gebhart/patrepeval huggingface dataset:
Engineered viral vaccine constructs with dual specificity: Avian influenza and Newcastle disease (2006)

Avian influenza viruses of the H5 and H7 hemagglutinin subtypes, and Newcastle disease virus (NDV), are important pathogens in poultry worldwide. Specifically, the highly pathogenic H5N1 avian influenza virus is a particular threat because it has now occurred in more than 40 countries on several continents. Inasmuch as most chickens worldwide are vaccinated with a live NDV vaccine, we embarked on the development of vaccine prototypes that would have dual specificity and would allow a single immunization against both avian influenza and Newcastle disease. Using reverse genetics, we constructed a chimeric avian influenza virus that expressed the ectodomain of the hemagglutinin-neuraminidase gene of NDV instead of the neuraminidase protein of the H5N1 avian influenza virus. Our second approach to creating a bivalent vaccine was based on expressing the ectodomain of an H7 avian influenza virus hemagglutinin in a fusogenic and attenuated NDV background. The insertion into the NDV genome of the foreign gene (containing only its ectodomain, with the transmembrane and cytoplasmic domains derived from the F protein of NDV) resulted in a chimeric virus with enhanced incorporation of the foreign protein into virus particles. A single immunization of chickens with this improved vaccine prototype virus induced not only a 90% protection against an H7N7 highly pathogenic avian influenza virus, but also complete immunity against a highly virulent NDV. We propose that chimeric constructs should be developed for convenient, affordable, and effective vaccination against avian influenza and Newcastle disease in chickens and other poultry.
Single‐feed circularly polarized triangular microstrip antenna with triangular slot for compact operation (2002)

Abstract Novel compact circular polarization (CP) designs of a single‐feed triangular microstrip antenna with a triangular slot or an inverted triangular slot are proposed and experimentally studied. For the design with a triangular slot, CP operation can easily be achieved by inserting a slit with a length about 24% of the slot's side length at the center of the inner bottom edge of the patch. As for the design with an inverted triangular slot, the insertion of a slit with a length about 12% of the slot's side length can result in CP radiation. Results also indicate that with the triangular slot embedded in the patch, the proposed CP design can have an antenna size reduction of about 30% as compared to the regular‐size CP design using a simple triangular patch. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 34: 263–266, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10433
Nucleic Acid Aptamers as Tools and Drugs: Recent Developments (2003)

Nucleic acid aptamers are molecules that bind to their ligands with high affinity and specificity. Unlike other functional nucleic acids such as antisense oligonucleotides, ribozymes, or siRNAs, aptamers almost never exert their effects on the genetic level. They manipulate their target molecules such as gene products or epitopes directly and site specifically, leaving nontargeted protein functions intact. In a similar way to antibodies, aptamers bind to many different kinds of target molecules with high specificity and can be made to order, but as a result of their different biochemical nature and size they can also be used complementary to antibodies. In some cases, aptamers might be more suitable or more specific than antibody approaches or small molecules, both as scientific and biotechnological tools and as therapeutic agents. Recent examples of characterization of aptamers as tools for scientific research to study regulatory circuits, as tools in diagnostic or biosensor development, and as therapeutic agents are discussed.
Expression Cloning and Characterization of NSIST, a Novel Sulfotransferase Expressed by a Subset of Neurons and Postsynaptic Targets (1998)

