gebhart/patrepeval huggingface dataset:
Selecting optimal oligonucleotide composition for maximal antisense effect following streptolysin O-mediated delivery into human leukaemia cells (1998)

It is widely accepted that most cell types efficiently exclude oligonucleotides in vitro and require specific delivery systems, such as cationic lipids, to enhance uptake and subsequent antisense effects. Oligonucleotides are not readily transfected into leukaemia cell lines using cationic lipid systems and streptolysin O (SLO) is used to effect their delivery. We wished to investigate the optimal oligonucleotide composition for antisense efficacy and specificity following delivery into leukaemia cells using SLO. For this study the well characterised chronic myeloid leukaemia cell line KYO-1 was selected and oligonucleotides (20mers) were targeted to an empirically identified accessible site of c- myc mRNA. The efficiency and specificity of antisense effect was measured 4 and 24 h after SLO-mediated delivery of the oligonucleotides. C5-propyne phosphodiester and phosphorothioate compounds were found to present substantial non-specific effects at 20 microM but were inactive at 0.2 microM. Indeed, no antisense-specific effect was noted at any concentration at either time. All of the other oligonucleotides tested induced some measurable antisense effect, except 7 (chimeric, all-phosphorothioate, 2'-methoxyethoxy termini) which was essentially inactive at 20 microM. The rank efficiency order of the remaining antisense compounds was 4 = 3 >> 9 >> 10 = 8 = 5 = 6 > 11. The efficient antisense effects induced by the chimeric methylphosphonate-phosphodiester compounds were found to be highly specific. Increased phosphorothioate content in the oligonucleotide backbone correlated with reduced antisense activity (efficacy: 2'-methoxyethoxy series 9 >> 8 >> 7, 2'-methoxytriethoxy series 10 > 11). No consistent evidence was obtained for increased activity correlating with increased oligonucleotide-mRNA heteroduplex thermal stability. In conclusion, the chimeric methylphosphonate-phosphodiester oligodeoxynucleotides present the most favourable characteristics of the compounds tested, for efficient and specific antisense suppression of gene expression following SLO-mediated delivery.
Monoclonal antibodies used in the detection and treatment of epithelial ovarian cancer (1995)

Conventional therapy for epithelial ovarian cancer, including aggressive cytoreductive surgery followed by combination chemotherapy regimens, has failed to reduce the number of deaths caused by this disease, which remains the most lethal of gynecologic malignancies. Monoclonal antibodies, which offer the promise of high selectivity for detection and therapy, may be targeted to tumor-associated antigens, growth factors, receptors, or oncogenes. They may be used alone as immunotherapeutic agents or conjugated to chemotherapeutic drugs, toxins, or radionuclides. Radioimmunoconjugates may also be used for preoperative or intraoperative tumor localization. The authors focused on the clinical utility, technical limitations, and potential of monoclonal antibodies in the detection and treatment of epithelial ovarian cancer with emphasis on radioimmunodetection and radioimmunotherapy.
Dynamics ofin vitropolymer degradation of polycaprolactone-based scaffolds: accelerated versus simulated physiological conditions (2008)

The increasing use of biodegradable devices in tissue engineering and regenerative medicine means it is essential to study and understand their degradation behaviour. Accelerated degradation systems aim to achieve similar degradation profiles within a shorter period of time, compared with standard conditions. However, these conditions only partially mimic the actual situation, and subsequent analyses and derived mechanisms must be treated with caution and should always be supported by actual long-term degradation data obtained under physiological conditions. Our studies revealed that polycaprolactone (PCL) and PCL-composite scaffolds degrade very differently under these different degradation conditions, whilst still undergoing hydrolysis. Molecular weight and mass loss results differ due to the different degradation pathways followed (surface degradation pathway for accelerated conditions and bulk degradation pathway for simulated physiological conditions). Crystallinity studies revealed similar patterns of recrystallization dynamics, and mechanical data indicated that the scaffolds retained their functional stability, in both instances, over the course of degradation. Ultimately, polymer degradation was shown to be chiefly governed by molecular weight, crystallinity susceptibility to hydrolysis and device architecture considerations whilst maintaining its thermodynamic equilibrium.
Characterization of Cytokine-Induced Myeloid-Derived Suppressor Cells from Normal Human Peripheral Blood Mononuclear Cells (2010)

