Academic literature on the topic 'PNA Probes'
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Journal articles on the topic "PNA Probes"
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Vilaivan, Tirayut. "Fluorogenic PNA probes." Beilstein Journal of Organic Chemistry 14 (January 29, 2018): 253–81. http://dx.doi.org/10.3762/bjoc.14.17.
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Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Tano, Hanna, Maryam Oroujeni, Anzhelika Vorobyeva, Kristina Westerlund, Yongsheng Liu, Tianqi Xu, Daniel Vasconcelos, Anna Orlova, Amelie Eriksson Karlström, and Vladimir Tolmachev. "Comparative Evaluation of Novel 177Lu-Labeled PNA Probes for Affibody-Mediated PNA-Based Pretargeting." Cancers 13, no. 3 (January 28, 2021): 500. http://dx.doi.org/10.3390/cancers13030500.
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Affibody-mediated PNA-based pretargeting is a promising approach to radionuclide therapy of HER2-expressing tumors. In this study, we test the hypothesis that shortening the PNA pretargeting probes would increase the tumor-to-kidney dose ratio. The primary probe ZHER2:342-SR-HP15 and the complementary secondary probes HP16, HP17, and HP18, containing 9, 12, and 15 nucleobases, respectively, and carrying a 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelator were designed, synthesized, characterized in vitro, and labeled with 177Lu. In vitro pretargeting was studied in HER2-expressing SKOV3 and BT474 cell lines. The biodistribution of these novel probes was evaluated in immunodeficient mice bearing SKOV3 xenografts and compared to the previously studied [177Lu]Lu-HP2. Characterization confirmed the formation of high-affinity duplexes between HP15 and the secondary probes, with the affinity correlating with the length of the complementary PNA sequences. All the PNA-based probes were bound specifically to HER2-expressing cells in vitro. In vivo studies demonstrated HER2-specific uptake of all 177Lu-labeled probes in xenografts in a pretargeting setting. The ratio of cumulated radioactivity in the tumor to the radioactivity in kidneys was dependent on the secondary probe’s size and decreased with an increased number of nucleobases. The shortest PNA probe, [177Lu]Lu-HP16, showed the highest tumor-to-kidney ratio. [177Lu]Lu-HP16 is the most promising secondary probe for affibody-mediated tumor pretargeting.
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Kim, Hyun-Joong, and Byron F. Brehm-Stecher. "Design and Evaluation of Peptide Nucleic Acid Probes for Specific Identification of Candida albicans." Journal of Clinical Microbiology 53, no. 2 (November 26, 2014): 511–21. http://dx.doi.org/10.1128/jcm.02417-14.
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Candida albicansis an important cause of systemic fungal infections, and rapid diagnostics for identifying and differentiatingC. albicansfrom otherCandidaspecies are critical for the timely application of appropriate antimicrobial therapy, improved patient outcomes, and pharmaceutical cost savings. In this work, two 28S rRNA-directed peptide nucleic acid-fluorescencein situhybridization (PNA-FISH) probes, P-Ca726 (targeting a novel region of the ribosome) and P-CalB2208 (targeting a previously reported region), were evaluated. Hybridization conditions were optimized by using both fluorescence microscopy (FM) and flow cytometry (FCM), and probes were screened for specificity and discriminative ability against a panel ofC. albicansand various nontargetCandidaspp. The performance of these PNA probes was compared quantitatively against that of DNA probes or DNA probe/helper combinations directed against the same target regions. Ratiometric analyses of FCM results indicated that both the hybridization quality and yield of the PNA probes were higher than those of the DNA probes. In FCM-based comparisons of the PNA probes, P-Ca726 was found to be highly specific, showing 2.5- to 5.5-fold-higher discriminatory power forC. albicansthan P-CalB2208. The use of formamide further improved the performance of the new probe. Our results reinforce the significant practical and diagnostic advantages of PNA probes over their DNA counterparts for FISH and indicate that P-Ca726 may be used advantageously for the rapid and specific identification ofC. albicansin clinical and related applications, especially when combined with FCM.
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Oliveira, Alexandre C., Hugo A. L. Filipe, and Luís M. S. Loura. "Fluorescent Probes cis- and trans-Parinaric Acids in Fluid and Gel Lipid Bilayers: A Molecular Dynamics Study." Molecules 28, no. 5 (February 28, 2023): 2241. http://dx.doi.org/10.3390/molecules28052241.
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Fluorescence probes are indispensable tools in biochemical and biophysical membrane studies. Most of them possess extrinsic fluorophores, which often constitute a source of uncertainty and potential perturbation to the host system. In this regard, the few available intrinsically fluorescent membrane probes acquire increased importance. Among them, cis- and trans-parinaric acids (c-PnA and t-PnA, respectively) stand out as probes of membrane order and dynamics. These two compounds are long-chained fatty acids, differing solely in the configurations of two double bonds of their conjugated tetraene fluorophore. In this work, we employed all-atom and coarse-grained molecular dynamics simulations to study the behavior of c-PnA and t-PnA in lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), representative of the liquid disordered and solid ordered lipid phases, respectively. All-atom simulations indicate that the two probes show similar location and orientation in the simulated systems, with the carboxylate facing the water/lipid interface and the tail spanning the membrane leaflet. The two probes establish interactions with the solvent and lipids to a similar degree in POPC. However, the almost linear t-PnA molecules have tighter lipid packing around them, especially in DPPC, where they also interact more with positively charged lipid choline groups. Probably for these reasons, while both probes show similar partition (assessed from computed free energy profiles across bilayers) to POPC, t-PnA clearly partitions more extensively than c-PnA to the gel phase. t-PnA also displays more hindered fluorophore rotation, especially in DPPC. Our results agree very well with experimental fluorescence data from the literature and allow deeper understanding of the behavior of these two reporters of membrane organization.
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Chim, Wilson, Abootaleb Sedighi, Christopher L. Brown, Ralph Pantophlet, and Paul C. H. Li. "Effect of buffer composition on PNA–RNA hybridization studied in the microfluidic microarray chip." Canadian Journal of Chemistry 96, no. 2 (February 2018): 241–47. http://dx.doi.org/10.1139/cjc-2017-0319.
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Herein, we report that peptide nucleic acid sequences (PNAs) have been used as the probe species for detection of RNA and that a microfluidic microarray (MMA) chip is used as the platform for detection of hybridizations between immobilized PNA probes and RNA targets. The RNA targets used are derived from influenza A sequences. This paper discusses the optimization of two probe technologies used for RNA detection and investigates how the composition of the probe buffer and the content of the hybridization solution can influence the overall results. Our data show that the PNA probe is a better choice than the DNA probe when there is low salt in the probe buffer composition. Furthermore, we show that the absence of salt (NaCl) in the hybridization buffer does not hinder the detection of RNA sequences. The results provide evidence that PNA probes are superior to DNA probes in term of sensitivity and adaptability, as PNA immobilization and PNA–RNA hybridization are less affected by salt content in the reaction buffers unlike DNA probes.
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Stender, Henrik, Cletus Kurtzman, Jens J. Hyldig-Nielsen, Ditte Sørensen, Adam Broomer, Kenneth Oliveira, Heather Perry-O'Keefe, Andrew Sage, Barbara Young, and James Coull. "Identification of Dekkera bruxellensis(Brettanomyces) from Wine by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid Probes." Applied and Environmental Microbiology 67, no. 2 (February 1, 2001): 938–41. http://dx.doi.org/10.1128/aem.67.2.938-941.2001.
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ABSTRACT A new fluorescence in situ hybridization method using peptide nucleic acid (PNA) probes for identification ofBrettanomyces is described. The test is based on fluorescein-labeled PNA probes targeting a species-specific sequence of the rRNA of Dekkera bruxellensis. The PNA probes were applied to smears of colonies, and results were interpreted by fluorescence microscopy. The results obtained from testing 127 different yeast strains, including 78 Brettanomycesisolates from wine, show that the spoilage organismBrettanomyces belongs to the species D. bruxellensis and that the new method is able to identifyBrettanomyces (D. bruxellensis) with 100% sensitivity and 100% specificity.
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Wilks, Sandra A., and C. William Keevil. "Targeting Species-Specific Low-Affinity 16S rRNA Binding Sites by Using Peptide Nucleic Acids for Detection of Legionellae in Biofilms." Applied and Environmental Microbiology 72, no. 8 (August 2006): 5453–62. http://dx.doi.org/10.1128/aem.02918-05.