Synapses are distinguished by localized concentrations of specific proteins, many of which bear the marks of posttranslational processing such as glycosylation and sulfation. One strategy to elucidate this posttranslational tailoring is to identify the enzymes that create these modifications. Monoclonal antibody 3B3 recognizes a carbohydrate-containing epitope expressed on dystroglycan and other constituents of Torpedo electric organ synaptic membranes. We used mAb 3B3 in an immunofluorescence-based expression-cloning method and isolated a cDNA clone conferring mAb-3B3 immunoreactivity to transfected COS cells. The deduced polypeptide has a predicted molecular weight of 51 kDa, a type II transmembrane topology, and four potential N-linked glycosylation sites. The polypeptide, which we term NSIST (nervous system involved sulfotransferase), shows extensive, although not complete, homology to a chondroitin-6-sulfotransferase and limited homology to other sulfotransferases. In NSIST-transfected COS cells, 35SO4 incorporation and chondroitin-sulfate-like immunoreactivity are increased. In vivo, NSIST occurs as a single 2.4 kb transcript abundant in Torpedo electric organ, moderately expressed in spinal cord and electric lobe, and undetectable in non-neural tissues. Immunohistochemistry shows that NSIST is expressed in a punctate distribution in the innervated portion of electrocytes. In the CNS, NSIST-like immunoreactivity is localized within the somas of motor neurons and neurons of the electromotor nucleus, whereas mAb-3B3 immunostaining is associated with cell surfaces and neuropil. Neuronal NSIST is therefore likely to exert its effects extracellularly; although NSIST is synthesized by neurons, its product, the 3B3 epitope, is found outside neuronal cell bodies. Our evidence indicates that NSIST participates in nervous system specific posttranslational modifications, perhaps including those at synapses.
Structural Basis for a Change in Substrate Specificity:  Crystal Structure of S113E Isocitrate Dehydrogenase in a Complex with Isopropylmalate, Mg2+, and NADP, (2001)

Isocitrate dehydrogenase (IDH) catalyzes the oxidative decarboxylation of isocitrate and has negligible activity toward other (R)-malate-type substrates. The S113E mutant of IDH significantly improves its ability to utilize isopropylmalate as a substrate and switches the substrate specificity (k(cat)/K(M)) from isocitrate to isopropylmalate. To understand the structural basis for this switch in substrate specificity, we have determined the crystal structure of IDH S113E in a complex with isopropylmalate, NADP, and Mg(2+) to 2.0 A resolution. On the basis of a comparison with previously determined structures, we identify distinct changes caused by the amino acid substitution and by the binding of substrates. The S113E complex exhibits alterations in global and active site conformations compared with other IDH structures that include loop and helix conformational changes near the active site. In addition, the angle of the hinge that relates the two domains was altered in this structure, which suggests that the S113E substitution and the binding of substrates act together to promote catalysis of isopropylmalate. Ligand binding results in reorientation of the active site helix that contains residues 113 through 116. E113 exhibits new interactions, including van der Waals contacts with the isopropyl group of isopropylmalate and a hydrogen bond with N115, which in turn forms a hydrogen bond with NADP. In addition, the loop and helix regions that bind NADP are altered, as is the loop that connects the NADP binding region to the active site helix, changing the relationship between substrates and enzyme. In combination, these interactions appear to provide the basis for the switch in substrate specificity.
CCCCXXIII.—Degradation of quaternary ammonium salts. Part I (1928)

T. S. Stevens, E. M. Creighton, A. B. Gordon and M. MacNicol, J. Chem. Soc., 1928, 3193 DOI: 10.1039/JR9280003193
Investigation of the Effects of Very Low Pressure Chemical Vapor Deposited TiSi2 on Device Electrical Characteristics (1989)

We report for the first time the effects of very low pressure chemical vapor deposited (VLPCVD) titanium silicide on device electrical characteristics. The compatibility of this material for VLSI technology is examined through careful characterization of the shallow junction and gate oxide integrities, sheet resistance, and contact resistivity. It is shown that the integrity of the shallow junctions is preserved if the silicon consumption during the silicide deposition is controlled. If this consumption is not controlled, a Schottky diode behavior is observed for the source/drain junctions. It is shown that titanium silicide lowers the specific contact resistivity of metal/source‐drain and metal/polysilicon structures by an order of magnitude and a factor of 4–5, respectively. The sheet resistance of the doped polysilicon (gate conductor) is reduced by more than two orders of magnitude through using a structure. In addition, it is shown that VLPCVD titanium silicide has no significant effect on the quality of the gate oxide. Slightly lower breakdown voltages for the capacitors are measured, which could be due to the stress induced by siliciding the gate. The results presented in this paper indicate the suitability of VLPCVD titanium silicide films for high quality device fabrication.
Tetracycline Actions Relevant to Rosacea Treatment (2009)

