gebhart/patrepeval huggingface dataset:
Preparation and properties of recombinant DNA derived tobacco mosaic virus coat protein (1990)

Recombinant DNA derived tobacco mosaic virus (vulgare strain) coat protein (r-TMVP) was obtained by cloning and expression in Escherichia coli and was purified by column chromatography, self-assembly polymerization, and precipitation. SDS-PAGE, amino terminal sequencing, and immunoblotting with polyclonal antibodies raised against TMVP confirmed the identify and purity of the recombinant protein. Isoelectric focusing in 8 M urea and fast atom bombardment mass spectrometry demonstrated that the r-TMVP is not acetylated at the amino terminus, unlike the wild-type protein isolated from the tobacco plant derived virus. The characterization of r-TMVP with regard to its self-assembly properties revealed reversible endothermic polymerization as studied by analytical ultracentrifugation, circular dichroism, and electron microscopy. However, the details of the assembly process differed from those of the wild-type protein. At neutral pH, low ionic strength, and 20 degrees C, TMVP forms a 20S two-turn helical rod that acts as a nucleus for further assembly with RNA and additional TMVP to form TMV. Under more acidic conditions, this 20S structure also acts as a nucleus for protein self-assembly to form viruslike RNA-free rods. The r-TMVP that is not acetylated carries an extra positive charge at the amino terminus and does not appear to form the 20S nucleus. Instead, it forms a 28S four-layer structure, which resembles in size and structure the dimer of the bilayer disk formed by the wild-type protein at pH 8.0, high ionic strength, and 20 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)
Cell surface expression of an endoplasmic reticulum resident heat shock protein gp96 triggers MyD88-dependent systemic autoimmune diseases (2003)

Heat shock proteins have been implicated as endogenous activators for dendritic cells (DCs). Without tissue distress or death, these intracellular molecules are inaccessible to surface receptor(s) on DCs, possibly to avoid uncontrolled DC activation and breakdown of immunologic tolerance. We herein addressed this hypothesis in transgenic mice by enforcing cell surface expression of gp96, a ubiquitous heat shock protein of the endoplasmic reticulum. Although a pan-specific promoter is used for transgene expression, neither the expression level nor the tissue distribution of the endogenous gp96 was altered by this maneuver. However, cell surface gp96 induced significant DC activations and spontaneous lupus-like autoimmune diseases, even though the development/functions of lymphocytic compartments were unaltered. Using a bone marrow chimera approach, we further demonstrated that both DC activation and autoimmunity elicited by cell surface gp96 are dependent on the downstream adaptor protein MyD88 for signaling by Toll/IL-1 receptor family. Our study not only established the proinflammatory property of cell surface gp96 in vivo, but also suggested a chronic stimulation of DCs by gp96 as a pathway to initiate spontaneous autoimmune diseases.
Estimation of local and nonlocal contributions to the current-induced magnetization switching (2006)

With the experimental results obtained with a special nanopillar structure and the calculations based on the one-dimensional diffusion equations, the respective contributions to the spin torque from spin accumulation and local spin current are quantitatively deduced. The results for a typical nanopillar structure show that the spin accumulation contributes to about 90% of the necessary torque for the antiparallel to parallel switching, while the parallel to antiparallel switching is totally dominated by the local spin current. Both the variations in spin accumulation and local spin current should be considered in any effort to reduce the critical switching current density. However it seems more effective to increase the local spin current in most cases.
Time-resolved, light scattering measurements of cartilage and cornea denaturation due to free electron laser radiation (2003)

Light scattering is used to monitor the dynamics and energy thresholds of laser-induced structural alterations in biopolymers due to irradiation by a free electron laser (FEL) in the infrared (IR) wavelength range 2.2 to 8.5 microm. Attenuated total reflectance (ATR) Fourier-transform IR (FTIR) spectroscopy is used to examine infrared tissue absorption spectra before and after irradiation. Light scattering by bovine and porcine cartilage and cornea samples is measured in real time during FEL irradiation using a 650-nm diode laser and a diode photoarray with time resolution of 10 ms. The data on the time dependence of light scattering in the tissue are modeled to estimate the approximate values of kinetic parameters for denaturation as functions of laser wavelength and radiant exposure. We found that the denaturation threshold is slightly lower for cornea than for cartilage, and both depend on laser wavelength. An inverse correlation between denaturation thresholds and the absorption spectrum of the tissue is observed for many wavelengths; however, for wavelengths near 3 and 6 microm, the denaturation threshold does not exhibit the inverse correlation, instead being governed by heating kinetics of tissue. It is shown that light scattering is useful for measuring the denaturation thresholds and dynamics for different biotissues, except where the initial absorptivity is very high.
Distribution of the folate receptor GP38 in normal and malignant cell lines and tissues. (1992)