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ABSTRACT Using fluorescence in situ hybridization to detect bacterial groups has several inherent limitations. DNA probes are generally used, targeting sites on the 16S rRNA. However, much of the 16S rRNA is highly conserved, with variable regions often located in inaccessible areas where secondary structures can restrict probe access. Here, we describe the use of peptide nucleic acid (PNA) probes as a superior alternative to DNA probes, especially when used for environmental samples. A complex bacterial genus (Legionella) was studied, and two probes were designed, one to detect all species and one targeted to Legionella pneumophila. These probes were developed from existing sequences and are targeted to low-binding-affinity sites on the 16S rRNA. In total, 47 strains of Legionella were tested. In all cases, the Legionella spp. PNA probe labeled cells strongly but did not bind to any non-Legionella species. Likewise, the specific L. pneumophila PNA probe labeled only strains of L. pneumophila. By contrast, the equivalent DNA probes performed poorly. To assess the applicability of this method for use on environmental samples, drinking-water biofilms were spiked with a known concentration of L. pneumophila bacteria. Quantifications of the L. pneumophila bacteria were compared using PNA hybridization and standard culture methods. The culture method quantified only 10% of the number of L. pneumophila bacteria found by PNA hybridization. This illustrates the value of this method for use on complex environmental samples, especially where cells may be in a viable but noncultivable state.
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Stender, Henrik, Kaare Lund, Kenneth H. Petersen, Ole F. Rasmussen, Poonpilas Hongmanee, Håkan Miörner, and Sven E. Godtfredsen. "Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes for Differentiation between Tuberculous and Nontuberculous Mycobacterium Species in Smears of Mycobacterium Cultures." Journal of Clinical Microbiology 37, no. 9 (1999): 2760–65. http://dx.doi.org/10.1128/jcm.37.9.2760-2765.1999.
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TB PNA FISH is a new fluorescence in situ hybridization (FISH) method using peptide nucleic acid (PNA) probes for differentiation between species of the Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria (NTM) in acid-fast bacillus-positive (AFB+) cultures is described. The test is based on fluorescein-labelled PNA probes that target the rRNA of MTC or NTM species applied to smears of AFB+ cultures for microscopic examination. Parallel testing with the two probes serves as an internal control for each sample such that a valid test result is based on one positive and one negative reaction. TB PNA FISH was evaluated with 30 AFB+ cultures from Denmark and 42 AFB+ cultures from Thailand. The MTC-specific PNA probe showed diagnostic sensitivities of 84 and 97%, respectively, and a diagnostic specificity of 100% in both studies, whereas the NTM-specific PNA probe showed diagnostic sensitivities of 91 and 64%, respectively, and a diagnostic specificity of 100% in both studies. The low sensitivity of the NTM-specific PNA probe in the Thai study was due to a relatively high prevalence of Mycobacterium fortuitum, which is not identified by the probe. In total, 63 (87%) of the cultures were correctly identified as MTC (n = 46) or NTM (n = 17), whereas the remaining 9 were negative with both probes and thus the results were inconclusive. None of the samples were incorrectly identified as MTC or NTM; thus, the predictive value of a valid test result obtained with TB PNA FISH was 100%.
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Mach, Kathleen E., Aniruddha M. Kaushik, Kuangwen Hsieh, Pak Kin Wong, Tza-Huei Wang, and Joseph C. Liao. "Optimizing peptide nucleic acid probes for hybridization-based detection and identification of bacterial pathogens." Analyst 144, no. 5 (2019): 1565–74. http://dx.doi.org/10.1039/c8an02194e.
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de Lima, Amanda L. R., Carmelita C. B. Cavalcanti, Mariana C. C. Silva, Patrícia M. G. Paiva, Luana C. B. B. Coelho, Eduardo I. C. Beltrão, and Maria T. dos S. Correia. "Histochemical Evaluation of Human Prostatic Tissues withCratylia mollisSeed Lectin." Journal of Biomedicine and Biotechnology 2010 (2010): 1–6. http://dx.doi.org/10.1155/2010/179817.
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Lectins, proteins which selectively recognize carbohydrates, have been used in histochemistry for the evaluation of changes in glycosylation in processes of cellular differentiation and/or dedifferentiation.Cratylia mollisseed lectins (Cramoll 1,4 and Cramoll 3), conjugated to horseradish peroxidase, were used as histochemical probes in human prostate tissues: normal (NP), hyperplasia (BPH), and prostate carcinoma (PCa). The staining pattern of Con-A and Cramoll 1,4 in BPH was more intense than in NP. These lectins also showed staining differences between BPH and PCa; the latter showing decreased staining intensity with an increased degree of malignancy. PNA and Cramoll 3 stained epithelial cells similarly in all diagnoses although they did present intense staining of PCa glands lumen. Corpora amylacea were not differentially recognized by any of the lectins. Cramoll 1,4 and Cramoll 3 seed lectins present themselves as candidates for histochemical probes for prostate pathologies when compared to commercial lectins such as Con-A and PNA.
Dissertations / Theses on the topic "PNA Probes"
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Ly, Danith. "Mechanism of electron transfer in double-stranded DNA and PNA-DNA hybrids, and the development of a fluorescence probe for DNA and RNA detection." Diss., Georgia Institute of Technology, 1998. http://hdl.handle.net/1853/30485.
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Park, Hyeyoung. "Kinetic and affinity analysis of hybridization reactions between PNA probes and DNA targets using surface plasmon field-enhanced fluorescence spectroscopy (SPFS)." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=976835673.
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Park, Hyeyoung. "Kinetic and affinity analysis of hybridization reactions between PNA probes and DNA targets using surface plasmon fiel enhanced fluorescence spectroscopy (SPFS)." Waabs GCA-Verl, 2005. http://deposit.ddb.de/cgi-bin/dokserv?id=2760979&prov=M&dok_var=1&dok_ext=htm.
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Coover, Robert A. "Development of Irreversible Substrate Competitive Probes for PKA Activity." VCU Scholars Compass, 2015. http://scholarscompass.vcu.edu/etd/3907.
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The current environment for drug discovery and disease treatment relies heavily on genomic analysis, structural biology and chemical biology techniques. With the enormous advances in genomic analysis and structural biology, the use of and desire for targeted therapies has increased. However, as more genomic data for cancer disease state pathology becomes available we must ask increasingly difficult questions and even produce new technologies, such as activity-based probes, to answer these questions.
In particular, targeted kinase inhibitors for the treatment of cancer has become a mainstay for drug development for both industry and academia, but it is evident that the genomic data is not always indicative of protein expression. Additionally, protein expression alone does not completely characterize functional activity. Therefore, in order to more accurately validate drug targets and predict drug efficacy, we must not only identify possible targets but also determine their activity in vivo.
The goal of this work was to develop a probe for Protein Kinase A that would act by alkylating a conserved cysteine in the substrate-binding pocket of the enzyme. We hypothesized that by targeting the substrate-binding pocket we could effectively utilize the natural substrate selectivity filters as well as take into account multiple endogenous regulatory mechanisms. We produced probes utilizing portions of the pseudosubstrate inhibitor PKI that demonstrate the ability to label the catalytic subunit of Protein Kinase A in an activity-dependent manner, thus making it an important first step in a new class of activity-based probes for the kinome.
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Moon, Gyo Sik. "An Algorithm for the PLA Equivalence Problem." Thesis, University of North Texas, 1995. https://digital.library.unt.edu/ark:/67531/metadc278922/.
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The Programmable Logic Array (PLA) has been widely used in the design of VLSI circuits and systems because of its regularity, flexibility, and simplicity. The equivalence problem is typically to verify that the final description of a circuit is functionally equivalent to its initial description. Verifying the functional equivalence of two descriptions is equivalent to proving their logical equivalence. This problem of pure logic is essential to circuit design. The most widely used technique to solve the problem is based on Binary Decision Diagram or BDD, proposed by Bryant in 1986. Unfortunately, BDD requires too much time and space to represent moderately large circuits for equivalence testing. We design and implement a new algorithm called the Cover-Merge Algorithm for the equivalence problem based on a divide-and-conquer strategy using the concept of cover and a derivational method. We prove that the algorithm is sound and complete. Because of the NP-completeness of the problem, we emphasize simplifications to reduce the search space or to avoid redundant computations. Simplification techniques are incorporated into the algorithm as an essential part to speed up the the derivation process. Two different sets of heuristics are developed for two opposite goals: one for the proof of equivalence and the other for its disproof. Experiments on a large scale of data have shown that big speed-ups can be achieved by prioritizing the heuristics and by choosing the most favorable one at each iteration of the Algorithm. Results are compared with those for BDD on standard benchmark problems as well as on random PLAs to perform an unbiased way of testing algorithms. It has been shown that the Cover-Merge Algorithm outperforms BDD in nearly all problem instances in terms of time and space. The algorithm has demonstrated fairly stabilized and practical performances especially for big PLAs under a wide range of conditions, while BDD shows poor performance because of its memory greedy representation scheme without adequate simplification.
