gebhart/patrepeval huggingface dataset:
Synthesis, Molecular Recognition, and Enzymology of Oligonucleotides Containing the Non‐standard Base Pair between 5‐Aza‐7‐deazaisoguanine and 6‐Amino‐3‐methylpyrazin‐2(1<i>H</i>)‐one, a Donor‐Acceptor‐Acceptor Purine Analog and an Acceptor‐Donor‐Donor Pyrimidine Analog (1996)

Abstract A 6‐aminopyrazin‐2(1 H )‐one (pyADD), when incorporated as a pyrimidine‐base analog into an oligonucleotide chain, presents a H‐bond acceptor‐donor‐donor pattern to 5‐aza‐7‐deazaisoguanine (puDAA), the complementrary donor‐acceptor‐acceptor purine analog. Reported here are the syntheses of the phosphoramidite of the 2′‐deoxyribonucleoside bearing the puDAA base, oligonucleotides containing this nucleoside unit, the enzyme‐assisted synthesis of oligoribonucleotides containing the pyADD ribonucleoside, and the molecular‐recognition properties of this non‐standard base pair in an oligonucleotide context. A series of melting experiments suggests that the pyADD · puDAA base pair contributes to the relative stability of a duplex structure approximately the same as an A · T base pair, and significantly more than mismatches between these non‐standard bases and certain standard nucleobases. The pyADD nucleoside bisphosphate is accepted by T4 RNA ligase, but the triphosphate of the pyADD nucleoside was not incorported by T7 RNA polymerase opposite the puDAA nucleobase in a template. Oligonucleotides containing the pyADD base slowly undergo a reversible first‐order reaction, presumably an epimerization process to give the α‐ D ‐anomer. These experiments provide the tools for laboratory‐based use of the pyADD · puDAA base pair as a component of an oligonucleotide‐like molecular‐recognition system based on an expanded genetic alphabet.
An application of reachable set analysis in power system transient stability assessment (2005)

A novel method to compute the stability region in power system transient stability analysis is presented. This method is based on the level set analysis. The key to this method is to construct the Hamilton-Jacobi-Isaacs (HJI) partial differential equation (PDE) of a nonlinear system, using which we can compute the backward reachable set by applying the level set methods. The backward reachable set of a stable equilibrium yields the stability region of the equilibrium point in power system transient stability assessment. The proposed method is applied to a single machine infinite bus system and a classical two-machine system yielding satisfactory results.
Microwave-Assisted Protection of Primary Amines as 2,5-Dimethylpyrroles and Their Orthogonal Deprotection (2013)

Primary amines can be readily doubly protected as N-substituted 2,5-dimethylpyrroles. Although this protecting group is stable toward strong bases and nucleophiles, long reaction times are required for both the protection and deprotection steps, generally resulting in low deprotection yields. By employing microwave irradiation, protection and deprotection reaction times are dramatically reduced. Furthermore, deprotection with dilute hydrochloric acid in ethanol increases reaction yields. Diverse deprotection conditions have been developed in conjunction with microwave irradiation, so that protection as an N-substituted 2,5-dimethylpyrrole can be orthogonal to other standard amine protecting groups, such as tert-butyloxycarbonyl (Boc), carbobenzyloxy (Cbz), and 9-fluorenylmethyloxycarbonyl (Fmoc).
Reversible Mode of Binding of Serum Proteins to DOTAP/Cholesterol Lipoplexes: A Possible Explanation for Intravenous Lipofection Efficiency (2005)

There are many indications that interaction of serum proteins with intravenously injected cationic lipoplexes disturbs lipofection in vitro and in vivo. However, transfection with certain lipid compositions such as N-[1- (2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTAP)/cholesterol appears to be more resistant to serum and more efficacious. We investigated the mechanism of interaction between fluorescently labeled lipoplexes of the above composition and fluorescently labeled serum proteins. Fluorescence resonance energy transfer measurements in vitro indicate that serum proteins interact instantly and closely with the DOTAP/cholesterol lipoplexes. In accord with this, preinjection of fluorescently labeled serum into mice before injection of lipoplexes showed an immediate association of proteins with lipoplexes. Serum proteins colocalized with the lipoplexes in the lung vasculature; however, they dissociated from the cationic lipid as soon as 1 hr postinjection, probably because of displacement of serum proteins from lipoplexes by extracellular proteoglycans. Indeed, this displacement was imitated by heparin, a typical glycosaminoglycan, and could be explained by the inability of weakly acidic serum proteins to neutralize the DOTAP/cholesterol electrical surface potential psi0. The stability of the cationic lipid psi0 in serum could be a key reason for the high lung association and transfection efficiency with this formulation.
Nanocrystal Arrested Precipitation in Supercritical Carbon Dioxide (2001)

