gebhart/patrepeval huggingface dataset:
Alterations in spinal cord gene expression after hindpaw formalin injection (2004)

Heme oxygenase type 2 (HO-2) is an enzyme that uses heme as a substrate to produce iron, biliverdin, and carbon monoxide (CO). This enzyme participates in regulation of nociceptive signal transmission in spinal cord tissue. We set out to identify genes undergoing alterations in expression in a model of inflammatory pain and to determine whether HO-2 participates in that regulation. After the hindpaw injection of formalin in mice, we measured changes in expression of immediate early genes including c-fos, c-jun, jun B, nerve growth factor induced genes (NGFI-A and NGFI-B) and activity-related cytoskeletal protein (ARC) using real-time PCR. The mRNA corresponding to these genes increased in abundance in the first hour after formalin injection and then slowly declined. Changes in the abundance of prodynorphin, extracellular signal related kinases (ERK1 and ERK2) and N-methyl-D-aspartate (NMDA) receptor R1 subunit mRNA generally peaked between 8 and 12 hr after formalin injection. In HO-2 null mutant mice, the enhancement of expression was less for all genes studied. We went on to quantify gene expression in superficial dorsal horn tissue using laser capture microdissection followed by RNA amplification and real-time PCR. The results confirmed that the changes in gene expression were occurring in regions of the spinal cord involved in nociceptive processing. We conclude that the hindpaw injection of formalin leads to enhanced early and late expression of many genes in spinal cord dorsal horn tissue, and that this enhancement of expression relies to a degree on the presence of HO-2.
Alternative Splicing in Colon, Bladder, and Prostate Cancer Identified by Exon Array Analysis (2008)

Alternative splicing enhances proteome diversity and modulates cancer-associated proteins. To identify tissue- and tumor-specific alternative splicing, we used the GeneChip Human Exon 1.0 ST Array to measure whole-genome exon expression in 102 normal and cancer tissue samples of different stages from colon, urinary bladder, and prostate. We identified 2069 candidate alternative splicing events between normal tissue samples from colon, bladder, and prostate and selected 15 splicing events for RT-PCR validation, 10 of which were successfully validated by RT-PCR and sequencing. Furthermore 23, 19, and 18 candidate tumor-specific splicing alterations in colon, bladder, and prostate, respectively, were selected for RT-PCR validation on an independent set of 81 normal and tumor tissue samples. In total, seven genes with tumor-specific splice variants were identified (ACTN1, CALD1, COL6A3, LRRFIP2, PIK4CB, TPM1, and VCL). The validated tumor-specific splicing alterations were highly consistent, enabling clear separation of normal and cancer samples and in some cases even of different tumor stages. A subset of the tumor-specific splicing alterations (ACTN1, CALD1, and VCL) was found in all three organs and may represent general cancer-related splicing events. In silico protein predictions suggest that the identified cancer-specific splice variants encode proteins with potentially altered functions, indicating that they may be involved in pathogenesis and hence represent novel therapeutic targets. In conclusion, we identified and validated alternative splicing between normal tissue samples from colon, bladder, and prostate in addition to cancer-specific splicing events in colon, bladder, and prostate cancer that may have diagnostic and prognostic implications.
Live oral Salmonella vaccines: potential use of attenuated strains as carriers of heterologous antigens to the immune system (1987)

Live attenuated strains of salmonellae are showing promise as live oral vaccines against human typhoid fever and other Salmonella infections of man and animals. Attenuation can be achieved by introducing genetically defined, non-reverting mutations into specific genes on the Salmonella chromosome. Mutations in the gal E or aroA genes of Salmonella inhibit the ability of the bacteria to grow in vivo, and strains carrying such lesions are effective vaccines against salmonellosis. Genetic determinants encoding for the expression of potentially protective antigens from heterologous, non-Salmonella pathogens can be readily introduced into these attenuated Salmonella strains. Expression of the heterologous antigen does not affect the ability of the Salmonella host to be used as a Salmonella vaccine. Mice infected orally with a Salmonella typhimurium aroA vaccine expressing the Escherichia coli heat-labile toxin B subunit developed both a secretory and serum antibody response to this antigen. These serum antibodies were able to neutralise the activity of E. coli heat-labile toxin in tissue culture assays. A humoral and cell-mediated (DTH) immune response was detected against beta galactosidase, an intracellular antigen, in mice infected with an aroA vaccine expressing this cloned antigen. The prospects for the development of live Salmonella vaccines as a method for delivering heterologous antigens derived from bacteria, viruses and parasites is discussed.
Epothilone B stabilizes microtubuli of macrophages like taxol without showing taxol-like endotoxin activity. (1997)

