gebhart/patrepeval huggingface dataset:
Retrovirus‐mediated transfer of anti‐MRD1 hammerhead ribozymes into multidrug‐resistant human leukemia cells: Screening for effective target sites (1999)

One of the underlying mechanisms of multidrug resistance (MDR) is cellular over-production of P-glycoprotein (P-gp), which acts as a drug efflux pump. P-gp is encoded by a small group of related genes termed MDR; only MDR1 is known to confer drug resistance. To overcome P-gp-mediated drug resistance, we have developed two anti-MDR1 hammerhead ribozymes driven by the β-actin promoter. Upon transduction of the ribozymes into MDR cells, vincristine resistance was decreased. These two ribozymes were constructed, which showed different cleavage activities. In this study, to determine suitable target sites for the anti-MDR1 ribozyme, the exon 1b–intron 1 boundary, the translation-initiation site, the intron 1–exon 2 boundary and the exon 2–intron 2 boundary, codons 179 and 196 of the MDR1 gene were selected as candidates. To improve the ribozyme activity, a retroviral vector containing RNA polymerase III promoter was used. Stable retrovirus producer cells were generated by transfecting the retroviral vector plasmids carrying the ribozyme into the packaging cell line. Retroviral vector transduction of human leukemia cell lines expressing MDR1 was accomplished by co-culturing these with virus producer cells. Stably transduced cells were selected by G418 and pooled to determine the efficacy of each ribozyme. These ribozyme-transduced cells became vincristine-sensitive concomitant with the decreases in MDR1 expression, P-gp amount and drug efflux pump function. Among the ribozymes tested, the anti-MDR1 ribozyme against the translation-initiation site exhibited the strongest efficacy. This retrovirus-mediated transfer of anti-MDR1 ribozyme may be applicable to the treatment of MDR cells as a specific means to reverse resistance. Int. J. Cancer81:944–950, 1999. © 1999 Wiley-Liss, Inc.
Two Computational Primitives for Algorithmic Self-Assembly:  Copying and Counting (2005)

Copying and counting are useful primitive operations for computation and construction. We have made DNA crystals that copy and crystals that count as they grow. For counting, 16 oligonucleotides assemble into four DNA Wang tiles that subsequently crystallize on a polymeric nucleating scaffold strand, arranging themselves in a binary counting pattern that could serve as a template for a molecular electronic demultiplexing circuit. Although the yield of counting crystals is low, and per-tile error rates in such crystals is roughly 10%, this work demonstrates the potential of algorithmic self-assembly to create complex nanoscale patterns of technological interest. A subset of the tiles for counting form information-bearing DNA tubes that copy bit strings from layer to layer along their length.
Resolution of Stroke Deficits Following Contralateral Grafts of Conditionally Immortal Neuroepithelial Stem Cells (2001)

MHP36 cells may improve functional outcome after MCAO by assisting spontaneous reorganization in both the damaged and intact hemispheres.
Development of Obesity and Insulin Resistance in the Israeli Sand Rat (Psammomys obesus) Does Leptin Play a Role? (1997)

The Israeli Sand Rat (Psammomys obesus) is an excellent polygenic model for the study of obesity and diabetes. The metabolic characteristics and the heterogeneous development of these defects, including elevated leptin levels, mimic those found in susceptible human populations. Interestingly, only animals that develop metabolic abnormalities demonstrate hyperleptinemia and, in these animals, leptin administration at the same dose that is effective in ob/ob mice is ineffective in reducing food intake or body weight. Perhaps leptin resistance needs to develop in Israeli Sand Rats to allow the development of obesity and, in fact, leptin resistance may be the "thrifty gene" that predisposes individuals to the development of obesity and subsequent metabolic abnormalities. However, there remain many unanswered questions about the physiological actions of leptin. The widespread tissue location of receptors and the actions of leptin independent of food intake highlight the need for further research aimed at determining the major physiological action of this newly discovered and exciting hormone.
Vitreous treatment of retinal pigment epithelial cells results in decreased expression of FGF-2. (1998)