Fluorocarbon-coated silver, iridium, and platinum nanocrystals ranging in size from 20 to 120 Å in diameter are synthesized in supercritical (sc)-CO2 by arrested precipitation from soluble organometallic precursors. The synthesis is performed in a single CO2 phase by reduction with H2 at elevated temperatures ranging from 60 to 100 °C. Precursor degradation and particle nucleation occur in the presence of stabilizing perfluorooctanethiol ligands, which bind to the surface of the metal agglomerates and quench particle growth. The ligands are sufficiently solvated by CO2 to provide a steric barrier to uncontrollable aggregation during synthesis. The particles redisperse in acetone and fluorinated solvents. The dominant mechanism to particle growth is through cluster agglomeration followed by ligand passivation, leading to self-similar size distributions with a standard deviation of ±47%. Additionally, the nanocrystal size is tunable with precursor concentration, with higher precursor loadings resulting in larger nanocrystal sizes.
High success rate of hematopoietic cell transplantation regardless of donor source in children with very high-risk leukemia (2011)

We evaluated 190 children with very high-risk leukemia, who underwent allogeneic hematopoietic cell transplantation in 2 sequential treatment eras, to determine whether those treated with contemporary protocols had a high risk of relapse or toxic death, and whether non-HLA-identical transplantations yielded poor outcomes. For the recent cohorts, the 5-year overall survival rates were 65% for the 37 patients with acute lymphoblastic leukemia and 74% for the 46 with acute myeloid leukemia; these rates compared favorably with those of earlier cohorts (28%, n = 57; and 34%, n = 50, respectively). Improvement in the recent cohorts was observed regardless of donor type (sibling, 70% vs 24%; unrelated, 61% vs 37%; and haploidentical, 88% vs 19%), attributable to less infection (hazard ratio [HR] = 0.12; P = .005), regimen-related toxicity (HR = 0.25; P = .002), and leukemia-related death (HR = 0.40; P = .01). Survival probability was dependent on leukemia status (first remission vs more advanced disease; HR = 0.63; P = .03) or minimal residual disease (positive vs negative; HR = 2.10; P = .01) at the time of transplantation. We concluded that transplantation has improved over time and should be considered for all children with very high-risk leukemia, regardless of matched donor availability.
A study of genomic instability in early preneoplastic colonic lesions (2012)

It is difficult to explain the differential rates of progression of premalignant colonic lesions and differences in behaviour of morphologically similar lesions. Heterogeneity for microsatellite instability (MSI) and promoter methylation in driving these phenomena forward may explain this; however, no previous analysis has examined this in detail at the gland level, the smallest unit of colorectal premalignant lesions. We aimed to carry out an analysis of gland level genomic instability for MSI and promoter methylation. MSI occurred significantly more frequently (20%) in colonic glands than has previously been observed in whole colorectal polyps. Significant promoter methylation was seen in MLH1, PMS2, MLH3 and MSH3 as well as significant heterogeneity for both MSI and promoter methylation. Methylation and MSI may have a significant role in driving forward colorectal carcinogenesis, although in the case of MSI, this association is less clear as it occurs significantly more frequently than previously thought, and may simply be a passenger in the adenoma-carcinoma sequence. Promoter methylation in MLH1, MLH3, MSH3 and PMS2 was also found to be significantly associated with MSI and should be investigated further. A total of 273 colorectal glands (126 hyperplastic, 147 adenomatous) were isolated via laser capture microdissection (targeted at regions of MLH1 loss) from 93 colonic polyps and tested for MSI, and promoter methylation of the DNA mismatch repair genes MLH1, MSH2, MLH3, MSH6, PMS2, MGMT and MLH3 via methylation specific multiplex ligation-dependent probe amplification. Logistic regression modelling was then used to identify significant associations between promoter methylation and gland histological type and MSI status.
Complexes of Alkylene-Linked Tacrine Dimers with <i>Torpedo c</i><i>alifornica</i> Acetylcholinesterase:  Binding of Bis(5)-tacrine Produces a Dramatic Rearrangement in the Active-Site Gorge (2006)

