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Daems, E. |
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Title |
Shaping up oligonucleotides : aptamer-target recognition investigated by native mass spectrometry |
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Doctoral thesis |
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Year |
2021 |
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235 p. |
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Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application. |
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Most recent IF: NA |
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UA @ admin @ c:irua:178116 |
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8517 |
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De Cocker, P.; Bessiere, Y.; Hernandez-Raquet, G.; Dubos, S.; Mercade, M.; Sun, X.Y.; Mozo, I.; Barillon, B.; Gaval, G.; Caligaris, M.; Martin Ruel, S.; Vlaeminck, S.E.; Sperandio, M. |
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Title |
Short and long term effect of decreasing temperature on anammox activity and enrichment in mainstream granular sludge process |
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P1 Proceeding |
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2017 |
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4 |
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50-54
T2 - Frontiers International Conference on W |
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P1 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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This study investigates the impact of lower temperature on short term and long term (down to 10 degrees C) on a completely anoxic anammox granular sludge process. This is the first time granular sludge Anammox is operated in pure anoxic condition in SBR and at low temperature. Conversion performance, kinetic parameters, sludge characteristics and microbial community were analyzed. |
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2017-05-04 |
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no |
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UA @ admin @ c:irua:151120 |
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8519 |
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Koutsenogii, P.K.; van Malderen, H.; Hoornaert, S.; Van Grieken, R.; Koutsenogii, K.P.; Boufetov, N.; Makarov, V.I.; Smoljakov, B.S.; Nemirovski, A.M.; Osipova, L.P.; Krjukov, J.A.; Ivakin, E.A.; Posukh, O.L.; Bronstein, E.L. |
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Title |
Siberian Haze: complex study of aerosols in Siberia |
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A3 Journal article |
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1996 |
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Optics of the atmosphere and ocean |
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9 |
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712-719 |
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A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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UA @ admin @ c:irua:14652 |
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8521 |
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Zhang, Q.; De Clippeleir, H.; Al-Omari, A.; Wett, B.; Vlaeminck, S.E.; Murthy, S. |
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Sidestream deammonification on thermal hydrolysis process digestate : strategies to overcome nitritation inhibition |
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P3 Proceeding |
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2015 |
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11 p.
T2 - IWA Nutrient Removal and Recovery 2015: |
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P3 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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UA @ admin @ c:irua:151147 |
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8522 |
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Piñera Hernández, I. |
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Simulation of atom displacements induced by photons and electrons in solids |
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Doctoral thesis |
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2014 |
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137 p. |
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Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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UA @ admin @ c:irua:116687 |
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8526 |
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van Malderen, H.; Van Grieken, R.; Khodzher, T.V.; Grachev, M.; Bufetov, N.S.; Koutsenogii, K.P. |
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Single particle analysis of aerosols from Siberia |
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P3 Proceeding |
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1994 |
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Proceedings of the Russian-Ukrainian-Austrian-German Analytical Symposium |
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P3 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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UA @ admin @ c:irua:9527 |
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8530 |
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Török, S.; Sandor, S.; Xhoffer, C.; Van Grieken, R.; Meszaros, E.; Molnar, A. |
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Single particle analysis of Hungarian background aerosol |
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A3 Journal article |
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1992 |
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Idojaras: quarterly journal of the Hungarian Meteorological Service |
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96 |
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223-233 |
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A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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no |
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Call Number |
UA @ admin @ c:irua:2847 |
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8532 |
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Author |
de Bock, L.A.; Van Grieken, R.E. |
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Title |
Single particle analysis techniques |
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H3 Book chapter |
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1999 |
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243-275
T2 - Analytical chemistry of aerosols / Sp |
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H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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UA @ admin @ c:irua:27599 |
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8534 |
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Jambers, W.; Van Grieken, R. |
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Single particle characterisation of inorganic North Sea suspensions |
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P3 Proceeding |
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1996 |
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P3 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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UA @ admin @ c:irua:14670 |
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8537 |
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Vlaeminck, S.E.; Courtens, E.N.P.; Vandekerckhove, T.G.L.; Boon, N. |
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Some like it hot : perspectives for thermophilic nitrogen removal |
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P3 Proceeding |
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2015 |
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4 p.
