gebhart/patrepeval huggingface dataset:
Pathophysiology of the heart in Chagas' disease: current status and new developments (2003)

In the present review we have summarized remarkable historical data on Chagas' disease studies putting special emphasis on histopathological findings and pathogenetic theories as well as recent discoveries based on the use of advanced modern technologies in pathology and immunology. A unified theory that links almost all of these findings is proposed. Chronic cardiac Chagas' disease represents the result of a close interaction between the host and the parasite, causing different clinical pictures: patients with an efficient immune response may adequately circumvent the parasitic infection and the individual will develop the indeterminate form. Deficient immune response of the host and/or a high initial parasitemia favor an immune imbalance that might lead to development of a permanent inadequate immunological response against the parasite. The inflammatory response, which is probably recurrent, undergoing periods of more accentuated exacerbation, is most likely responsible for progressive neuronal damage, microcirculatory alterations, heart matrix deformations and consequent organ failure.
Characterization of a Fibrin Glue-Gdnf Slow-Release Preparation (1998)

One novel method to deliver trophic factor locally in the CNS is to mix it into fibrin glue. In the present studies, [ 125 I]-labeled GDNF-containing fibrin glue balls were used to determine binding and spread of the trophic factor. First, the binding of different concentrations of [ 125 I]-labelèd GDNF in fibrin glue was determined in vitro. Within the six concentrations used (from 200 nM to 0.004 nM, 0 M as control), there was a strong linear correlation between the [ 125 I]-GDNF concentration and the recovered radioactivity (r = 0.992). The mean bound radioactivity in 16 samples with 4 nM [ 125 I]-GDNF was 71262 + 2710 CPM, and accounted for 89.8% of the mean initial count of free [ 125 I]-GDNF (79369 + 3499 CPM). Second, [ 125 I]-GDNF-containing glue balls were implanted into the anterior chamber of adult rats. The implanted fibrin glue balls decreased in size with time, but could still be identified on the irises 2 wk after implantation. Radioactivity was concentrated at the implantation sites in the early stages with a distribution in the surrounding iris tissue, which became separated into focal radioactive spots at the third week. Counts of radioactivity were significantly higher in the [ 125 I]-GDNF glue ball-implanted irises than controls until 14 days after implantation. A study of the [ 125 I] decay over time using least-squares linear regression demonstrated first-order kinetics (r = —0.98, p &lt; 0.02) with k = 0.0091 and T 1/2 = 76 h. Finally, [ 125 I]-GDNF–containing glue balls were implanted in the spinal cord of adult rats. Radioactivity was concentrated at the implantation sites in the early stages and was later distributed more widely in the surrounding thoracic cord. The [ 125 I]-GDNF–containing glue degraded over time and became a porous meshwork with decreasing radioactivity at the later time points. Radioactivity in the spinal cords subjected to implantation of [ 125 I]-GDNF–containing glue balls was higher than in controls for 14 days. Study of the [ 125 I] decay by time with least-squares linear regression demonstrated first-order kinetics (r = -0.97, p = 0.001) with T 1/2 = 75.6 h. We conclude that the trophic factor GDNF becomes bound in the fibrin glue matrix from which it is gradually released. Our results suggest that fibrin glue is an effective substrate for keeping a trophic factor localized in situ for a finite period, protected from the circulation, surrounding aqueous humor or CSF.
Resveratrol induces MMP-9 and cell migration via the p38 kinase and PI-3K pathways in HT1080 human fibrosarcoma cells (2012)

Trans-3,4',5-trihydroxystilbene (resveratrol) is a grape polyphenol present in various plants, food products, red wine and grapes. Resveratrol has anti-inflammatory, anticarcinogenic, anti-oxidant and anti-aging properties. Matrix metalloproteinases (MMPs) are key enzymes involved in the degradation of the extracellular matrix, and their expression may be regulated in cancer metastasis. In the present study, we aimed to evaluate the effect of resveratrol on MMPs and cell migration, and to understand the mechanism of action in HT1080 human fibrosarcoma cells. We found that resveratrol inhibited HT1080 cell viability at various concentrations as detected by the MTT assay and FACS analysis. However, resveratrol dramatically increased the activation and expression of MMP-9 in a dose- and time-dependent manner, as determined by gelatin zymography assay and western blot analysis. We also discovered that resveratrol enhanced the migratory ability of HT1080 cells, as determined by the wound healing assay, and decreased the phosphorylation of p38 kinase. Moreover, the Akt kinase was inhibited by resveratrol in the HT1080 cells. The inhibition of p38 and Akt kinases with SB203580 and LY294002 further increased resveratrol-induced MMP-9 as well as cell migration in the HT1080 cells. Our results suggest that resveratrol regulates MMP-9 and migratory abilities through the p38 kinase and PI-3K pathways in HT1080 human fibrosarcoma cells.
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats (2007)

Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php.
Epitaxial Growth of Ferroelectric YMnO3 Thin Films on Si (111) Substrates by Molecular Beam Epitaxy (1998)

Ferroelectric YMnO 3 thin films are grown on Si (111) substrates using Y 2 O 3 buffer layers by molecular beam epitaxy (MBE). In situ reflection high-energy electron diffraction (RHEED) analyses show that both Y 2 O 3 and YMnO 3 films are epitaxially grown on Si substrates. X-ray rocking curve measurements also show that the best full-width at half maximum (FWHM) values for Y 2 O 3 and YMnO 3 films are 0.4° and 1.5°, respectively. Concerning the electrical properties, capacitance–voltage ( C – V ) characteristics of Al/YMnO 3 /Y 2 O 3 /Si structures indicate the ferroelectric properties of YMnO 3 films with a memory window of 0.3 V.
The All-Electric Airplane as an Energy Efficient Transport (1980)

&lt;div class="htmlview paragraph"&gt;The concern for energy conservation and the escalating fuel costs, threatens to impact adversely on the economic viability of the aerospace industry. This paper discusses the role of the All-Electric Airplane in assuaging the problems of fuel costs; it also evaluates the ability of an all-electric secondary power system to take over the functions and services historically in the province of the hydraulic and pneumatic systems.&lt;/div&gt;
Blockade of Delta-Like Ligand 4 Signaling Inhibits Both Growth and Angiogenesis of Pancreatic Cancer (2010)

These results suggests that cell-to-cell interaction via DLL4-Notch signaling pathway has been implicated in tumor angiogenesis, and control of this pathway can be a new therapeutic approach to solid tumor.
A Physical Map of the Escherichia coli K12 Genome (1987)

A physical map of a genome is the structure of its DNA. Construction of such a map is a first step in the complete characterization of that DNA. The restriction endonuclease Not I cuts the genome of Escherichia coli K12 into 22 DNA fragments ranging from 20 kilobases (20,000 base pairs) to 1000 kilobases. These can be separated by pulsed field gel electrophoresis. The order of the fragments in the genome was determined from available E. coli genetic information and analysis of partial digest patterns. The resulting ordered set of fragments is a macrorestriction map. This map facilitates genetic and molecular studies on E. coli, and its construction serves as a model for further endeavors on larger genomes.
Antigen capture assay for detection of a 43-kilodalton Mycobacterium tuberculosis antigen (1990)

This study describes the development of an enzyme-linked immunosorbent assay (ELISA) to detect Mycobacterium tuberculosis antigens in body fluids. A double-antibody sandwich procedure that used human and rabbit anti-M. tuberculosis immunoglobulin G antibodies was followed. The ELISA was able to detect as little as 0.8 micrograms of protein of M. tuberculosis sonic extract. Of 253 cerebrospinal fluid specimens submitted for analysis, 11 (4.3%) false-positive results were recorded. Analysis of 317 pleural and ascitic fluid specimens resulted in 6 (1.9%) false-positive recordings. No false-negative results were recorded for any of the body fluids tested. This technique is rapid (5.5 h) and sensitive, may be developed and used in many laboratories with limited resources, and may prove useful in the diagnosis of extrapulmonary and pulmonary tuberculoses. Analysis of these body fluids by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western immunoblotting indicated that the antibody used in the ELISA detects a mycobacterial antigen of 43 kDa. Such antigens were not detected in body fluids of nontuberculous patients.
Chromatographic selectivity for amino acid esters and alkali metal ions on a silica bonded calix[4]arene tetraester stationary phase (1994)

A silica bonded tetrameric calix[4]arene ester stationary phase has been used in the chromatographic separation of alkali metal ions and amino acid esters. Under reversed phase conditions, baseline resolution of a standard test mixture of benzamide, benzophenone and biphenyl was achieved using an MeOH—H2O mobile phase. In the chromatography of the amino acid ester hydrochlorides, retention appears to be related to the hydrophobicity of the esters studied, with tryptophan methyl ester being the longest retained.
Programmable protein circuits in living cells (2018)

Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.
Correlation And Kullback Matching Approaches: Application To Blind Channel Estimation In Ostbc Systems (2008)

Publication in the conference proceedings of EUSIPCO, Lausanne, Switzerland, 2008
The antagonism between MCT-1 and p53 affects the tumorigenic outcomes (2010)

The oppositions between MCT-1 and p53 are firstly confirmed at multistage processes that include transcription control, mRNA metabolism, and protein expression. MCT-1 oncogenicity can overcome p53 function that persistently advances the tumor development.
Approaches to analogs of dehydrogliotoxin. 6. An efficient synthesis of a gliotoxin analog with anti-reverse transcriptase activity (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApproaches to analogs of dehydrogliotoxin. 6. An efficient synthesis of a gliotoxin analog with anti-reverse transcriptase activityHenricus C. J. Ottenheijm, Jacobus D. M. Herscheid, Gerardus P. C. Kerkhoff, and Tom F. SpandeCite this: J. Org. Chem. 1976, 41, 21, 3433–3438Publication Date (Print):October 1, 1976Publication History Published online1 May 2002Published inissue 1 October 1976https://pubs.acs.org/doi/10.1021/jo00883a024https://doi.org/10.1021/jo00883a024research-articleACS PublicationsRequest reuse permissionsArticle Views322Altmetric-Citations41LEARN 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
Molecular Pathways to Prostate Cancer (2003)

The identification of molecular markers specific to early and late events in prostate cancer progression is critical for the development of improved detection and prognostication strategies. While there is evidence to support the association between inflammation and prostate cancer, the exact mechanisms by which these processes occur are not well defined. The significant contribution of somatic and epigenetic defects to prostate carcinogenesis underscores the need to develop therapeutic approaches that specifically target these molecular alterations.
B Subunit of Shiga Toxin-Based Vaccines Synergize with α-Galactosylceramide to Break Tolerance against Self Antigen and Elicit Antiviral Immunity (2007)

The nontoxic B subunit of Shiga toxin (STxB) targets in vivo Ag to dendritic cells that preferentially express the glycolipid Gb(3) receptor. After administration of STxB chemically coupled to OVA (STxB-OVA) or E7, a polypeptide derived from HPV, in mice, we showed that the addition of alpha-galactosylceramide (alpha-GalCer) resulted in a dramatic improvement of the STxB Ag delivery system, as reflected by the more powerful and longer lasting CD8(+) T cell response observed even at very low dose of immunogen (50 ng). This synergy was not found with other adjuvants (CpG, poly(I:C), IFN-alpha) also known to promote dendritic cell maturation. With respect to the possible mechanism explaining this synergy, mice immunized with alpha-GalCer presented in vivo the OVA(257-264)/K(b) complex more significantly and for longer period than mice vaccinated with STxB alone or mixed with other adjuvants. To test whether this vaccine could break tolerance against self Ag, OVA transgenic mice were immunized with STxB-OVA alone or mixed with alpha-GalCer. Although no CTL induction was observed after immunization of OVA transgenic mice with STxB-OVA, tetramer assay clearly detected specific anti-OVA CD8(+) T cells in 8 of 11 mice immunized with STxB-OVA combined with alpha-GalCer. In addition, vaccination with STxB-OVA and alpha-GalCer conferred strong protection against a challenge with vaccinia virus encoding OVA with virus titers in the ovaries reduced by 5 log compared with nonimmunized mice. STxB combined with alpha-GalCer therefore appears as a promising vaccine strategy to more successfully establish protective CD8(+) T cell memory against intracellular pathogens and tumors.
Biosynthesis of Flavocytochrome b 558 (1999)

The redox center of the phagocyte NADPH oxidase is flavocytochrome b 558 , a transmembrane protein with two subunits, gp91 phox and p22 phox . In this study we investigated the identity, subcellular localization, and maturation of a putative 65-kDa gp91 phox precursor (p65). Expressing the gp91 phox cDNA in an in vitro transcription and translation system, we found that synthesis of p65 required endoplasmic reticulum (ER) microsomes. Sucrose density gradient centrifugation of postnuclear supernatants obtained from a PLB-985 derived cell line with a constitutively expressed gp91 phox transgene demonstrated that p65 co-sedimented with the ER marker protein calreticulin and myeloperoxidase precursors. Unexpectedly, the majority of p22 phox was found in subcellular compartments containing the mature 91-kDa form of gp91 phox and not with p65, suggesting that heterodimer formation may occur in a post-ER compartment. The heme synthesis inhibitor, succinyl acetone, reduced the abundance of mature gp91 phox and p22 phox but had little or no impact on p65. These studies demonstrate (a) gp91 phox is synthesized as a glycosylated 65-kDa precursor in the ER, (b) heterodimer formation is not a co-translational process, and (c) heme insertion is a determinant in the formation of a stable heterodimer but does not appear to affect the stability of p65.
Thiopurine S-methyltransferase pharmacogenetics (2003)

