gebhart/patrepeval huggingface dataset:
Regulation of U6 Promoter Activity by Transcriptional Interference in Viral Vector-Based RNAi (2010)

The direct negative impact of the transcriptional activity of one component on the second one in cis is referred to as transcriptional interference (TI). U6 is a type III RNA polymerase III promoter commonly used for driving small hairpin RNA (shRNA) expression in vector-based RNAi. In the design and construction of viral vectors, multiple transcription units may be arranged in close proximity in a space-limited vector. Determining if U6 promoter activity can be affected by TI is critical for the expression of target shRNA in gene therapy or loss-of-function studies. In this research, we designed and implemented a modified retroviral system where shRNA and exogenous gene expressions were driven by two independent transcriptional units. We arranged U6 promoter driving shRNA expression and UbiC promoter in two promoter arrangements. In primary macrophages, we found U6 promoter activity was inhibited by UbiC promoter when in the divergent arrangement but not in tandem. In contrast, PKG promoter had no such negative impact. Instead of enhancing U6 promoter activity, CMV enhancer had significant negative impact on U6 promoter activity in the presence of UbiC promoter. Our results indicate that U6 promoter activity can be affected by TI in a proximal promoter-specific and arrangement-dependent manner.
Binding of host collectins to the pathogenic yeast Cryptococcus neoformans: human surfactant protein D acts as an agglutinin for acapsular yeast cells (1995)

Cryptococcus neoformans is an opportunistic pathogen in AIDS patients causing disseminated disease and lethal meningitis after inhalation of acapsular or sparsely encapsulated yeast cells. In this study we have investigated whether a recently described family of primitive opsonins, termed collectins, contribute to innate resistance against C. neoformans. The pulmonary surfactant proteins SP-A and SP-D as well as the serum collectins mannose-binding protein and CL-43 bound in a calcium-dependent manner to acapsular C. neoformans in vitro. Binding was concentration dependent and abolished by competition with defined mono- and oligosaccharides. In contrast, no binding of the collectins was observed with the encapsulated form of the yeast. Furthermore, binding of purified collectin SP-D, but not SP-A, mannose-binding protein, or CL-43, led to a concentration-dependent agglutination of acapsular C. neoformans. These data indicate that collectins recognize carbohydrate structures in the cell wall of an initial infectious form of C. neoformans and may play a role in early antifungal defenses in the lung.
TNF-R1 Signaling: A Beautiful Pathway (2002)

Tumor necrosis factor (TNF) is a major mediator of apoptosis as well as inflammation and immunity, and it has been implicated in the pathogenesis of a wide spectrum of human diseases, including sepsis, diabetes, cancer, osteoporosis, multiple sclerosis, rheumatoid arthritis, and inflammatory bowel diseases. The interaction of TNF with TNF receptor-1 (TNF-R1) activates several signal transduction pathways. A common feature of each pathway is the TNF-induced formation of a multiprotein signaling complex at the cell membrane. Over the past decade, many of the components and mechanisms of these signaling pathways have been elucidated. We provide an overview of current knowledge of TNF signaling and introduce an STKE Connections Map that depicts a canonical view of this process.
Oligonucleosides: synthesis of a novel methylhydroxylamine-linked nucleoside dimer and its incorporation into antisense sequences (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOligonucleosides: synthesis of a novel methylhydroxylamine-linked nucleoside dimer and its incorporation into antisense sequencesJean Jacques Vasseur, Francoise Debart, Yogesh S. Sanghvi, and P. Dan CookCite this: J. Am. Chem. Soc. 1992, 114, 10, 4006–4007Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/ja00036a076https://doi.org/10.1021/ja00036a076research-articleACS PublicationsRequest reuse permissionsArticle Views341Altmetric-Citations93LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Indanylacetic Acid Derivatives Carrying 4-Thiazolyl-phenoxy Tail Groups, a New Class of Potent PPAR α/γ/δ Pan Agonists:  Synthesis, Structure−Activity Relationship, and In Vivo Efficacy (2007)