Vitreous treatment of RPE cells in culture results in decreased expression of FGF-2 mRNA and protein. Because supplementation of FGF-2 prevents some of the vitreous-mediated effects, this may indicate that modulation of FGF-2 levels by the vitreous may play an important role in the phenotypic changes seen in RPE cells exposed to vitreous.
Syntheses of Indoles via a Palladium-Catalyzed Annulation between Iodoanilines and Ketones (1997)

ADVERTISEMENT RETURN TO ISSUECommunicationNEXTSyntheses of Indoles via a Palladium-Catalyzed Annulation between Iodoanilines and KetonesCheng-yi Chen, David R. Lieberman, Robert D. Larsen, Thomas R. Verhoeven, and Paul J. ReiderView Author Information Department of Process Research, Merck Research Laboratories, Division of Merck & Co., Inc., P.O. Box 2000, Rahway, New Jersey 07065 Cite this: J. Org. Chem. 1997, 62, 9, 2676–2677Publication Date (Web):May 2, 1997Publication History Received14 February 1997Published online2 May 1997Published inissue 1 May 1997https://pubs.acs.org/doi/10.1021/jo970278ihttps://doi.org/10.1021/jo970278irapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views5950Altmetric-Citations153LEARN 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 SUBJECTS:Addition reactions,Amines,Byproducts,Indoles,Ketones Get e-Alerts
Principal long-term adverse effects of imatinib in patients with chronic myeloid leukemia in chronic phase (2010)

Imatinib mesylate (IM), an original Abl tyrosine kinase inhibitor, entered the clinics in 1998 for the treatment of patients with chronic myeloid leukemia (CML). The drug is universally considered the treatment of choice for most, if not all, patients with CML. Importantly, lessons learned from patients with CML have been applied successfully for the treatment of patients with other disorders where IM has since been found to be active by virtue of its ability to target other kinases, such as c-kit in patients with gastrointestinal stromal tumors. IM is associated with mild to moderate toxicity, mostly reversible by dose reduction or discontinuation of the drug. Most adverse effects occur within the first 2 years of starting therapy; however, late effects, many being unique, are now being recognized. In this report, we assess the toxicity associated with IM, with an emphasis on the long-term adverse effects.
Second order total generalized variation (TGV) for MRI (2010)

Total variation was recently introduced in many different magnetic resonance imaging applications. The assumption of total variation is that images consist of areas, which are piecewise constant. However, in many practical magnetic resonance imaging situations, this assumption is not valid due to the inhomogeneities of the exciting B1 field and the receive coils. This work introduces the new concept of total generalized variation for magnetic resonance imaging, a new mathematical framework, which is a generalization of the total variation theory and which eliminates these restrictions. Two important applications are considered in this article, image denoising and image reconstruction from undersampled radial data sets with multiple coils. Apart from simulations, experimental results from in vivo measurements are presented where total generalized variation yielded improved image quality over conventional total variation in all cases.
Green Fluorescent Protein (2005)

BACKGROUND. The Discovery of Green Fluorescent Protein. Photons for Reporting Molecular Events: Green Fluorescent Protein and Four Luciferase Systems. BIOCHEMISTRY AND MOLECULAR BIOLOGY OF GREEN FLUORESCENT PROTEIN. Biochemical and Physical Properties of Green Fluorescent Protein. The Three--Dimensional Structure of Green Fluorescent Protein and Its Implications for Function and Design. Molecular Biology and Mutation of Green Fluorescent Protein. APPLICATIONS OF GREEN FLUORESCENT PROTEIN. The Uses of Green Fluorescent Protein in Caenorhabditis elegans. The Uses of Green Fluorescent Protein in Prokaryotes. The Uses of Green Fluorescent Protein in Yeasts. The Uses of Green Fluorescent Protein in Drosophila. The Uses of Green Fluorescent Protein in Plants. The Uses of Green Fluorescent Protein in Trangenic Vertebrates. The Uses of Green Fluorescent Protein in Mammalian Cells. METHODS AND PROTOCOLS. Expressioin of Green Fluorescent Protein. Specimen Preparation. Visualization of Green Fluorescent Protein. Documenting Green Fluorescent Protein. Appendix. Index.
Structures of allosamidins, novel insect chitinase inhibitors, produced by actinomycetes. (1987)

