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2. External validation of the PAGE-B score for HCC risk prediction in people living with HIV/HBV coinfection

Author

Abela, I., Aebi-Popp, K., Anagnostopoulos, A., Battegay, M., Bernasconi, E., Braun, D.L., Bucher, H.C., Calmy, A., Cavassini, M., Ciuffi, A., Dollenmaier, G., Egger, M., Elzi, L., Fehr, J., Fellay, J., Furrer, H., Fux, C.A., Günthard, H.F., Hachfeld, A., Haerry, D., Hasse, B., Hirsch, H.H., Hoffmann, M., Hösli, I., Huber, M., Jackson-Perry, D., Kahlert, C.R., Kaiser, L., Keiser, O., Klimkait, T., Kouyos, R.D., Kovari, H., Kusejko, K., Labhardt, N., Leuzinger, K., de Tejada B, Martinez, Marzolini, C., Metzner, K.J., Müller, N., Nemeth, J., Nicca, D., Notter, J., Paioni, P., Pantaleo, G., Perreau, M., Rauch, A., Salazar-Vizcaya, L., Schmid, P., Speck, R., Stöckle, M., Tarr, P., Trkola, A., Wandeler, G., Weisser, M., Yerly, S., van der Valk, M., Geerlings, S.E., Goorhuis, A., Harris, V.C., Hovius, J.W., Lempkes, B., Nellen, F.J.B., van der Poll, T., Prins, J.M., Spoorenberg, V., van Vugt, M., Wiersinga, W.J., Wit, F.W.M.N., Bruins, C., van Eden, J., Hylkema-van den Bout, I.J., van Hes, A.M.H., Pijnappel, F.J.J., Smalhout, S.Y., Weijsenfeld, A.M., Back, N.K.T., Berkhout, B., Cornelissen, M.T.E., van Houdt, R., Jonges, M., Jurriaans, S., Schinkel, C.J., Wolthers, K.C., Zaaijer, H.L., Peters, E.J.G., van Agtmael, M.A., Autar, R.S., Bomers, M., Sigaloff, K.C.E., Heitmuller, M., Laan, L.M., van den Berge, M., Stegeman, A., Baas, S., Hage de Looff, L., van Arkel, A., Stohr, J., Wintermans, B., Pronk, M.J.H., Ammerlaan, H.S.M., de Munnik, E.S., Deiman, B., Jansz, A.R., Scharnhorst, V., Tjhie, J., Wegdam, M.C.A., van Eeden, A., Hoornenborg, E., Nellen, J., Alers, W., Elsenburg, L.J.M., Nobel, H., van Kasteren, M.E.E., Berrevoets, M.A.H., Brouwer, A.E., de Kruijf-van de Wiel, B.A.F.M., Adams, A., Rijkevoorsel, M. Pawels-van, Buiting, A.G.M., Murck, J.L., Rokx, C., Anas, A.A., Bax, H.I., van Gorp, E.C.M., de Mendonça Melo, M., van Nood, E., Nouwen, J.L., Rijnders, B.J.A., Schurink, C.A.M., Slobbe, L., de Vries-Sluijs, T.E.M.S., Bassant, N., van Beek, J.E.A., Vriesde, M., van Zonneveld, L.M., de Groot, J., van Kampen, J.J.A., Koopmans, M.P.G., Rahamat-Langendoen, J.C., Branger, J., Douma, R.A., Cents-Bosma, A.S., Duijf-van de Ven, C.J.H.M., Schippers, E.F., van Nieuwkoop, C., Geilings, J., van Winden, S., van der Hut, G., van Burgel, N.D., Leyten, E.M.S., Gelinck, L.B.S., Mollema, F., Wildenbeest, G.S., Nguyen, T., Groeneveld, P.H.P., Bouwhuis, J.W., Lammers, A.J.J., van