Compounds that simultaneously activate the three peroxisome proliferator-activated receptor (PPAR) subtypes alpha, gamma, and delta hold potential to address the adverse metabolic and cardiovascular conditions associated with diabetes and the metabolic syndrome. We recently identified the indanylacetic acid moiety as a well-tunable PPAR agonist head group. Here we report the synthesis and structure-activity relationship (SAR) studies of novel aryl tail group derivatives that led to a new class of potent PPAR pan agonists. While most of the tail group modifications imparted potent PPAR delta agonist activity, improvement of PPAR alpha and gamma activity required the introduction of new heterocyclic substituents that were not known in the PPAR literature. Systematic optimization led to the discovery of 4-thiazolyl-phenyl derivatives with potent PPAR alpha/gamma/delta pan agonistic activity. The lead candidate from this series was found to exhibit excellent ADME properties and superior therapeutic potential compared to known PPAR gamma activating agents by favorably modulating lipid levels in hApoA1 mice and hyperlipidemic hamsters, while normalizing glucose levels in diabetic rodent models.
Depressive illness, depressive symptomatology and regional cerebral blood flow in elderly people with sub-clinical cognitive impairment (1999)

In dementia, there may be two separate and interacting depressive syndromes whose differentiation may be clinically important.
Gene Transfer via Reversible Plasmid Condensation with Cysteine-Flanked, Internally Spaced Arginine-Rich Peptides (2003)

Nonviral gene transfer offers biosafety, stability, and expense advantages over viruses; however, it has suffered from poor efficiency. Because arginine-rich peptides facilitate uptake of macromolecules such as proteins, liposomes, and iron nanoparticles, we explored their potential in enhancing plasmid DNA delivery. In their unmodified form, known protein transduction sequences, including hepta-arginine and Tat(47-57), failed to support effective gene delivery. However, by flanking a core of consecutive arginines with amino- and carboxy-terminal cysteines in vitro gene transfer was observed. Furthermore, interspersing arginines with glycine and histidine residues achieved reversible plasmid condensation and dramatically increased transfection levels in a variety of cell types. Unlike most available cationic homopolymers that function only in vitro, these new peptides also increased gene expression in both murine and human tissue in vivo. Thus, cysteine-flanked, internally spaced arginine-rich (CFIS-R) peptides represent a new approach to efficient nonviral plasmid delivery using rationally designed protein transduction domains.
781 Sensitive DNA Marker Panel for Detection of Pancreatic Cancer by Assay in Pancreatic Juice (2014)

G A A b st ra ct s Ectopic expression of Spdef in tumors caused by treatment with azoxymethane (AOM) and dextran sodium sulfate (DSS), or spontaneously formed in ApcMin/+ mice was sufficient to drive cell cycle exit of tumor cells in both mouse models. Furthermore, loss of Spdef lead to a significant increase in colonic tumor number from both mouse models (AOM+DSS and ApcMin/+ ), defining Spdef as a tumor suppressor in the colon. Importantly, our previous study indicates that SPDEF expression is often silenced in human colon cancer and this SPDEF silencing in colon cancer is tightly correlated to ATOH1 silencing, suggesting SPDEF as a mediator of ATOH1's function in intestinal homeostasis and tumorigenesis. Therefore, we hypothesize that Spdef is a key effector of Notch-Atoh1 effects in intestinal tumors. Here, we assess the requirement of Spdef for Atoh1-directed growth inhibition in colonic tumors, and extend the analysis to elucidate the sufficiency of Spdef to promote cell cycle exit and goblet cell differentiation in Atoh1-null colonic tumors that mimic human colon cancer. Method: All analysis was performed in transgenic mice. The sufficiency of Spdef was tested by re-expressing Spdef in colonic tumors that lack Atoh1. The requirement of Spdef was tested by inducing Atoh1 expression through inhibition of the Notch activity in tumors that lack Spdef. Progenitor cell proliferation, Lgr5+ stem cell population and differentiation were immunohistologically assessed. Results: In Atoh1-null tumors, proliferation and Lgr5+ stem cell population was significantly reduced upon expression of SPDEF without induction of goblet cell markers. In response to Atoh1 induction by Notch inhibitor treatment, cell proliferation was inhibited and goblet cell differentiation was induced in colonic tumors; this response was prevented in Spdef-/mice. In contrast, Lgr5+ stem cell population was similarly reduced in tumors from both control and Spdef-/mice. Conclusions: SPDEF mediates the effect on tumor cell proliferation of Atoh1 induced by Notch inhibitors. The sufficiency and requirement for Spdef in promoting cell cycle exit in intestinal tumors suggest Spdef as a potential therapeutic target for colon cancer. Future studies will investigate the Notch-Atoh1 independent mechanisms to activate expression of SPDEF, which can be utilized as a colon cancer therapy.
High sensitivity three-dimensional insulator-based dielectrophoresis (2012)

