gebhart/patrepeval huggingface dataset:
Mechanisms of interferon-induced inhibition of Toxoplasma gondii replication in human retinal pigment epithelial cells (1996)

Inflammation associated with retinochoroiditis is a major complication of ocular toxoplasmosis in infants and immunocompetent individuals. Moreover, Toxoplasma gondii-induced retinal disease causes serious complications in patients with AIDS and transplant patients. The retinal pigment epithelial (RPE) cell is an important regulatory cell within the retina and is one of the cells infected with T. gondii in in vivo. We have developed a human RPE (HRPE) cell in vitro model system to evaluate T. gondii replication and the regulation of this replication by cytokines. T. gondii replication was quantitated by counting the foci of infection (plaque formation) and the numbers of tachyzoites released into the supernatant fluids. Pretreatment of cultures with recombinant human tumor necrosis factor alpha, alpha interferon (IFN-alpha), IFN-beta, or IFN-gamma for 24 h prior to inoculation inhibited T. gondii replication in a dose-dependent manner. Of these cytokines, IFN-gamma was the most potent, and T. gondii replication was completely inhibited at a concentration of 100 U/ml. The anti-toxoplasmotic activity of IFN-gamma was significantly blocked by monoclonal antibody to IFN-gamma. Treatment of the cultures with IFN-gamma from day 1 or 2 postinoculation with T. gondii also offered protection against the parasite. The anti-toxoplasmotic activity of tumor necrosis factor alpha or IFN-alpha, -beta, or -gamma in these cultures was found to be independent of the nitric oxide (NO) pathway, since NO production was not found in HRPE cells treated with these cytokines. However, addition of tryptophan to IFN-gamma-treated cells significantly reversed the inhibitory effects of IFN-gamma, suggesting that IFN-gamma acts by depleting cellular tryptophan. This effect was further confirmed by reverse transcription-PCR and Northern (RNA) blot analysis, which indicated induction of indoleamine 2,3-dioxygenase (IDO), an enzyme that converts tryptophan to kynurenine. These results indicated that interferons inhibited T. gondii replication in HRPE by NO-independent but IDO-dependent mechanisms. This in vitro model of T. gondii replication in HRPE may be useful in evaluating the effects of cytokines and drugs on T. gondii replication within the retina.
The Autonomous, the Universal and the Future of Sociology (2005)

The universal concepts of sociology are those that form the basic foundation of the discipline found in all human societies and valid for all times. Examples are the concepts of sanction, class, social stratification, social mobility, group, culture, values, religion, custom and others. These concepts are universally valid in the general and abstract sense but their historical and concrete manifestations are conditioned by their temporal, spatial and cultural frameworks. It is in the studies of these unique historical phenomena that the autonomous tradition has its roots. What is lacking in the non-western world is an autonomous social science tradition, generated and developed by local scholars, guided by the selection of problems from within the society, applying an independent concept of relevance in the collection and accumulation of research data and comparative attention to problems outside the country or region.
Raman Dye-Labeled Nanoparticle Probes for Proteins (2003)

In this paper, we demonstrate how one can chemically design Raman dye-functionalized nanoparticle probes with specific protein-binding affinities and use these probes, coupled with surface-enhanced Raman scattering (SERS) spectroscopy, to perform multiplexed screening of protein-small molecule interactions and protein-protein interactions in a protein microarray format.
Noggin-mediated antagonism of BMP signaling is required for growth and patterning of the neural tube and somite (1998)