Hulzen, A.G.W., Kraan, S., Kruiper, M.S.M., van der Bliek, G.L., Bor, P.C.J., Debast, S.B., Wagenvoort, G.H.J., Roukens, A.H.E., de Boer, M.G.J., Jolink, H., Lambregts, M.M.C., Scheper, H., Dorama, W., van Holten, N., Claas, E.C.J., Wessels, E., Hollander, J.G. den, El Moussaoui, R., Pogany, K., Brouwer, C.J., Heida-Peters, D., Mulder, E., Smit, J.V., Struik-Kalkman, D., van Niekerk, T., Pontesilli, O., van Tienen, C., Lowe, S.H., Lashof, A.M.L. Oude, Posthouwer, D., van Wolfswinkel, M.E., Ackens, R.P., Burgers, K., Elasri, M., Schippers, J., Havenith, T.R.A., van Loo, M., van Vonderen, M.G.A., Kampschreur, L.M., van Broekhuizen, M.C., S, Faber, Al Moujahid, A., Kootstra, G.J., Delsing, C.E., van der Burg-van de Plas, M., Scheiberlich, L., Kortmann, W., van Twillert, G., Renckens, R., Wagenaar, J., Ruiter-Pronk, D., van Truijen-Oud, F.A., Stuart, J.W.T. Cohen, Hoogewerf, M., Rozemeijer, W., Sinnige, J.C., Brinkman, K., van den Berk, G.E.L., Lettinga, K.D., de Regt, M., Schouten, W.E.M., Stalenhoef, J.E., Veenstra, J., Vrouenraets, S.M.E., Blaauw, H., Geerders, G.F., Kleene, M.J., Knapen, M., Kok, M., van der Meché, I.B., Toonen, A.J.M., Wijnands, S., Wttewaal, E., Kwa, D., van de Laar, T.J.W., van Crevel, R., van Aerde, K., Dofferhoff, A.S.M., Henriet, S.S.V., Hofstede, H.J.M. ter, Hoogerwerf, J., Richel, O., Albers, M., Grintjes-Huisman, K.J.T., de Haan, M., Marneef, M., McCall, M., Burger, D., Gisolf, E.H., Claassen, M., Hassing, R.J., Beest, G. ter, van Bentum, P.H.M., Gelling, M., Neijland, Y., Swanink, C.M.A., Velderman, M. Klein, van Lelyveld, S.F.L., Soetekouw, R., van der Prijt, L.M.M., van der Swaluw, J., Kalpoe, J.S., Wagemakers, A., Vahidnia, A., Lauw, F.N., Verhagen, D.W.M., van Wijk, M., Bierman, W.F.W., Bakker, M., van Bentum, R.A., van den Boomgaard, M.A., Kleinnijenhuis, J., Kloeze, E., Middel, A., Postma, D.F., Schenk, H.M., Stienstra, Y., Wouthuyzen-Bakker, M., Boonstra, A., de Jonge, H., Maerman, M.M.M., de Weerd, D.A., van Eije, K.J., Knoester, M., van Leer-Buter, C.C., Niesters, H.G.M., T.Mudrikova, Barth, R.E., Bruns, A.H.W., Ellerbroek, P.M., Hensgens, M.P.M., Oosterheert, J.J., Schadd, E.M., Verbon, A., van Welzen, B.J., Berends, H., Santen, B.M.G. Griffioen-van, de Kroon, I., Lunel, F.M. Verduyn, Wensing, A.M.J., Zaheri, S., Boyd, A.C., Bezemer, D.O., van Sighem, A.I., Smit, C., Hillebregt, M.M.J., Woudstra, T.J., Rutkens, T., Bergsma, D., Brétin, N.M., Lelivelt, K.J., van de Sande, L., van der Vliet, K.M. Visser.S.T., Paling, F., de Groot-Berndsen, L.G.M., van den Akker, M., Alexander, R., Bakker, Y., El