The structures of allosamidin (1) and methylallosamidin (2), novel insect chitinase inhibitors, were elucidated as 1 and 2 by acid hydrolysis experiments and analyses of 2D-NMR spectra. They are unique basic pseudotrisaccharides consisting of 2-acetamido-2-deoxy-D-allose (N-acetyl-D-allosamine) and a novel aminocyclitol derivative (3), termed allosamizoline.
A short history ofSHELX (2007)

An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Array Signal Processing: Concepts and Techniques (1993)

1. Introduction 2. Signals in Space and Time 3. Apertures and Arrays 4. Conventional Array Processing 5. Detection Theory 6. Estimation Theory 7. Adaptive Array Processing 8. Tracking Appendices References List of Symbols Index.
HADOF: defense against routing disruptions in mobile ad hoc networks (2005)

HADOF is a set of mechanisms to protect mobile ad hoc networks against routing disruption attacks launched by inside attackers. First, each node launches a route traffic observer to monitor the behavior of each valid route in its route cache, and to collect the packet forwarding statistics submitted by the nodes on this route. Since malicious nodes may submit false reports, each node also keeps cheating records for other nodes. If a node is detected as dishonest, this node will be excluded from future routes, and the other nodes will stop forwarding packets for it. Third, each node will try to build friendship with other nodes to speed up malicious node detection. Route diversity will be explored by each to discover multiple routes to the destination, which can increase the chance of defeating malicious nodes who aim to prevent good routes from being discovered. In addition, adaptive route rediscovery will be applied to determine when new routes should be discovered. HADOF can handle various attacks and introduces little overhead to the existing protocols. Both analysis and simulation studies have confirmed the effectiveness of HADOF.
Electrical Stimulation Accelerates Motor Functional Recovery in the Rat Model of 15-mm Sciatic Nerve Gap Bridged by Scaffolds With Longitudinally Oriented Microchannels (2010)

Brief ES may accelerate axonal regeneration and motor recovery after focal peripheral nerve transection when repaired with optimally tissue-engineered grafts.
Crystal-induced neutrophil activation. IV. Specific inhibition of tyrosine phosphorylation by colchicine. (1993)

We recently demonstrated that pathologically relevant inflammatory microcrystals, namely triclinic monosodium urate (MSU) and calcium pyrophosphate dihydrate (CPPD) crystals, potently stimulate a characteristic protein tyrosine phosphorylation pattern in human neutrophils that differed from that observed in response to other soluble or particulate agonists. In this study, the effects of colchicine on protein tyrosine phosphorylation induced by MSU and CPPD crystals in human blood neutrophils were investigated. Immunoblot analysis with antiphosphotyrosine antibodies demonstrated that colchicine dose-dependently inhibited the tyrosine phosphorylation of all the proteins phosphorylated in response to MSU and CPPD crystals. Other microtubule-disruptive agents such as vinblastine, nocodazole, and colcemid also inhibited crystal-induced protein tyrosine phosphorylation while lumicolchicine and trimethylcolchicinic acid were without effect. Indomethacin and phenylbutazone were similarly without effect on microcrystal-induced tyrosine phosphorylation. Colchicine, as well as the other active alkaloids, failed to inhibit the protein tyrosine phosphorylation elicited by FMLP, C5a, leukotriene B4, and unopsonized zymosan. Overall, these results demonstrate that colchicine specifically and significantly inhibits the protein tyrosine phosphorylation induced by MSU and CPPD crystals and suggest that its effects are associated, at least in part, with its interaction with microtubules. Furthermore, the use of microtubule-disrupting drugs demonstrate that the mechanisms implicated in the induction of protein tyrosine phosphorylation by microcrystals differed from those involved in response to other soluble or particulate agonists.
Tyrphostins. 3. Structure-activity relationship studies of .alpha.-substituted benzylidenemalononitrile 5-S-aryltyrphostins (1993)