Embryonic patterning in vertebrates is dependent upon the balance of inductive signals and their specific antagonists. We show that Noggin, which encodes a bone morphogenetic protein (BMP) antagonist expressed in the node, notochord, and dorsal somite, is required for normal mouse development. Although Noggin has been implicated in neural induction, examination of null mutants in the mouse indicates that Noggin is not essential for this process. However, Noggin is required for subsequent growth and patterning of the neural tube. Early BMP-dependent dorsal cell fates, the roof plate and neural crest, form in the absence of Noggin. However, there is a progressive loss of early, Sonic hedgehog (Shh)-dependent ventral cell fates despite the normal expression of Shh in the notochord. Further, somite differentiation is deficient in both muscle and sclerotomal precursors. Addition of BMP2 or BMP4 to paraxial mesoderm explants blocks Shh-mediated induction of Pax-1, a sclerotomal marker, whereas addition of Noggin is sufficient to induce Pax-1. Noggin and Shh induce Pax-1 synergistically. Use of protein kinase A stimulators blocks Shh-mediated induction of Pax-1, but not induction by Noggin, suggesting that induction is mediated by different pathways. Together these data demonstrate that inhibition of BMP signaling by axially secreted Noggin is an important requirement for normal patterning of the vertebrate neural tube and somite.
Role of Rho-Associated Kinase in Neointima Formation After Vascular Injury (2001)

Y27632 inhibited neointima formation by enhancing SMC apoptosis and probably by suppressing early SMC migration. Therefore, a role of Rho-kinase is suggested in neointima formation after vascular injury.
Preparation of Enamides via Reductive Acylation of N-Acetoxyimino Compounds by Use of Fe3(CO)12 (1987)

Abstract Treatment of N-acetoxyimino compounds with Fe3(CO)12 in the presence of acyl halides and triethylamine gave enamides in good yields.
Treatment of systemic lupus erythematosus by inhibition of T cell costimulation with anti‐CD154: A randomized, double‐blind, placebo‐controlled trial (2002)

IDEC-131 administered at doses ranging 2.5-10.0 mg/kg over 16 weeks was safe and well tolerated in patients with SLE. Efficacy of the drug compared with placebo was not demonstrated. There were statistically significant improvements from baseline in all groups, including the placebo group.
Antibodies :a practical approach (1988)

Properties of antibodies and antigens Production and quality control of polyclonal antibodies Murine monoclonal antibodies Human monoclonal antibodies Imunoaffinity chromatography Gel immunodiffusion, immunoeletrophoresis and immunostaining methods Haemagglutination and haemolysis assays
Osmoregulation of gene expression. I. DNA sequence of the ompR gene of the ompB operon of Escherichia coli and characterization of its gene product. (1982)

The ompB region on the Escherichia coli chromosome codes for two genes, ompR and envZ, which are required for the osmolarity sensitive biosynthetic regulation of the outer membrane matrix proteins (porins), OmpF and ompC. A part of the ompB region containing the ompR gene has been cloned (Wurtzel, E. T., Movva, N. R., Ross, F. L., and Inouye, M. (1981) J. Mol. Appl. Genet. 1, 61-69). We have determined the DNA sequence, including the promoter and structural regions encompassed in a 1.3-kilobase pair Ava I-Eco RI subfragment. This fragment codes for the entire ompR gene as well as the 5' end of the envZ gene. The ompR gene codes for a protein of 32,489 daltons, consisting of 284 amino acid residues. This was confirmed by identifying the gene product by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and determining a partial amino acid sequence of the NH2-terminal region of the gene product. A sequence of 57 amino acid residues located in the COOH-terminal region of the protein is extremely basic. It contains 10 arginine plus lysine residues in contrast to 1 glutamic acid residue in this region. In vitro transcription of the DNA from this region indicates that ampR and envZ are co-transcribed as a polycistronic mRNA from a promoter located 5' to the ompR gene. Translation of the am pR gene terminates at two tandem TAS codons and translation of the envZ gene initiates 29 nucleotides downstream. Cloning of the promoter region of ompB at a site 5' to the structural portion of the beta-galactosidase gene indicates that transcription of ompB is under positive control by cAMP.
3-D STRUCTURES FROM STABLE GELS (2002)