Tumor immune tolerance can derive from the recruitment of suppressor cell populations, including myeloid-derived suppressor cells (MDSCs). In cancer patients, increased MDSCs correlate with more aggressive disease and a poor prognosis. Expression of 15 immune factors (TGFbeta, IL-1beta, IL-4, IL-6, IL-10, GM-CSF, M-CSF, IDO, fms-related tyrosine kinase 3 ligand, c-kit ligand, inducible NO synthase, arginase-1, TNF-alpha, cyclo-oxygenase 2, vascular endothelial growth factor [VEGF]) by MDSC-inducing human solid tumor cell lines was evaluated by RT-PCR. Based upon these data, cytokine mixtures were then tested for their ability to generate suppressive CD33(+) cells from healthy donor PBMCs in vitro by measuring their ability to inhibit the proliferation of, and IFN-gamma production by, fresh autologous human T cells after CD3/CD28 stimulation. Induced MDSCs were characterized with respect to their morphology, surface phenotype, and gene expression profile. MDSC-inducing cancer cell lines demonstrated multiple pathways for MDSC generation, including overexpression of IL-6, IL-1beta, cyclo-oxygenase 2, M-CSF, and IDO. CD33(+) cells with potent suppressive capacity were best generated in vitro by GM-CSF and IL-6, and secondarily by GM-CSF + IL-1beta, PGE(2), TNF-alpha, or VEGF. Characterization studies of cytokine-induced suppressive cells revealed CD33(+)CD11b(+)CD66b(+)HLA-DR(low)IL-13R alpha2(int) large mononuclear cells with abundant basophilic cytoplasm. Expression of inducible NO synthase, TGFbeta, NADPH oxidase, VEGF, and/or arginase-1 was also upregulated, and Transwell studies showed suppression of autologous T cells to be contact dependent. Suppressive CD33(+) cells generated from PBMCs by GM-CSF and IL-6 were consistent with human MDSCs. This study suggests that these cytokines are potential therapeutic targets for the inhibition of MDSC induction in cancer patients.
Viewdata: the evolution of home and business terminals (1979)

The paper briefly considers the background to viewdata development during the 1970s. It goes on to discuss a number of aspects of a full terminal which affect, or are affected by, the viewdata system: the display, display control, data controller, user interface, terminating unit, autodialler and auto-identifier, keypage, home terminals and business terminals. The paper continues with possible developments to the basic system such as editing station, foreign languages, security, and high-resolution graphics. Finally, the paper looks to the future and how the viewdata concept can be extended, not only in the home and in the office but in many other fields.
On the Regiochemistry of Cycloaddition of Unsymmetrical Aryne with Nitrone Remarkable Effect of Trialkylsilyl Substituent (1993)

Regioselectivity of the aryne-nitrone cycloaddition was studied. Various unsymmetrical arynes with C(3)-substituent were generated at -78 °C by halogen-lithium exchange of ortho-haloaryl triflate and trapped with a nitrone. The sense and magnitude of the regio-controlling effect posed by the substituent is discussed based on the electronic and steric grounds by assuming the non-synchronous, charge-controlled transition state. The trialkylsilyl group, by its strong electron-releasing property, poses a remarkable effect on the regioselectivity.
Stimulus-response coupling in human platelets activated by monoclonal antibodies to the CD9 antigen, a 24 kDa surface-membrane glycoprotein (1990)