In some epithelial cells studied in vitro a membrane-bound folate receptor initiates the process for cell accumulation of 5-methyltetrahydrofolic acid. This receptor was found to be GP38, an overexpressed, glycosyl-phosphatidylinositol anchored glycoprotein, recognized by two monoclonal antibodies, designated MOv18 and MOv19. Using immunoblotting with MOv19, radioimmunoassay with MOv18 and 19, Northern blot analysis, and radioligand binding when possible, we describe the limited expression of the folate receptor in a large number of normal tissues from four autopsies. The immunoblot technique detected as little as 40 pg (approximately 1 fmol) of receptor protein. Choroid plexus consistently had the largest amount of folate receptor. Other tissues containing substantial amounts of receptor included lung, thyroid, and kidney. The liver, intestines, muscle, cerebellum, cerebrum, and spinal cord were immunologically nonreactive. Folate receptor gene expression determined by Northern blot analysis confirmed these observations. We also show that several malignant cell lines express significantly more receptor than normal epithelial cells or fibroblasts. Specifically, malignant cells bound greater than or equal to 20 pmol [3H]folate/10(6) cells, while normal epithelial cells and fibroblasts bound less than or equal to 1 pmol radioligand/10(6) cells. We also demonstrate that 4 of 6 brain tumors overexpress the folate receptor. These studies reveal the limited normal tissue distribution of the folate receptor, a cell surface protein which may be a useful immunological or pharmacological target for the development of selective cancer therapy.
9-cis Retinoic Acid Inhibition of Activation-Induced Apoptosis Is Mediated via Regulation of Fas Ligand and Requires Retinoic Acid Receptor and Retinoid X Receptor Activation (1995)

T-cell hybridomas, thymocytes, and T cells can be induced to undergo apoptotic cell death by activation through the T-cell receptor. This process requires macromolecular synthesis and thus gene expression, and it has been shown to be influenced by factors regulating transcription. Recently, activation, T-cell hybridomas rapidly express the Fas/CD95 receptor and its ligand, Fas ligand (FasL), which interact to transduce the death signal in the activated cell. Retinoids, the active metabolites of vitamin A, modulate expression of specific target genes by binding to two classes of intracellular receptors, retinoic acid receptors (RARs) and retinoid X receptors (RXRs). They are potent modulators of apoptosis in a number of experimental models, and they have been shown to inhibit activation-induced apoptosis in T-cell hybridomas and thymocytes. Particularly effective is the prototypic pan-agonist 9-cis retinoic acid (9-cis RA), which has high affinity for both RARs and RXRs. We report here that 9-cis RA inhibits T-cell receptor-mediated apoptosis in T-cell hybridomas by blocking the expression of Fas ligand following activation. This inhibition appears to be at the level of FasL mRNA, with the subsequent failure to express cell surface FasL. RAR-selective (TTNPB) or RXR-selective (LG100268) ligands alone were considerably less potent than RAR-RXR pan-agonists. However, the addition of both RAR- and RXR-selective ligands was as effective as the addition of 9-cis RA alone. The demonstrates that the inhibitory effect requires the ligand-mediated activation of both retinoid receptor signaling pathways.
Cloud Physical Property of Sea Fog Induced by Yamase in the Sanriku Seashore. (1997)