Berkaoui, A., Bezemer-Goedhart, M., Djoechro, E.A., Groters, M., Koster, L.E., Lodewijk, C.R.E., Lucas, E.G.A., Munjishvili, L., Peeck, B.M., Ree, C.M.J., Regtop, R., van Rijk, A.F., Ruijs-Tiggelman, Y.M.C., Schnörr, P.P., Schoorl, M.J.C., Tuijn, E.M., Veenenberg, D.P., Witte, E.C.M., Bretin, N.M., Karpov, I., Losso, M., Lundgren, J., Rockstroh, J., Aho, I., Rasmussen, L.D., Novak, P., Pradier, C., Chkhartishvili, N., Matulionyte, R., Oprea, C., Kowalska, J.D., Begovac, J., Miró, J.M., Guaraldi, G., Paredes, R., Peters, L., Larsen, J.F., Neesgaard, B., Jaschinski, N., Fursa, O., Raben, D., Kristensen, D., Fischer, A.H., Jensen, S.K., Elsing, T.W., Gardizi, M., Mocroft, A., Phillips, A., Reekie, J., Cozzi-Lepri, A., Pelchen-Matthews, A., Roen, A., Tusch, E.S., Bannister, W., Bellecave, P., Blanco, P., Bonnet, F., Bouchet, S., Breilh, D., Cazanave, C., Desjardin, S., Gaborieau, V., Gimbert, A., Hessamfar, M., Lacaze-Buzy, L., Lacoste, D., Lafon, M.E., Lazaro, E., Leleux, O., Le Marec, F., Le Moal, G., Malvy, D., Marchand, L., Mercié, P., Neau, D., Pellegrin, I., Perrier, A., Petrov-Sanchez, V., Vareil, M.O., Wittkop, L., Bernard, N., Chaussade, D. Bronnimann H., Dondia, D., Duffau, P., Faure, I., Morlat, P., Mériglier, E., Paccalin, F., Riebero, E., Rivoisy, C., Vandenhende, M.A., Barthod, L., Dauchy, F.A., Desclaux, A., Ducours, M., Dutronc, H., Duvignaud, A., Leitao, J., Lescure, M., Nguyen, D., Pistone, T., Puges, M., Wirth, G., Courtault, C., Camou, F., Greib, C., Pellegrin, J.L., Rivière, E., Viallard, J.F., Imbert, Y., Thierry-Mieg, M., Rispal, P., Caubet, O., Ferrand, H., Tchamgoué, S., Farbos, S., Wille, H., Andre, K., Caunegre, L., Gerard, Y., Osorio-Perez, F., Chossat, I., Iles, G., Labasse-Depis, M., Lacassin, F., Barret, A., Castan, B., Koffi, J., Rouanes, N., Saunier, A., Zabbe, J.B., Dumondin, G., Beraud, G., Catroux, M., Garcia, M., Giraud, V., Martellosio, J.P., Roblot, F., Pasdeloup, T., Riché, A., Grosset, M., Males, S., Bell, C. Ngo, Carpentier, C., Bellecave, Virology P., Tumiotto, C., Miremeont-Salamé, G., Arma, D., Arnou, G., Blaizeau, M.J., Camps, P., Decoin, M., Delveaux, S., Diarra, F., Gabrea, L., Lawson-Ayayi, S., Lenaud, E., Plainchamps, D., Pougetoux, A., Uwamaliya, B., Zara, K., Conte, V., Gapillout, M., Surial, Bernard, Ramírez Mena, Adrià, Roumet, Marie, Limacher, Andreas, Smit, Colette, Leleux, Olivier, Mocroft, Amanda, van der Valk, Marc, Bonnet, Fabrice, Peters, Lars, Rockstroh, Jürgen K., Günthard, Huldrych F., Berzigotti, Annalisa, Rauch, Andri, and Wandeler, Gilles