Insulator-based dielectrophoresis (iDEP) is a very promising technique for sorting microparticles based on their electrical properties. The need for microfabricated electrode arrays is eliminated by using constrictions in a microchannel to induce large electric field gradients. In this work, micro-milling is used to build devices with three-dimensional features that exhibit very large constriction ratios. These three-dimensional insulator-based dielectrophoresis (3DiDEP) devices allow for trapping microparticles at average electric fields one order of magnitude lower than two-dimensional designs with the same footprint. Low voltage operation minimizes Joule heating effects that have limited previous systems, opening up the possibility for new biological applications of iDEP.
Exendin(9-39)amide is an antagonist of glucagon-like peptide-1(7-36)amide in humans. (1998)

The gastrointestinal hormone, glucagon-like peptide-1(7-36)amide (GLP-1) is released after a meal. The potency of synthetic GLP-1 in stimulating insulin secretion and in inhibiting glucagon secretion indicates the putative physiological function of GLP-1. In vitro, the nonmammalian peptide, exendin(9-39)amide [ex(9-39)NH2], is a specific and competitive antagonist of GLP-1. This in vivo study examined the efficacy of ex(9-39)NH2 as an antagonist of exogenous GLP-1 and the physiological role of endogenous GLP-1. Six healthy volunteers underwent 10 experiments in random order. In each experiment, a 30-min period of euglycemia was followed by an intravenous infusion of glucose for 150 min that established a stable hyperglycemia of 8 mmol/liter. There was a concomitant intravenous infusion of one of the following: (1) saline, (2) GLP-1 (for 60 min at 0.3 pmol . kg-1 . min-1 that established physiological postprandial plasma levels, and for another 60 min at 0.9 pmol . kg-1 . min-1 to induce supraphysiological plasma levels), (3-5) ex(9-39)NH2 at 30, 60, or 300 pmol . kg-1 . min-1 + GLP-1, (6-8) ex(9-39)NH2 at 30, 60, or 300 pmol . kg-1 . min-1 + saline, (9 and 10) GIP (glucose-dependent insulinotropic peptide; for 60 min at 0.8 pmol . kg-1 . min-1, with saline or ex(9-39)NH2 at 300 pmol . kg-1 . min-1). Each volunteer received each of these concomitant infusions on separate days. ex(9-39)NH2 dose-dependently reduced the insulinotropic action of GLP-1 with the inhibitory effect declining with increasing doses of GLP-1. ex(9-39)NH2 at 300 pmol . kg-1 . min-1 blocked the insulinotropic effect of physiological doses of GLP-1 and completely antagonized the glucagonostatic effect at both doses of GLP-1. Given alone, this load of ex(9-39)NH2 increased plasma glucagon levels during euglycemia and hyperglycemia. It had no effect on plasma levels of insulin during euglycemia but decreased plasma insulin during hyperglycemia. ex(9-39)NH2 did not alter GIP-stimulated insulin secretion. These data indicate that in humans, ex(9-39)NH2 is a potent GLP-1 antagonist without any agonistic properties. The pancreatic A cell is under a tonic inhibitory control of GLP-1. At hyperglycemia, the B cell is under a tonic stimulatory control of GLP-1.
Role of Natural Interferon-α Producing Cells (Plasmacytoid Dendritic Cells) in Autoimmunity (2003)