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Oguz, Alaattin. "The Interplay Between Turkish And Hungarian Nationalism: Ottoman Pan-turkism And Hungarian Turanism (1890-1918)." Master's thesis, METU, 2005. http://etd.lib.metu.edu.tr/upload/12606629/index.pdf.
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This thesis dealt with the issues of the emergence of Pan-Turkism in Ottoman Empire and of Pan-Turanism in Hungary between the years 1890 and 1920. The theoretical discussion and literature review related to the subject exhibited that these two nationalisms were possible only when a state bureaucrats and intellectuals try to save the state from collapse and make discussions on the national issues, or when a state elites and noble classes aim to use national ideology for protecting the state from external threats and providing benefits on behalf of national interest. While former suits to Ottoman Pan-Turkism, latter describes Hungarian Pan-Turanism.
The thesis consisted of three main and related parts. The first part focused on the historical and theoretical development of nationalism and pan movements, and condition of pan movement in the context of theories of nationalism. In the second part, the emergence of Turkish nationalism and Pan-Turkism was analysed in the historical context. The third part dwelt upon the genesis of Pan-Turanism in Hungary, and its relations with Ottoman Pan-Turkism until the end of the First World War. For that reason, firstly, historical roots of Turkish nationalism and Pan-Turkism were sought so that it is able to see how the attempts to modernization in the Ottoman state provided a ground for the spreading of Western political concepts and ideas and the emergence of a secular nationalist intelligentsia. Also the role of Turcology and the influence of Russian Turks on the development and politicization of Turkish nationalism and Pan-Turkism could be assessed. Secondly, the political condition of Hungary in the nineteenth century was exposed in order to explain the emergence and development of Pan-Turanism. Then, the focus was made on the linguistic debates of Hungarian academic circles on the origin of Hungarians. Exposing the political and cultural conditions could facilitate to project the partnership between Pan-Turkism and Pan-Turanism.
Throughout the thesis, it was tried to be demonstrated that Ottoman Empire and Hungarian state had different political conditions and necessities. While Ottoman state bureaucrats and intellectuals aimed to save the stateHungarian elites and intellectuals urged on the Hungarian national interests. Although some strong relations and partnerships were manifest in political and cultural areas, Hungarian Pan-Turanists and Ottoman Pan-Turkists belonged to different state traditions. Turkish nationalism and Pan-Turkism had an aim to save the state and create a new national identity. Nevertheless, Hungarian nationalism and Pan-Turanism tended towards the national interests of Hungarians through expansionist policy. That was the reason why the relations between Pan-Turkists and Pan-Turanists remained temporary.
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Cvitkovic, John Peter. "From All-Atom Molecular Mechanics to Coarse- Grained Lattice Models: Computational Approaches to Problems in Protein Biochemistry." Digital WPI, 2019. https://digitalcommons.wpi.edu/etd-dissertations/524.
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Computational simulations of chemical systems play an ever-increasing role in many areas of biochemical research from rational drug design to probing fundamental physiological processes. Depending on the method, a vast array of properties are able to be predicted. Here we report the design and implementation of two methods for investigating diverse problems in protein biochemistry.
In order to better understand protein–metal interactions—most importantly for the difficult to model transition metal ions— empirical force field parameters were developed for Pt(II), cisplatin, and other Pt(II) coordination compounds. Two force field frameworks were used: a modified version of the fixed- charge OPLS-AA and the polarizable POSSIM force field. A seven-site model was used for the Pt(II) ion. The produced parameters are compatible with the OPLS-AA and POSSIM force fields and can be used in protein–metal binding simulations in which—contrary to the common treatment of metal ions in such simulations—the position or even coordination of the ion does not have to be constrained using preexisting knowledge. It has been demonstrated that the produced models are capable of reproducing key properties of relevant Pt(II) complexes but that the POSSIM formalism yields more accurate values for energies of formation than the OPLS-AA model. This Pt(II) model was employed—along with previously developed Cu(I) parameters—to investigate the binding of platinum to the protein Atox1, a human copper chaperone implicated in the resistance mechanism of cisplatin and other platinum antitumor compounds. In collaboration with the Dmitriev and Bernholc groups, we used our models to inform and refine spectroscopic experiments as well as to serve as starting points for high-performance quantum calculations. It was shown that under physiological redox conditions, copper(I) and cisplatin can form large polymers with glutathione. These polymers were capable of transferring copper(I) to apo-Atox1 or to platinum(II) to copper-loaded Atox1. Analysis of the simultaneous binding of copper(I) and platinum(II) to Atox1 was found to occur through the formation of copper–sulfur–platinum bridges, where copper is coordinated by three sulfur atoms and platinum by four sulfur atoms. With the goal of using a simple model to be able to quickly estimate the acid disassociation constants of proteins, PKA17 has been developed and tested. PKA17 is a coarse-grain grid-based method and software tool for accurately and rapidly calculating protein pKa values given an input PDB structure file. During development, parameter fitting was carried out using a compilation of 442 Asp, Glu, His, and Lys residues that had both high-resolution PDB structures and published experimental pKa values available. Applying our PKA17 model, the calculated average unsigned error and RMSD for the residue set were found to be 0.628 and 0.831 pH units, respectively. As a benchmark for comparison, the same residue set was evaluated with the PROPKA software package which resulted in an average unsigned error of 0.761 pH units and an RMSD of 1.063 pH units. Finally, a web interface for the PKA17 software was developed and deployed (http://users.wpi.edu/~jpcvitkovic/pka_calc.html) to make PKA17 available to the wider scientific community.
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Hüsken, Nina [Verfasser], Nils [Gutachter] Metzler-Nolte, and Wolfgang [Gutachter] Schuhmann. "Ferrocene-PNA recognition layers : probe design, interfacial and electron transfer studies and DNA detection strategies / Nina Hüsken ; Gutachter: Nils Metzler-Nolte, Wolfgang Schuhmann ; Fakultät für Chemie und Biochemie." Bochum : Ruhr-Universität Bochum, 2012. http://d-nb.info/122317199X/34.
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Bodén, Ida. "Near infrared and skin impedance spectroscopic in vivo measurements on human skin : development of a diagnostic tool for skin cancer." Doctoral thesis, Umeå universitet, Kirurgi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-50605.
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Every year approximately 2800 Swedes are diagnosed with malignant melanoma, the form of cancer that is most rapidly increasing in incidence in the Western world. The earlier we can identify and diagnose a malignant melanoma, the better is the prognosis. In Sweden, 155 000 benign naevi, harmless skin tumours or moles, are surgically excised each year, many of them because melanoma cannot be dismissed by non-invasive methods. The excisions result in substantial medical costs and cause unrest and suffering of the individual patient. For untrained physicians, it is often difficult to make an accurate diagnosis of melanoma, thus a tool that could help to strengthen the diagnosis of suspected melanomas would be highly valuable. This thesis describes the development and assessment of a non-invasive method for early skin cancer detection. Using near infrared (NIR) and skin impedance spectroscopy, healthy and diseased skin of various subjects was examined to develop a new instrument for detecting malignant melanoma. Due to the complex nature of skin and the numerous variables involved, the spectroscopic data were analysed multivariately using Principal Component Analysis (PCA) and partial leas square discriminant analysis (PLS-DA). The reproducibility of the measurements was determined by calculating Scatter Values (SVs), and the significance of separations between overlapping groups in score plots was determined by calculating intra-model distances. The studies indicate that combining skin impedance and NIR spectroscopy measurements adds value, therefore a new probe-head for simultaneous NIR and skin impedance measurements was introduced. Using both spectroscopic techniques it was possible to separate healthy skin at one body location from healthy skin at another location due to the differences in skin characteristics at various body locations. In addition, statistically significant differences between overlapping groups of both age and gender in score plots were detected. However, the differences in skin characteristics at different body locations had stronger effects on the measurements than both age and gender. Intake of coffee and alcohol prior to measurement did not significantly influence the outcome data. Measurements on dysplastic naevi were significantly separated in a score plot and the influence of diseased skin was stronger than that of body location. This was confirmed in a study where measurements were performed on 12 malignant melanomas, 19 dysplastic naevi and 19 benign naevi. The malignant melanomas were significantly separated from both dysplastic naevi and benign naevi. Overall, the presented findings show that the instrument we have developed provides fast, reproducible measurements, capable of distinguishing malignant melanoma from dysplastic naevi and benign naevi non-invasively with 83% sensitivity and 95% specificity. Thus, the results are highly promising and the instrument appears to have high potential diagnostic utility.