Published
2023
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4. A method for mechanical generation of radio frequency fields in nuclear magnetic resonance force microscopy

Author

Wagenaar, J. J. T., Haan, A. M. J. den, Donkersloot, R. J., Marsman, F., de Wit, M., Bossoni, L., and Oosterkamp, T. H.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Instrumentation and Detectors
Abstract

We present an innovative method for magnetic resonance force microscopy (MRFM) with ultra-low dissipation, by using the higher modes of the mechanical detector as radio frequency (rf) source. This method allows MRFM on samples without the need to be close to an rf source. Furthermore, since rf sources require currents that give dissipation, our method enables nuclear magnetic resonance experiments at ultra-low temperatures. Removing the need for an on-chip rf source is an important step towards a MRFM which can be widely used in condensed matter physics., Comment: 7 pages, 5 figures, to be submitted to Physical Review Applied

Published
2016
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5. Observing 'Quantized' Conductance Steps in Silver Sulfide: Two Parallel Resistive Switching Mechanisms

Author

Wagenaar, J. J. T., Morales-Masis, M., and van Ruitenbeek, J. M.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

We demonstrate that it is possible to distinguish two conductance switching mechanisms in silver sulfide devices at room temperature. Experiments were performed using a Ag$_2$S thin film deposited on a wide Ag bottom electrode, which was contacted by the Pt tip of a scanning tunneling microscope. By applying a positive voltage on the silver electrode the conductance is seen to switch to a state having three orders of magnitude higher conductance, which is related to the formation of a conductive path inside the Ag$_2$S thin film. We argue this to be composed of a metallic silver nanowire accompanied by a modification of the surrounding lattice structure. Metallic silver nanowires decaying after applying a negative voltage allow observing conductance steps in the breaking traces characteristic for atomic-scale contacts, while the lattice structure deformation is revealed by gradual and continuously decreasing conductance traces., Comment: 6 pages, 6 figures

Published
2016
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6. Probing the Nuclear Spin-Lattice Relaxation Time at the Nanoscale

Author

Wagenaar, J. J. T., Haan, A. M. J. den, de Voogd, J. M., Bossoni, L., de Jong, T. A., de Wit, M., Bastiaans, K. M., Thoen, D. J., Endo, A., Klapwijk, T. M., Zaanen, J., and Oosterkamp, T. H.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Physics - Instrumentation and Detectors
Abstract

Nuclear spin-lattice relaxation times are measured on copper using magnetic resonance force microscopy performed at temperatures down to 42 mK. The low temperature is verified by comparison with the Korringa relation. Measuring spin-lattice relaxation times locally at very low temperatures opens up the possibility to measure the magnetic properties of inhomogeneous electron systems realized in oxide interfaces, topological insulators and other strongly correlated electron systems such as high-Tc superconductors., Comment: We revised the manuscript by including the supplemental material. The manuscript is changed from a Letter to a Research Article after change of journal

Published
2016
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7. Handleiding Productief Kruidenrijk Grasland

Author

Janssen, P., Bruinenberg, M., Eekeren, N. van, Hoekstra, N., Pijlman, J., Schie, T. van, Wagenaar, J-P., Wit, J. de, Janssen, P., Bruinenberg, M., Eekeren, N. van, Hoekstra, N., Pijlman, J., Schie, T. van, Wagenaar, J-P., and Wit, J. de

