gebhart/patrepeval huggingface dataset:
Long-Term Transmission of Defective RNA Viruses in Humans and <i>Aedes</i> Mosquitoes (2006)

In 2001, dengue virus type 1 (DENV-1) populations in humans and mosquitoes from Myanmar acquired a stop-codon mutation in the surface envelope (E) protein gene. Within a year, this stop-codon strain had spread to all individuals sampled. The presence of truncated E protein species within individual viral populations, along with a general relaxation in selective constraint, indicated that the stop-codon strain represents a defective lineage of DENV-1. We propose that such long-term transmission of defective RNA viruses in nature was achieved through complementation by coinfection of host cells with functional viruses.
Prophylactic Administration of Fucoidan Represses Cancer Metastasis by Inhibiting Vascular Endothelial Growth Factor (VEGF) and Matrix Metalloproteinases (MMPs) in Lewis Tumor-Bearing Mice (2015)

Fucoidan, a heparin-like sulfated polysaccharide, is rich in brown algae. It has a wide assortment of protective activities against cancer, for example, induction of hepatocellular carcinoma senescence, induction of human breast and colon carcinoma apoptosis, and impediment of lung cancer cells migration and invasion. However, the anti-metastatic mechanism that fucoidan exploits remains elusive. In this report, we explored the effects of fucoidan on cachectic symptoms, tumor development, lung carcinoma cell spreading and proliferation, as well as expression of metastasis-associated proteins in the Lewis lung carcinoma (LLC) cells-inoculated mice model. We discovered that administration of fucoidan has prophylactic effects on mitigation of cachectic body weight loss and improvement of lung masses in tumor-inoculated mice. These desired effects are attributed to inhibition of LLC spreading and proliferation in lung tissues. Fucoidan also down-regulates expression of matrix metalloproteinases (MMPs), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and vascular endothelial growth factor (VEGF). Moreover, the tumor-bearing mice supplemented with fucoidan indeed benefit from an ensemble of the chemo-phylacticity. The fact is that fucoidan significantly decreases viability, migration, invasion, and MMPs activities of LLC cells. In summary, fucoidan is suitable to act as a chemo-preventative agent for minimizing cachectic symptoms as well as inhibiting lung carcinoma metastasis through down-regulating metastatic factors VEGF and MMPs.
Co-evolving stability and conformational homogeneity of the human adenosine A<sub>2a</sub>receptor (2008)

Structural studies on mammalian integral membrane proteins have long been hampered by their instability in detergent. This is particularly true for the agonist conformation of G protein-coupled receptors (GPCRs), where it is thought that the movement of helices that occurs upon agonist binding results in a looser and less stable packing in the protein. Here, we show that mutagenesis coupled to a specific selection strategy can be used to stabilize the agonist and antagonist conformations of the adenosine A(2a) receptor. Of the 27 mutations identified that improve the thermostability of the agonist conformation, only three are also present in the 17 mutations identified that improve the thermostability of the antagonist conformation, suggesting that the selection strategies used were specific for each conformation. Combination of the stabilizing mutations for the antagonist- or agonist-binding conformations resulted in mutants that are more stable at higher temperatures than the wild-type receptor by 17 degrees C and 9 degrees C, respectively. The mutant receptors both showed markedly improved stability in short-chain alkyl-glucoside detergents compared with the wild-type receptor, which will facilitate their structural analysis.
Involvement of the outer membrane in gentamicin and streptomycin uptake and killing in Pseudomonas aeruginosa (1981)

Induction of a major outer membrane protein, H1, in Pseudomonas aeruginosa resulted in decreased susceptibility to gentamicin and streptomycin. Mutants which overproduce protein H1 and cells in which H1 is induced in response to growth conditions had altered kinetics of uptake and killing. It was further demonstrated that gentamicin and streptomycin interact with the outer membrane to permeabilize it to lysozyme and to increase the permeation of a chromogenic beta-lactam, nitrocefin. Experiments with inhibitors of aminoglycoside uptake showed that uptake was not required to increase permeability. Mg2+ at 1 mM totally inhibited aminoglycoside-mediated outer membrane permeabilization. We propose that the uptake and killing by these aminoglycosides requires interaction with an Mg2+ binding site at the outer membrane, permitting aminoglycoside uptake into the periplasm.
Silicon temperature measurement by infrared transmission for rapid thermal processing applications (1990)