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Mohnani, Stefan. "Synthetic approaches towards modified peptide nucleic acids (PNAs) for biomimetical nanostructured surfaces." Doctoral thesis, Università degli studi di Trieste, 2011. http://hdl.handle.net/10077/4814.
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2009/2010“There is plenty of room at the bottom”. These were the famous words of Richard P. Feynman in 1959 that led to the birth of nanotechnology and nanoscience. Electronic devices based on inorganic semiconductors have been part of our daily lives for the last 60 years. Their miniaturisation has occurred gradually over the years, however, according to Moore’s law the contemporary microelectronic industry’s “top-down” manufacturing technique will soon reach its limits. Therefore, the recent development and increased knowledge of organic semiconductors has led to a tendency to explore alternative avenues with a focus on the creation of electronic devices based on organic molecules. The invention of techniques such STM (1981) and AFM (1986) have facilitated this research, allowing the imaging and manipulation of surfaces and molecules at the nanometre scale (0.1-100 nm). The next step is therefore the development of methods for the controlled fabrication of molecular assemblies and their integration into usable macroscopic systems. In this respect, the “bottom-up” approach offers considerable advantages over any other methodology (i.e. “top-down”) for the construction of nanoscale functional materials and devices. This approach generally exploits the hierarchical self-assembly of functional molecules through multiple non-covalent interactions to prepare long range ordered and defect-free assemblies barely accessible through conventional covalent synthesis. However, an intrinsic drawback of investigating such systems in solution or in a crystal is that molecular components cannot be directly addressed on a nanometric scale. As a consequence, the best engineering methodology involves modifying the surfaces of bulk materials such as metals or semiconductors by deposition of functional organic materials. The modified surfaces are then characterised using scanning probe microscopies (e.g. STM, AFM). To this end, surface-confined, supramolecularly constructed, bi-dimensional (2D) networks, featuring regular porous domains (controllable both in shape and size) are of particular significance in this research domain because their cavities can be used as receptors for the confinement of other remotely controlled functional molecules (e.g. molecular switches, luminescent chromophores). Since these complex nanostructures could ultimately find applications as optoelectronic devices, research efforts in this domain have been gathering momentum in recent years. In Chapter 1, the reader is introduced to the methods employed to construct porous networks on surfaces via supramolecular interactions. The second part of the chapter deals with recent examples of recognition, selection and immobilisation of guest molecules within the cavities of the networks, which is followed in the third part with a discussion about surface assemblies that display structural features or functionality in the third dimension. The last section of the chapter is devoted to the construction of porous networks on surfaces via the interactions of biomimetic molecules (e.g. DNA), which leads to the objectives of the present doctoral project. Inspired by the self-assembly of DNA into nanoporous arrays, it was postulated that the Watson-Crick base pairing of oligonucleotide’s nucleobases would be ideal in preparing 2D porous networks with large receptor cavities. The idea was to covalently attach complementary single stranded oligonucleotides to rigid angular and linear unit core modules respectively, and then allow the two units to self-assemble on surfaces. However, instead of using DNA oligonucleotides, the use of peptide nucleic acid (PNA) oligonucleotides was proposed since more robust architectures would be obtained due to the higher duplex stability displayed by this class of biomimetic molecules. This doctoral dissertation describes the synthetic steps taken towards achieving this goal. The design of the angular and linear units bearing complementary PNA oligomers, required for the preparation of self-assembled nanoporous arrays are described. However, prior to synthesizing these complex molecules, a simpler proof of principle was required to confirm that PNA duplexes could be formed on surfaces and also, whether the presence of chromophoric moieties (e.g. porphyrin) appended to the PNA strands had any effect on duplex formation and duplex stability. The molecule designed for this proof of principle was a self-complementary PNA dodecamer bearing a porphyrin adduct. The synthesis of the self-complementary PNA oligomer required for the preparation of the PNA-porphyrin adduct is described in the first part of Chapter 2. The main synthetic routes and protecting-group strategies used to prepare PNA monomers and oligomers are described first. This is followed by a discussion of the orthogonal protecting group strategies chosen for our project that would allow the isolation of PNA oligomers bearing protected nucleobases following resin-cleavage. This is contrary to the general norm in existing strategies wherein resin-cleavage and nucleobase deprotection is carried out in situ, however, it was required in our synthetic strategy since the terminal amino group of the PNA oligomers was required for further solution phase reactions. To this end, two protecting group strategies were proposed, a Fmoc/Mmt and Fmoc/Cbz-protecting group strategies. The solid support chosen for the Fmoc/Mmt strategy was Tentagel featuring a base-cleavable linker. Due to the failure to hydrolyse the linker during the resin-cleavage step, the Fmoc/Mmt strategy was abandoned. In the second strategy, an acid-cleavable Rink amide resin was chosen as the solid support, therefore a Fmoc/Cbz-protecting group strategy was chosen since it would allow the TFA-mediated cleavage of the oligomer from the resin, without the deprotection of the Cbz groups from the nucleobases. The preparation of the target PNA oligomer (sequence: TTAATTAATTAA) using the Fmoc/Cbz strategy is described in the next section. First, the required monomers for the oligomer synthesis were prepared using established procedures. Then, following reports of the advances in microwave assisted solid phase peptide synthesis claiming improved purity of oligomer products using short coupling times, the solid phase PNA oligomerisation was attempted using microwave irradiation. Three attempts were performed. The first, using a standard laboratory microwave, resulted in a complex mixture of products at the dodecamer stage. An improvement was observed in the results using the CEM discover SPS microwave which was specifically designed for solid phase synthesis, however, the crude dodecamer obtained was still inseparable from the by-products. Similar results were obtained with the CEM liberty microwave, which was an automated solid phase synthesis setup. Finally, utilising manual solid phase synthesis, the target PNA dodecamer was obtained. The HPLC chromatogram of crude PNA dodecamer obtained following resin cleavage displayed a single major product, which was subsequently purified. The oligomer was then deprotected by treatment with TMSI, and was analysed by mass spectrometry, which confirmed that the target dodecamer had been isolated. Section 2.2 described our efforts to prepare PNA-chromophore adducts. Following the isolation of the PNA dodecamer, attempts to covalently attach a porphyrin moiety to the resin-bound oligomer via an amide linkage failed, possibly due to steric hindrance. Subsequently, an azide linker was appended to the oligomer, and attempts to attach an acetylene functionalised porphyrin using a Cu(I)-catalysed 1,3-dipolar cycloaddition were performed. Unfortunately, this approach also did not yield the target adduct. These unsuccessful results paved the way to the development of a Cu(I)-free 1,3-dipolar cycloaddition that enabled the attachment of chromophores to the PNA oligomer. Recently published reports of Cu(I)-free 1,3-dipolar cycloaddition reactions applied on DNA oligomers offered inspiration towards this goal. The reported strategies involved the generation of a nitrile oxide species, which then reacted with either an alkene or an alkyne to form an isoxazoline or an isoxazole. Two methods of generating the nitrile oxide species were evaluated using anthracene derivatives. The first method involved the base-mediated dehydrochlorination of anthracene hydroximoyl chloride to yield the nitrile oxide, which then reacted with a dipolarophile that was introduced into the reaction mixture. The second approach to generating a nitrile oxide species involved treating an O-silylated hydroxamic acid derivative of anthracene with trifluoromethanesulfonic anhydride in the presence of a base (Carreira’s method). Following successful trapping of the nitrile oxides generated by both methods using trimethylsilyl ethylene as the dipolarophile, the reactions were applied on a resin-bound, acetylene-functionalised PNA dodecamer. Both methods yielded the target PNA-anthracene adduct. Since the nitrile oxide-acetylene 1,3-dipolar cycloaddition reaction had never been applied on porphyrins, a method had to be developed. Attempts to prepare a hydroximoyl chloride derivative of a porphyrin resulted in the decomposition of the macrocycle upon treatment with chlorinating agents (NCS, tert-BuOCl, and 1-chlorobenzotriazole), therefore, the hydroximoyl chloride method was abandoned in favour of the Carreira method. An O-silylated hydroxamic acid derivative of porphyrin was synthesized, and upon exposure to trifluoromethanesulfonic anhydride and Et3N, the nitrile oxide was generated and was trapped with a large excess (200 eq.) of trimethylsilyl ethylene yielding the target tetra-isoxazole porphyrin derivative in 62% yield, which corresponded to a yield of 89% per 1,3-dipolar cycloaddition. Optimisation of the reaction conditions using phenyl acetylene as the dipolarophile allowed similar yields to be obtained with only a 10 eq. excess of the acetylene. Having developed a protocol that was compatible with both PNA and porphyrin, the utility of the method to prepare a variety of PNA-chromophore adducts was tested. Hydroxamate derivatives of pyrene, porphyrin, phenanthroline and fluorescein chromophores were prepared. Subsequently, the corresponding nitrile oxide species were generated and were reacted with the resin-bound, acetylene-functionalised PNA dodecamer. The PNA-pyrene adduct was successfully isolated (Figure v), however, the other target PNA-chromophore products were not isolated. The porphyrin nitrile oxide derivative was insoluble in the reaction medium, thus preventing the cycloaddition reaction from proceeding. In the case of the fluorescein hydroxamate, the presence of nucleophilic functional groups in the starting material were probably reactive towards the trifluoromethanesulfonic anhydride reagent, therefore it was unlikely that the nitrile oxide species was formed, and thus the cycloaddition reaction could not proceed. Finally, the reaction with the phenanthroline derivative yielded a new product, however mass spectrometry analysis indicated that it did not correspond the target PNA-phenanthroline adduct. Further work is currently underway to re-evaluate these reactions. In parallel to the synthetic work, a preliminary study into the deposition of PNA onto mica surfaces was investigated using AFM imaging. Deposition of drops of an aqueous solution of deprotected self-complementary PNA dodecamer onto clean mica surfaces using spin coating resulted in aggregates of PNA on the surface. Following annealing of the solution, a repeated deposition of a single drop of the solution resulted in a completely different surface assembly. The surface was saturated by what was thought to be PNA duplexes. This was confirmed by the deposition of drop of a solution that was diluted ten-fold which resulted in an AFM image where bright spot were intermitted by clean mica surface. Topographical analysis of the surface indicated that the bright spots were an average in 1 nm in height, which closely corresponds to the expected height of PNA duplexes, thus confirming that PNA duplexes could be deposited onto surfaces.