RETURN TO ISSUEPREVNewsNEXT3-D STRUCTURES FROM STABLE GELSAutomated method builds precision parts from tailor-made colloidal inksMITCH JACOBYCite this: Chem. Eng. News 2002, 80, 26, 7Publication Date (Print):July 1, 2002Publication History Published online13 November 2010Published inissue 1 July 2002https://doi.org/10.1021/cen-v080n026.p007Copyright © 2002 American Chemical SocietyArticle Views8Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (579 KB) SUBJECTS:Materials Get e-Alerts
Precise determination of lattice parameter and thermal expansion coefficient of silicon between 300 and 1500 K (1984)

The lattice parameter of high-purity silicon is measured as a function of temperature between 300 and 1500 K, and the linear thermal expansion coefficient is accurately determined. Precise measurements are made by the high-temperature attachment for Bond’s x-ray method to a few parts per million. It is found that the temperature dependence of the linear thermal expansion coefficient α(t) is empirically given by α(t)=(3.725{1−exp[−5.88×10−3{(t−124)} +5.548×10−4t)×10−6 (K−1), where t is the absolute temperature ranging from 120 to 1500 K. It is shown that the lattice parameter in the above temperature range can be calculated using α(t) and the lattice parameter at 273.2 K (0.5430741 nm). Measured values of the lattice parameter and the thermal expansion coefficient for high-purity float-zoned (100 kΩ cm) and Czochralski-grown (30 Ω cm) single crystals are uniformly distributed within ±1×10−5 nm and ±2×10−7 K−1 with respect to the values obtained from the above empirical formula.
A study of metabolism of deaminated and sulfoconjugated iodothyronines by rat placental iodothyronine 5-monodeiodinase (1992)

The interaction of the rat placental type III iodothyronine 5-monodeiodinase (5-MD) with acetic acid (AA), propionic acid (PA), and sulfoconjugate (SA) derivatives of thyroid hormones has been investigated in comparison with hepatic iodothyronine type I MD. PA and AA derivatives of both T3 and T4 were potent inhibitors of 5-monodeiodination of [125I]T3 by rat placental microsomes. 3,5,3'-Triiodothyroacetic acid (T3AA) and 3,5,3'-triiodothyropropionic acid (T3PA) were comparable to T3 in their ability to inhibit 5-monodeiodination of [125I]T3, whereas T4AA and T4PA were more potent than T4. 3,5,3'-triiodothyrosulfonic acid (T3SA), T4SA, and rT3SA caused little or no inhibition of placental 5-MD activity. Among various analogs of T3 or T4, the order of relative potency of inhibition of hepatic 5'-MD was PA > AA > SA > parent iodothyronine. The metabolism of T3 and its derivatives by rat placental microsomes was studied by determining the rates of disappearance of the various substrates and the production of the metabolites generated by inner ring monodeiodination of the substrate. T3AA and T3PA were metabolized at a rate comparable to that of T3. Under the same conditions, essentially 100% of T3SA remained intact. Kinetic studies of placental inner ring monodeiodination of T3, T3AA, and T3PA demonstrated comparable values for Km (1.3, 1.8, and 2.3 nM, respectively) and maximum velocity (44, 57, and 74 fmol/micrograms.h, respectively). All derivatives of T3 studied were deiodinated by hepatic type I MD more avidly than the parent iodothyronine. Our data suggest that 1) deamination does not appreciably influence, while sulfoconjugation markedly inhibits type III 5-monodeiodination of T3; and 2) deamination may be even more conducive to degradation of thyroid hormone than sulfoconjugation.
Elastomeric Ionomers (1984)

Abstract Ionomers are a class of materials which are emerging as important commercial polymers but yet have many intriguing scientific characteristics. Typically, ionomers consist of a low level of inorganic salt groups pendent to a polymer chain. For this article, we will consider ionomers to possess a maximum level of about 10 mol% ionic groups pendent to a hydrocarbon polymer chain. While this definition is somewhat arbitrary, it is one generally accepted in the polymer field. Unlike homogeneous polymer systems, the pendent ionic groups can interact to form ion-rich aggregates contained in the nonpolar polymer matrix. The resulting ionic interactions can have a major influence on polymer properties and applications which have made this area an extremely fertile one for research and development.
State-of-the-art Adsorption and Membrane Separation Processes for Carbon Dioxide Production from Carbon Dioxide Emitting Industries (2009)