Until today, the pathogenesis of rosacea is not known in detail. Yet in recent years evidence has been accumulating that rosacea with its common symptoms such as inflammatory lesions, erythema, telangiectasia, phymatous changes, and ocular symptoms is of inflammatory nature. Tetracycline derivatives like doxycycline successfully used in the treatment of skin diseases like acne and rosacea seem to inhibit different inflammatory pathways involved in the pathogenesis by various modes of action. Although data for skin diseases are relatively scanty, the following modes of action of tetracyclines seem to be most relevant for an effective treatment of acne and rosacea: inhibition of matrix metalloproteinases, downmodulation of cytokines, inhibition of cell movement and proliferation, inhibition of granuloma formation, inhibition of reactive oxygen species, nitric oxide, and angiogenesis, whereas inhibition of phospholipase A2 seems to be of lower importance. The role of the saprophytic mite Demodex folliculorum remains to be clarified. Additional studies are necessary to further elucidate how tetracyclines work in rosacea treatment.
Fabrication of large area subwavelength antireflection structures on Si using trilayer resist nanoimprint lithography and liftoff (2003)

In this article we report on the fabrication of subwavelength antireflection structures on silicon substrates using a trilayer resist nanoimprint lithography and liftoff process. We have fabricated cone-shaped nanoscale silicon pillars with a continuous effective index gradient, which greatly enhances its antireflective performances. Our measurements show that the two-dimensional subwavelength structure effectively suppresses surface reflection over a wide spectral bandwidth and a large field of view. A reflectivity of 0.3% was measured at 632.8 nm wavelength, which is less than 1% of the flat silicon surface reflectivity.
STUDIES ON 6 : 7-DIHYDROXY-4-METHYLCOUMARIN AND ITS METHYL ETHERS (1960)

6 : 7-Dihydroxy-4-methylconmarin and its dimethyl ether, on bromination with one mole of bromine, urnish the 3 -bromo compound, and wtih two moles of bromine, the 3 : 8-dibromo compound. The methoxy derivative, however, affords the 3 : 5-dibromo compound with two moles of bromine. In nitration, the 7-rnethoxy derivative yields the 5-nitro derivative whereas the 6 : 7-dimethoxy derivative furnishes the 3-nitro derivative.
Lactobacillus kunkeei sp. nov. : a spoilage organism associated with grape juice fermentations (1998)

A Gram-positive rod was isolated from a commercial grape wine undergoing a sluggish/stuck alcoholic fermentation. The organism produced L-lactic acid from glucose, possessed weak catalase activity, and fermented relatively few carbohydrates, i.e. glucose, fructose, sucrose, raffinose (weakly) and mannitol. The 16S rRNA gene sequence analysis revealed that the isolate was phylogenetically a member of the genus Lactobacillus and formed a distinct subline within the Lact. casei cluster of species. Based on phenotypic and phylogenetic evidence, a new species is proposed, Lact. kunkeei. The type strain of Lact. kunkeei is ATCC 700308.
Inter-domain Identity-based Proxy Re-encryption (2008)

Proxy re-encryption is a cryptographic primitive developed to delegate the decryption right from one party (the delegator) to another (the delegatee). So far, research efforts have only been devoted to the intra-domain setting, where the delegator and the delegatee are registered in the same domain. In this paper, we investigate the proxy re-encryption in the inter-domain setting, where the delegator and the delegatee are from different domains, and focus on the identity-based case. We analyze the trust relationships and possible threats to the plaintext privacy, and provide rigorous security definitions. We propose a new inter-domain identity-based proxy re-encryption scheme and prove its security in our security model. An interesting property of the proposed scheme is that, to achieve the chosen plaintext security for the delegator, the delegatee’s IBE only needs to be one-way. 1
Heat-Stable Inhibitor Protein Derived Peptide Substrate Analogs: Phosphorylation by cAMP-Dependent and cGMP-Dependent Protein Kinases (1995)