The type I interferons (IFNs) have antiviral, cytostatic and prominent immunomodulatory effects, which all are of great importance during viral infections. However, prolonged exposure of the immune system to type I IFN can break tolerance and initiate an autoimmune reaction, eventually leading to autoimmune disease. Recent observations in patients with systemic lupus erythematosus (SLE) have revealed that such individuals have endogenous IFN-alpha inducers, causing an ongoing IFN-alpha production and consequently a continuous stimulation of the immune system. These IFN-alpha inducers consist of small immune complexes (IC) containing DNA or RNA and act on the principal IFN-alpha producing cell, the natural IFN-alpha producing cell (NIPC), also termed the plasmacytoid dendritic cell (PDC). The NIPC/PDC is a key cell in both the innate and adaptive immune response but can also, either directly or via produced IFN-alpha, have a pivotal role in autoimmunity. In this review we summarize recent data concerning NIPC/PDC, including their activation, regulation, function and possible role in autoimmune diseases, especially SLE.
Gene Transfer of a Chimeric Trans-Activator Is Immunogenic and Results in Short-Lived Transgene Expression (2002)

Pharmacologic gene regulation is a key technology, necessary to achieve safe, long-term gene transfer. The approaches described in the scientific literature all share in common the creation of artificial transcription factors by fusing a DNA-binding domain, a drug-binding domain and a transcription activation domain. These transcription factors activate the transgene expression upon binding of the pharmacologic agent (antibiotics of the tetracycline family, insect hormone, progesterone antagonist, or immunosuppressor drug) to the drug-binding domain. The major limitations to the use of these systems for human gene and cell therapies are the toxicity of the inducer molecule and the immunogenicity of the chimeric transcription factor. Thus, the gene regulation systems should operate with clinically approved drugs with safety records that do not conflict with the therapeutic gene expression regimen. This work focuses on the characterization of the immunogenicity of a tetracycline-activated transcription factor commonly used in preclinical gene therapy, rtTA2-M2, and its impact on reporter gene expression. We demonstrate that intramuscular injection of plasmid or adenoviral vectors encoding rtTA-M2 in outbred primates generates a cellular and humoral immune response to this transcription factor. The immune response to rtTA2-M2 blunts the duration of the expression the rtTA2-M2-controlled transgene in primates, presumably by destruction of the cells that coexpress rtTA2-M2 and the reporter or therapeutic gene. This immune response may result directly from the vectors used in this study, which prompts the development of new gene transfer vectors enabling safe and efficient pharmacologic gene regulation in clinic.
Probing Glycosyltransferase Activities with the Staudinger Ligation (2003)

The development of rapid screening methods for probing glycosyltransferase activities is essential for advancing the field of glycobiology. While assays for specific glycosyltransferases exist, there is no generalizable method that can be applied across the enzyme superfamily. Herein we describe a novel glycosyltransferase assay that exploits their unnatural substrate tolerance and the unique chemical reactivity of the azide. We applied this "azido-ELISA" to the family of polypeptide alpha-N-acetylgalactosaminyltransferases (ppGalNAcTs), all of which were able to transfer N-azidoacetylgalactosamine (GalNAz) from the unnatural nucleotide sugar donor UDP-GalNAz. The azide was detected and quantified by Staudinger ligation with a phosphine probe in a microtiter plate format. This approach should be applicable to any glycosyltransferase or group-transfer enzyme that tolerates unnatural azido substrates.
Expression and characterization of the Plasmodium falciparum haemoglobinase falcipain-3 (2001)

