gebhart/patrepeval huggingface dataset:
Differential Activation of Acute Phase Response Factor/Stat3 and Stat1 via the Cytoplasmic Domain of the Interleukin 6 Signal Transducer gp130 (1996)

Distinct yet overlapping sets of STAT transcription factors are activated by different cytokines. One example is the differential activation of acute phase response factor (APRF, also called Stat3) and Stat1 by interleukin 6 and interferon-gamma. Interleukin 6 activates both factors while, at least in human cells, interferon-gamma recruits only Stat1. Stat1 activation by interferon-gamma is mediated through a cytosolic tyrosine motif, Y440, of the interferon-gamma receptor. In an accompanying paper (Gerhartz, C., Heesel, B., Sasse, J., Hemmann, U., Landgraf, C., Schneider-Mergener, J., Horn, F., Heinrich, P. C., and Graeve, L. (1996) J. Biol. Chem. 271, 12991-12998), we demonstrated that two tyrosine motifs within the cytoplasmic part of the interleukin 6 signal transducer gp130 specifically mediate APRF activation while two others can recruit both APRF and Stat1. By expressing a series of Stat1/APRF domain swap mutants in COS-7 cells, we now determined which domains of Stat1 and APRF are involved in the specific recognition of phosphotyrosine motifs. Our data demonstrate that the SH2 domain is the sole determinant of specific STAT factor recruitment. Furthermore, the SH2 domain of Stat1 is able to recognize two unrelated types of phosphotyrosine motifs, one represented by the interferon-gamma receptor Y440DKPH peptide, and the other by two gp130 YXPQ motifs. By molecular modeling, we propose three-dimensional model structures of the Stat1 and APRF SH2 domains which allow us to explain the different binding preferences of these factors and to predict amino acids crucial for specific peptide recognition.
Antibodies to Hepatitis B Surface Antigen (HBsAg) Elicited by Immunization with a Synthetic Peptide Covalently Linked to Liposomes (1984)

SUMMARY Peptides synthesized for potential application as antiviral vaccines have been mostly tested in the form of conjugates with carrier proteins. The possible use of several distinct synthetic vaccines in prophylaxis would be facilitated by the availability of fully synthetic immunogens. A synthetic peptide corresponding to residues 135 to 155 (P135–155) of hepatitis B surface antigen (HBsAg) failed to elicit in free form anti-peptide antibodies or anti-HBs. However, polymers of P135–155 (prepared by linking to diaminoalkanes) and synthetic conjugates prepared by binding P135–155 to liposomes or polylysine were immunogenic. A poor correlation was observed between anti-peptide and anti-HBs responses elicited by these conjugates. Glutaraldehyde-fixed liposomes appeared to be the carriers of choice for inducing anti-HBs.
The lepidopteran transposon vector, piggyBac , mediates germ-line transformation in the Mediterranean fruit fly (1998)

The piggyBac (IFP2) short inverted terminal repeat transposable element from the cabbage looper Trichoplusia ni was tested for gene transfer vector function as part of a bipartite vector-helper system in the Mediterranean fruit fly Ceratitis capitata. A piggyBac vector marked with the medfly white gene was tested with a normally regulated piggyBac transposase helper at two different concentrations in a white eye host strain. Both experiments yielded transformants at an approximate frequency of 3-5%, with a total of six lines isolated having pigmented eyes with various levels of coloration. G1 transformant siblings from each line shared at least one common integration, with several sublines having an additional second integration. For the first transformant line isolated, two integrations were determined to be stable for 15 generations. For five of the lines, a piggyBac-mediated transposition was verified by sequencing the insertion site junctions isolated by inverse PCR that identified a characteristic piggyBac TTAA target site duplication. The efficient and stable transformation of the medfly with a lepidopteran vector represents transposon function over a relatively large evolutionary distance and suggests that the piggyBac system will be functional in a broad range of insects.
Prediction of bacterial proteins carrying a nuclear localization signal and nuclear targeting of HsdM from Klebsiella pneumoniae (2009)

Nuclear targeting of bacterial proteins is an emerging pathogenic mechanism whereby bacterial proteins can interact with nuclear molecules and alter the physiology of host cells. The fully sequenced bacterial genome can predict proteins that target the nuclei of host cells based on the presence of nuclear localization signal (NLS). In the present study, we predicted bacterial proteins with the NLS sequences from Klebsiella pneumoniae by bioinformatic analysis, and 13 proteins were identified as carrying putative NLS sequences. Among them, HsdM, a subunit of KpnAl that is a type I restriction-modification system found in K. pneumoniae, was selected for the experimental proof of nuclear targeting in host cells. HsdM carried the NLS sequences, (7)KKAKAKK(13), in the N-terminus. A transient expression of HsdM-EGFP in COS-1 cells exhibited exclusively a nuclear localization of the fusion proteins, whereas the fusion proteins of HsdM with substitutions in residues lysine to alanine in the NLS sequences, (7)AAAKAAA(13), were localized in the cytoplasm. HsdM was co-localized with importin o in the nuclei of host cells. Recombinant HsdM alone methylated the eukaryotic DNA in vitro assay. Although HsdM tested in this study has not been considered to be a virulence factor, the prediction of NLS motifs from the full sequenced genome of bacteria extends our knowledge of functional genomics to understand subcellular targeting of bacterial proteins.
Plasmid-mediated tetracycline resistance in Campylobacter jejuni: expression in Escherichia coli and identification of homology with streptococcal class M determinant (1986)