The use of optical transmission at 1.3 and 1.55 μm is reported to measure the temperature of silicon wafers in a rapid thermal processing environment. Physically, as the wafer temperature increases, infrared transmission drops due to band-gap reduction and an increased phonon population. This method has been used to measure wafer temperature with a resolution of several degrees from 400 to 800 °C, and is compatible with the thick quartz walls of the processing chamber. As part of this work, the absorption constant of silicon at 1.3 and 1.55 μm from 400 to 800 °C has also been measured.
Supramolecular Layer-by-Layer Assembly of 3D Multicomponent Nanostructures via Multivalent Molecular Recognition (2008)

The supramolecular layer-by-layer assembly of 3D multicomponent nanostructures of nanoparticles is demonstrated. Nanoimprint lithography (NIL) was used as the patterning tool for making patterned beta-cyclodextrin (CD) self-assembled monolayers (SAMs) and for the confinement of nanoparticles on the substrate. A densely packed and multilayered nanoparticle structure was created by alternating assembly steps of complementary guest- (Fc-SiO(2), 60 nm) and host-functionalized (CD-Au, 3 nm) nanoparticles. The effects induced by the order of the nanoparticle assembly steps, going from large to small and from small to large nanoparticles by using Fc-SiO(2), CD-Au, and CD-SiO(2) (350 nm) nanoparticles, were compared. AFM height profiles revealed that the specific supramolecular assembly of nanoparticles was self-limited, i.e. one nanoparticle layer per assembly step, allowing the control over the thickness of the supramolecular hybrid nanostructure by choosing the size of the nanoparticles, irrespective of the core material of the nanoparticles. The roughness of structure, observed by AFM imaging of the top layer, was directly influenced by the size and packing of the underlying nanoparticle layers.
Quantum Dot Solar Cells with Multiple Exciton Generation (2005)

We have measured the quantum yield of the multiple exciton generation (MEG) process in quantum dots (QDs) of the lead-salt semiconductor family (PbSe, PbTe, and PbS) using fs pump-probe transient absorption measurements. Very high quantum yields (up to 300%) for charge carrier generation from MEG have been measured in all of the Pb-VI QDs. We have calculated the potential maximum performance of various MEG QD solar cells in the detailed balance limit. We examined a two-cell tandem PV device with singlet fission (SF), QD, and normal dye (N) absorbers in the nine possible series-connected combinations to compare the tandem combinations and identify the combinations with the highest theoretical efficiency. We also calculated the maximum efficiency of an idealized single-gap MEG QD solar cell with M multiplications and its performance under solar concentration.
Automated Observer-independent Acquisition of Cardiac Short-Axis MR Images: A Pilot Study (2001)

The authors compared an automated observer-independent acquisition planning method for short-axis multisection multiphase cardiac magnetic resonance imaging studies with conventional manual image planning. Systematic and random differences and reproducibility of left ventricular function measurements and image geometry were evaluated in five healthy adult volunteers and 20 patient studies. Results with the automated planning method were as accurate and reproducible as those with the manual planning method.
EXPLORING METHODS TO IMPROVE PRESSURE ULCER DETECTION: SPECTROSCOPIC ASSESSMENT OF THE BLANCH RESPONSE (2006)

Pressure damage in intact skin is difficult to detect, particularly in individuals with dark skin, because color changes and tissue blanching are masked by the skin's pigmentation. Tissue reflectance spectroscopy (TRS) may be able to detect the blanch response regardless of skin color by measuring the change in total hemoglobin (delta tHb) that occurs when pressure is applied to the skin. The objective of this dissertation was to examine the ability of TRS to detect the blanch response at sites at risk for pressure ulcer development in individuals with various levels of skin pigmentation. Three studies were conducted to address this objective. In Study 1, delta tHb was assessed at the heel and sacrum of light and dark-skinned healthy participants using a portable TRS system. Study 1 showed that a significant decrease (p less than 0.001) in tHb could be measured in both light and dark skinned-participants with good intra-rater reliability (ICC greater than or equal to 0.80) at the heel, but not at the sacrum. Study 2 was conducted to identify a reliable method of skin color description for use in subsequent studies of the spectroscopic blanch response. Two examiners (B and C) performed three skin color assessments at the volar forearm of ten healthy participants using Munsell color tile matching and colorimetry. Intra and inter-rater reliability was excellent for colorimetry (ICCs typically greater than or equal to 0.90). Reliability for Munsell color tile matching was highest for Munsell value within Examiner B (93% agreement, kappa 0.87-1.00), which was determined to be sufficiently high for use in subsequent studies. In Study 3, delta tHb was assessed at the heels of light, moderate, and dark-skinned elderly nursing home residents at risk for pressure ulcers. As in the pilot study, a significant decrease in tHb was observed in all skin color groups (p less than 0.05). Intra-rater reliability for delta tHb was moderate or greater (ICC greater than or equal to 0.61). In combination, the results of Study 1 and Study 3 demonstrated that a significant spectroscopic blanch response could be detected with moderate or greater intra-rater reliability at the heel regardless of age or pressure ulcer risk status.
Synthesis, Anticlotting and Antiplatelet Effects of 1,2,3-Triazoles Derivatives (2016)