In this study we describe an extension of our previous studies on cis-benzylidenemalononitrile tyrphostins. We have introduced S-aryl substituents in the 5 position (meta vis-a-vis the malononitrile moiety). We find that these compounds are potent blockers of EGFR kinase and its homolog HER-2 kinase. Interestingly, we find that certain S-aryltryphostins discriminate between EGFR and HER-2 kinase in favor of the HER-2 kinase domain by almost 2 orders of magnitude. When examined in intact cells it was found that these selective S-aryltrphostins are equipotent in inhibiting EGF dependent proliferation of NIH 3T3 harboring either the EGF receptor or the chimera EGF/neu (HER1-2). These findings suggest that the antiproliferative activity of these tyrphostins is mainly due to the inhibition of a mitogenic signaling element downstream to the growth receptor kinase.
Nonlymphocyte-Derived Tumor Necrosis Factor Is Required for Induction of Colitis in Recombination Activating Gene (Rag)2−/− Mice upon Transfer of Cd4+Cd45rbhi T Cells (1999)

In this study, we addressed the role of tumor necrosis factor (TNF)-alpha and lymphotoxin (LT)-alpha in the development of colitis and defined the cellular sources (T cells versus non-T cells) of TNF (TNF-alpha and LT-alpha) relevant to disease development. After adoptive transfer of TNF(+/+) CD4(+)CD45RB(hi) splenocytes into TNF(+/+) recombination activating gene (RAG)2(-/-) mice, the recipients develop massive inflammation of the large intestinal mucosa concurrent with massive weight loss. In contrast, clinical signs of disease are completely absent in TNF(-/-)RAG2(-/-) recipients of TNF(-/-) CD4(+)CD45RB(hi) T cells, although elevated numbers of interferon-gamma-producing cells are present in the colonic mucosa. Surprisingly, upon transfer of TNF(-/-)CD4(+)CD45RB(hi) T cells into TNF(+/+)RAG2(-/-) recipients, colitis develops with kinetics similar to those upon transfer of TNF(+/+)CD4(+)CD45RB(hi) donor cells. In contrast, no clinical signs of colitis are observed in TNF(-/-)RAG2(-/-) recipients of TNF(+/+)CD4(+)CD45RB(hi) T cells. This protection from colitis is not a consequence of the absence of LT-alpha, as TNF-alpha(-/-)RAG2(-/-) recipients of TNF-alpha(-/-) CD4(+)CD45RB(hi) T cells are also protected from colitis induction. These results demonstrate the importance of TNF production by non-T cells of the colonic mucosa in the pathogenesis of colitis and provide direct evidence for a nonredundant role of TNF-alpha in this mouse model of colitis.
Protein interactions with oligo(ethylene glycol) (OEG) self-assembled monolayers: OEG stability, surface packing density and protein adsorption (2007)

We present a study of protein adsorption on oligo(ethylene glycol) (OEG) self-assembled monolayers (SAMs) at a range of OEG surface densities. OEG SAMs were formed in mixed ethanol and water solutions at different assembly temperatures to adjust the packing density of EG4-SAMs. These SAMs were characterized using X-ray photoelectron spectroscopy (XPS). Fibrinogen adsorption on these surfaces was measured by a surface plasmon resonance (SPR) sensor at different temperatures. This work is aimed at addressing three important issues for protein-OEG interactions, i.e., (i) OEG stability, (ii) the correlation between OEG surface densities and surface non-fouling properties, and (iii) protein adsorption on OEG surfaces at different temperatures.
Synthesis and biological activity of spirocyclic benzopyran imidazolone potassium channel openers (1993)