The phosphorylation of substrate peptides derived from PKI, the heat-stable inhibitor protein of the cAMP-dependent protein kinase (PKA), has been studied with both PKA and the cGMP-dependent protein kinase (PKG) using a variety of substitution and deletion analogs. On the basis of Km, kcat and kcat/Km values, (Ser21)PKI alpha(14-22) amide (numbering based upon native PKI alpha) is the most effective peptide substrate yet discovered for either kinase, although other peptides, while phosphorylated considerably less efficiently by PKG, are more specific. Although the inhibitory peptide corresponding to this sequence (i.e., with an Ala at position 21) is a much more potent inhibitor of PKA than of PKG (approximately 250-fold), PKG actually exhibits a 60% higher kcat than does PKA with the (Ser21)PKI alpha(14-22) amide substrate peptide, with only a 20-fold higher Km value. The two key PKI residues within this peptide which were found to be essential for substrate activity with both kinases were Arg18 (P-3) and Ile22 (P+1). The Arg19 (P-2) residue, which contributes significantly to both PKI-based peptide inhibitors and substrates of PKA, was only a more minor contributor to PKG substrate efficacy. Of particular note, the Phe10 (P-11) residue, which contributes very substantially to high affinity binding of both PKI and longer PKI peptide inhibitors, neither positively nor negatively affects the kinetics of either PKA or PKG with PKI-based substrates.(ABSTRACT TRUNCATED AT 250 WORDS)
Generation of tumor-specific CTLs from melanoma patients by using peripheral blood stimulated with allogeneic melanoma tumor cell lines. Fine specificity and MART-1 melanoma antigen recognition. (1995)

PBLs were isolated from 13 patients with metastatic melanoma. Mixed lymphocyte tumor cell cultures (ML TCs) were established (15 times) by using irradiated HLA-matched (one class I locus) allogeneic melanoma tumor cell lines (13 times) or autologous melanoma tumor cell lines (two times) in medium containing 120 IU/ml IL-2 and 100 IU/ml IL-4. PBLs grew to levels that could be assessed for functional reactivity 9 of 15 times. In seven of nine cases, CD3+CD8+ CTLs grew from MLTCs that were tumor specific; five were restricted by HLA-A2 and two were restricted by HLA-A24. Four of the tumor-specific CTL lines lysed autologous fresh tumor cells. Tumor-specific CTLs from two of three patients had cytolytic activity identical with tumor-infiltrating lymphocytes (TIL) derived from tumor biopsies removed earlier and grown in high concentrations (6000 IU/ml) of IL-2. Three of the HLA-A2-restricted tumor-specific CTLs were shown to recognize 293 cells transfected with HLA-A2.1 cDNA and the gene encoding the melanoma Ag, MART-1. In addition, these CTLs recognized the T2 cell line pulsed exogenously with the peptide MART-1(27-35), which is the nine-amino acid immunodominant epitope of the MART-1 Ag recognized on melanoma tumor cells by nearly all HLA-A2-restricted TIL. Thus, we have demonstrated the ability to generate tumor-specific CTLs from PBLs that are similar in their reactivity to TIL. This technique obviates the need for autologous tumor tissue and suggests that PBLs contain sufficient CTL precursors for use in generating antitumor CTLs for cellular immunotherapy trials.
Modulation of macrophage phenotype by cell shape (2013)

Phenotypic polarization of macrophages is regulated by a milieu of cues in the local tissue microenvironment. Although much is known about how soluble factors influence macrophage polarization, relatively little is known about how physical cues present in the extracellular environment might modulate proinflammatory (M1) vs. prohealing (M2) activation. Specifically, the role of cell shape has not been explored, even though it has been observed that macrophages adopt different geometries in vivo. We and others observed that macrophages polarized toward different phenotypes in vitro exhibit dramatic changes in cell shape: M2 cells exhibit an elongated shape compared with M1 cells. Using a micropatterning approach to control macrophage cell shape directly, we demonstrate here that elongation itself, without exogenous cytokines, leads to the expression of M2 phenotype markers and reduces the secretion of inflammatory cytokines. Moreover, elongation enhances the effects of M2-inducing cytokines IL-4 and IL-13 and protects cells from M1-inducing stimuli LPS and IFN-γ. In addition shape- but not cytokine-induced polarization is abrogated when actin and actin/myosin contractility are inhibited by pharmacological agents, suggesting a role for the cytoskeleton in the control of macrophage polarization by cell geometry. Our studies demonstrate that alterations in cell shape associated with changes in ECM architecture may provide integral cues to modulate macrophage phenotype polarization.
In vitro activity of Triclisia patens and some bisbenzylisoquinoline alkaloids against eishmania donovani and Trypanosoma brucei brucei (2002)