The CD9 molecule is a 24 kDa surface-membrane glycoprotein present on platelets and a variety of haematopoetic and non-haematopoetic tissues. In the present study we utilized specific inhibitors of thromboxane A2 (TxA2) formation (aspirin), protein kinase C [H-7 [1-(5-isoquinolinesulphonyl)-2-methylpiperazine]] and autocrine stimulation by secreted ADP (apyrase) to modify platelet activation by a monoclonal antibody ALB-6 to the CD9 antigen. This activation is only partially inhibited by aspirin alone but, in combination with either H-7 or apyrase, more than 50% inhibition of platelet aggregation and secretion was observed. This combination of inhibitors was also required to inhibit effectively the phosphorylation of myosin light chain and the 47 kDa substrate of protein kinase C. Intracellular Ca2+ flux monitored by the fluorescent dye fura-2 showed that this was almost completely mediated by the aspirin-sensitive TxA2 pathway. We suggest that the aspirin-insensitive pathway is primarily mediated by phospholipase C formation of diacylglycerol to activate protein kinase C. The inhibition by apyrase suggests a strong dependency on autocrine stimulation by secreted ADP to fully activate both phospholipase C and express fibrinogen-binding sites mediating platelet aggregation. This alternate pathway of phospholipase C activation by ALB-6 may be mediated by cytoplasmic alkalinization [monitored by SNARF-1 (5'(6')-carboxy-10-bismethylamino-3-hydroxy-spiro-[7H- benzo[c]xanthine-1',7(3H)-isobenzofuran]-3'-one) fluorescence of the dye]. Both activation pathways are dependent on intact antibodies, since F(ab')2 fragments of SYB-1, a monoclonal antibody against the CD9 antigen with activation characteristics identical with those of ALB-6, do not elicit activation. Besides thrombin, collagen is another physiological agonist shown to induce aspirin-insensitive activation. Similarities to ALB-6 in collagen sensitivity to apyrase in combination with aspirin inhibitors were noted with respect to aggregation and secretion, as well as a complete block of Ca2+ flux by aspirin. However, it is unlikely that collagen activation is mediated by the CD9 antigen, since SYB-1 F(ab')2 fragments had no effect on collagen activation and aspirin also completely blocked the alkalinization response to collagen, in contrast with ALB-6.
XRCC4 suppresses medulloblastomas with recurrent translocations in p53-deficient mice (2006)

Inactivation of the XRCC4 nonhomologous end-joining factor in the mouse germ line leads to embryonic lethality, in association with apoptosis of newly generated, postmitotic neurons. We now show that conditional inactivation of the XRCC4 in nestin-expressing neuronal progenitor cells, although leading to no obvious phenotype in a WT background, leads to early onset of neuronally differentiated medulloblastomas (MBs) in a p53-deficient background. A substantial proportion of the XRCC4/p53-deficient MBs have high-level N-myc gene amplification, often intrachromosomally in the context of complex translocations or other alterations of chromosome 12, on which N-myc resides, or extrachromosomally within double minutes. In addition, most XRCC4/p53-deficient MBs harbor clonal translocations of chromosome 13, which frequently involve chromosome 6 as a partner. One copy of the patched gene (Ptc), which lies on chromosome 13, was deleted in all tested XRCC4/p53-deficient MBs in the context of translocations or interstitial deletions. In addition, Cyclin D2, a chromosome 6 gene, was amplified in a subset of tumors. Notably, amplification of Myc-family or Cyclin D2 genes and deletion of Ptc also have been observed in human MBs. We therefore conclude that, in neuronal cells of mice, the nonhomologous end-joining pathway plays a critical role in suppressing genomic instability that, in a p53-deficient background, routinely contributes to genesis of MBs with recurrent chromosomal alterations.
Collective Theory for Surface Enhanced Raman Scattering (1996)

We present an implementation of Maxwell's equations on adaptive meshes in order to study interaction of light with metal surfaces. For the first time it is possible to handle surfaces consisting of complex particles close enough to interact strongly. A fully retarded implementation allows treatment of large particles as well as small. By way of example we model a rough silver surface as an array of half-cylinders embedded in a silver surface. Very localized plasmon modes, created by strong electromagnetic coupling between touching metallic objects, dominate the surface enhanced Raman scattering response.
Improvement of the Glutaryl-7-Aminocephalosporanic Acid Acylase Activity of a Bacterial γ-Glutamyltranspeptidase (2008)