Epothilones are a new class of potential antitumor compounds that were isolated from the myxobacterium Sorangium cellulosum. Epothilones have effects on the cytoskeleton similar to those of the antineoplastic drug Taxol. Both compounds inhibit cell proliferation by stabilizing microtubuli, and they compete for the same binding site. In addition, Taxol displays endotoxin-like properties in that it activates macrophages to synthesize proinflammatory cytokines and nitric oxide. We measured nitric oxide release by IFN-gamma-treated murine macrophages as an indicator of macrophage activation by epothilone B. Although epothilone B showed the expected effects on the microtubuli, there was no indication of macrophage stimulatory activity by epothilone B, nor did epothilone B inhibit lipopolysaccharide-mediated nitric oxide release. We conclude that, unlike Taxol, epothilone-mediated microtubuli stabilization does not trigger endotoxin-signaling pathways. Moreover, because the endotoxin-like activity of Taxol may be the cause of some nonhematological clinical side effects, it is to be expected that such effects may not occur with epothilones.
Molecular Imaging of a Micropatterned Biological Ligand on an Activated Polymer Surface (2000)

We report here molecular characterization of a new method derived from reactive microcontact printingmicrostamping on an activated polymer surface (MAPS)which enables biological ligands and proteins to be patterned on a polymer surface with a spatial resolution of at least 5 μm and good reproducibility. MAPS is a multistep procedure: first, the surface of a polymer is modified, in one or more steps, to introduce a reactive group of interest. In a subsequent step, an elastomeric stamp, inked with a biological ligand containing a complementary terminal reactive group, is brought into contact with the activated surface of the polymer. This results in spatially resolved transfer and coupling of the biological ligand to the reactive surface of the polymer. We used MAPS to pattern biotin on carboxylic acid derivatized poly(ethylene terephthalate) (PET), and subsequently with streptavidin, mediated by the high affinity streptavidin−biotin interaction. X-ray photoelectron spectroscopy of biotin-derivatized PET showed that approximately one in five PET repeat units in the top 50−100 Å were functionalized with biotin. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) suggested an increased concentration of PET oligomers in the top 10 Å due to chain scission during modification and clearly identified the derivatization of PET with biotin. TOF-SIMS imaging mapped biotin and streptavidin to the stamped regions. TOF-SIMS also imaged the spatial distribution of residual reagents from the multistep derivatization in MAPS, such as pentafluorophenol, Tween 20 surfactant, as well as poly(dimethylsiloxane) (PDMS), which was transferred from the elastomeric PDMS stamp to the surface during MAPS.
Effects of Polymer Matrixes on the Time-Resolved Luminescence of a Ruthenium Complex Quenched by Oxygen (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffects of Polymer Matrixes on the Time-Resolved Luminescence of a Ruthenium Complex Quenched by OxygenSonja Draxler, Max E. Lippitsch, Ingo Klimant, Heinz Kraus, and Otto S. WolfbeisCite this: J. Phys. Chem. 1995, 99, 10, 3162–3167Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://pubs.acs.org/doi/10.1021/j100010a029https://doi.org/10.1021/j100010a029research-articleACS PublicationsRequest reuse permissionsArticle Views676Altmetric-Citations108LEARN 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 options Get e-Alerts
Basic Principles of Cell Culture (2005)

This chapter contains sections titled: Introduction Types of Cell Culture Isolation of Cells for Culture Subculture Cryopreservation Characterization and Validation Sources of Materials References
Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults (2009)

In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota--referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16,000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose-response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition.
Characterization of rat ovarian lutropin receptor (1989)