Plasmid pUA466, a 45-kilobase transmissible tetracycline resistance plasmid from Campylobacter jejuni was mapped with AvaI, AvaII, BclI, HincII, PstI, XhoI, and XbaI. The resistance determinant was cloned and expressed in Escherichia coli and was homologous with a class M determinant from Streptococcus spp.
Role of the vector genome and underlying factor IX mutation in immune responses to AAV gene therapy for hemophilia B (2014)

The nature of the AAV genome can impact the CD8⁺ T cell response to the therapeutic transgene product. In mice with endogenous hF.IX expression, however, this enhanced immunogenicity did not break tolerance to hF.IX, suggesting that the underlying mutation is a more important risk factor for transgene-specific immunity than the molecular form of the AAV genome.
Directed diffusion for wireless sensor networking (2003)

Advances in processor, memory, and radio technology enable small and cheap nodes capable of sensing, communication, and computation. Networks of such nodes can coordinate to perform distributed sensing of environmental phenomena. We explore the directed diffusion paradigm for such coordination. Directed diffusion is data-centric in that all communication is for named data. All nodes in a directed-diffusion-based network are application aware. This enables diffusion to achieve energy savings by selecting empirically good paths and by caching and processing data in-network (e.g., data aggregation). We explore and evaluate the use of directed diffusion for a simple remote-surveillance sensor network analytically and experimentally. Our evaluation indicates that directed diffusion can achieve significant energy savings and can outperform idealized traditional schemes (e.g., omniscient multicast) under the investigated scenarios.
Glycoproteins gB, gD, and gHgL of Herpes Simplex Virus Type 1 Are Necessary and Sufficient To Mediate Membrane Fusion in a Cos Cell Transfection System (1998)

Herpes simplex virus type 1 glycoproteins gB, gD, and gHgL were expressed by transient transfection of Cos cells. Polykaryocyte formation above the background level seen in untransfected controls was observed only if all three components were expressed. Thus, gB, gD, and gHgL are necessary and sufficient to induce membrane fusion.
Assessing serotonin receptor mRNA editing frequency by a novel ultra high-throughput sequencing method (2010)

RNA editing is a post-transcriptional modification of pre-mRNA that results in increased diversity in transcriptomes and proteomes. It occurs in a wide variety of eukaryotic organisms and in some viruses. One of the most common forms of pre-mRNA editing is A-to-I editing, in which adenosine is deaminated to inosine, which is read as guanosine during translation. This phenomenon has been observed in numerous transcripts, including the mammalian 5-HT(2C) receptor, which can be edited at five distinct sites. Methods used to date to quantify 5-HT(2C) receptor editing are labor-intensive, expensive and provide limited information regarding the relative abundance of 5-HT(2C) receptor editing variants. Here, we present a novel, ultra high-throughput method to quantify 5-HT(2C) receptor editing, compare it to a more conventional method, and use it to assess the effect of a range of genetic and pharmacologic manipulations on 5-HT(2C) editing. We conclude that this new method is powerful and economical, and we provide evidence that alterations in 5-HT(2C) editing appear to be a result of regional changes in brain activity, rather than a mechanism to normalize 5-HT(2C) signaling.
Effect of deferiprone on urinary zinc excretion in multiply transfused children with thalassemia major. (2005)

A prospective multi-centric study was conducted to determine if iron-chelating agent deferiprone also chelates zinc. Twenty four-hour urinary zinc levels were compared in multiply transfused children with thalassemia major not receiving any chelation therapy (Group A, n = 28), those receiving deferiprone (Group B, n = 30) and age and sex-matched controls of subjects in Group B (Group C, n = 29) by a colorimetric method. The 24-hour mean urinary excretion of zinc was significantly higher in Group B than in the other two groups indicating that deferiprone chelates zinc.
Light Response of Retinal ON Bipolar Cells Requires a Specific Splice Variant of Gαo (2002)