1,2,3-triazoles are potential candidates for molecular modeling of new antithrombotic drugs.
Activation of human α1 and α2 homomeric glycine receptors by taurine and GABA (2001)

1. Two ligand binding alpha subunits, alpha1 and alpha2, of the human (H) glycine receptor (GlyR) are involved at inhibitory synapses in the adult and neonatal spinal cord, respectively. The ability of homomeric alphaH1 and alphaH2 GlyRs to be activated by glycine, taurine and GABA was studied in Xenopus oocytes or in the human embryonic kidney HEK-293 cell line. 2. In outside-out patches from HEK cells, glycine, taurine and GABA activated both GlyRs with the same main unitary conductance, i.e. 85 +/- 3 pS (n = 6) for alphaH1, and 95 +/- 5 pS (n = 4) for alphaH2. 3. The sensitivity of both alphaH1 and alphaH2 GlyRs to glycine was highly variable. In Xenopus oocytes the EC50 for glycine (EC50gly) was between 25 and 280 microM for alphaH1 (n = 44) and between 46 and 541 microM for alphaH2 (n = 52). For both receptors, the highest EC50gly values were found on cells with low maximal glycine responses. 4. The actions of taurine and GABA were dependent on the EC50gly: (i) their EC50 values were linearly correlated to EC50gly, with EC50tau approximately 10 EC50gly and EC50GABA approximately 500-800 EC50gly; (ii) they could act either as full or weak agonists depending on the EC50gly. 5. The Hill coefficient (n(H)) of glycine remained stable regardless of the EC50gly whereas n(H) for taurine decreased with increasing EC50tau. 6. The degree of desensitization, evaluated by fast application of saturating concentrations of agonist on outside-out patches from Xenopus oocytes, was similar for glycine and taurine on both GlyRs and did not exceed 50 %. 7. Our data concerning the variations of EC50gly and the subsequent behaviour of taurine and GABA could be qualitatively described by the simple del Castillo-Katz scheme, assuming that the agonist gating constant varies whereas the binding constants are stable. However, the stability of the Hill coefficient for glycine was not explained by this model, suggesting that other mechanisms are involved in the modulation of EC50.
Technology affordances (1991)

Article Technology affordances Share on Author: William W. Gaver Rank Xerox Cambridge EuroPARC, 61 Regent Street, Cambridge CB2 1AB, U.K. Rank Xerox Cambridge EuroPARC, 61 Regent Street, Cambridge CB2 1AB, U.K.View Profile Authors Info & Claims CHI '91: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsApril 1991 Pages 79–84https://doi.org/10.1145/108844.108856Online:01 March 1991Publication History 464citation11,156DownloadsMetricsTotal Citations464Total Downloads11,156Last 12 Months1,252Last 6 weeks153 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
The effect of copper and zinc on the shell growth of <i>Mytilus edulis</i> measured by a laser diffraction technique (1984)

The effects of copper and zinc on the daily shell growth of Mytilus edulis have been measured with a laser diffraction measuring technique accurate to 3 µm. The results show that within three days 10 ppb added copper has a significant inhibitory effect on shell growth. Longer term experiments have been undertaken which show that the effects of 10 ppb added copper become more severe as exposure time increases. Recovery of near normal shell growth does occur on transfer to clean sea water even after a 14 day exposure to this concentration. The effects of zinc on shell growth are less severe. Transferring animals from their natural environment to the laboratory causes a measurable disturbance of shell growth for up to a week.
Long-Term Expression of the Biologically Active Growth Hormone in Genetically Modified Fibroblasts after Implantation into a Hypophysectomized Rat (1995)