Abstract

ZuivelNL heeft een inventarisatie gedaan naar de kennisbehoefte onder melkveehouders. Hieruit kwam naar voren dat het onderwerp kruidenrijk grasland erg leeft en met name hoe dit te combineren met melkproductie. Productief kruidenrijk grasland is een relatief nieuwe vorm van grasland die nog lang niet bij alle veehouders bekend is. Het is in tegenstelling tot extensief kruidenrijk grasland gericht op een goede productie van melkvee die samengaat met een verbeterde biodiversiteit van het melkveebedrijf. Het biedt mogelijkheden op het gebied van grasproductie, droogtetolerantie, voederwaarde, diergezondheid, biodiversiteit, bodemkwaliteit, milieu en sectorimago. Kruidenrijk grasland kan naast functionele voordelen ook een meerwaarde betekenen voor de melkprijs in diverse trajecten van zuivelverwerkers en binnen het GLB. Voor de praktijk ontbrak het echter aan een handzaam overzichtswerk met handreikingen, terwijl er inmiddels veel bekend is over het onderwerp. In diverse PPS’en (Publiek-Private Samenwerking) is onderzoek gedaan naar mengsels, management en de waarde van productief kruidenrijk grasland. Het betreft dan met name PPS DZK C2 Living lab, PPS Ruwvoer, Bodem en Kringlooplandbouw, PPS KLIMAP en PPS Met precisie naar meer biodiversiteit. Daarnaast is er veel praktijkervaring opgenomen. Deze direct toepasbare kennis is hier samengebracht. De informatie is actueel en onderbouwd met onderzoeksresultaten.

Published
2024

8. Spin-mediated dissipation and frequency shifts of a cantilever at milliKelvin temperatures

Author

Haan, A. M. J. den, Wagenaar, J. J. T., de Voogd, J. M., Koning, G., and Oosterkamp, T. H.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

We measure the dissipation and frequency shift of a magnetically coupled cantilever in the vicinity of a silicon chip, down to $25$ mK. The dissipation and frequency shift originates from the interaction with the unpaired electrons, associated with the dangling bonds in the native oxide layer of the silicon, which form a two dimensional system of electron spins. We approach the sample with a $3.43$ $\mu$m-diameter magnetic particle attached to an ultrasoft cantilever, and measure the frequency shift and quality factor as a function of temperature and the distance. Using a recent theoretical analysis [J. M. de Voogd et al., arXiv:1508.07972 (2015)] of the dynamics of a system consisting of a spin and a magnetic resonator, we are able to fit the data and extract the relaxation time $T_1=0.39\pm0.08$ ms and spin density $\sigma=0.14\pm0.01$ spins per nm$^2$. Our analysis shows that at temperatures $\leq500$ mK magnetic dissipation is an important source of non-contact friction., Comment: 5 pages, 3 figures

Published
2015
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9. Dissipation and resonance frequency shift of a resonator magnetically coupled to a semiclassical spin

Author

de Voogd, J. M., Wagenaar, J. J. T., and Oosterkamp, T. H.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Quantum Physics
Abstract

We calculate the change of the properties of a resonator, when coupled to a semiclassical spin by means of the magnetic field. Starting with the Lagrangian of the complete system, we provide an analytical expression for the linear response function for the motion of the resonator, thereby considering the influence of the resonator on the spin and vice versa. This analysis shows that the resonance frequency and effective dissipation factor can change significantly due to the relaxation times of the spin. We first derive this for a system consisting of a spin and mechanical resonator and thereafter apply the same calculations to an electromagnetic resonator. Moreover, the applicability of the method is generalized to a resonator coupled to general two and more level systems, providing a key to understand some of the problems of two level systems in quantum devices., Comment: 10 pages, 4 figures, Appendices A-D included (page 8-10)

Published
2015

10. Local control of single atom magneto-crystalline anisotropy

Author

Bryant, B., Spinelli, A., Wagenaar, J. J. T., Gerrits, M., and Otte, A. F.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Individual Fe atoms on a Cu2N/Cu(100) surface exhibit strong magnetic anisotropy due to the crystal field. Using atom manipulation in a low-temperature STM we demonstrate that the anisotropy of one Fe atom is significantly influenced by local strain due to a second Fe atom placed nearby. Depending on the relative positions of the two atoms on the Cu2N lattice we can controllably enhance or reduce the uniaxial anisotropy. We present a model that explains the observed behavior qualitatively in terms of first principles., Comment: Three figures, one table

Published
2013
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12. Detection and control of individual nuclear spins using a weakly coupled electron spin

Author

Taminiau, T. H., Wagenaar, J. J. T., van der Sar, T., Jelezko, F., Dobrovitski, V. V., and Hanson, R.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics, Quantum Physics
Abstract

