gebhart/patrepeval huggingface dataset:
Autoimmune effector cells. V.A monoclonal antibody specific for rat helper T lymphocytes inhibits adoptive transfer of autoimmune encephalomyelitis. (1983)

The in vitro activation of spleen cells from donor rats immunized with myelin basic protein results in enhanced adoptive transfer of experimental allergic encephalomyelitis to syngeneic recipients. In this study, adoptive transfer was inhibited when monoclonal antibody W3/25, which defines an antigen on rat helper T lymphocytes, was included in the in vitro cultures. Partial inhibition was achieved with monoclonal antibody OX-3, which recognizes la antigen, whereas other anti-T cell monoclonal reagents were ineffective. These results support the conclusion that W3/25+T cells play an essential role in the induction of this autoimmune response.
Changes in gas composition in the swimbladder of the European eel (Anguilla anguilla) infected withAnguillicola crassus(Nematoda) (1996)

The effect of Anguillicola crassus (Nematoda) on gas composition in the swimbladder of eels (Anguilla anguilla) was studied using mass spectrometry in feral eels from two German rivers and in experimentally infected eels. In both naturally and experimentally infected eels significant correlations were observed between the proportion of oxygen in the swimbladder and level of infection with Anguillicola crassus. In swimbladders of naturally infected feral eels the contribution of oxygen to swimbladder gas was reduced by 36-62.9% and in experimentally infected eels it was reduced by 11.4-57% compared to uninfected controls. The proportion of CO2 appeared to be lower in infected swimbladders compared to uninfected ones. However, this change was not significant. The findings are discussed in relation to an altered structure of the swimbladder wall due to the parasite.
Isolation and Characterization of Three Streptococcus pneumoniae Transformation-Specific Loci by Use of a lacZ Reporter Insertion Vector (1998)

Although more than a dozen new proteins are produced when Streptococcus pneumoniae cells become competent for genetic transformation, only a few of the corresponding genes have been identified to date. To find genes responsible for the production of competence-specific proteins, a random lacZ transcriptional fusion library was constructed in S. pneumoniae by using the insertional lacZ reporter vector pEVP3. Screening the library for clones with competence-specific beta-galactosidase (beta-Gal) production yielded three insertion mutants with induced beta-Gal levels of about 4, 10, and 40 Miller units. In all three clones, activation of the lacZ reporter correlated with competence and depended on competence-stimulating peptide. Chromosomal loci adjacent to the integrated vector were subcloned from the insertion mutants, and their nucleotide sequences were determined. Genes at two of the loci exhibited strong similarity to parts of Bacillus subtilis com operons. One locus contained open reading frames (ORFs) homologous to the comEA and comEC genes in B. subtilis but lacked a comEB homolog. A second locus contained four ORFs with homology to the B. subtilis comG gene ORFs 1 to 4, but comG gene ORFs 5 to 7 were replaced in S. pneumoniae with an ORF encoding a protein homologous to transport ATP-binding proteins. Genes at all three loci were confirmed to be required for transformation by mutagenesis using pEVP3 for insertion duplications or an erm cassette for gene disruptions.
Biochemical and Immunological Characterization of MP65, a Major Mannoprotein Antigen of the Opportunistic Human Pathogen Candida albicans (2000)

In the search of the antigenic determinants of a 65-kDa mannoprotein (MP65) of Candida albicans, tryptic fragments of immunoaffinity-purified MP65 preparations were tested for their ability to induce lymphoproliferation of human peripheral blood mononuclear cells (PBMC). Five major peptides (T1 to T5) were shown to induce a vigorous proliferation of PBMC from the majority of the eight healthy human subjects tested. With the use of synthetic peptides, critical amino acid sequences of the two most immunoactive (T1 and T2) peptides were determined. Similar to what was found for the MP65 molecule, no PBMC multiplication was induced by the antigenic peptides in cultures of naive cord blood cells. The amino acid sequence analysis of tryptic and chymotryptic peptides of MP65 demonstrated a substantial homology with the deduced sequences of two cell wall proteins of Saccharomyces cerevisiae, encoded by the genes YRM305C and YGR279C. However, the antigenic peptides were those showing the least similarity with the corresponding regions of the above proteins. In particular, the lymphoproliferation-inducing sequence of the T1 peptide scored only 20% identity with the homologous regions of S. cerevisiae proteins. Besides disclosing the amino acid sequence of MP65, this study provides an initial characterization of some of its antigenic determinants, as well as of synthetic peptides of potential use to detect specific immune responses against MP65, a major target of anticandidal cell-mediated immunity in humans.
The role of the second growth-factor domain of human factor IXa in binding to platelets and in factor-X activation (1995)