We employed the hypophysectomized rats as an animal model to explore the feasibility of using genetically engineered fibroblast cells for growth hormone gene therapy. An internal ribosome entry site (IRES)-directed bicistronic retroviral vector, PSN, which contained a porcine growth hormone (pGH) cDNA at the first cistron and a Neo(r) gene at the second cistron was used to infect primary rat embryo fibroblast (REF) cells. The infected cells (5 x 10(6) cells/rat) were injected directly into the peritoneum of syngeneic hypophysectomized rats. We demonstrate that the implanted PSN-infected REF cells could secrete biologically active pGH in vivo, leading to significant growth of the tibia at day 15 and day 57 post-implantation. We also treated the PSN-infected REF cells with collagen to form a tissue-like structure. The skin-like discs were grafted underneath the skin on the back of rats and cells were retrieved at different times. Using two criteria, semiquantitative reverse transcription-polymerase chain reaction on the pGH RNA extracted from the explants and G418 resistance conferred from the explanted cells, we demonstrate that pGH was expressed in the implanted fibroblasts up to 70 days. Despite the fact that the total pGH RNA level was reduced in the explants of long-time post-implantation, which was probably due to the reduction of transduced cells retained in the explants, the specific efficiencies of pGH RNA expression from these explants were maintained as high as the primary PSN-infected REF prior implantation. These results suggest that fibroblast cells are capable of expressing the foreign genes persistently in vivo.
Handbook of radiation and scattering of waves (1995)

Acoustic Waves in Fluids: Cartesian Tensors and Their Properties Integral-Transformation Methods Basic Equations of the Theory of Acoustic Waves in Fluids The Principle of Superposition and Its Application to Acoustic Wave Fields in Configurations with Geometrical Symmetry The Acoustic Wave Equations, Constitutive Relations, and Boundary Conditions in the Time Laplace-Transform Domain (Complex Frequency Domain) Acoustic Radiation from Sources in an Unbounded, Homogeneous, Isotropic Fluid Acoustic Reciprocity Theorems and Their Applications Plane-Wave Scattering by an Object in an Unbounded, Homogeneous, Isotropic, Lossless Embedding. Elastic Waves in Solids: Cartesian Tensors and Their Properties Integral-Transformation Methods Basic Equations of the Theory of Elastic Waves in Solids The Principle of Superposition and Its Application to Electromagnetic Fields in Configurations with Geometrical Symmetry The Elastic Wave Equations, Constitutive Relations, and Boundary Conditions in the Time Laplace-Transform Domain (Complex Frequency Domain) Elastodynamic Radiation from Sources in an Unbounded, Homogeneous, Isotropic Solid Plane Elastic Waves in Homogeneous Solids Elastodynamic Reciprocity Theorems and Their Applications Plane-Wave Scattering by an Object in an Unbounded, Homogeneous, Isotropic, Lossless Embedding. Electromagnetic Waves: Cartesian Tensors and Their Properties Integral-Transformation Methods The Electromagnetic Constitutive Relations The Electromagnetic Boundary Conditions Exchange of Energy in the Electromagnetic Field Vector Potentials, Point-Source Solutions, and Green's Function in the Theory of Electromagnetic Radiation from Sources The Principle of Superposition and Its Application to Electromagnetic Fields in Configuration with Geometrical Symmetry The Electromagnetic Field Equations, Constitutive Relations, and Boundary Conditions in the Time Laplace-Transform Domain (Complex Frequency Domain) Complex Frequency Domain Vector Potentials Point-Source Solutions and Green's Functions in the Theory of Electromagnetic Radiation from Sources Electromagnetic Radiation from Sources in an Unbounded, Homogeneous, Isotropic Medium Plane Electromagnetic Waves in Homogeneous Media Electromagnetic Reciprocity Theorems and Their Applications Plane-Wave Scattering by an Object in an Unbounded, Homogeneous, Isotropic, Lossless Embedding Interference and Shielding of Electromagnetic Systems Accessible via Low-Frequency Terminations Electromagnetic Compatibility (EMC).
Novel Nanoporous Au−Pd Alloy with High Catalytic Activity and Excellent Electrochemical Stability (2010)