T2 - IWA Nutrient Removal and Recovery 2015: |
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P3 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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no |
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UA @ admin @ c:irua:151145 |
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8552 |
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Kuczumow, A.; Vekemans, B.; Schalm, O.; Vincze, L.; Dorriné, W.; Gysels, K.; Van Grieken, R. |
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Some new applications of auxiliary signals in X-ray fluorescence and electron microprobe analysis |
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P1 Proceeding |
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1999 |
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197-201
T2 - Proceedings of the European Conferenc |
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P1 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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000081658400032 |
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UA @ admin @ c:irua:24716 |
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8553 |
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Caratelli, D.; Gielis, J.; Ricci, P.E.; Tavkhelidze, I. |
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Some properties of “bulky” links, generated by Generalized Möbius Listing's bodies GML4n |
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P3 Proceeding |
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2013 |
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P3 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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UA @ admin @ c:irua:108672 |
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8555 |
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Van Grieken, R.; Kontozova, V.; Godoi, R.H.M.; Spolnik, Z.; Worobiec, A.; Deutsch, F.; Bencs, L. |
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Some studies of the effect of indoor and outdoor pollutants on cultural heritage items |
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P3 Proceeding |
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2005 |
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P3 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP) |
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UA @ admin @ c:irua:57632 |
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8556 |
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Author |
Török, S.; Szandor, S.; Xhoffer, C.; Van Grieken, R. |
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Source apportionment of individual aerosol particles at Hungarian background stations |
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1993 |
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Abbreviated Journal |
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32-331
T2 - Photo-oxidants: precursors and product |
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H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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UA @ admin @ c:irua:6265 |
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8559 |
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Author |
Vos, L.; Van Grieken, R. |
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Spark source mass spectrometry for trace analysis of diverse biological matrices |
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1983 |
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Abbreviated Journal |
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303-306
T2 - Mass spectrometry advances 1982 / Sch |
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H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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UA @ admin @ c:irua:117486 |
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8564 |
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Author |
Bencs, L.; Ravindra, K.; Van Grieken, R. |
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Title |
Spatial and temporal variation of anthropogenic palladium in the environment |
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H3 Book chapter |
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Year |
2006 |
Publication |
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Abbreviated Journal |
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Volume |
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Issue |
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Pages |
433-454
T2 - Palladium emissions in the environmen |
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Keywords |
H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Additional Links |
UA library record |
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Impact Factor |
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Open Access |
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Notes |
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Approved |
no |
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Call Number |
UA @ admin @ c:irua:54922 |
Serial |
8565 |
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Permanent link to this record |
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Author |
Ravindra, K.; Wauters, E.; Van Grieken, R. |
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Title |
Spatial and temporal variations in particulate Polycyclic Aromatic Hydrocarbon (PAH) levels over Menen (Belgium) and their relation with air mass trajectories |
Type |
H3 Book chapter |
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Year |
2007 |
Publication |
|
Abbreviated Journal |
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Volume |
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Issue |
|
Pages |
838-841
T2 - Air pollution modeling and its applic |
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Keywords |
H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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ISBN |
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Additional Links |
UA library record |
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Impact Factor |
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Times cited |
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Open Access |
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Notes |
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Approved |
no |
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|
Call Number |
UA @ admin @ c:irua:65571 |
Serial |
8566 |
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Permanent link to this record |
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Author |
Bruynseels, F.; Van Grieken, R. |
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Title |
Speciation and distribution of sulfur and nitrogen in individual aerosol particles measured by LAMMA |
Type |
P3 Proceeding |
|
Year |
1984 |
Publication |
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Abbreviated Journal |
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Volume |
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Issue |
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Pages |
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Keywords |
P3 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Edition |
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ISSN |
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ISBN |
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Additional Links |
UA library record |
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Impact Factor |
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Times cited |
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Open Access |
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|
Notes |
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Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:117494 |
Serial |
8568 |
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Permanent link to this record |
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Author |
Szalóki, I.; Ro, C.-U.; Osán, J.; de Hoog, J.; Van Grieken, R. |
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|
Title |
Speciation and surface analysis of single particles using electron-excited X-ray emission spectrometry |
Type |
H3 Book chapter |
|
Year |
2004 |
Publication |
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Abbreviated Journal |
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|
Volume |
|
Issue |
|
Pages |
569-592
T2 - X-ray spectrometry: recent technologi |
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Keywords |
H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
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Wos |
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Series Issue |
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Edition |
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|
|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
|
|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:43878 |
Serial |
8570 |
|
Permanent link to this record |
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Author |
Injuk, J.; Van Grieken, R.; Blank, A.; Eksperiandova, L.; Buhrke, V. |
|
|
Title |
Specimen preparation |
Type |
H3 Book chapter |
|
Year |
2006 |
Publication |
|
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
411-432
T2 - Handbook of practical X-ray fluoresce |
|
|
Keywords |
H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
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Address |
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Series Issue |
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Edition |
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ISSN |
|
ISBN |
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Additional Links |
UA library record |
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|
Impact Factor |
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Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:58854 |
Serial |
8573 |
|
Permanent link to this record |
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Author |
Zhang, Q.; Vlaeminck, S.E.; DeBarbadillo, C.; Suzuki, R.; Kharkar, S.M.; Al-Omari, A.; Wett, B.; Chandran, K.; Murthy, S.; De Clippeleir, H. |
|
|
Title |
Startup strategies of deammonification reactors treating reject water from thermally hydrolyzed solids |
Type |
P3 Proceeding |
|
Year |
2017 |
Publication |
|
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
5 p.