Rat ovarian lutropin receptor occurs predominantly as a monomer of an apparent molecular mass of 70 or 80 kDa determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis under nonreducing and reducing conditions, respectively. The receptor contains 0.4% free cysteine and 1.9% cysteine as cystine, determined by amino acid analysis of the S-carboxymethyl receptor prepared before and after reduction. The presence of free thiol groups was further shown by the specific adsorption of the receptor on p-chloromercuribenzoate-agarose and its susceptibility to 3H labeling with [3H]N-ethylmaleimide or [3H]iodoacetic acid. The receptor readily undergoes association into homo-oligomers. Evidence suggests that the association was caused by the intermolecular oxidation of the free -SH groups to form disulfide bonds. The aggregation could be induced by H2O2 or molecular O2 and was inhibited by sulfhydryl protecting agents such as N-ethylmaleimide, iodoacetic acid, dithiothreitol, cysteine, and Zn(II). The oligomers could be dissociated by reduction into a monomer. 125I-Labeling of the S-carboxymethyl- or N-ethylmaleyl receptor gave a single band of molecular mass 70 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Furthermore, S-alkylation of the receptor did not affect its binding to the ligand. On reduction, however, it lost its ability to bind to the ligand, but the reduced receptor retained its ability to bind to a specific polyclonal rabbit antireceptor antibody indicating the separation of the ligand and antibody binding sites. Endoproteinase Glu-C cleaved the receptor at a single glutamyl residue to give two components, 46 and 36 kDa. The 36-kDa component was extracellularly located since it contained the carbohydrate. On deglycosylation with endoglycosidase F, it yielded two components, 27 and 25 kDa. The deglycosylation of the reduced intact receptor (80 kDa) with endoglycosidase F occurred in two steps giving 73- and 64-kDa polypeptides, indicating the presence of about 20% carbohydrate contained in two or more N-linked chains.
Role of 4‐hydroxy‐2,3‐nonenal in the pathogenesis of fibrosis (2005)

Transient activation of fibroblasts or fibroblast-like cells to proliferate and to produce elevated quantities of extracellular matrix is essential to fibrosis. This activation is regulated by several cytokines produced by various inflammation-associated cells. Among these, transforming growth factor beta1 (TGFbeta1) is considered of major importance. Many studies have shown that lipid peroxidation play a key role in the initiation and progression of fibrosis in different organs. In fact, 4-hydroxy-2,3-nonenal (HNE), the major aldehydic product of lipid peroxidation, is able to induce TGFbeta1 expression and synthesis, and activation of activator protein-1 (AP-1) transcription factor. In this study, using the murine macrophage line J774-A1, we show that these effects are strictly related to the chemical structure of HNE, since neither 2-nonenal nor nonanal are biologically active to the same extent. Moreover, we demonstrate that HNE can indeed contribute to the onset of fibrosis by stimulating AP-1 binding to DNA and consequently inducing TGFbeta1 expression, since thiol-group reagents, such as N-ethylmaleimide and 4-(chloro-mercuri)-benzenesulfonic acid, that down-modulate HNE entrance and localisation inside the cell, prevent both phenomena. The possibility to control fibrogenic cytokine levels by means of antioxidant or dietetic treatments opens new potential pharmacological and nutritional horizons in the treatment of many chronic diseases characterised by excessive fibrosis.
Pragmatic naturalism & realism (2003)

Pragmatism, the philosophy native to America, has once again grown to prominence in philosophical debate around the world. Today, the type of pragmatism that is proving to be of greatest value for fostering discussions with other worldviews is pragmatic naturalism. The fourteen provocative essays in this original collection are all by philosophers who describe themselves as pragmatic naturalists and who are active in the present-day revival of American pragmatism.
Expression of growth arrest???specific gene 6 and its receptors in a rat model of chronic renal transplant rejection (2002)

These findings suggest that Gas6 and its receptors have an as yet undefined role in kidney function and/or development and may be involved in the pathogenesis of CR. The action of Gas6 in rat kidney is mainly mediated through the Rse receptors rather than the Axl and Mer receptors.
Evaluation of Topical Drug Treatment in Psoriasis (1998)

An optimal treatment of psoriasis requires a spectrum of topical drugs and their formulations in different vehicles.
Three forms of RPTP-? are differentially expressed during gliogenesis in the developing rat brain and during glial cell differentiation in culture (1996)

In situ hybridization and Northern analysis demonstrate that the three splicing variants of RPTP-beta have different spatial and temporal patterns of expression in the developing brain. The 9.5-kb and 6.4-kb transcripts, which encode transmembrane protein tyrosine phosphatases with different extracellular domains, are predominantly expressed in glial progenitors located in the subventricular zone (SVZ). The 8.4-kb transcript, which encodes a secreted chondroitin sulfate proteoglycan (phosphacan), is expressed at high levels by more mature glia that have migrated out of the SVZ. The three transcripts are also differentially expressed in glial cell cultures; O2A progenitors express high levels of the 9.5- and 8.4-kb transcript, whereas type 1 astrocyte progenitors predominantly express the 6.4-kb transcript. C6 gliomas also express high levels of the 6.4-kb transcript. Treating C6 cells with the differentiating agent dibutyryl cyclic-AMP (DBcAMP), induces a decrease in the 6.4-kb transcript and a corresponding increase in the 8.4-kb transcript. O2A cells grown in the presence of basic fibroblast growth factor (bFGF) and platelet-derived growth factor (PDGF) remain highly proliferative and undifferentiated, and continue to express high levels of RPTP-beta. However, when O2A cells are grown in conditions that induce oligodendrocyte differentiation, there is a marked decrease in the expression of the transmembrane forms of RPTP-beta, as determined by immunofluorescence. These results demonstrate that RPTP-beta expression is regulated during glial cell differentiation and suggest that the different forms of RPTP-beta perform distinct functions during brain development.
Additional data on the population distribution of human serum albumin genes; three new variants (1973)