XXII Ciclo
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Books on the topic "PNA Probes"
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Franck, Pellestor, ed. PRINS and PNA technologies in chromosomal investigations. New York: Nova Biomedical Books, 2007.
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Pan, Jun. Pan Jun san wen =: Pan Jun's selected proses. [Hangzhou]: Zhejiang wen yi chu ban she, 2000.
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Cai pan de fa li. Beijing: Ren min chu ban she, 2007.
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translator, Ge Yaojun, ed. Shen pan. Taibei Shi: Huang guan wen hua chu ban you xian gong si, 2016.
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Shang di zen yang shen pan. Beijing: Zhongguo fa zhi chu ban she, 2000.
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Encontro, de Agentes de Projetos (1998 Salvador Brazil). Caminhos: Planejamento, Monitoramento, Avaliação - PMA. Salvador, Bahia, Brasil: CESE, 1999.
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Encontro de Agentes de Projetos (1998 Salvador, Brazil). Caminhos: Planejamento, Monitoramento, Avaliação - PMA. Salvador, Bahia, Brasil: CESE, 1999.
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1933-, Paris Peter J., ed. Religion and poverty: Pan-African perspectives. Durham: Duke University Press, 2009.
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1933-, Paris Peter J., and Olupọna Jacob Obafẹmi Kẹhinde, eds. Religion and poverty: Pan-African perspectives. Durham: Duke University Press, 2009.
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S, Hipólito Gill. La Individualización judicial de la pena. [Panama?]: Gabinete de Estudios Culturales, 1996.
Find full textBook chapters on the topic "PNA Probes"
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Kato, Takamitsu A. "Nontraditional Method for Telomere Staining by PNA Probes." In Methods in Molecular Biology, 111–16. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2433-3_13.
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Knoll, Andrea, Susann Kummer, Felix Hövelmann, Andreas Herrmann, and Oliver Seitz. "Life Cell Imaging of mRNA Using PNA FIT Probes." In Concepts and Case Studies in Chemical Biology, 351–64. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527687503.ch24.
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Piro, Benoît, Vincent Noël, and Steeve Reisberg. "DNA and PNA Probes for DNA Detection in Electroanalytical Systems." In RNA Technologies, 47–80. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17305-4_3.
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Gorska, Katarzyna, and Nicolas Winssinger. "Rapid miRNA Imaging in Cells Using Fluorogenic Templated Staudinger Reaction Between PNA-Based Probes." In Peptide Nucleic Acids, 179–92. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-553-8_15.
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Kato, Takamitsu A. "Telomere Aberration Detection by PNA FISH Probe." In Methods in Molecular Biology, 105–10. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2433-3_12.
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Lammer, J., F. Karnel, E. Pilger, F. Olbert, and H. Schreyer. "Nd-YAG Laser Angioplasty with Contact Probes." In Pros and Cons in PTA and Auxiliary Methods, 68–78. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-73736-7_9.
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Lomholt, Bodil, Sune Frederiksen, and Peter E. Nielsen. "PNA as Specific Probe forIn SituHybridization to Metaphase Chromosomes." In Nonradioactive Analysis of Biomolecules, 478–83. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-57206-7_42.
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Löding, Christof, and Anton Pirogov. "Ambiguity, Weakness, and Regularity in Probabilistic Büchi Automata." In Lecture Notes in Computer Science, 522–41. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-45231-5_27.
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AbstractProbabilistic Büchi automata are a natural generalization of PFA to infinite words, but have been studied in-depth only rather recently and many interesting questions are still open. PBA are known to accept, in general, a class of languages that goes beyond the regular languages. In this work we extend the known classes of restricted PBA which are still regular, strongly relying on notions concerning ambiguity in classical $$\omega $$ ω -automata. Furthermore, we investigate the expressivity of the not yet considered but natural class of weak PBA, and we also show that the regularity problem for weak PBA is undecidable.
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Hua, Yihe, Desmond T. B. Yeo, and Thomas K. F. Foo. "Peripheral Nerve Stimulation (PNS) Analysis of MRI Head Gradient Coils with Human Body Models." In Brain and Human Body Modelling 2021, 39–57. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-15451-5_3.
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AbstractThe main objective of this chapter is to provide a comprehensive and intuitive introduction to MRI gradient coil related PNS modeling with human body models. We will present the fundamental concepts and analytical processes behind gradient coil-induced peripheral nerve stimulation (PNS) modeling and also show some new results of our work. We first describe the process of performing electromagnetic simulation of a gradient coil, the neurodynamic simulation of nerves, and the gradient coil design. Then, we present improvements of two existing human body models by adding more nerve trajectories in the head and upper body to reduce the discrepancies between the simulated and measured results for PNS thresholds in head gradient coils. Further, we apply the modified human body models to analyze three folded and non-folded gradient coils and reveal the relationship between the eddy current flow in the human body and the gradient coil wire pattern and its impact on the PNS. We also show the connection between concomitant fields and PNS and assess the accuracy of PNS calculations in human body models with simplified tissue properties. Finally, we give our thoughts on the future direction of this work.
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Roelens, Ben, and Dominik Bork. "An Evaluation of the Intuitiveness of the PGA Modeling Language Notation." In Enterprise, Business-Process and Information Systems Modeling, 395–410. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-49418-6_27.
Full textConference papers on the topic "PNA Probes"
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Regonda, Suresh, Lisa Spurgin, and Walter Hu. "Ultrasensitive electronic detection of DNA using Si nanograting FETs coated with PNA probes." In 2013 IEEE 13th International Conference on Nanotechnology (IEEE-NANO). IEEE, 2013. http://dx.doi.org/10.1109/nano.2013.6720911.
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Bethge, Lucas, and Oliver Seitz. "New cyanine dyes as base surrogates in peptide nucleic acid (PNA): extending the utility of forced intercalation probes (FIT-probes)." In XIVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2008. http://dx.doi.org/10.1135/css200810317.