The Pacific side of Tohoku district has been frequently suffered from cool foggy easterly (Yamase) in summer times, resulting in severe decrease of rice production. The penetration of sea fog into inland area gives important effects on solar radiation impinging on crop fields.This study was made to make clear cloud physical characteristics of sea fogs penetrated from the sea into the Taneichi region. The observations were made during the sea fog seasons from May to August in 1990 and 1991, respectively. The fog penetrates more frequently in periods of weak or no solar radiation, such as evening, night, and morning, than in daytimes. It was also observed that the sea fog into crop field is more frequent and strong under weather conditions with the wind directions from E to S.The size distribution of sea fogs was measured by the Poval film method at the each observation point with different distances from the Taneichi seashore. The average size of sea fogs decreases linearly with the distance from the Taneichi seashore. This reason was mainly due to water evaporation on fog droplet surface. The results were compared with average size of sea fogs estimated indirectly from Eq. (2). Although there is relatively large scatter of points, it is reasonable to say that Eq. (2) can be used to estimate average values for droplet size from the data of visivility and fog water content.
Long‐term storage at −80°C of hematopoietic progenitor cells with 5‐percent dimethyl sulfoxide as the sole cryoprotectant (1999)

HPCs can be cryopreserved at -80 degrees C with 5-percent DMSO and stored at -80 degrees C no longer than 6 months. A 5-percent DMSO concentration is comparable to a with 10-percent concentration in terms of recovery and MNC viability.
Surfactant Removal for Colloidal Nanoparticles from Solution Synthesis: The Effect on Catalytic Performance (2012)

Colloidal nanoparticles prepared by solution synthesis with robust control over particle size, shape, composition, and structure have shown great potential for catalytic applications. However, such colloidal nanoparticles are usually capped with organic ligands (as surfactants) and cannot be directly used as catalyst. We have studied the effect of surfactant removal on the electrocatalytic performance of Pt nanoparticles made by organic solution synthesis. Various methods were applied to remove the oleylamine surfactant, which included thermal annealing, acetic acid washing, and UV-Ozone irradiation, and the treated nanoparticles were applied as electrocatalysts for the oxygen reduction reaction. It was found that the electrocatalytic performance, including electrochemically active surface area and catalytic activity, was strongly dependent on the pretreatment. Among the methods studied here, low-temperature thermal annealing (∼185 °C) in air was found to be the most effective for surface cleaning without inducing particle size and morphology changes.
Tubby-like protein 1 homozygous splice-site mutation causes early-onset severe retinal degeneration. (1999)

This TULP1 splice-site mutation in homozygotes causes early-onset, severe retinal degeneration involving macular and peripheral cones and rods. The constellation of phenotypic findings suggests that the TULP1 gene product is critically important for normal photoreceptor function and may play a role in retinal development.
Monocytes and macrophages synthesize and secrete thrombospondin (1985)

Thrombospondin, one of the major glycoproteins released from alpha-granules of thrombin-stimulated platelets, is a disulfide-linked trimer of 160,000-dalton subunits. Cultured human monocytes secreted thrombospondin (determined by an enzyme-linked immunosorbent assay) into the culture medium in a time-dependent manner (1.45 micrograms/10(6) cells/24 hr); secretion was totally blocked by cycloheximide (1 microgram/mL). 35S-thrombospondin was isolated from 35S-methionine-labeled human monocyte postculture medium with rabbit polyclonal anti-thrombospondin coupled to protein A-Sepharose. The immunoisolated 35S-thrombospondin migrated in sodium dodecyl sulfate-polyacrylamide gels after reduction with a molecular weight of 159,000. Similar results were obtained using mouse resident peritoneal macrophages. Elicited peritoneal macrophages harvested from mice pretreated with endotoxin, casein, or thioglycollate secreted much less thrombospondin than did resident macrophages harvested from control mice. Thus, monocytes and macrophages from two different species synthesize and secrete thrombospondin, and the rate of synthesis of thrombospondin appears to depend on the state of activation of the cells.
Immune ageing and Alzheimerʼs disease (1995)

The implications of immune ageing are considered with respect to Alzheimer's disease. In the course of immune ageing a population of activated autoreactive T cells appears which is proposed to cross the undamaged blood-brain barrier and to initiate overactivation of brain microglia. The development of highly activated microglia appears to be sufficient to induce the inflammatory neurotoxic process characteristic of the brain in Alzheimer's disease. The model thus emerging for sporadic Alzheimer's disease is that of a T cell-mediated chronic autoimmune syndrome following the age-dependent loss of thymic function. This view is consistent with available data and provides testable predictions.
Enrichment of human hematopoietic stem cell activity in the CD34+Thy- 1+Lin- subpopulation from mobilized peripheral blood (1995)