T2 - WEFTEC.17, 30 September 4 October 2017, |
|
|
Keywords |
P3 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Edition |
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ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:151113 |
Serial |
8579 |
|
Permanent link to this record |
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Author |
Playford, K.; Colin, J.L.; Pacyna, J.M.; Pirrone, N.; Schulz, M.; Van Grieken, R.; Wrembel, Z. |
|
|
Title |
State-of-the-art and research needs for trace metals |
Type |
H3 Book chapter |
|
Year |
1998 |
Publication |
|
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
7-11
T2 - Sea-air exchange: processes and modellin |
|
|
Keywords |
H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
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Address |
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Wos |
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Series Issue |
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Edition |
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|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:20972 |
Serial |
8580 |
|
Permanent link to this record |
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|
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Author |
Van Grieken, R. |
|
|
Title |
Stof : begrippen, bronnen en analysmethoden |
Type |
P3 Proceeding |
|
Year |
1985 |
Publication |
|
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
|
|
|
Keywords |
P3 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
|
|
Abstract |
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Address |
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Wos |
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Series Issue |
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Edition |
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|
ISSN |
|
ISBN |
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Additional Links |
UA library record |
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|
Impact Factor |
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Times cited |
|
Open Access |
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|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:117501 |
Serial |
8582 |
|
Permanent link to this record |
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|
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Author |
Injuk, J.; de Bock, L.; Van Grieken, R. |
|
|
Title |
Structural heterogeneity within airborne particles |
Type |
H3 Book chapter |
|
Year |
1998 |
Publication |
|
Abbreviated Journal |
|
|
|
Volume |
|
Issue |
|
Pages |
173-202
T2 - Atmospheric particles / Harrison, R.M |
|
|
Keywords |
H3 Book chapter; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
|
|
Abstract |
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Address |
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Thesis |
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Place of Publication |
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Language |
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Wos |
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Publication Date |
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Series Title |
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Abbreviated Series Title |
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Series Issue |
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Edition |
|
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|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:20969 |
Serial |
8586 |
|
Permanent link to this record |
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Author |
de Araujo, J.L.B.; Munarin, F.F.; Farias, G.A.; Peeters, F.M.; Ferreira, W.P. |
|
|
Title |
Structure and reentrant percolation in an inverse patchy colloidal system |
Type |
A1 Journal article |
|
Year |
2017 |
Publication |
Physical Review E |
Abbreviated Journal |
|
|
|
Volume |
95 |
Issue |
6 |
Pages |
062606 |
|
|
Keywords |
A1 Journal article; Condensed Matter Theory (CMT) |
|
|
Abstract |
Two-dimensional systems of inverse patchy colloids modeled as disks with a central charge and having their surface decorated with oppositely pointlike charged patches are investigated using molecular dynamics simulations. The self-assembly of the patchy colloids leads to diverse ground state configurations ranging from crystalline arrangements of monomers to linear clusters, ramified linear clusters and to percolated configurations. Two structural phase diagrams are constructed: (1) as a function of the net charge and area fraction, and (2) as a function of the net charge and the range of the pair interaction potential. An interesting reentrant percolation transition is obtained as a function of the net charge of the colloids. We identify distinct mechanisms that lead to the percolation transition. |
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Corporate Author |
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Wos |
000404545700005 |
Publication Date |
2017-06-27 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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|
ISSN |
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ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
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Times cited |
5 |
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:152628 |
Serial |
8587 |
|
Permanent link to this record |
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Author |
Tavkhelidze, I.; Gielis, J. |
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|
Title |