The X-ray crystal structures were solved for complexes with Torpedo californica acetylcholinesterase of two bivalent tacrine derivative compounds in which the two tacrine rings were separated by 5- and 7-carbon spacers. The derivative with the 7-carbon spacer spans the length of the active-site gorge, making sandwich interactions with aromatic residues both in the catalytic anionic site (Trp84 and Phe330) at the bottom of the gorge and at the peripheral anionic site near its mouth (Tyr70 and Trp279). The derivative with the 5-carbon spacer interacts in a similar manner at the bottom of the gorge, but the shorter tether precludes a sandwich interaction at the peripheral anionic site. Although the upper tacrine group does interact with Trp279, it displaces the phenyl residue of Phe331, thus causing a major rearrangement in the Trp279-Ser291 loop. The ability of this inhibitor to induce large-scale structural changes in the active-site gorge of acetylcholinesterase has significant implications for structure-based drug design because such conformational changes in the target enzyme are difficult to predict and to model.
Controlling strength and toughness of multilayer films: A new multiscalar approach (1993)

Multiscalar films are produced in order to combine both toughness and strength into a multilayer film. These structures incorporate both a strengthening phase and a toughening phase in a compositionally modulated microcomposite. The mechanical properties and microstructure for thick (∼50 μm) Mo/W multiscalar films have been characterized. A detailed microstructural analysis (including transmission electron microscopy, scanning electron microscopy, and x-ray techniques) of Mo/W multiscalar films has shown that large single-crystal columns of Mo interspersed with epitaxial layers of W extend for the entire film thickness. The microstructure is a zone-II-type microstructure, yet the temperatures during deposition are well below the lower limit (0.3 T/Tm) previously reported for such microstructures. Hardness and tensile tests have shown that a multiscalar approach is capable of tailoring a desired strength and toughness into a multilayered film.
Common control of the heat shock gene and early adenovirus genes: evidence for a cellular E1A-like activity. (1984)

We have employed an antiserum specific to the 70-kilodalton human heat shock protein and a cDNA clone specific to the mRNA for this protein to analyze the expression of the gene under noninducing conditions. Expression of the heat shock gene can be detected in the absence of heat induction, and this uninduced level of expression depends greatly on the particular cell type. For instance, the basal expression of the heat shock gene is at least 50 times higher in HeLa cells than in WI38 cells at both the mRNA and protein levels. We have previously shown that the inducer of transcription of the early adenovirus genes, the E1A gene product, also induces the heat shock gene, suggesting that these genes may be subject to the same regulation. We have, therefore, investigated the control of the adenovirus genes in relation to the cellular control of the heat shock gene. We find that human cells that allow a high level of uninduced expression of the heat shock gene (i.e., HeLa cells) also allow expression of the early adenovirus genes in the absence of the E1A inducer. The same is also true for the mouse F9 teratocarcinoma cell line. F9 stem cells, which constitutively express the heat shock protein, allow early adenovirus gene expression in the absence of E1A; upon differentiation induced by retinoic acid and cyclic AMP, the cells become restrictive and early viral gene expression requires the E1A gene product. Coordinately, upon differentiation there is also a loss of heat shock protein expression.
An Investigation into the New Product Process: Steps, Deficiencies, and Impact (1986)

In a comprehensive study of 252 new product histories at 123 firms, Robert Cooper and Elko Kleinschmidt looked critically at the new products management process. Each company was shown a set of 13 activities which formed a general “skeleton” of a new product process. This article examines how this structure was modified by the companies and how well various stages of the process were reportedly executed. The results show a variety of practices among the surveyed companies. While the presence of activities cannot guarantee successful new products, certain activities were singled out as particularly weak. Firms should consider placing more emphasis on market studies, initial screening activities, and preliminary market assessment. The article provides a thoughtful assessment of the level of implementation of current practices in new products management.
A Reliable and Accurate Method for Measuring Orthosis Wearing Time (2002)