We experimentally isolate, characterize and coherently control up to six individual nuclear spins that are weakly coupled to an electron spin in diamond. Our method employs multi-pulse sequences on the electron spin that resonantly amplify the interaction with a selected nuclear spin and at the same time dynamically suppress decoherence caused by the rest of the spin bath. We are able to address nuclear spins with interaction strengths that are an order of magnitude smaller than the electron spin dephasing rate. Our results provide a route towards tomography with single-nuclear-spin sensitivity and greatly extend the number of available quantum bits for quantum information processing in diamond.

Published
2012
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13. Real-world effectiveness and tolerability of switching to doravirine-based antiretroviral therapy in people with HIV: a nationwide, matched, prospective cohort study

Author

Oomen, Patrick G A, Wit, Ferdinand W N M, Brinkman, Kees, Vrouenraets, Saskia M E, Mudrikova, Tania, van Welzen, Berend J, van der Valk, Marc, van Agtmael, M.A., Bomers, M., Geerlings, S.E., Goorhuis, A., Harris, V.C., Hovius, J.W., Lemkes, B., Nellen, F.J.B., Peters, E.J.G., van der Poll, T., Prins, J.M., Sigaloff, K.C.E., Spoorenberg, V., van Vugt, M., Wiersinga, W.J., Bruins, C., van Eden, J., Hylkema-van den Bout, I.J., Laan, L.M., Pijnappel, F.J.J., Smalhout, S.Y., Spelbrink, M.E., Weijsenfeld, A.M., Back, N.K.T., Cornelissen, M.T.E., van Houdt, R., Jonges, M., Jurriaans, S., Schinkel, C.J., Welkers, M.R.A., Wolthers, K.C., van den Berge, M., Stegeman, A., Baas, S., Hage de Looff, L., van Arkel, A., Stohr, J., Wintermans, B., Pronk, M.J.H., Ammerlaan, H.S.M., de Bree, C., de Munnik, E.S., Phaf, S., Deiman, B., Jansz, A.R., Scharnhorst, V., Tjhie, J., Wegdam, M.C.A., Nellen, J., van Eeden, A., Hoornenborg, E., de Stoppelaar, S., Alers, W., Elsenburg, L.J.M., Nobel, H., Schinkel, C.J., van Kasteren, M.E.E., Berrevoets, M.A.H., Brouwer, A.E., de Kruijf-van de Wiel, B.A.F.M., Adams, A., Pawels-van Rijkevoorsel, M., Murck, J.L., Rokx, C., Anas, A.A., Bax, H.I., van Gorp, E.C.M., de Mendonça Melo, M., van Nood, E., Nouwen, J.L., Rijnders, B.J.A., Schurink, C.A.M., Slobbe, L., de Vries-Sluijs, T.E.M.S., Bassant, N., van Beek, J.E.A., Vriesde, M., van Zonneveld, L.M., de Groot, J., van Kampen, J.J.A., Koopmans, M.P.G., Rahamat-Langendoen, J.C., Branger, J., Douma, R.A., Cents-Bosma, A.S., Mulder, M.A., Schippers, E.F., van Nieuwkoop, C., Geilings, J., van de Ven, E., van der Hut, G., van Burgel, N.D., Leyten, E.M.S., Gelinck, L.B.S., Mollema, F., Langbein, M., Wildenbeest, G.S., Nguyen, T., Groeneveld, P.H.P., Bouwhuis, J.W., Lammers, A.J.J., van Hulzen, A.G.W., Kraan, S., Kruiper, M.S.M., Debast, S.B., Wagenvoort, G.H.J., Roukens, A.H.E., de