To study the structural requirements for factor IXa binding to platelets, we have carried out equilibrium binding studies with human factor IXa after replacing the second epidermal growth factor (EGF) domain by the corresponding polypeptide region of factor X. The chimeric protein, factor IX(Xegf2), and the wild-type, factor IXwt, produced in embryonic kidney cells 293 were radiolabelled with 125I and activated with factor XIa. Direct binding studies with thrombin-activated platelets showed normal stoichiometry and affinity of binding of factor IXawt in the presence of factor VIIIa (2 units/ml) and factor X (1.5 microM). However, under similar experimental conditions, factor IXa(Xegf2) was bound to a smaller number of sites (396 sites/platelet) with decreased affinity, i.e. a dissociation constant (Kd) of 1.4 nM, compared with normal factor IXa, factor IXaN (558 sites/platelet; Kd 0.67 nM), or factor IXawt (590 sites/platelet; Kd 0.61 nM). The concentrations of factor IXaN and factor IXawt required for half-maximal rates of factor-X activation were 0.63 nM and 0.7 nM, indicating a close correspondence of the Kd,app. for binding of factor IXawt to the factor-X activating complex on activated platelets to the Kd obtained in equilibrium binding studies. In contrast, kinetic parameters for factor-X activation by factor IXa(Xegf2) showed a decreased affinity (Kd 1.5 nM), in agreement with results of binding studies. These studies with factor IX(Xegf2) suggest that the EGF-2 domain may be important for specific high-affinity factor IXa binding to platelets in the presence of factor VIIIa and factor X.
A Three-Dimensional Cellular Model of the Human Respiratory Tract to Study the Interaction with Particles (2005)

A novel triple co-culture model of the human airway barrier was designed to simulate the cellular part of the air-blood barrier of the respiratory tract represented by macrophages, epithelial cells, and dendritic cells. When epithelial cells (A549 cells) were grown on filter inserts with pores of 3.0 mum in diameter in a two-chamber system, they formed monolayers with polarization into apical and basolateral domains. The epithelial cell cultures were then supplemented with human blood monocyte-derived macrophages and dendritic cells on the apical and basal aspect, respectively. The single-cell cultures as well as the triple co-cultures were characterized in terms of a number of typical features, for example, morphology of cell types, integrity of epithelial layer, and expression of specific cell surface markers (CD14 for macrophages and CD86 for dendritic cells). The interplay of epithelial cells with macrophages and dendritic cells during the uptake of polystyrene particles (1 mum in diameter) was investigated with confocal laser scanning and conventional transmission electron microscopy. Particles were found in all three cell types, although dendritic cells were not directly exposed to the particles. More investigations are needed to understand the translocation pathway.
Transcription-Based Reporters of Wnt/β-Catenin Signaling (2009)

INTRODUCTION The Wnt/β-catenin pathway is the best characterized Wnt pathway largely as a result of powerful assays that allow measurement of in vivo and in vitro pathway activation. Early assays for Wnt/β-catenin signaling included phenotypic assays in Drosophila , dorsal axis duplication in Xenopus , and proliferation of C57MG mammary epithelial cells. More recent characterizations rely on direct measurement of pathway activation. The Wnt/β-catenin signaling pathway culminates with T-cell factor/lymphoid enhancer factor (TCF/LEF)-dependent regulation of target gene transcription; assaying such transcription with reporters containing multimerized TCF/LEF DNA-binding sites is a reliable measure of pathway activation. These reporters have helped characterize the Wnt/β-catenin signaling pathway and will be critical to further studies of pathway regulation and in the development of therapeutic mechanisms to combat diseases arising from aberrant signaling. This protocol describes a variety of methods for using an improved Wnt/β-catenin reporter system, the β-catenin-activated reporter (BAR), and its accompanying control reporter system, found-unresponsive BAR (fuBAR). Procedures are presented for transient and stable transfection of the reporter. Transient transfection is very robust and does not require lentiviral production, although it has a slightly smaller dynamic range relative to stably integrated BAR. The stable transduction system can be used to generate stable reporter cell lines, assay Wnt/β-catenin signaling in cells that might be otherwise difficult to transfect, or assay signaling in vivo. The BAR system, with its improved sensitivity, greater dynamic range, and lentiviral-based reporter system, provides a vital tool for future studies of this signaling pathway.
Tunable Redox-Responsive Hybrid Nanogated Ensembles (2008)