Abstract With the growing concern about global warming placing greater demands on improving energy efficiency and reducing CO2 emissions, the need for improving the energy intensive, separation processes involving CO2 is well recognized. The US Department of Energy estimates that the separation of CO2 represents 75% of the cost associated with its separation, storage, transport, and sequestration operations. Hence, energy efficient, CO2 separation technologies with improved economics are needed for industrial processing and for future options to capture and concentrate CO2 for reuse or sequestration. The overall goal of this review is to foster the development of new adsorption and membrane technologies to improve manufacturing efficiency and reduce CO2 emissions. This study focuses on the power, petrochemical, and other CO2 emitting industries, and provides a detailed review of the current commercial CO2 separation technologies, i.e., absorption, adsorption, membrane, and cryogenic, an overview of the emerging adsorption and membrane technologies for CO2 separation, and both near and long term recommendations for future research on adsorption and membrane technologies. Flow sheets of the principal CO2 producing processes are provided for guidance and new conceptual flow sheets with ideas on the placement of CO2 separations technologies have also been devised.
Synthesis, spectral properties, and use of 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan). A thiol-selective, polarity-sensitive fluorescent probe. (1983)

Fluorophores processing a 6-acyl-2-dimethylaminonaphthalene moiety show fluorescence that is extremely sensitive to solvent polarity (Weber, G., and Farris, F. J. (1979) Biochemistry 18, 3075-3078). We have synthesized and characterized 6-acryloyl-2-dimethylaminonaphthalene (Acrylodan) which selectively labels thiol moieties in proteins. The quantum yield of this agent is markedly enhanced after reaction with thiols, and as expected, the fluorescent derivatives are very sensitive to dipolar perturbation from their environments. The usefulness of Acrylodan in the study of "hydrophobic" domains, conformational changes, and dipolar relaxation processes in proteins is demonstrated by measurements of fluorescence spectra and lifetimes of a mercaptoethanol adduct dissolved in different solvents and of adducts of this agent with parvalbumin, troponin C, papain, and carbonic anhydrase.
Novel peptide-based HIV-1 immunotherapy (2004)

Therapeutic immunisation of human immunodeficiency virus type 1-infected individuals should be actively pursued in the first instance to augment highly active antiretroviral therapy regimens. Peptide-based immunotherapeutic strategies offer considerable advantages over conventional approaches, particularly regarding safety. Peptide design itself is becoming increasingly sophisticated, with the rapid evolution of bioinformatics tools that can analyse not only T cell epitopes, but also their potential for successful presentation on diverse human leukocyte antigen (HLA) class I or II following intracellular processing by antigen-presenting cells (APCs). By targeting conserved viral domains, peptides acquire improved reactivity to diverse viral strains. Dendritic cells represent a powerful route of administration, as they are the most potent APCs and can present exogenous peptides on both HLA class I and II through the process of cross-presentation. In this way, soluble peptides can thereby stimulate both CD4+ and CD8+ T cells.
Ultramicroscopy as a novel tool to unravel the tropism of AAV gene therapy vectors in the brain (2016)

Recombinant adeno-associated viral (AAV) vectors have advanced to the vanguard of gene therapy. Numerous naturally occurring serotypes have been used to target cells in various tissues. There is a strong need for fast and dynamic methods which efficiently unravel viral tropism in whole organs. Ultramicroscopy (UM) is a novel fluorescence microscopy technique that images optically cleared undissected specimens, achieving good resolutions at high penetration depths while being non-destructive. UM was applied to obtain high-resolution 3D analysis of AAV transduction in adult mouse brains, especially in the hippocampus, a region of interest for Alzheimer's disease therapy. We separately or simultaneously compared transduction efficacies for commonly used serotypes (AAV9 and AAVrh10) using fluorescent reporter expression. We provide a detailed comparative and quantitative analysis of the transduction profiles. UM allowed a rapid analysis of marker fluorescence expression in neurons with intact projections deep inside the brain, in defined anatomical structures. Major hippocampal neuronal transduction was observed with both vectors, with slightly better efficacy for AAV9 in UM. Glial response and synaptic marker expression did not change post transduction.We propose UM as a novel valuable complementary tool to efficiently and simultaneously unravel tropism of different viruses in a single non-dissected adult rodent brain.
Redesign of retrovirus packaging cell lines to avoid recombination leading to helper virus production. (1986)