Peer Reviewed
Protection From Ischemic Heart Injury by a Vigilant Heme Oxygenase-1 Plasmid System (2004)

Although human heme oxygenase-1 (hHO-1) could provide a useful approach for cellular protection in the ischemic heart, constitutive overexpression of hHO-1 may lead to unwanted side effects. To avoid this, we designed a hypoxia-regulated hHO-1 gene therapy system that can be switched on and off. This vigilant plasmid system is composed of myosin light chain-2v promoter and a gene switch that is based on an oxygen-dependent degradation domain from the hypoxia inducible factor-1-alpha. The vector can sense ischemia and switch on the hHO-1 gene system, specifically in the heart. In an in vivo experiment, the vigilant hHO-1 plasmid or saline was injected intramyocardially into myocardial infarction mice or sham operation mice. After gene transfer, expression of hHO-1 was only detected in the ischemic heart treated with vigilant hHO-1 plasmids. Masson trichrome staining showed significantly fewer fibrotic areas in vigilant hHO-1 plasmids-treated mice compared with saline control (43.0%+/-4.8% versus 62.5%+/-3.3%, P<0.01). The reduction of interstitial fibrosis is accompanied by an increase in myocardial hHO-1 expression in peri-infarct border areas, concomitant with higher Bcl-2 levels and lower Bax, Bak, and caspase 3 levels in the ischemic myocardium compared with saline control. By use of a cardiac catheter, heart from vigilant hHO-1 plasmids-treated mice showed improved recovery of contractile and diastolic performance after myocardial infarction compared with saline control. This study documents the beneficial regulation and therapeutic potential of vigilant plasmid-mediated hHO-1 gene transfer. This novel gene transfer strategy can provide cardiac-specific protection from future repeated bouts of ischemic injury.
BIOLOGIC MECHANISMS OF THE PROTECTIVE ROLE OF LUTEIN AND ZEAXANTHIN IN THE EYE (2003)

The macular region of the primate retina is yellow in color due to the presence of the macular pigment, composed of two dietary xanthophylls, lutein and zeaxanthin, and another xanthophyll, meso-zeaxanthin. The latter is presumably formed from either lutein or zeaxanthin in the retina. By absorbing blue-light, the macular pigment protects the underlying photoreceptor cell layer from light damage, possibly initiated by the formation of reactive oxygen species during a photosensitized reaction. There is ample epidemiological evidence that the amount of macular pigment is inversely associated with the incidence of age-related macular degeneration, an irreversible process that is the major cause of blindness in the elderly. The macular pigment can be increased in primates by either increasing the intake of foods that are rich in lutein and zeaxanthin, such as dark-green leafy vegetables, or by supplementation with lutein or zeaxanthin. Although increasing the intake of lutein or zeaxanthin might prove to be protective against the development of age-related macular degeneration, a causative relationship has yet to be experimentally demonstrated.
Activation of Platinum(IV) Prodrugs By Motexafin Gadolinium as a Redox Mediator (2016)

Abstract Water‐soluble platinum(IV) prodrugs, which proved kinetically stable to reduction in the presence of physiological concentration of ascorbate, were quickly reduced to their active form, oxaliplatin, when co‐incubated with a macrocycle metallotexaphyrin (i.e., Motexafin Gadolinium (MGd)). The reduction of Pt IV to Pt II promoted by MGd occurs in cell culture as well, leading to an increase in the antiproliferative activity of the Pt IV species in question. The mediated effect is proportional to the concentration of MGd and gives rise to an enhancement when the prodrug is relatively hydrophilic. MGd is known to localize/accumulate preferentially in tumor tissues. Thus, the present “activation by reduction” approach may allow for the cancer‐selective enhancement in the cytotoxicity of Pt IV prodrugs.