A new redox-responsive hybrid nanogated ensemble has been developed by introducing the disulfide-linked polymeric network at the outlet of mesoporous silica. The cross-linked polymer works as gatekeeper to control molecule release from mesoporous silica. The presence of disulfide reducing agent can effectively open the polymeric network and release the loading in a tunable manner.
Ant colony optimization approach for classification of occupational low back disorder risks (2008)

Abstract Manual material handling (MMH) tasks, the leading cause of low back disorders (LBDs), are still extensively used in industry in spite of the advanced technology. Classification of industrial jobs related to LBD risks has great significance in preventing injuries and designing workplaces. In this article, industrial jobs have been classified into two categories, low risk and high risk, using ant colony optimization (ACO). ACO classification (ACOCLASS) has obtained better results than studies that used the same experimental data. Ergonomic interventions can be done by means of obtained classification schema for future reductions in low back injuries. © 2008 Wiley Periodicals, Inc.
The plant 2‐Cys peroxiredoxin BAS1 is a nuclear‐encoded chloroplast protein: its expressional regulation, phylogenetic origin, and implications for its specific physiological function in plants (1997)

2-Cys peroxiredoxins constitute a family of enzymes which catalyze the transfer of electrons from sulfhydryl residues to peroxides and are ubiquitously distributed among all organisms. This paper characterizes the higher plant 2-Cys-peroxiredoxin BAS1. (i) Escherichia coli over-expressing BAS1 exhibit increased tolerance for alkyl hydroperoxides in vivo. This result substantiates the peroxiredoxin function of BAS1. (ii) BAS1 protein is associated with the soluble chloroplast fraction of mesophyll protoplasts. Import and processing of in vitro-transcribed and cell-free translated BAS1 protein into isolated chloroplasts provides conclusive evidence that the plant-specific N-terminal extension of bas1 encodes the chloroplast import signal which targets the pre-form of BAS1 to the chloroplast stroma where it is cleaved to its mature size. (iii) Genomic analysis reveals that the targeting signal is encoded by a separate exon in Arabidopsis thalina. (iv) The amino acid sequence of the BAS1 core protein of higher plants has a higher degree of similarity to open reading frames in the genome of the bluegreen algae Synechochystis PCC sp. 6803 and in the plastome of the red algae Porphyra purpurea than to any other nuclear-encoded 2-Cys peroxiredoxin. Therefore, it is tempting to speculate that the chloroplast import signal was added to an ancestor gene of endosymbiotic origin in the course of plant evolution. (v) The bas1 gene expression is regulated under the control of the cellular redox state which is in accordance with the anti-oxidant function of the enzyme. While oxidative stressors increased expression only slightly, antioxidants such as reduced thiols strongly suppressed the transcript level. The implications of these findings are discussed with respect to the possible physiological functions of BAS1.
In vitro differentiation of retinal cells from human pluripotent stem cells by small-molecule induction (2009)

The use of stem-cell therapy to treat retinal degeneration holds great promise. However, definitive methods of retinal differentiation that do not depend on recombinant proteins produced in animal or Escherichia coli cells have not been devised. Here, we report a defined culture method using low-molecular-mass compounds that induce differentiation of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells into retinal progenitors, retinal pigment epithelium cells and photoreceptors. The casein kinase I inhibitor CKI-7, the ALK4 inhibitor SB-431542 and the Rho-associated kinase inhibitor Y-27632 in serum-free and feeder-free floating aggregate culture induce retinal progenitors positive for RX, MITF, PAX6 and CHX10. The treatment induces hexagonal pigmented cells that express RPE65 and CRALBP, form ZO1-positive tight junctions and exhibit phagocytic functions. Subsequent treatment with retinoic acid and taurine induces photoreceptors that express recoverin, rhodopsin and genes involved in phototransduction. Both three-factor (OCT3/4, SOX2 and KLF4) and four-factor (OCT3/4, SOX2, KLF4 and MYC) human iPS cells could be successfully differentiated into retinal cells by small-molecule induction. This method provides a solution to the problem of cross-species antigenic contamination in cell-replacement therapy, and is also useful for in vitro modeling of development, disease and drug screening.
FGFR3 and FGFR4 Do not Mediate Renal Effects of FGF23 (2008)