A series of novel spirocyclic benzopyran imidazolones were synthesized as rigid analogues of cromakalim. These compounds cause a dose-dependent membrane hyperpolarization of A10 rat aorta cells. This hyperpolarization was blocked by pretreatment with glyburide, indicating that the spirocyclic benzopyran imidazolones were acting by increasing the open probability of ATP-sensitive potassium channels in A10 cells. Representative compounds also showed potent in vivo activity as hypotensive agents in normotensive rats. Many of the compounds described are much more potent than cromakalim both in vitro and in vivo, with one of the most potent compounds being 2,3-dihydro-2,2-dimethyl-6-nitro-2'-(propylamino)spiro[4H-1-benzopyran- 4,4'-[4H]imidazol]-5'(1'H)-one (5r). It is concluded that the N1' nitrogen of the imidazolone is an effective substitute for the carbonyl oxygen of cromakalim. The rigid spirocyclic ring fusion holds this nitrogen in an optimum orientation relative to the benzopyran ring.
Methods for characterization of Streptomyces species (1966)

The methods used by collaborators in the International Streptomyces Project (ISP) for emendation of descriptions of type and neotype strains of the genus Streptomyces (Actinomycetales) are presented.
Production of specific‐structured triacylglycerols by lipase‐catalyzed interesterification in a laboratory‐scale continuous reactor (1998)

Abstract A laboratory‐scale continuous reactor was constructed for production of specific structured triacylglycerols containing essential fatty acids and medium‐chain fatty acids (MCFA) in the sn ‐2 and sn ‐1,3 positions, respectively. Different parameters in the lipase‐catalyzed interesterification were elucidated. The reaction time was the most critical factor. Longer reaction time resulted in higher yield, but was accompanied by increased acyl migration. The concentration of the desired triacylglycerol (TAG) in the interesterification product increased significantly with reaction time, even though there was only a slight increase in the incorporation of MCFA. Increased reactor temperature and content of MCFA in the initial reaction substrate improved the incorporation of MCFA and the yield of the desired TAG in the products. Little increase of acyl migration was observed. Increasing the water content from 0.03 to 0.11% (w/w substrate) in the reaction substrate had almost no effect on either the incorporation or the migration of MCFA, or on the resulting composition of TAG products and their free fatty acid content. Therefore, we conclude that the water in the original reaction substrate is sufficient to maintain the enzyme activity in this continuous reactor. Since the substrates were contacted with a large amount of lipase, the reaction time was shorter compared with a batch reactor, resulting in reduced acyl migration. Consequently, the purity of the specific structured TAG produced was improved. Interesterification of various vegetable oils and caprylic acid also demonstrated that the incorporation was affected by the reaction media. Reaction conditions for lipase‐catalyzed synthesis of specific structured TAG should be optimized according to the oil in use.
[Oncogenic activation of p21ras or pp60c-src in human colonic Caco-2 cells induces post-translation alterations of syndecan-1]. (1997)

The protein encoded by ras and src protooncogenes are frequently activated in a constitutive state in human colorectal cancer. In this study, we investigated the effect of oncogenic p21ras and Py-MT/pp60c-src on the synthesis of syndecan-1, a membrane anchored proteoglycan playing a role in cell-matrix interaction and neoplastic growth control. To this end, we used Caco-2 cells transfected with an activated (Val-12) human Ha-ras gene or the polyoma middle T (Py-MT) oncogene, a constitutive activator of pp60c-src tyrosine kinase activity. As compared to control vector-transfected Caco-2 cells, both oncogene-transfected cells exhibited: (1) a decrease in syndecan-1 specific activity; (2) a decrease in size and sulfation of syndecan-1 ectodomain glycosaminoglycan side chains; and (3) an active heparanase specifically degrading the heparan sulfate chains. In conclusion, the tumorigenic progression induced by oncogenic p21ras or Py-MT/pp60c-src is associated with marked alterations of syndecan-1 at the post-translational level.