency for ozone production was obtained using high voltage pulses of approximately 150 ns duration in Ar/O2 mixtures with the maximum efficiency (energy yield) of 23 g kW h−1 for 40% argon content.
Development of Effective Solvent Modifiers for the Solvent Extraction of Cesium from Alkaline High‐Level Tank Waste (2003)

Abstract A series of novel alkylphenoxy fluorinated alcohols were prepared and investigated for their effectiveness as modifiers in solvents containing calix[4]arene‐bis‐(tert‐octylbenzo)‐crown‐6 for the extraction of cesium from alkaline nitrate media. The structure of the fluorinated portion of the modifier influences the chemical stability, and a modifier that contained a terminal 1,1,2,2‐tetrafluoroethoxy group was found to decompose following long‐term exposure to warm alkaline solutions. However, replacement of the tetrafluoroethoxy group with a 2,2,3,3‐tetrafluoropropoxy group led to a series of modifiers that possessed the alkaline stability required for a solvent extraction process. Within this series of modifiers, the structure of the alkyl substituent (tert‐octyl, tert‐butyl, tert‐amyl, and sec‐butyl) of the alkylphenoxy moiety was found to have a profound impact on the phase behavior of the solvent in liquid–liquid contacting experiments, and hence on the overall suitability of the modifier for a solvent extraction process. The sec‐butyl derivative [1‐(2,2,3,3‐tetrafluoropropoxy)‐3‐(4‐sec‐butylphenoxy)‐2‐propanol] (Cs‐7SB) was found to possess the best overall balance of properties with respect to third phase and coalescence behavior, cleanup following degradation, resistance to solids formation, and cesium distribution behavior. Accordingly, this modifier was selected for use as a component of the solvent employed in the Caustic‐Side Solvent Extraction (CSSX) process designed for the removal of cesium from high‐level nuclear waste (HLW) at the U.S. Department of Energy's (DOE) Savannah River Site. In batch equilibrium experiments, this solvent has also been successfully shown to extract cesium from both simulated and actual solutions generated from caustic leaching of HLW tank sludge stored in tank B‐110 at the DOE's Hanford Site.
The Cricket location-support system (2000)

This paper presents the design, implementation, and evaluation of Cricket, a location-support system for in-building, mobile, location-dependent applications. It allows applications running on mobile and static nodes to learn their physical location by using listeners that hear and analyze information from beacons spread throughout the building. Cricket is the result of several design goals, including user privacy, decentralized administration, network heterogeneity, and low cost. Rather than explicitly tracking user location, Cricket helps devices learn where they are and lets them decide whom to advertise this information to; it does not rely on any centralized management or control and there is no explicit coordination between beacons; it provides information to devices regardless of their type of network connectivity; and each Cricket device is made from off-the-shelf components and costs less than U.S. $10. We describe the randomized algorithm used by beacons to transmit information, the use of concurrent radio and ultrasonic signals to infer distance, the listener inference algorithms to overcome multipath and interference, and practical beacon configuration and positioning techniques that improve accuracy. Our experience with Cricket shows that several location-dependent applications such as in-building active maps and device control can be developed with little effort or manual configuration.
The Role of the Tyrosine Kinase Domain of the Insulin-like Growth Factor-I Receptor in Intracellular Signaling, Cellular Proliferation, and Tumorigenesis (1995)

Insulin and insulin-like growth factor (IGF-I) receptors are heterotetrameric proteins consisting of two alpha-and two beta-subunits and members of the transmembrane tyrosine kinase receptors. Specific ligand binding to the receptor triggers a cascade of intracellular events, which begins with autophosphorylation of several tyrosine residues of the beta-subunit of the receptor. The triple cluster in the tyrosine kinase domain of the beta-subunit is the earliest and major autophosphorylation site. Previous studies have shown that substitutions of these three tyrosines by phenylalanines of both insulin and IGF-I receptors practically abolish any activation of cellular signaling pathways. We have studied the effect of double tyrosine mutations on IGF-I induced receptor autophosphorylation, activation of Shc and IRS-1 pathways, and cell proliferation and tumorigenicity. Substitution of tyrosines 1131/1135 blocks any detectable autophosphorylation, whereas substitution of tyrosines 1131/1136 or 1135/1136 only reduces autophosphorylation levels in some clones by approximately 50%. Nevertheless, all the cells expressing IGF-I receptors with double tyrosine substitutions demonstrated markedly reduced signaling through Shc and IRS-1 pathways. In addition, they were unable to respond to IGF-I-stimulated cell growth in culture, and tumor formation in nude mice was abrogated. These data suggest that the presence of tyrosine 1131 or 1135 essential for receptor autophosphorylation, whereas the presence of each of these tyrosines is necessary for a fully functional receptor.