In the malaria parasite Plasmodium falciparum, erythrocytic trophozoites hydrolyse haemoglobin to provide amino acids for parasite protein synthesis. Cysteine protease inhibitors block parasite haemoglobin hydrolysis and development, indicating that cysteine proteases are required for these processes. Three papain-family cysteine protease sequences have been identified in the P. falciparum genome, but the specific roles of their gene products and other plasmodial proteases in haemoglobin hydrolysis are uncertain. Falcipain-2 was recently identified as a principal trophozoite cysteine protease and potential drug target. The present study characterizes the related P. falciparum cysteine protease falcipain-3. As is the case with falcipain-2, falcipain-3 is expressed by trophozoites and appears to be located within the food vacuole, the site of haemoglobin hydrolysis. Both proteases require a reducing environment and acidic pH for optimal activity, and both prefer peptide substrates with leucine at the P(2) position. The proteases differ, however, in that falcipain-3 undergoes efficient processing to an active form only at acidic pH, is more active and stable at acidic pH, and has much lower specific activity against typical papain-family peptide substrates, but has greater activity against native haemoglobin. Thus falcipain-3 is a second P. falciparum haemoglobinase that is particularly suited for the hydrolysis of native haemoglobin in the acidic food vacuole. The redundancy of cysteine proteases may offer optimized hydrolysis of both native haemoglobin and globin peptides. Consideration of both proteases will be necessary to evaluate cysteine protease inhibitors as antimalarial drugs.
A Unique Placental Lactogen Receptor: Implications for Fetal Growth* (1987)

To determine whether there are structural differences between the binding sites for placental lactogen (PL) and GH, we have compared the molecular weights of complexes formed by the covalent cross-linking of [125I]ovine (o) PL and [125I]oGH to hepatic membranes from fetal and pregnant sheep in mid- and late gestation and from postnatal nonpregnant sheep at 3 days to 7 months of age. Specific [125I]oPL binding sites in fetal liver were detected as early as midgestation, and cross-linking of [125I]oPL to fetal hepatic membranes yielded a major radiographic band with a mol wt of 60 +/- 5 K (mean +/- SD). Unlabeled oPL at low concentrations (0.9-9 nM) specifically competed with [125I]oPL for binding to the 60 K complex. In contrast, oGH and oPRL competed for binding to the 60 K complex only at much higher concentrations (greater than or equal to 90 nM). In addition, no specific cross-linking of [125I]oGH or [125I]oPRL to fetal hepatic membranes was observed. These findings suggest the presence of a distinct and unique PL binding site in ovine fetal liver. Since the mol wt of oPL is 22 K, the estimated mol wt of the oPL receptor protein is 38 +/- 5 K. During the first week after birth, there was a striking increase in the number of [125I]oGH binding sites. Cross-linking of [125I]oGH to postnatal liver yielded radiographic bands with apparent mol wts of 75 K and 140 K. The relative potencies of oPL, oGH, and oPRL in competing for binding to the 75 K and 140 K complexes were similar to the relative potencies of these hormones in competing for [125I]oGH binding sites in postnatal liver, suggesting that the 75 K and 140 K bands represent subunits of the oGH receptor bound covalently to [125I]oGH. Cross-linking of [125I]oPL to pregnant and postnatal nonpregnant liver yielded three radiographic bands with mol wts of 60 K, 75 K, and 140 K. The intensities of all three bands were reduced by low concentrations (0.9-9 nM) of oPL. Higher concentrations of oGH abolished the 75 K and 140 K bands but reduced the intensity of the 60 K band by only 20-30%. oPRL had minimal effect on band intensities. These observations suggest the presence of two functionally and structurally distinct receptors in pregnant liver: the oPL receptor, which has high affinity for oPL and low affinity for oGH and oPRL.(ABSTRACT TRUNCATED AT 400 WORDS)
The clinical and biological impact of new pathogen inactivation technologies on platelet concentrates (2014)

Since 1990, several techniques have been developed to photochemically inactivate pathogens in platelet concentrates, potentially leading to safer transfusion therapy. The three most common methods are amotosalen/UVA (INTERCEPT Blood System), riboflavin/UVA-UVB (MIRASOL PRT), and UVC (Theraflex-UV). We review the biology of pathogen inactivation methods, present their efficacy in reducing pathogens, discuss their impact on the functional aspects of treated platelets, and review clinical studies showing the clinical efficiency of the pathogen inactivation methods and their possible toxicity.
Cooperative work in the Andrew message system (1988)

The Andrew Message System, a distributed system for multi-media electronic communication, has a number of special features that support cooperative work. After a brief discussion of the system itself, these features are described and discussed in more detail. Examples of how organizations actually use these features are then presented and discussed, with particular attention paid to the “Advisor” system for electronic consulting.