In the search for antiprotozoal compounds from natural sources, Triclisia patens displayed activity against L. donovani promastigotes (IC(50) = 1.5 microg/mL) and T. b. brucei blood stream trypomastigote forms (IC(50) = 31.25 microg/mL). In addition, a total of 20 bisbenzylisoquinoline alkaloids were screened for antileishmanial and antitrypanosomal activity in vitro. Fangchinoline (IC(50) = 0.39 microM) was found to be as active as the standard pentamidine against Leishmania donovani promastigotes. Phaeanthine was three-fold more active (IC(50) = 2.41 microM; 1.5 microg/mL) than the standard drug Pentostam against L. donovani amastigotes, but at this concentration was toxic to murine macrophages. In contrast, cocsoline (IC(50) = 12.3 microM; 6.76 microg/mL) was as active as Pentostam, and was not toxic to macrophages at this concentration. Thalisopidine showed the strongest activity (IC(50) = 1.14 microM) against Trypanosoma brucei brucei blood stream form trypomastigotes, but was less active than pentamidine.
Eph Receptors and Ephrin Ligands: Important Players in Angiogenesis and Tumor Angiogenesis (2010)

Eph receptors and their ephrin ligands were identified in the late 1980's. Subsequently, they were linked to different physiological and pathophysiological processes like embryonic development, angiogenesis, and tumorigenesis. In this regard, recent work focused on the distribution and effects of Eph receptors and ephrins on tumor cells and tumor microenvironment. The purpose of this review is to outline the role of these molecules in physiological angiogenesis and pathophysiological tumor angiogenesis. Furthermore, novel therapeutical approaches are discussed as Eph receptors and ephrins represent attractive targets for antiangiogenic therapy.
A comparison between bromodeoxyuridine and 3H thymidine labeling in human breast tumors. (1991)

The fraction of tumor cells in the DNA synthesis (S) phase of the cell cycle is a strong prognostic indicator in human breast cancer. Most studies measuring S-phase in primary tumors have used either in vitro labeling with 3H thymidine or DNA flow cytometry. The former involves a cumbersome and time-consuming radioactive assay, while the latter is heavily dependent on the quality of the preparation and the effectiveness of the algorithms used. In this study, in vivo or in vitro labeling with bromodeoxyuridine (BrdUrd) was compared with in vitro labeling using 3H thymidine in a series of 33 human breast tumors. Thymidine labeling showed strong correlation with both in vitro (r = 0.96) and in vivo (r = 0.83) BrdUrd incorporation. The reliability between observers was higher for BrdUrd counting (r = 0.94) than for thymidine counting (r = 0.87). The mean labeling index of 15 tumors labeled in vivo with BrdUrd was 5.9% compared to 4.7% for 18 tumors labeled in vitro (p = 0.34). There was poor correlation between flow cytometric and microscopic analysis of BrdUrd incorporation (r = 0.37). We conclude that microscopic analysis of in vivo or in vitro BrdUrd incorporation is a rapid and reliable method to estimate breast tumor proliferation.
Accuracy performance of star trackers - a tutorial (2002)

An autonomous star tracker is an avionics instrument used to provide the absolute 3-axis attitude of a spacecraft utilizing star observations. It consists of an electronic camera and associated processing electronics. The processor has the capability to perform star identification utilizing an internal star catalog stored in firmware and to calculate the attitude quaternion autonomously. Relevant parameters and characteristics of an autonomous star tracker are discussed in detail.
Combining Milatuzumab with Bortezomib, Doxorubicin, or Dexamethasone Improves Responses in Multiple Myeloma Cell Lines (2009)

The therapeutic efficacies of bortezomib, doxorubicin, and dexamethasone are enhanced in MM cell lines when given in combination with milatuzumab, suggesting testing these combinations clinically.
Stretching DNA (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStretching DNAJohn F. Marko and Eric D. SiggiaCite this: Macromolecules 1995, 28, 26, 8759–8770Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/ma00130a008https://doi.org/10.1021/ma00130a008research-articleACS PublicationsRequest reuse permissionsArticle Views10256Altmetric-Citations2037LEARN 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