7-Aminocephalosporanic acid (7-ACA) is an important material in the production of semisynthetic cephalosporins, which are the best-selling antibiotics worldwide. 7-ACA is produced from cephalosporin C via glutaryl-7-ACA (GL-7-ACA) by a bioconversion process using d-amino acid oxidase and cephalosporin acylase (or GL-7-ACA acylase). Previous studies demonstrated that a single amino acid substitution, D433N, provided GL-7-ACA acylase activity for gamma-glutamyltranspeptidase (GGT) of Escherichia coli K-12. In this study, based on its three-dimensional structure, residues involved in substrate recognition of E. coli GGT were rationally mutagenized, and effective mutations were then combined. A novel screening method, activity staining followed by a GL-7-ACA acylase assay with whole cells, was developed, and it enabled us to obtain mutant enzymes with enhanced GL-7-ACA acylase activity. The best mutant enzyme for catalytic efficiency, with a k(cat)/K(m) value for GL-7-ACA almost 50-fold higher than that of the D433N enzyme, has three amino acid substitutions: D433N, Y444A, and G484A. We also suggest that GGT from Bacillus subtilis 168 can be another source of GL-7-ACA acylase for industrial applications.
Aza Diels-Alder reactions in aqueous solution: cyclocondensation of dienes with simple iminium salts generated under Mannich conditions (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAza Diels-Alder reactions in aqueous solution: cyclocondensation of dienes with simple iminium salts generated under Mannich conditionsScott D. Larsen and Paul A. GriecoCite this: J. Am. Chem. Soc. 1985, 107, 6, 1768–1769Publication Date (Print):March 1, 1985Publication History Published online1 May 2002Published inissue 1 March 1985https://pubs.acs.org/doi/10.1021/ja00292a057https://doi.org/10.1021/ja00292a057research-articleACS PublicationsRequest reuse permissionsArticle Views3004Altmetric-Citations250LEARN 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
Four-channel wavelength division multiplexers and bandpass filters based on elliptical Bragg reflectors (1990)

Four-channel multiplexers and four-wavelength bandpass filters based on elliptical Bragg reflectors (EBRs) are discussed. The channel spacing is 50 AA near 1.56 mu m. The EBRs are narrowband elliptical mirrors that can refocus light from an input waveguide to any one of a number of output waveguides. Spectrally, they perform similarly to Bragg reflectors. The devices were fabricated on silicon using silica-based waveguide technology. The elliptical gratings with 0.53- mu m periods were patterned using deep UV spatial frequency doubling photolithography. Multiplexers with single filtering and double filtering were demonstrated. With single filtering, the fiber-to-fiber insertion loss was 3.0+or-0.5 dB, and the crosstalk was -20 dB; with double filtering, the insertion loss was 4.0+or-0.5 dB, and the crosstalk was -30 dB. About 2 dB of this loss was due to coupling between the fibers and the waveguide. The additive loss associated with the EBR, including propagation, Bragg reflection, and coupling between input and output waveguides, was about 1 dB.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Preparation and Characterization of Individual Peptide-Wrapped Single-Walled Carbon Nanotubes (2004)

Two challenges for effectively exploiting the remarkable properties of single-walled carbon nanotubes (SWNTs) are the isolation of intact individual nanotubes from the raw material and the assembly of these isolated SWNTs into useful structures. In this study, we present atomic force microscopy (AFM) evidence that we can isolate individual peptide-wrapped SWNTs, possibly connected end-to-end into long fibrillar structures, using an amphiphilic alpha-helical peptide, termed nano-1. Transmission electron microscopy (TEM) and well-resolved absorption spectral features further corroborate nano-1's ability to debundle SWNTs in aqueous solution. Peptide-assisted assembly of SWNT structures, specifically in the form of Y-, X-, and intraloop junctions, was observed in the AFM and TEM images.
Inclusion of the Hepatic Locus Control Region, an Intron, and Untranslated Region Increases and Stabilizes Hepatic Factor IX Gene Expression in Vivo but Not in Vitro (2000)