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Zhang, Pengfei, Aniruddha Kaushik, Kuangwen Hsieh, and Tza-Huei lJeff' Wang. "DropPNA-GO: A Single-cell Uropathogen Sensor Based on PNA Probes and Graphene Oxide in Picoliter Droplets." In 2020 IEEE 15th International Conference on Nano/Micro Engineered and Molecular System (NEMS). IEEE, 2020. http://dx.doi.org/10.1109/nems50311.2020.9265521.
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Baker, J. B., M. P. McGrogan, C. Simonsen, R. L. Gronke, and B. W. Festoff. "STRUCTURE AND PROPERTIES OF PROTEASE NEXIN I." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644765.
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Human foreskin fibroblasts secrete several different serine protease inhibitors which differ in size and protease specificities. These proteins, called protease nexins (PNs) all form SDS-resistant complexes with their protease targets. Fibroblast surface receptors recognize the protease-PN complexes and mediate their delivery to lysosomes. PNI is a 45 kilodalton glycoprotein that rapidly inhibits several arg or lys-specific proteases including trypsin, thrombin, and urokinase (k assoc.∼ 4×l06,∼ 6×105 and ∼ 2×105, m−1s−1 respectively). Like antithrombin III, PNI binds heparin and inhibits thrombin at a vastly accelerated rate in the presence of this glycoaminoglycan. Immunofluorescence studies show that in addition to secreting PNI foreskin fibroblasts carry this inhibitor on their surfaces. PNI cDNA has been cloned and sequenced. A mixed oligonucleotide probe derived from PNI N-terminal sequence was used to probe a foreskin fibroblast cDNA library constructed with λGT10. Identification of PNI cDNAs has been verified by sequencing and by expressing active PNI protein in mammalian cells. The full amino acid sequence of PNI, deduced from cDNA sequencing, is 392 residues long and has 30% homology to antithrombin III. An arg-ser pair 32 residues from the C-terminus of the inhibitor is proposed as the reactive center P1-P1 residues. In the hinge region a lys residue is present in a position occupied by a ginor glu residue in other serpins. PNI mRNA exists in 2 slightly different forms:One (αPNI) yields a thr-arg-ser sequence wherethe other βPNI) yields a thr-thr-gly-ser sequence. The presence of the appropriate splice acceptor sites in the genome indicates that these forms are generated from a single gene by alternative splicing. Expressed aPNI and 0PNI proteins both bind thrombin and urokinase. In foreskin fibroblaststhe α form of PNI mRNA predominates over the β form by about 2:1. In foreskin fibroblast cultures secreted PNI inhibits the mitogenic response to thrombin and regulate secreted urokinase. Purified PNI added to human fibrosarcoma (HT1080) cells inhibitsthe tumor cell-mediated destruction of extracellular matrix and transiently, but dramatically, inhibits tumor cell growth. PNI or PNI-like inhibitors may function at multiple physiological sites. The β form of PNI is virtually identical to a glia-derived neurite promoting factor, the cDNA for which has been recently cloned and sequenced by Gloor et al (1). The neurite outgrowth activity of PNI may result from inhibition of a thrombin-like protease that is associated with neurons, since a number of thrombin inhibitors stimulate neurite extension. Recent immunofluoresence experiments, carried out with D. Hantai (Inserm; Paris) demonstrate that anti-PNI antibody intensely stains neuromuscular synapses. In addition, a PNI-like inhibitor is associated with platelets. At low (0.5 nM <) 125I-thrombin concentrations formation of 125I-thrombin-platelet PNI complexes accounts for most of the specific binding of 125I-thrombin to platelets (2). Although the platelet-associated form of PNI is electrophoretically and immunologically indistinguishable from fibroblast PNI, it does not bind urokinase, suggesting that it may be distinct.(1) Gloor, S., K. Odink, J. Guenther, H. Nick, and D. Monard. (1986) Cell 47:687-693.(2) Gronke, R.S., B.L. Bergman, and J.B. Baker. (1987) J. Biol. Chem. (in press)
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Charbonnel, Corinne. "Post-AGB Stars and PNe: Crucial Probes of Stellar Nucleosynthesis." In PLANETARY NEBULAE AS ASTRONOMICAL TOOLS: International Conference on Planetary Nebulae as Astronomical Tools. AIP, 2005. http://dx.doi.org/10.1063/1.2146246.
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Segura, Luis Javier, Christian Narváez Muñoz, Chi Zhou, and Hongyue Sun. "Sketch-Based Tensor Decomposition for Non-Parametric Monitoring of Electrospinning Processes." In ASME 2020 15th International Manufacturing Science and Engineering Conference. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/msec2020-8367.
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Abstract Electrospinning is a promising process to fabricate functional parts from macrofibers and nanofibers of bio-compatible materials including collagen, polylactide (PLA), and polyacrylonitrile (PAN). However, the functionality of the produced parts highly rely on quality, repeatability, and uniformity of the electrospun fibers. Due to the variations in material composition, process settings, and ambient conditions, the process suffers from large variations. In particular, the fiber formation in the stable regime (i.e., Taylor cone and jet) and its propagation to the substrate plays the most significant role in the process stability. This work aims to designing a fast process monitoring tool from scratch for monitoring the dynamic electrospinning process based on the Taylor cone and jet videos. Nevertheless, this is challenging since the videos are of high frequency and high dimension, and the monitoring statistics may not have a parametric distribution. To achieve this goal, a framework integrating image analysis, sketch-based tensor decomposition, and non-parametric monitoring, is proposed. In particular, we use Tucker tensor-sketch (Tucker-TS) based tensor decomposition to extract the sparse structure representations of the videos. Additionally, the extracted monitoring variables are non-normally distributed, hence non-parametric bootstrap Hotelling T2 control chart is deployed to handle this issue during the monitoring. The framework is demonstrated by electrospinning a PAN-based polymeric solution. Finally, it is demonstrated that the proposed framework, which uses Tucker-TS, largely outperformed the computational speed of the alternating least squares (ALS) approach for the Tucker tensor decomposition, i.e., Tucker-ALS, in various anomaly detection tasks while keeping the comparable anomaly detection accuracy.
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Ham, Seaung Lok, and Nojun Kwak. "Boosted-PCA for binary classification problems." In 2012 IEEE International Symposium on Circuits and Systems - ISCAS 2012. IEEE, 2012. http://dx.doi.org/10.1109/iscas.2012.6271455.
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Park, Young H. "Stable Evaluation of Probabilistic Constraint in Reliability-Based Design Optimization for Large Deformation Problem." In ASME 2001 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2001. http://dx.doi.org/10.1115/detc2001/dac-21112.
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Abstract In this paper, Reliability-Based Design Optimization (RBDO) is carried out using two distinct ways, the Reliability Index Approach (RIA) and the Performance Measure Approach (PMA). It has been theoretically explained that RIA shows instability but PMA is stable and efficient in identifying a probabilistic failure mode in the RBDO process. The PMA is compared to RIA with regard to the stable evaluation of a probabilistic constraint in the RBDO using a large deformation problem. In addition, an efficient Design Sensitivity Analysis (DSA) method is developed to support reliability analysis and reliability-based optimization for a hyper-elastic structure with factional contact using a meshfree method. A numerical result is presented to demonstrate the comparative study between RIA and PMA.
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Okura, Masayuki, Shinya Takahashi, Takuma Kobayashi, Hikaru Saijo, and Takeo Takahashi. "Improvement of Impact Strength of Polyglycolic Acid for Self-Degradable Tools for Low-Temperature Wells." In SPE Middle East Unconventional Resources Conference and Exhibition. SPE, 2015. http://dx.doi.org/10.2118/spe-172969-ms.
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Abstract Recent increases in the stage count of hydraulic fracturing has increased the time and cost for well completion. Simplifying time-consuming processes is crucial for economic success. The use of degradable materials for components of downhole tools has several advantages, such as eliminating or simplifying the recovery process of the tools. Polyglycolic acid (PGA), a hydrolyzable polymer, is a suitable material for these components. PGA has already been used in frac balls because of its high mechanical strength and appropriate degradation characteristics. However, in low-temperature wells close to the glass transition temperature of PGA, there are problems with tool breakage during installation or stimulation because of the changes in the mechanical properties of PGA at low temperatures. This paper focuses on the improvement of the impact strength of PGA. A study of modifiers identified the additives that are highly compatible with PGA. Morphological studies of mixtures showed finely dispersed additive domains within a PGA matrix. The impact strength of the mixture was twice as high as that of neat PGA. A formulation was identified that optimized the impact strength while retaining degradability, processability, and machinability similar to that of neat PGA. The improvement of the impact strength broadens the range of applications that PGA tooling is suitable for and helps to reduce the cost and time of the well completion process.