As indicated by the regression analyses, the compliance monitor accurately quantified the orthosis wearing-time intervals during the laboratory climate tests and the tests with normal volunteers.
Formation of viscoelastic protein layers on polymeric surfaces relevant to platelet adhesion (2005)

The hemocompatibility of biomaterials is highly dependent on the adhesion and activation of platelets. Surface-adsorbed fibrinogen has a dominant role in promoting platelet adhesion to artificial surfaces by binding glycoprotein IIb-IIIa (GPIIb-IIIa), the major platelet membrane receptor. Using quartz crystal microbalance with dissipation monitoring (QCM-D), we have investigated the material-dependent binding kinetics of purified GPIIb-IIIa to polymer-adsorbed fibrinogen. The following ranking of polymer-adsorbed mass (fibrinogen and GPIIb-IIIa) to test polymers could be established: poly[desaminotyrosyl-tyrosine ethyl (DTE) carbonate]/poly(lactide-co-glycolide)>poly[DTE co-5% poly(ethylene glycol) carbonate]. The QCM-D fibrinogen adsorption data were confirmed using an immunofluorescence assay. A synthetic RGD-containing peptide, but not a control peptide, inhibited GPIIb-IIIa binding to polymer-adsorbed fibrinogen, demonstrating the specificity of binding. Importantly, the binding efficiency of purified GPIIb-IIIa to polymer-adsorbed fibrinogen correlated with increased platelet adhesion in an in vitro model. Theoretical simulations using a Voight-based model provided quantitative data on the thickness and viscoelastic properties of the polymer-adsorbed protein layers. The precision of the modeling technique was limited with respect to the shear moduli values, leading to large variations. However, the other modeling parameters showed reproducible results. The thickness of both protein layers was polymer-dependent and ranged from 5 to 35 nm and the viscosity from 0.001 to 0.005 kg/ms, whereas the protein layer densities showed little differences between the test polymers. These results suggest that material-dependent changes in the thickness and viscoelastic properties of adsorbed fibrinogen-GPIIb-IIIa layers are crucial factors in the binding behavior of platelets to biomaterials.
Polarization-insensitive arrayed-waveguide grating wavelength multiplexer on silicon (1992)

A wavelength-division multiplexer with no polarization dependence is demonstrated. It is based on an arrayed-waveguide grating fabricated with silica-based optical waveguides on a silicon substrate. The polarization dependence that is due to the birefringence of the waveguide is eliminated by inserting a quartz lambda/2 plate in the middle of the arrayed waveguide. Moreover the grating is designed to operate in the 115th order for high wavelength resolution. The polarization insensitivity and the high resolution lead to the successful multiplexing of 13 wavelength channels with 1-nm spacing. A passband width of 0.3 nm and a cross-talk level of -30 dB are achieved.
Efficient and regulated erythropoietin production by naked DNA injection and muscle electroporation (1999)

We show that an electric treatment in the form of high-frequency, low-voltage electric pulses can increase more than 100-fold the production and secretion of a recombinant protein from mouse skeletal muscle. Therapeutical erythopoietin (EPO) levels were achieved in mice with a single injection of as little as 1 microgram of plasmid DNA, and the increase in hematocrit after EPO production was stable and long-lasting. Pharmacological regulation through a tetracycline-inducible promoter allowed regulation of serum EPO and hematocrit levels. Tissue damage after stimulation was transient. The method described thus provides a potentially safe and low-cost treatment for serum protein deficiencies.
<i>Indian Hedgehog</i> coordinates endochondral bone growth and morphogenesis via <i>Parathyroid Hormone related-Protein</i>-dependent and -independent pathways (2000)