Fibroblast growth factor 23 (FGF23) is a phosphaturic factor that suppresses both sodium-dependent phosphate transport and production of 1,25-dihydroxyvitamin D [1,25(OH)(2)D] in the proximal tubule. In vitro studies suggest that FGFR3 is the physiologically relevant receptor for FGF23 in the kidney, but this has not been established in vivo. Here, immunohistochemical analysis of the mouse kidney revealed that the proximal tubule expresses FGF receptor 3 (FGFR3) but not FGFR1, FGFR2, or FGFR4. Compared with wild-type mice, Hyp mice, which have elevated circulating levels of FGF23, exhibited low levels of serum phosphate and 1,25(OH)(2)D, reduced expression of the sodium-dependent phosphate transporter NPT2a in the proximal tubules, and low bone mineral density as a result of osteomalacia. In contrast, neither the serum phosphate nor 1,25(OH)(2)D levels were altered in FGFR3-null mice. For examination of the role of FGFR3 in mediating the effects of FGF23, Hyp mice were crossed with FGFR3-null mice; interestingly, this failed to correct the aforementioned metabolic abnormalities of Hyp mice. Ablation of FGFR4 also failed to correct hypophosphatemia in Hyp mice. Because the ablation of neither FGFR3 nor FGFR4 inhibited the renal effects of excess FGF23, the kidney localization of FGFR1 was investigated. FGFR1 co-localized with Klotho, the co-factor required for FGF23-dependent FGFR activation, in the distal tubule. In summary, neither FGFR3 nor FGFR4 is the principal mediator of FGF23 effects in the proximal tubule, and co-localization of FGFR1 and Klotho suggests that the distal tubule may be an effector site of FGF23.
Controlled synthesis of a large fraction of metallic single-walled carbon nanotube and semiconducting carbon nanowire networks (2011)

Controlled synthesis of both single-walled carbon nanotube and carbon nanowire networks using the same CVD reactor and Fe/Al(2)O(3) catalyst by slightly altering the hydrogenation and temperature conditions is demonstrated. Structural, bonding and electrical characterization using SEM, TEM, Raman spectroscopy, and temperature-dependent resistivity measurements suggest that the nanotubes are of a high quality and a large fraction (well above the common 33% and possibly up to 75%) of them are metallic. On the other hand, the carbon nanowires are amorphous and semiconducting and feature a controlled sp(2)/sp(3) ratio. The growth mechanism which is based on the catalyst nanoisland analysis by AFM and takes into account the hydrogenation and temperature control effects explains the observed switch-over of the nanostructure growth modes. These results are important to achieve the ultimate control of chirality, structure, and conductivity of one-dimensional all-carbon networks.
Strong field theory of low loss optical switching and three-wave mixing in a semiconductor quantum well (1994)

A density matrix analysis based on radiative renormalization predicts significant changes in band-edge absorption, index of refraction, and three-wave-mixing susceptibility in a quantum well when two conduction subbands are strongly coupled by an electromagnetic field.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fast DNA Translocation through a Solid-State Nanopore (2005)

We report experiments and modeling of translocation of double-strand DNA through a siliconoxide nanopore. Long DNA molecules with different lengths ranging from 6500 to 97000 base pairs have been electrophoretically driven through a 10 nm pore. We observe a power-law caling of the translocation time with the length, with an exponent of 1.27. This nonlinear scaling is strikingly different from the well-studied linear behavior observed in similar experiments performed on protein pores. We present a theoretical model where hydrodynamic drag on the ection of the polymer outside the pore is the dominant force counteracting the electrical driving force. We show that this applies to our experiments, and we derive a power-law scaling with an exponent of 1.22, in good agreement with the data.
Factor VIII immunogenicity (1998)