The number of CD34+ cells in the peripheral blood of cancer patients is known to be increased following the administration of high dose chemotherapy and hematopoietic growth factors. These so-called peripheral blood stem cell grafts are now frequently used for autologous transplantation of patients with malignancies. In this report, we address the question of whether true long-term repopulating pluripotent hematopoietic stem cells (PHSC) are mobilized into peripheral blood following chemotherapy plus granulocyte/macrophage colony-stimulating factor (GM-CSF) or granulocyte colony-stimulating factor (G-CSF) mobilization. We have examined the presence of stem cells in mobilized peripheral blood (MPB) by using an antibody to the human Thy-1 molecule to stain the CD34+Lineage- (Lin-) population. The kinetics of mobilization of CD34+Thy-1+ Lin- cells into peripheral blood were studied, and the percentage of cells with this phenotype was found to vary widely depending on the day of leukapheresis. A CD34+Thy-1+Lin- cell population, potentially containing PHSCs, was isolated by fluorescence activated cell sorting (FACS) and analyzed for activity. The multilineage differentiative capacity of this candidate stem cell-containing population in MPB was determined using an in vitro long-term culture system, in which cobblestone area formation was used as a means of detecting PHSCs. We also measured repopulating capacity by using two in vivo models in which severe combined immunodeficiency (SCID)-hu mice were implanted with human fetal bone or thymus grafts. Using these assays, we show that the highest frequency of cobblestone area-forming cells (CAFC) after 7 weeks of culture was observed in a subpopulation of CD34+Lin- cells, which expressed low levels of Thy-1. This cell population was capable of producing both B and myeloid cells, and maintaining CD34+Lin- cells in these long term cultures. Moreover, the CD34+Thy-1+Lin- cell subset possessed a higher ability to engraft and to demonstrate multilineage differentiative potential at 8 weeks in the SCID-hu bone assay. However, in the SCID-hu thymus model, both Thy-1+ and Thy-1- subpopulations were capable of donor T-cell engraftment at 6 weeks, suggesting the presence of cells capable of initiating T lymphopoiesis in both populations.(ABSTRACT TRUNCATED AT 400 WORDS)
Transloading of tumor antigen-derived peptides into antigen-presenting cells (1997)

The discovery of a steadily growing number of tumor antigens (TAs) has made generic, cell-free, peptide-based cancer vaccines a possible alternative to cytokine-transfected autologous cellular cancer vaccines. The major drawback of peptide vaccines, however, is the poor immunogenicity of peptides. It is commonly thought that for the induction of an effective anticancer immune response, antigen-presenting cells (APCs) have to display TA-derived peptides to T lymphocytes. Polycationic amino acids have been employed in the past to enhance transport of proteins into cells. In a systematic study, the ability of different cationic polymers to transfer fluorescence-tagged peptides to APCs was investigated. We were able to show that several compounds enhance uptake of fluorescence-labeled peptides by APCs to different degrees. The most efficient compound identified, polyarginine (pArg), enhanced peptide delivery by more than 2 logs as compared with cells treated with peptide alone, whereas polylysine (pLys) treatment resulted in approximately 10-fold increased levels of fluorescence. Augmentation of peptide uptake was concentration-dependent, and the molecular weight of pArg or pLys also influenced peptide delivery. Furthermore, highly negatively charged peptides appear to be delivered with higher efficiency, although neutral peptides were also taken up at enhanced rates. Whereas peptide uptake mediated by pLys appears to be due to an at least transient permeabilization of cell membranes, peptide delivery in the presence of pArg may rely on endocytic processes. TA-derived peptides applied as cancer vaccines in conjunction with polycations afforded antitumor protection in animal models.
Sulfated glycosaminoglycans modify growth factor‐induced neurite outgrowth in PC12 cells (1988)