Indian hedgehog (Ihh) and Parathyroid Hormone-related Protein (PTHrP) play a critical role in the morphogenesis of the vertebrate skeleton. Targeted deletion of Ihh results in short-limbed dwarfism, with decreased chondrocyte proliferation and extensive hypertrophy, features shared by mutants in PTHrP and its receptor. Activation of Ihh signaling upregulates PTHrP at the articular surface and prevents chondrocyte hypertrophy in wild-type but not PTHrP null explants, suggesting that Ihh acts through PTHrP. To investigate the relationship between these factors during development of the appendicular skeleton, mice were produced with various combinations of an Ihh null mutation (Ihh(-/-)), a PTHrP null mutation (PTHrP(-/-)), and a constitutively active PTHrP/Parathyroid hormone Receptor expressed under the control of the Collagen II promoter (PTHrPR*). PTHrPR* rescues PTHrP(-/-) embryos, demonstrating this construct can completely compensate for PTHrP signalling. At 18.5 dpc, limb skeletons of Ihh, PTHrP compound mutants were identical to Ihh single mutants suggesting Ihh is necessary for PTHrP function. Expression of PTHrPR* in chondrocytes of Ihh(-/-) mice prevented premature chondrocyte hypertrophy but did not rescue either the short-limbed dwarfism or decreased chondrocyte proliferation. These experiments demonstrate that the molecular mechanism that prevents chondrocyte hypertrophy is distinct from that which drives proliferation. Ihh positively regulates PTHrP, which is sufficient to prevent chondrocyte hypertrophy and maintain a normal domain of cells competent to undergo proliferation. In contrast, Ihh is necessary for normal chondrocyte proliferation in a pathway that can not be rescued by PTHrP signaling. This identifies Ihh as a coordinator of skeletal growth and morphogenesis, and refines the role of PTHrP in mediating a subset of Ihh's actions.
Positron emission tomographic measurement of blood-to-brain and blood-to-tumour transport of<sup>82</sup>Rb. I: Error analysis and computer simulations (1989)

Unidirectional blood-to-brain and blood-to-tumour transport rate constants (K1) for 82Rb (half-life 76 s) and plasma water volume per unit mass of brain/tumour tissue (Vp) can be estimated in vivo using dynamic positron emission tomography (PET). The accuracy of these estimates depends upon the accuracy of PET measurements of regional brain/tumour radioactivity and scintillation well detector measurements of whole-blood radioactivity, which, in turn, depend upon the time course of arterial blood radioactivity. A two-compartmental model has been employed to derive estimates for K1, k2 (efflux rate constant) and Vp from 82Rb/PET data. Errors in these parameter estimates have been studied (1) qualitatively using sensitivity function analysis and (2) quantitatively using computer simulations. The effect of adding a third irreversible compartment and its unidirectional rate constant, k3, has also been investigated. The advantages and disadvantages of bolus injection vs continuous infusion protocols are discussed. Precision in estimated parameters from actual patient data is compared to that obtained from computer simulations in part II of this paper.
A Learning Journal as a Tool to Promote Lifelong Learning Skills. (1988)

Women's studies is not only an emerging content area, but also a feminist perspective on knowledge, teaching and learning. Feminist education includes a commitment to help students, or, as I prefer to call them, learners, acquire the skills to let them keep learning throughout their lives. This commitment furthers the political agenda of feminist education by empowering learners, and it furthers the development of women's studies content by assisting learners as they do research that contributes to what we know about women. By making the development of lifelong learning skills an explicit goal of women's studies classes, we expand feminist pedagogy in a way that will help us to avoid creating women's studies as yet another traditionally defined and taught discipline. Regardless of our subject areas or the level at which we teach, we need to know that learners leave our classroom
Steroidal Sapogenins. XVII. Stereochemistry of the Spiroketal Side Chain<sup>2</sup> (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSteroidal Sapogenins. XVII. Stereochemistry of the Spiroketal Side Chain2Monroe E. Wall, Samuel Serota, and C. Roland EddyCite this: J. Am. Chem. Soc. 1955, 77, 5, 1230–1237Publication Date (Print):March 1, 1955Publication History Published online1 May 2002Published inissue 1 March 1955https://pubs.acs.org/doi/10.1021/ja01610a040https://doi.org/10.1021/ja01610a040research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations12LEARN 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