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Ma, Ming, and Owen F. Hughes. "Permanent Means of Access Structural Design Using Multi-Objective Optimization." In ASME 2011 30th International Conference on Ocean, Offshore and Arctic Engineering. ASMEDC, 2011. http://dx.doi.org/10.1115/omae2011-49259.
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Permanent means of access (PMA) of oil tankers and bulk carries consists of a wide platform for walk through inspection. Since PMA structures have a tall web plate, they are vulnerable to elastic tripping. A previous paper [1] proposed a Rayleigh-Ritz method to analyze elastic tripping behavior of PMA structures. The method is parametric formulated, mesh free, computational efficient, and is able to predict both the flange plate critical tripping stress as well as the web plate local buckling stress; therefore the solution process is suitable for design space exploration. In this paper, multi-objective optimization methods are used to determine the Pareto solutions of a PMA structure based on the proposed tripping algorithm. The objective is to solve a design problem aimed at simultaneously minimizing the weight of a PMA structure and maximizing its critical buckling stress. Three multi-objective methods, Pareto Simulated Annealing (PSA), Ulungu Multi-objective Simulated Annealing (UMOSA) and Multi-objective Genetic Algorithm (MOGA) are presented for a case study. The numerical results show that all three methods can efficiently and effectively solve such optimization problems within a short search time. The critical buckling stress of the final optimal designs is validated by the linear and non-linear buckling analysis of NX-NASTRAN [2].
Reports on the topic "PNA Probes"
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Balthasar, Andreas, Frédéric Varone, and Daniel Meierhans. Synthèse thématique «Acceptation» du PNR «Energie». Swiss National Science Foundation (SNSF), June 2019. http://dx.doi.org/10.46446/publication_pnr70_pnr71.2019.1.fr.
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Que faut-il pour que les Suissesses et les Suisses changent leur comportement de consommation? Qu’est-ce qui est déterminant pour le soutien des technologies et des projets d’infrastructure? Le PNR Énergie a identifié de nombreux facteurs d’acceptation. Cette synthèse les consolide et va jusqu’à recommander des actions concrètes.
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Guidati, Gianfranco, and Domenico Giardini. Synthèse conjointe «Géothermie» du PNR «Energie». Swiss National Science Foundation (SNSF), February 2020. http://dx.doi.org/10.46446/publication_pnr70_pnr71.2020.4.fr.
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La géothermie de faible profondeur avec des pompes à chaleur correspond à l’état actuel de la technique et est déjà largement répandue en Suisse. Au sein du futur système énergétique, la géothermie de moyenne à grande profondeur (1 à 6 km) devrait également jouer un rôle important, notamment en matière de fourniture de chaleur pour les bâtiments et les process industriels. Cette forme d’utilisation de la chaleur géothermique nécessite un sous-sol bien perméable, permettant à un fluide – généralement de l’eau – d’engranger la chaleur naturellement présente dans la roche et de la transporter jusqu’à la surface. Dans les roches sédimentaires, cette condition est généralement vérifiée du fait de la structure naturelle, tandis que dans les granites et les gneiss la perméabilité doit être générée artificiellement par injection d’eau. La chaleur ainsi récupérée augmente au fur et à mesure de la profondeur de forage : la température souterraine atteint environ 40°C à 1 km de profondeur et environ 100°C à 3 km de profondeur. Pour entraîner une turbine à vapeur en vue de produire de l’électricité, des températures supérieures à 100°C sont nécessaires. Étant donné que cela implique de forer à des profondeurs de 3 à 6 km, le risque de sismicité induite augmente en conséquence. Le sous-sol peut également servir à stocker de la chaleur ou des gaz, par exemple de l’hydrogène ou du méthane, ou encore à enfouir de façon permanente du CO2. À cet effet, les mêmes exigences que pour l’extraction de chaleur doivent être vérifiées et le réservoir doit en outre être surmonté d’une couche étanche, empêchant le gaz de s’échapper. Le projet conjoint « Énergie hydroélectrique et géothermique » du PNR « Énergie » était avant tout consacré à la question de savoir où en Suisse trouver des couches de sol appropriées, répondant de manière optimale aux exigences des différentes utilisations. Un deuxième grand axe de recherche concernait les mesures visant à réduire la sismicité induite par les forages profonds et les dommages aux structures qui en résultent. Par ailleurs, des modèles et des simulations ont été élaborés dans le but de mieux comprendre les processus souterrains qui interviennent dans la mise en œuvre et l’exploitation des ressources géothermiques. En résumé, les résultats de recherche montrent que la Suisse jouit de bonnes conditions pour l’utilisation de la géothermie de moyenne profondeur (1-3 km), tant pour le parc de bâtiments que pour les processus industriels. L’optimisme est également de mise en ce qui concerne le stockage saisonnier de chaleur et de gaz. Le potentiel de stockage définitif de CO2 dans des quantités pertinentes s’avère en revanche plutôt limité. Concernant la production d’électricité à partir de la chaleur issue de la géothermie profonde (> 3 km), il n’existe pas encore de certitude définitive quant à l’importance du potentiel économiquement exploitable du sous-sol. Des installations de démonstration exploitées industriellement sont absolument nécessaires à cet égard, afin de renforcer l’acceptation par la population et les investisseurs.
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Morgan, Lozev, and Spencer. L52051 Further Investigation of AUT Defect Detection and Sizing. Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), March 2005. http://dx.doi.org/10.55274/r0011327.
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The objective of the work was to improve the reliability of detection and the accuracy of defect size measurement for defects in mechanised girth welds when using automated ultrasonic testing (AUT) methods. By amalgamating data from two previous studies in a single database the intention was to quantify the reliability of detection and accuracy of sizing for the different types of weld defects encountered in practice. Through the improved understanding of the impact of defect vagaries on ultrasonic signal responses the work intended to point the way to more robust procedures. The report concludes that unusual defect/signal types can often be identified, so that a wider error margin can be used for the more common defect types. Time of Flight Diffraction (ToFD) sizing is not so error-prone as amplitude-based methods and should be used wherever the signal allows. Where a Phased Array (PA) system is used, separate ToFD probes are advantageous. PA systems also allow the application of electronic sectorial scanning (s-scan), which can give good size estimates, using the same probes as for normal linear scanning.
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Morrison, Mark, Joshuah Miron, Edward A. Bayer, and Raphael Lamed. Molecular Analysis of Cellulosome Organization in Ruminococcus Albus and Fibrobacter Intestinalis for Optimization of Fiber Digestibility in Ruminants. United States Department of Agriculture, March 2004. http://dx.doi.org/10.32747/2004.7586475.bard.
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Improving plant cell wall (fiber) degradation remains one of the highest priority research goals for all ruminant enterprises dependent on forages, hay, silage, or other fibrous byproducts as energy sources, because it governs the provision of energy-yielding nutrients to the host animal. Although the predominant species of microbes responsible for ruminal fiber degradation are culturable, the enzymology and genetics underpinning the process are poorly defined. In that context, there were two broad objectives for this proposal. The first objective was to identify the key cellulosomal components in Ruminococcus albus and to characterize their structural features as well as regulation of their expression, in response to polysaccharides and (or) P AA/PPA. The second objective was to evaluate the similarities in the structure and architecture of cellulosomal components between R. albus and other ruminal and non-ruminal cellulolytic bacteria. The cooperation among the investigators resulted in the identification of two glycoside hydrolases rate-limiting to cellulose degradation by Ruminococcus albus (Cel48A and CeI9B) and our demonstration that these enzymes possess a novel modular architecture specific to this bacterium (Devillard et al. 2004). We have now shown that the novel X-domains in Cel48A and Cel9B represent a new type of carbohydrate binding module, and the enzymes are not part of a ceiluiosome-like complex (CBM37, Xu et al. 2004). Both Cel48A and Cel9B are conditionally expressed in response to P AA/PPA, explaining why cellulose degradation in this bacterium is affected by the availability of these compounds, but additional studies have shown for the first time that neither PAA nor PPA influence xylan degradation by R. albus (Reveneau et al. 2003). Additionally, the R. albus genome sequencing project, led by the PI. Morrison, has supported our identification of many dockerin containing proteins. However, the identification of gene(s) encoding a scaffoldin has been more elusive, and recombinant proteins encoding candidate cohesin modules are now being used in Israel to verify the existence of dockerin-cohesin interactions and cellulosome production by R. albus. The Israeli partners have also conducted virtually all of the studies specific to the second Objective of the proposal. Comparative blotting studies have been conducted using specific antibodies prepare against purified recombinant cohesins and X-domains, derived from cellulosomal scaffoldins of R. flavefaciens 17, a Clostridium thermocellum mutant-preabsorbed antibody preparation, or against CbpC (fimbrial protein) of R. albus 8. The data also suggest that additional cellulolytic bacteria including Fibrobacter succinogenes S85, F. intestinalis DR7 and Butyrivibrio fibrisolvens Dl may also employ cellulosomal modules similar to those of R. flavefaciens 17. Collectively, our work during the grant period has shown that R. albus and other ruminal bacteria employ several novel mechanisms for their adhesion to plant surfaces, and produce both cellulosomal and non-cellulosomal forms of glycoside hydrolases underpinning plant fiber degradation. These improvements in our mechanistic understanding of bacterial adhesion and enzyme regulation now offers the potential to: i) optimize ruminal and hindgut conditions by dietary additives to maximize fiber degradation (e.g. by the addition of select enzymes or PAA/PPA); ii) identify plant-borne influences on adhesion and fiber-degradation, which might be overcome (or improved) by conventional breeding or transgenic plant technologies and; iii) engineer or select microbes with improved adhesion capabilities, cellulosome assembly and fiber degradation. The potential benefits associated with this research proposal are likely to be realized in the medium term (5-10 years).