Glutamate released onto retinal ON bipolar neurons binds to a metabotropic receptor to activate a heterotrimeric G-protein (G(o)) that ultimately closes a nonspecific cation channel. Signaling requires the alpha subunit (Galpha(o)), but its effector is unknown. Because Galpha(o) is transcribed into two splice variants (alpha(o1) and alpha(o2)) that differ in the key GTPase domain, the next step in elucidating this pathway was to determine which splice variant carries the signal. Here we show by reverse transcription-PCR and Western blots that retina expresses both splice variants. Furthermore, in situ hybridization and immunostaining on mouse retina deficient in one splice variant or the other show that both alpha(o1) and alpha(o2) are expressed by ON bipolar cells but that alpha(o1) is much more abundant. Finally, electroretinography performed on mice deficient for one splice variant or the other shows that the positive b-wave (response of ON bipolar cells to rod and cone input) requires alpha(o1) but not alpha(o2). Thus, the light response of the ON bipolar cell is probably carried by its strongly expressed splice variant, Galpha(o1).
Compatibility of thioamides with reverse turn features: synthesis and conformational analysis of two model cyclic pseudopeptides containing thioamides as backbone modifications (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCompatibility of thioamides with reverse turn features: synthesis and conformational analysis of two model cyclic pseudopeptides containing thioamides as backbone modificationsDouglas B. Sherman and Arno F. SpatolaCite this: J. Am. Chem. Soc. 1990, 112, 1, 433–441Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/ja00157a064https://doi.org/10.1021/ja00157a064research-articleACS PublicationsRequest reuse permissionsArticle Views443Altmetric-Citations63LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Transient blockade of the inducible costimulator pathway generates long-term tolerance to factor VIII after nonviral gene transfer into hemophilia A mice (2008)

Formation of inhibitory antibodies is a common problem encountered in clinical treatment for hemophilia. Human factor VIII (hFVIII) plasmid gene therapy in hemophilia A mice also leads to strong humoral responses. We demonstrate that short-term therapy with an anti-ICOS monoclonal antibody to transiently block the inducible costimulator/inducible costimulator ligand (ICOS/ICOSL) signaling pathway led to sustained tolerance to hFVIII in hFVIII plasmid-treated hemophilia A mice and allowed persistent, high-level FVIII functional activity (100%-300% of normal). Anti-ICOS treatment resulted in depletion of ICOS(+)CD4(+) T cells and activation of CD25(+)Foxp3(+) Tregs in the peripheral blood, spleen, and lymph nodes. CD4(+) T cells from anti-ICOS-treated mice did not proliferate in response to hFVIII stimulation and produced high levels of regulatory cytokines, including interleukin-10 and transforming growth factor-beta. Moreover, CD4(+)CD25(+) Tregs from tolerized mice adoptively transferred dominant tolerance in syngeneic hFVIII plasmid-treated hemophilia A mice and reduced the production of antibodies against FVIII. Anti-ICOS-treated mice tolerized to hFVIII generated normal primary and secondary antibody responses after immunization with the T-dependent antigen, bacteriophage Phix 174, indicating maintenance of immune competency. Our data indicate that transient anti-ICOS monoclonal antibody treatment represents a novel single-agent immunomodulatory strategy to overcome the immune responses against transgene product after gene therapy.
Translocation Inhibitors Define Specificity of Protein Kinase C Isoenzymes in Pancreatic β-Cells (1997)

The protein kinase C (PKC) family consists of 11 isoenzymes. Following activation, each isoenzyme translocates and binds to a specific receptor for activated C kinase (RACK) (Mochly-Rosen, D. (1995) Science 268, 247-251) that provides an anchoring site in close proximity to the isoenzyme's specific substrate. Pancreatic islet cells contain at least six PKC isoenzymes (Knutson, K. L., and Hoenig, M. (1994) Endocrinology 135, 881-886). Although PKC activation enhances insulin release, the specific function of each isoenzyme is unknown. Here we show that following stimulation with glucose, alphaPKC and epsilonPKC translocate to the cell's periphery, while deltaPKC and zetaPKC translocate to perinuclear sites. betaC2-4, a peptide derived from the RACK1-binding site in the C2 domain of betaPKC, inhibits translocation of alphaPKC and reduces insulin response to glucose. Likewise, epsilonV1-2, an epsilonPKC-derived peptide containing the site for its specific RACK, inhibits translocation of epsilonPKC and reduces insulin response to glucose. Inhibition of islet-glucose metabolism with mannoheptulose blocks translocation of both alphaPKC and epsilonPKC and diminishes insulin response to glucose while calcium-free buffer inhibits translocation of alphaPKC but not epsilonPKC and lowers insulin response by 50%. These findings illustrate the unique ability of specific translocation inhibitors to elucidate the isoenzyme-specific functions of PKC in complex signal transduction pathways.
From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing (2013)

Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and editing, and regulatory module activity. Despite great progress recently, substantial challenges remain, including discriminating biological variation from technical noise. Here we apply the SMART-seq single-cell RNA-seq protocol to study the reference lymphoblastoid cell line GM12878. By using spike-in quantification standards, we estimate the absolute number of RNA molecules per cell for each gene and find significant variation in total mRNA content: between 50,000 and 300,000 transcripts per cell. We directly measure technical stochasticity by a pool/split design and find that there are significant differences in expression between individual cells, over and above technical variation. Specific gene coexpression modules were preferentially expressed in subsets of individual cells, including one enriched for mRNA processing and splicing factors. We assess cell-to-cell variation in alternative splicing and allelic bias and report evidence of significant differences in splice site usage that exceed splice variation in the pool/split comparison. Finally, we show that transcriptomes from small pools of 30-100 cells approach the information content and reproducibility of contemporary RNA-seq from large amounts of input material. Together, our results define an experimental and computational path forward for analyzing gene expression in rare cell types and cell states.
Antiviral and Interferon-Inducing Activity of a New Glutarimide Antibiotic, 9-Methylstreptimidone (1976)

The antiviral effect of 9-methylstreptimidone (9-MS) was examined in mice infected with mouse-adapted influenza A(2) (H(2)N(2)) virus. Both a single and continuous prophylactic administration of 9-MS protected mice from virus infection, and comparison between the minimal effective and the 50% lethal dose gave a therapeutic index of 60. When the treatment was started after infection, however, no antiviral effect was demonstrated. After a single intraperitoneal administration of 9-MS, a highly potent virus-inhibitory factor was detected in the lungs (10 h later) and the sera (16 h later) of uninfected mice, which was assumed to be an interferon on the basis of the biological characteristics. These results suggest that the protective activity of the antibiotic is due to interferon induction in mice.
BAY 43-9006: Preclinical Data (2002)

The drug design and discovery efforts described in the previous section led to the development of a novel, small molecule Raf-1 kinase inhibitor, BAY 43-9006, which belongs to a class that can be broadly described as bis-aryl ureas (Figure 1). BAY 43-9006 was identified during a large medicinal chemistry optimization program, and this compound was selected for further pharmacological characterization based on its potent inhibition of Raf-1 (IC(50) 12 nM) and its favorable kinase selectivity profile. In vitro and in vivo experiments were designed to demonstrate effective blockade of the Raf/MEK/ERK signaling pathway in tumor cells and for anti tumor efficacy in human xenograft models.
Complications of Level I and II Axillary Dissection in the Treatment of Carcinoma of the Breast (1999)

The characterization of a level I and II axillary dissection as a procedure with significant complications does not appear justified based on this experience.
Gene Expression Patterns in Human Liver Cancers (2002)

Hepatocellular carcinoma (HCC) is a leading cause of death worldwide. Using cDNA microarrays to characterize patterns of gene expression in HCC, we found consistent differences between the expression patterns in HCC compared with those seen in nontumor liver tissues. The expression patterns in HCC were also readily distinguished from those associated with tumors metastatic to liver. The global gene expression patterns intrinsic to each tumor were sufficiently distinctive that multiple tumor nodules from the same patient could usually be recognized and distinguished from all the others in the large sample set on the basis of their gene expression patterns alone. The distinctive gene expression patterns are characteristic of the tumors and not the patient; the expression programs seen in clonally independent tumor nodules in the same patient were no more similar than those in tumors from different patients. Moreover, clonally related tumor masses that showed distinct expression profiles were also distinguished by genotypic differences. Some features of the gene expression patterns were associated with specific phenotypic and genotypic characteristics of the tumors, including growth rate, vascular invasion, and p53 overexpression.
Ductal carcinoma in situ: Value of sentinel lymph node biopsy (2006)

Sentinel lymph node biopsy is valuable in patients with diffuse DCIS or DCISM who are scheduled for mastectomy in order to search for axillary micrometastases and occult breast microinvasion.
Science and environment education : views from developing countries (1999)

Currently, there is an increasing understanding that teaching and learning good school science may produce extensive contributions to economic development. The importance of scientifically literate citizens and workers is likely to increase further in the coming decades as a result of the fast replacement of traditional technologies by new, efficient, science-based technologies. This volume, the first in the Secondary Education series, contains articles written by science educators from various countries which give an overview of some of the current best practices in school science and environment education. One of the main purposes of this book is to demonstrate that valuable information is available in developing countries, several of which have attempted to implement significant science education reforms in recent years. The papers collected in this volume come from Latin America and the Caribbean, Africa, Asia, Europe, and North America. While the majority address reforms in specific developing nations, some papers look at issues that cross national barriers. For example, two papers address the use of low-cost/no cost equipment to deliver hands-on science instruction. One paper examines extremely high technology--high cost methods of enhancing science instruction--methods that, although more commonly used in industrial nations, are now spreading to the wealthier developing countries.