Retrovirus vectors can be made in the absence of helper virus by using retrovirus packaging cell lines. Helper-free virus is critical for a variety of gene transfer studies. The most useful packaging cell lines contain helper virus DNA from which the signal required for packaging of the viral RNA genome into virions has been deleted. However, we showed that the ability to package virus is conferred at very low frequency to cells infected with virus from these packaging cell lines, presumably by low-frequency transmission of the deleted virus genome. In addition, these packaging cell lines can interact with some retroviral vectors to yield replication-competent virus. We constructed packaging cell lines containing helper virus DNA that had several alterations in addition to deletion of the packaging signal. The new packaging cells retained the useful features of previously available lines but did not yield helper virus after introduction of any of the vectors tested, and transfer of the packaging function was not detected.
Present Trends in the Application of Genetic Algorithms to Heterogeneous Catalysis (2004)

This chapter contains sections titled: Introduction Theoretical and Methodological Principles Genetic Algorithms Artificial Neural Networks Automatically Generated Problem-tailored Genetic Algorithms Integrating Genetic Algorithms with Neural Networks Conclusions References
Lead Discovery Using Stochastic Cluster Analysis (SCA):  A New Method for Clustering Structurally Similar Compounds (1998)

We have developed an algorithm that clusters structural databases using topological similarity. The first step in this procedure is to identify a set of probe structures that all fall outside a defined similarity score cutoff with respect to one another. This list of probes is then used to bin the remaining compounds in the database. In the last step, some housekeeping is performed to ensure that each compound in the dataset is either a probe or is contained in one and only one bin. We have applied this clustering method to a database of ∼27 000 compounds for which we have screening level biological data. Analysis of the resulting clusters shows that clusters defined by an active probe are much more likely to contain other active compounds than clusters defined by an inactive probe. Indeed, the incidence of active compounds in bins with active probes is anywhere from 6 to 10 times greater than the incidence of active compounds in the database as a whole. This results demonstrates the power of simple two-dimensional topological descriptors, and serves to validate our clustering algorithm.
Table-lookup methods for improved performance-driven routing (1998)

The inaccuracy of Elmore delay [3] for inter conne ct delay estimation is well-documented. However it remains a popular delay measur e to drive p erformance optimization procedur es such as wire-sizing and topolo gy construction. This p aper studies the merits of incorp orating “b etter-than-Elmore” delay measur es into the optimization process. The proposed delay metrics use a table-lo okup method to incorporatebetter load modeling and approximate the effect of signal slew. We demonstrate that the proposed metrics exhibit a much narrower error distribution than Elmore delay, eliminating Elmore's frequent gross delay over-estimation. Finally we show the improvement in solution quality which can b e had by inc orp orating the new metrics into a timing driven topology construction algorithm.
AGE-RAGE in Multiple Sclerosis Brain (2010)

This pilot study used immunohistochemical techniques to investigate the advanced glycation end-product (AGE) Nepsilon-(carboxymethyl)lysine (CML) and its receptor (RAGE) in the brains of multiple sclerosis (MS) patients, comparing them with the brains of patients with Alzheimer's disease (AD) (positive controls) and with age-matched control subjects (negative controls). Postmortem slides derived from the hippocampi of MS patients, AD patients, and controls were stained with monoclonal antibodies for CML and human RAGE. Results showed increased AGE and RAGE immunostaining in the hippocampi of MS patients, similar to AD patients.