The immunogenicity of factor VIII depends on the interaction of multiple parametres including host susceptibility and characteristics of the factor VIII preparations. We briefly review here the basic mechanisms by which tolerance to self is established, maintained, and possibly broken in the context of haemophilia A, with special emphasis on the severity of the disease. Reference is also made to the situation observed in healthy individuals and patients with autoantibodies to factor VIII.
Overexpression of 3-Ketoacyl-Acyl-Carrier Protein Synthase IIIs in Plants Reduces the Rate of Lipid Synthesis (2001)

A cDNA coding for 3-ketoacyl-acyl-carrier protein (ACP) synthase III (KAS III) from spinach (Spinacia oleracea; So KAS III) was used to isolate two closely related KAS III clones (Ch KAS III-1 and Ch KAS III-2) from Cuphea hookeriana. Both Ch KAS IIIs are expressed constitutively in all tissues examined. An increase in the levels of 16:0 was observed in tobacco (Nicotiana tabacum, WT-SR) leaves overexpressing So KAS III when under the control of the cauliflower mosaic virus-35S promoter and in Arabidopsis and rapeseed (Brassica napus) seeds overexpressing either of the Ch KAS IIIs driven by napin. These data indicate that this enzyme has a universal role in fatty acid biosynthesis, irrespective of the plant species from which it is derived or the tissue in which it is expressed. The transgenic rapeseed seeds also contained lower levels of oil as compared with the wild-type levels. In addition, the rate of lipid synthesis in transgenic rapeseed seeds was notably slower than that of the wild-type seeds. The results of the measurements of the levels of the acyl-ACP intermediates as well as any changes in levels of other fatty acid synthase enzymes suggest that malonyl-ACP, the carbon donor utilized by all the 3- ketoacyl-ACP synthases, is limiting in the transgenic plants. This further suggests that malonyl-coenzyme A is a potential limiting factor impacting the final oil content as well as further extension of 16:0.
Glomerular filtration barrier (2009)

Glomerular diseases account for 90% of chronic kidney disease requiring dialysis and transplantation at an annual cost of $20 billion in the USA. In clinical practice, we lack specific treatment of these diseases, giving us plenty of room for improvement. Future research should be directed toward deeper understanding of the signaling pathways involved in different conditions of proteinuria, the cross-talk between cell types in the glomerulus, and the identification of novel targets for treatment of acquired kidney disease.
Role of the LXCXE Binding Site in Rb Function (2000)

Oncoproteins from DNA tumor viruses such as adenovirus E1a, simian virus 40 T antigen, and human papillomavirus E7 contain an LXCXE sequence, which they use to bind the retinoblastoma protein (Rb) and inhibit its function. Cellular proteins such as histone deacetylases 1 and 2 (HDAC1 and -2) also contain an LXCXE-like sequence, which they use to interact with Rb. The LXCXE binding site in Rb was mutated to assess its role in Rb function. These mutations inhibited binding to HDAC1 and -2, which each contain an LXCXE-like sequence, but had no effect on binding to HDAC3, which lacks an LXCXE-like sequence. Mutation of the LXCXE binding site inhibited active transcriptional repression by Rb and prevented it from effectively repressing the cyclin E and A gene promoters. In contrast, mutations in the LXCXE binding site did not prevent Rb from binding and inactivating E2F. Thus, the LXCXE mutations appear to separate Rb's ability to bind and inactivate E2F from its ability to efficiently recruit HDAC1 and -2 and actively repress transcription. In transient assays, several of the LXCXE binding site mutants caused an increase in the percentage of cells in G(1) by flow cytometry, suggesting that they can arrest cells. However, this effect was transient, as none of the mutants affected cell proliferation in longer-term assays examining bromodeoxyuridine incorporation or colony formation. Our results then suggest that the LXCXE binding site is important for full Rb function. Mutation of the LXCXE binding site does not inhibit binding of the BRG1 ATPase component of the SWI/SNF nucleosome remodeling complex, which has been shown previously to be important for Rb function. Indeed, overexpression of BRG1 and Rb in cells deficient for the proteins led to stable growth inhibition, suggesting a cooperative role for SWI/SNF and the LXCXE binding site in efficient Rb function.