Thiopurine S-methyltransferase (TPMT) catalyses the S-methylation of thiopurine drugs such as 6-mercaptopurine. A common genetic polymorphism for TPMT is associated with large individual variations in thiopurine drug toxicity and therapeutic efficacy. TPMT*3A, the most common variant allele in Caucasians, has two alterations in amino acid sequence, resulting in striking decreases in TPMT protein levels. This phenomenon results, in part, from rapid degradation through a ubiquitin-proteasome-mediated process. We set out to test the hypothesis that chaperone proteins might be involved in targeting TPMT for degradation. As a first step, hsp90, hsp70 and the cochaperone hop were immunoprecipitated from a rabbit reticulocyte lysate (RRL) that included radioactively labelled *3A and wild-type TPMT. TPMT*3A was much more highly associated with all three chaperones than was the wild-type enzyme. The RRL was also used to confirm the accelerated degradation of *3A compared to wild-type TPMT. Treatment of RRL with the hsp90 inhibitor geldanamycin resulted in enhanced association of hsp90 with wild-type TPMT, an observation that correlated with accelerated ubiquitin-dependent degradation of wild-type TPMT. Geldanamycin treatment of COS-1 cells transfected with FLAG-tagged wild-type also resulted in a time and geldanamycin concentration-dependent decrease in TPMT activity and protein, which was compatible with results obtained in the RRL. These observations indicate that TPMT is a client protein for hsp90 and suggest that chaperone proteins, especially hsp90, are involved in targeting both TPMT*3A and, in the presence of geldanamycin, the wild-type allozyme for degradation. Therefore, chaperone proteins play an important mechanistic role in this clinically significant example of pharmacogenetic variation in drug metabolism.
Obfuscation of executable code to improve resistance to static disassembly (2003)

A great deal of software is distributed in the form of executable code. The ability to reverse engineer such executables can create opportunities for theft of intellectual property via software piracy, as well as security breaches by allowing attackers to discover vulnerabilities in an application. The process of reverse engineering an executable program typically begins with disassembly, which translates machine code to assembly code. This is then followed by various decompilation steps that aim to recover higher-level abstractions from the assembly code. Most of the work to date on code obfuscation has focused on disrupting or confusing the decompilation phase. This paper, by contrast, focuses on the initial disassembly phase. Our goal is to disrupt the static disassembly process so as to make programs harder to disassemble correctly. We describe two widely used static disassembly algorithms, and discuss techniques to thwart each of them. Experimental results indicate that significant portions of executables that have been obfuscated using our techniques are disassembled incorrectly, thereby showing the efficacy of our methods.
Cish attenuates proximal TCR-signaling and CD8+ T cell immunity (2014)

Meeting abstracts CD8+ T cells are potent killers of infected cells and tumors, specifically recognizing their targets through the T cell receptor (TCR). While much has been revealed about the activation of TCR signaling, negative regulation of this pathway remains incompletely elucidated. We
Monitoring transfected cells without selection agents by using the dual-cassette expression EGFP vectors (2001)

Conventional methods of selecting gene transfected cells by toxic agents may yield ambiguous results. It is difficult to determine whether cell death is due to selection agents or gene transfection, owing to the substantial overlap of the time-courses for both effects. Therefore, to determine transfection-induced cell toxicity, the mammalian expression vector pEGFP-N1 (CLONTECH Lab., Palo Alto, CA, USA) has been modified to the dual-cassette expression vectors named pEGFP-Ks by the relocation of its EGFP expression cassette. We have precisely monitored the cells transfected with this vector on our custom culture dishes, thereby bypassing the need for selection agent or fluorescent cell sorting. This is a useful method to screen genes encoding potential toxic or useful proteins without performing undesirable selection agent and also can be used to monitor the transfected cells for various purposes, either the inhibition or proliferation of mammalian cells for applications in biotechnology.