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Habert, Guillaume, and Francesco Pittau. Synthèse conjointe «Constructions durables en béton» du PNR «Energie». Swiss National Science Foundation (SNSF), February 2020. http://dx.doi.org/10.46446/publication_pnr70_pnr71.2020.5.fr.
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À l’échelle de leur cycle de vie, toutes les constructions de Suisse – c’est-à-dire les bâtiments, les routes, les ouvrages d’infrastructure, etc. – représentent environ 50 % des besoins d’énergie finale de la Suisse. De plus, elles sont responsables de plus de 30 % des émissions de CO2, un gaz à effet de serre. Au cours des dernières décennies, les besoins énergétiques et les émissions de CO2 liées à l’utilisation des bâtiments ont fortement diminué. L’énergie grise contenue dans les bâtiments et les émissions de CO2 issues de la production des matériaux de construction, de la rénovation et du démantèlement sont cependant restées élevées. Le potentiel d’amélioration est considérable à cet égard. Le projet conjoint « Béton à basse énergie » jette les fondements d’une transformation de l’industrie de la construction en un secteur durable. Il se concentre notamment sur le béton en tant que matériau de construction engendrant des niveaux particulièrement élevés d’énergie grise et d’émissions de CO2. Les résultats de ce projet conjoint sont résumés et interprétés dans la présente synthèse « Constructions durables en béton ». Le projet conjoint s’est avant tout concentré sur les objectifs suivants : Réduire les émissions de CO2 et l’énergie grise par une diminution drastique du clinker dans le ciment. Réduire l’énergie grise en remplaçant l’acier d’armature et de précontrainte dans les structures en béton par du bois et des matériaux de synthèse. Allonger la durée de vie des ouvrages grâce à une surveillance professionnelle et des mesures de rénovation adéquates, ce qui réduit les moyennes annuelles d’énergie grise et d’émissions de CO2. Les recherches montrent que les émissions de CO2 causées par le béton et les structures en béton peuvent être réduites d’un facteur 4 et l’énergie grise mobilisée d’un facteur 3.
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Baker, Anthony P. Proper Role of Special Operations Forces in the Pan Sahel Region of Africa. Fort Belvoir, VA: Defense Technical Information Center, October 2006. http://dx.doi.org/10.21236/ada463309.
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Lambert, D. P., C. S. Boley, and R. A. Jacobs. Large Precipitate Hydrolysis Aqueous (PHA) Heel Process Development for the Defense Waste Processing Facility (DWPF). Office of Scientific and Technical Information (OSTI), June 1998. http://dx.doi.org/10.2172/656910.
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Melanie, Haupt, and Hellweg Stefanie. Synthèse du projet conjoint du PNR 70 «Gestion des déchets pour soutenir la transition énergétique (wastEturn)». Swiss National Science Foundation (SNSF), January 2020. http://dx.doi.org/10.46446/publication_pnr70_pnr71.2020.2.fr.
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Les déchets renferment de grandes quantités d’énergie aussi bien directe qu’indirecte. Les déchets ménagers incinérés chaque année en Suisse représentent une valeur énergétique de quelque 60 pétajoules. L’énergie qui en est directement tirée couvre environ 4 % des besoins en énergie finale. Le plus gros potentiel en matière de gestion des déchets réside cependant dans le recyclage des matériaux, afin de leur donner une seconde vie et d’éviter ainsi indirectement la production énergivore de matières premières Pour optimiser la contribution de la gestion des déchets à la transition énergétique, il s’agit dans un premier temps d’améliorer la transparence et la documentation des flux de matières et d’argent et, sur cette base, de hiérarchiser l’impact énergétique des diverses solutions de valorisation et d’élimination. Les catégories de déchets identifiées comme ayant le plus grand potentiel d’amélioration sont le papier, le carton ainsi que le plastique. En ce qui concerne le papier et le carton, les énormes quantités traitées promettent des résultats significatifs. À l’exception des bouteilles en PET, le tri sélectif des plastiques usagés demeure encore peu développé. Un potentiel d’optimisation notable a également été identifié au niveau de l’efficacité énergétique des usines d’incinération. Pour permettre une utilisation plus efficace de la chaleur générée par les usines d’incinération d’ordures ménagère (UIOM), les consommateurs de vapeur et d’énergie thermique doivent toutefois être implantés à proximité. Un facteur décisif pour progresser vers une gestion des déchets plus efficace sur le plan énergétique est la collaboration entre les nombreux acteurs du secteur à l’échelle fédérale. Ceux-ci doivent d’une part mieux s’organiser tout au long de la chaîne de création de valeur et d’autre part tirer profit de la marge de manœuvre que procure la souplesse du fédéralisme pour tester différentes approches.
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Ferguson, Matthew, and Marin Kress. AIS data case study : dredge material placement site evaluation in Frederick Sound near Petersburg, Alaska. Engineer Research and Development Center (U.S.), May 2022. http://dx.doi.org/10.21079/11681/44141.
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The purpose of this Coastal and Hydraulics Laboratory Technical Note (CHETN) is to present an application of historic vessel position information acquired through the Automatic Identification System (AIS), which provides geo-referenced and time-stamped vessel position information. The US Army Corps of Engineers, Alaska District (POA), needed to evaluate potential placement sites for dredged material near Petersburg, AK, and possible impacts to navigation were considered as part of the evaluation process.
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Rusk, Todd, Ryan Siegel, Linda Larsen, Tim Lindsey, and Brian Deal. Technical and Financial Feasibility Study for Installation of Solar Panels at IDOT-owned Facilities. Illinois Center for Transportation, August 2021. http://dx.doi.org/10.36501/0197-9191/21-024.
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The Smart Energy Design Assistance Center assessed the administrative, technical, and economic aspects of feasibility related to the procurement and installation of photovoltaic solar systems on IDOT-owned buildings and lands. To address administrative feasibility, we explored three main ways in which IDOT could procure solar projects: power purchase agreement (PPA), direct purchase, and land lease development. Of the three methods, PPA and direct purchase are most applicable for IDOT. While solar development is not free of obstacles for IDOT, it is administratively feasible, and regulatory hurdles can be adequately met given suitable planning and implementation. To evaluate IDOT assets for solar feasibility, more than 1,000 IDOT sites were screened and narrowed using spatial analytic tools. A stakeholder feedback process was used to select five case study sites that allowed for a range of solar development types, from large utility-scale projects to small rooftop systems. To evaluate financial feasibility, discussions with developers and datapoints from the literature were used to create financial models. A large solar project request by IDOT can be expected to generate considerable attention from developers and potentially attractive PPA pricing that would generate immediate cash flow savings for IDOT. Procurement partnerships with other state agencies will create opportunities for even larger projects with better pricing. However, in the near term, it may be difficult for IDOT to identify small rooftop or other small on-site solar projects that are financially feasible. This project identified two especially promising solar sites so that IDOT can evaluate other solar site development opportunities in the future. This project also developed a web-based decision-support tool so IDOT can identify potential sites and develop preliminary indications of feasibility. We recommend that IDOT begin the process of developing at least one of their large sites to support solar electric power generation.