Structure of the dm knives and process of cutting of GML(man) or GRT(man) bodies |
Type |
A3 Journal article |
|
Year |
2019 |
Publication |
Sn – 1512-0066 |
Abbreviated Journal |
|
|
|
Volume |
33 |
Issue |
|
Pages |
|
|
|
Keywords |
A3 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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Abstract |
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Address |
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Place of Publication |
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Wos |
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Series Issue |
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Edition |
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|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
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Times cited |
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Open Access |
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|
Notes |
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Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:164897 |
Serial |
8588 |
|
Permanent link to this record |
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|
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Author |
Grunert, O.; Robles Aguilar, A.A.; Hernandez-Sanabria, E.; Vandekerckhove, T.; Reheul, D.; Van Labeke, M.-C.; Vlaeminck, S.; Boon, N.; Jablonowski, N.D. |
|
|
Title |
Struvite and organic fertilizer impacting the rhizosphere microbial community, nutrient turnover and plant growth performance |
Type |
P3 Proceeding |
|
Year |
2016 |
Publication |
|
Abbreviated Journal |
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|
|
Volume |
|
Issue |
|
Pages |
12 p.
T2 - WEF/IWA Nutrient Removal and Recovery C |
|
|
Keywords |
P3 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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|
Abstract |
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Address |
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Corporate Author |
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Place of Publication |
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Wos |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:151135 |
Serial |
8589 |
|
Permanent link to this record |
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Author |
Muys, M.; Derese, S.; Verliefde, A.; Vlaeminck, S.E. |
|
|
Title |
Struvite solubilisation rates enable direct addition To single cell protein bioreactors |
Type |
P3 Proceeding |
|
Year |
2016 |
Publication |
|
Abbreviated Journal |
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|
Volume |
|
Issue |
|
Pages |
10 p.
T2 - WEF/IWA Nutrient Removal and Recovery C |
|
|
Keywords |
P3 Proceeding; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) |
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|
Abstract |
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Address |
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Wos |
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Series Editor |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:151129 |
Serial |
8590 |
|
Permanent link to this record |
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Author |
Samek, L.; Worobiec, A.; Spolnik, Z.; Van Grieken, R. |
|
|
Title |
Studia sezonowych zmian wewnetrznego składu powietrza atmosferycznego w kościołach zabytkowych w kontekście doboru i modyfikacji metod konserwacji obiektów zabytkowych |
Type |
H3 Book chapter |
|
Year |
2005 |
Publication |
|
Abbreviated Journal |
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|
|
Volume |
|
Issue |
|
Pages |
59-64
T2 - Technika jadrowa w przemyśle, medycynie |
|
|
Keywords |
H3 Book chapter; Laboratory Experimental Medicine and Pediatrics (LEMP); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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|
Abstract |
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Address |
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Thesis |
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Editor |
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Language |
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Wos |
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Publication Date |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
|
Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:53886 |
Serial |
8591 |
|
Permanent link to this record |
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|
|
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Author |
Cholewa, M.; Legge, G.J.F.; Eeckhaoudt, S.; Van Grieken, R. |
|
|
Title |
A study of aluminium-exposed fish using a scanning proton microprobe |
Type |
P3 Proceeding |
|
Year |
1994 |
Publication |
Proceedings of the Australian Conference on Nuclear Techniques of Analysis |
Abbreviated Journal |
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Volume |
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Issue |
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Pages |
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Keywords |
P3 Proceeding; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
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Address |
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Language |
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Wos |
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Publication Date |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
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Times cited |
|
Open Access |
|
|
|
Notes |
|
Approved |
no |
|
|
Call Number |
UA @ admin @ c:irua:9517 |
Serial |
8594 |
|
Permanent link to this record |