Glycosaminoglycans (GAGs), localized on the surfaces of cells and in the basement membrane, modulate the growth and differentiation of many cell types. Recent studies have shown that heparin, a GAG found in mast cells, potentiates the ability of acidic fibroblast growth factor (aFGF) to induce neurite outgrowth in pheochromocytoma (PC12) cells. We examined the effect of a variety of GAGs on aFGF, basic fibroblast growth factor (bFGF), and nerve growth factor (NGF)-induced neurite outgrowth in PC12 cells. The effects observed were dependent upon the specific GAG, the concentration of the GAG, and the growth factor. Heparin potentiated aFGF-induced neurite outgrowth in a concentration-dependent fashion; potentiation increased with increasing heparin concentrations of 0.01-100 micrograms/ml. At concentrations greater than 100 micrograms/ml, heparin potentiation decreased. The maximally active concentration of heparin (100 micrograms/ml) increased the potency of aFGF 102-fold. Increasing concentrations of heparan sulfate, dermatan sulfate, and chondroitin sulfate correlated with increasing aFGF potentiation. The maximally active concentrations of heparan sulfate (100 micrograms/ml), dermatan sulfate (10 mg/ml), and chondroitin sulfate (1 mg/ml) increased the activity of aFGF 11-, 110-, and 11-fold, respectively. Hyaluronic acid did not affect the neurite outgrowth-promoting activity of aFGF. Heparin also altered the activity of bFGF; increasing concentrations of heparin (0.01-1 micrograms/ml) correlated with increased potentiation. At concentrations greater than 1 microgram/ml, heparin concentration was inversely correlated with potentiation. Chondroitin sulfate only increased the percentage of neurite-bearing cells at concentrations greater than 10 micrograms/ml. Maximally active concentrations of heparin (1 microgram/ml) and chondroitin sulfate (1 mg/ml) increased the potency of bFGF 5-fold. The highest concentration of heparan sulfate studied (1 mg/ml) inhibited the activity of bFGF. Dermatan sulfate and hyaluronic acid (0.01-1000 micrograms/ml) had no effect on bFGF activity. Heparan sulfate and chondroitin sulfate showed concentration-dependent potentiation of NGF; maximally active concentrations of heparan sulfate (100 micrograms/ml) and chondroitin sulfate (1 mg/ml) increased the potency of NGF 3-fold, whereas heparin, dermatan sulfate and hyaluronic acid had no effect. None of the GAGs had any effect on PC12 neurite outgrowth when added alone. The specificity of the activity of the GAGs was verified by selective enzyme degradation.(ABSTRACT TRUNCATED AT 400 WORDS)
Toward spontaneous interaction with the Perceptive Workbench (2000)

Until now, we have interacted with computers mostly by using wire-based devices. Typically, the wires limit the distance of movement and inhibit freedom of orientation. In addition, most interactions are indirect. The user moves a device as an analog for the action created in the display space. We envision an untethered interface that accepts gestures directly and can accept any objects we choose as interactors. We discuss methods for producing more seamless interaction between the physical and virtual environments through the Perceptive Workbench. We applied the system to an augmented reality game and a terrain navigating system. The Perceptive Workbench can reconstruct 3D virtual representations of previously unseen real-world objects placed on its surface. In addition, the Perceptive Workbench identifies and tracks such objects as they are manipulated on the desk's surface and allows the user to interact with the augmented environment through 2D and 3D gestures.
Post-translational Formylglycine Modification of Bacterial Sulfatases by the Radical S-Adenosylmethionine Protein AtsB (2004)

C(alpha)-Formylglycine (FGly) is the catalytic residue of sulfatases. FGly is generated by post-translational modification of a cysteine (prokaryotes and eukaryotes) or serine (prokaryotes) located in a conserved (C/S)XPXR motif. AtsB of Klebsiella pneumoniae is directly involved in FGly generation from serine. AtsB is predicted to belong to the newly discovered radical S-adenosylmethionine (SAM) superfamily. By in vivo and in vitro studies we show that SAM is the critical co-factor for formation of a functional AtsB.SAM.sulfatase complex and for FGly formation by AtsB. The SAM-binding site of AtsB involves (83)GGE(85) and possibly also a juxtaposed FeS center coordinated by Cys(39) and Cys(42), as indicated by alanine scanning mutagenesis. Mutation of these and other conserved cysteines as well as treatment with metal chelators fully impaired FGly formation, indicating that all three predicted FeS centers are crucial for AtsB function. It is concluded that AtsB oxidizes serine to FGly by a radical mechanism that is initiated through reductive cleavage of SAM, thereby generating the highly oxidizing deoxyadenosyl radical, which abstracts a hydrogen from the serine-C(beta)H(2)-OH side chain.