We systematically compared human factor IX gene expression from a variety of plasmids containing different cis-regulatory sequences after transfection into different hepatocyte cell lines, or in vivo, after their injection into the livers of mice. Although there was a 1.5- to 2.0-fold variation in gene expression from cultured cells, a 65-fold variation was observed in the in vivo studies. We found that a plasmid containing the apolipoprotein E locus control region (HCR), human alpha1-antitrypsin (hAAT) promoter, hFIX minigene (hFIXmg) sequence including a portion of the first intron (intron A), 3'-untranslated region (3'-UTR), and a bovine growth hormone polyadenylation signal (bpA) produced the highest serum level of human factor IX, reaching 18 microg/ml (normal = 5 microg/ml) 1 day after injection. Although most of the plasmid DNAs resulted in transient gene expression, inclusion of an intron, a polyadenylation signal from either the 1.7-kb 3'-UTR or the 0.3-kb bpA, and the HCR resulted in persistent and therapeutic levels of hFIX gene expression, ranging from 0.5 to 2 microg/ml (10 to 40% of normal) for 225 days (length of experiment). These data underscore the importance of cis sequences for enhancing in vivo hepatic gene expression and reemphasize the lack of correlation of gene expression in tissue culture and in vivo studies.
IL-17 is produced by nickel-specific T lymphocytes and regulates ICAM-1 expression and chemokine production in human keratinocytes: synergistic or antagonist effects with IFN-gamma and TNF-alpha. (1999)

IL-17 is a novel T cell-derived cytokine that can regulate the functions of a variety of cell types. In this study, we investigated whether hapten-specific T cells isolated from patients with allergic contact dermatitis (ACD) to nickel produce IL-17 and the effects of IL-17 alone or in combination with IFN-gamma or TNF-alpha on the immune activation of keratinocytes. Skin affected with ACD to nickel and skin-derived, nickel-specific CD4+ T cell lines expressed IFN-gamma, TNF-alpha, and IL-17 mRNAs. Four of seven nickel-specific CD4+ T cell clones positive for the skin-homing receptor, cutaneous lymphocyte-associated Ag, were shown to corelease IL-17, IFN-gamma, and TNF-alpha. In contrast, two nickel-specific CD8+ T cell clones failed to synthesize IL-17. Normal human keratinocytes were found to express constitutively the IL-17 receptor gene. IL-17 specifically and dose-dependently augmented IFN-gamma-induced ICAM-1 expression on keratinocytes at both the mRNA and the protein level, whereas HLA-DR, MHC class I, and CD40 levels were not modulated by IL-17. On the other hand, IL-17 alone did not affect ICAM-1 or enhance TNF-alpha-induced ICAM-1. In addition, IL-17, both directly and in synergism with IFN-gamma and/or TNF-alpha, stimulated synthesis and release of IL-8 by keratinocytes. In contrast, IFN-gamma- and TNF-alpha-induced production of RANTES was markedly inhibited by IL-17, and the synthesis of macrophage chemotactic protein 1 was not changed. Taken together, the results suggest that IL-17 is an important player of T cell-mediated skin immune responses, with synergistic or antagonist effects on IFN-gamma- and TNF-alpha-stimulated keratinocyte activation.
Algorithmic collision analysis for evaluating cryptographic systems and side-channel attacks (2011)

Side-channel attacks have emerged as a kind of effective security threat targeting system implementation of cryptographic algorithms. Evaluating a cryptographic system's resilience to side-channel attacks is therefore important for secure system design. This paper proposes a novel analysis method for resilience evaluation of cryptographic algorithms, which takes DES as example and reveals inherent algorithmic properties related to side-channel attacks. Collision and confusion coefficients are defined as the algorithmic parameters. The analysis shows that in addition to the side-channel leakage, another algorithm-dependent factor determines the effectiveness of side-channel attacks. With such factor considered, a metric is proposed to evaluate side-channel attacks and system resilience. Experiment results demonstrate the effectiveness and efficiency of the metric.