A novel nanoporous gold−palladium alloy has been successfully fabricated by electrochemically dealloying a multicomponent metallic glass. In comparison with conventional nanoporous gold prepared by dealloying Au−Ag alloys, the nanoporous gold−palladium alloy shows much higher catalytic activity for electrooxidation of methanol as a free-standing electrode. Moreover, a small amount of palladium in the nanoporous alloy is found to dramatically improve the electrochemical stability of nanoporous gold.
Peroxisome Biogenesis Disorders (2006)

Abstract Peroxisome biogenesis disorders are progressive disorders characterized by loss of multiple peroxisomal metabolic functions. These diseases, consisting of 12 complementation groups, are inherited in an autosomal recessive manner and are caused by defects in peroxisome assembly.
The Adenovirus E1B 55-Kilodalton and E4 Open Reading Frame 6 Proteins Limit Phosphorylation of eIF2α during the Late Phase of Infection (2009)

During a productive infection, species C adenovirus reprograms the host cell to promote viral translation at the expense of cellular translation. The E1B 55-kilodalton (E1B-55K) and E4 open reading frame 6 (E4orf6) proteins are important in this control of gene expression. As part of a ubiquitin-protein ligase, these viral proteins stimulate viral mRNA export, inhibit cellular mRNA export, promote viral gene expression, and direct the degradation of certain host proteins. We report here that the E1B-55K and E4orf6 proteins limited phosphorylation of eIF2alpha and the activation of the eIF2alpha kinase PKR. Phospho-eIF2alpha levels were observed to rise and fall at least twice during infection. The E1B-55K and E4orf6 proteins prevented a third increase at late times of infection. PKR appeared to phosphorylate eIF2alpha only in the absence of E1B-55K/E4orf6 function. PKR activation and eIF2alpha phosphorylation was unrelated to the cytoplasmic levels of the adenovirus inhibitor of PKR, VA-I RNA. Nonetheless, expression of a PKR inhibitor, the reovirus double-stranded RNA-binding protein sigma 3, prevented PKR activation and eIF2alpha phosphorylation. The sigma 3 protein largely corrected the defect in viral late protein synthesis associated with the E1B-55K and E4orf6 mutant viruses without affecting cytoplasmic levels of the late viral mRNA. The ubiquitin-protein ligase activity associated with the E1B-55K/E4orf6 complex was necessary to prevent activation of PKR and phosphorylation of eIF2alpha. These findings reveal a new contribution of the E1B-55K/E4orf6 complex to viral late protein synthesis and the existence of multiple layers of regulation imposed on eIF2alpha phosphorylation and PKR activation in adenovirus-infected cells.
Feedback Control of an LVAD Supporting a Failing Cardiovascular System Regulated by the Baroreflex (2006)

The baroreflex is an internal feedback mechanism that stabilizes the blood pressure in the circulatory system. Its function in patients with congestive heart failure is preserved fairly well. When these patients are implanted with a left ventricular assist device (LVAD), the baroreflex plays an important role in interacting with the controller that regulates the pump speed. In this paper, we consider a combined model of the cardiovascular system, the baroreflex mechanism, and an LVAD. We present results that will describe the interaction mechanisms between these three subsystems. We then propose a feedback controller for the LVAD which automatically adjust its speed based on the systemic vascular resistance (SVR) and heart rate (HR) under varying patient conditions. Simulation results show that the combined model is capable of reproducing human responses to exercise and the proposed controller is able to respond to change in physiological state of patients with heart failure
Multi-label informed latent semantic indexing (2005)

Latent semantic indexing (LSI) is a well-known unsupervised approach for dimensionality reduction in information retrieval. However if the output information (i.e. category labels) is available, it is often beneficial to derive the indexing not only based on the inputs but also on the target values in the training data set. This is of particular importance in applications with multiple labels, in which each document can belong to several categories simultaneously. In this paper we introduce the multi-label informed latent semantic indexing (MLSI) algorithm which preserves the information of inputs and meanwhile captures the correlations between the multiple outputs. The recovered "latent semantics" thus incorporate the human-annotated category information and can be used to greatly improve the prediction accuracy. Empirical study based on two data sets, Reuters-21578 and RCV1, demonstrates very encouraging results.