Boer, M.G.J., Jolink, H., Lambregts, M.M.C., Scheper, H., van Holten, N., van der Sluis, D., Claas, E.C.J., Wessels, E., den Hollander, J.G., El Moussaoui, R., Pogany, K., Brouwer, C.J., Heida-Peters, D., Mulder, E., Smit, J.V., Struik-Kalkman, D., van Niekerk, T., Pontesilli, O., van Tienen, C., Lowe, S.H., Oude Lashof, A.M.L., Posthouwer, D., Stoop, A., van Wolfswinkel, M.E., Ackens, R.P., Elasri, M., Houben-Pintaric, K., Schippers, J., Havenith, T.R.A., van Loo, M., van Vonderen, M.G.A., Kampschreur, L.M., Timmer, C., van Broekhuizen, M.C., Faber, S., Al Moujahid, A., Kootstra, G.J., Delsing, C.E., van der Burg-van de Plas, M., Scheiberlich, L., Kortmann, W., van Twillert, G., Renckens, R., Wagenaar, J., Ruiter-Pronk, D., Stander, B., Cohen Stuart, J.W.T., Hoogewerf, M., Rozemeijer, W., Sinnige, J.C., Brinkman, K., van den Berk, G.E.L., Lettinga, K.D., de Regt, M., Schouten, W.E.M., Stalenhoef, J.E., Blaauw, H., Geerders, G.F., Kleene, M.J., Knapen, M., Kok, M., van der Meché, I.B., Toonen, A.J.M., Wijnands, S., Wttewaal, E., Kwa, D., van de Laar, T.J.W., van Crevel, R., van Aerde, K., Dofferhoff, A.S.M., Henriet, S.S.V., ter Hofstede, H.J.M., Hoogerwerf, J., Richel, O., Albers, M., Grintjes-Huisman, K.J.T., de Haan, M., Marneef, M., McCall, M., Rahamat-Langendoen, J., Ruizendaal, E., Burger, D., Gisolf, E.H., Claassen, M., Hassing, R.J., ter Beest, G., van Bentum, P.H.M., Neijland, Y., Valette, M., Swanink, C.M.A., Klein Velderman, M., van Lelyveld, S.F.L., Soetekouw, R., van der Prijt, L.M.M., van der Swaluw, J., Kalpoe, J.S., Wagemakers, A., Vahidnia, A., Lauw, F.N., Verhagen, D.W.M., van Wijk, M., Bierman, W.F.W., Bakker, M., van Bentum, R.A., van den Boomgaard, M.A., Kleinnijenhuis, J., Kloeze, E., Middel, A., Postma, D.F., Schenk, H.M., Stienstra, Y., Wouthuyzen-Bakker, M., Boonstra, A., Maerman, M.M.M., de Weerd, D.A., van Eije, K.J., Knoester, M., van Leer-Buter, C.C., Niesters, H.G.M., Barth, R.E., Bruns, A.H.W., Ellerbroek, P.M., Hensgens, M.P.M., Oosterheert, J.J., Schadd, E.M., Verbon, A., Griffioen-van Santen, B.M.G., de Kroon, I., Schuurman, R., Verduyn Lunel, F.M., Wensing, A.M.J., van der Valk, M., Zaheri, S., Boyd, A.C., Bezemer, D.O., Jongen, V.W., van Sighem, A.I., Smit, C., Wit, F.W.M.N., Hillebregt, M.M.J., Woudstra, T.J., Rutkens, T., Bergsma, D., Brétin, N.M., Koster, L.E., Lelivelt, K.J., van de Sande, L., Schoorl, M.J.C., Visser, K.M., van der Vliet, S.T., Paling, F., van den Akker, M., Akpomukai, O.M., Alexander, R., Bakker, Y.M., Bastos Sales, L., El Berkaoui, A., Bezemer-Goedhart, M., Djoechro, E.A., Grolleman, J.M., El Hammoud, I., Khouw, M.R., Lodewijk, C.R.E., Lucas, E.G.A., van Meerveld-Derks, S., Mulder, H.W., Munjishvili, L., Ree, C.M.J., Regtop, R., van Rijk, A.F., Ruijs-Tiggelman, Y.M.C., Schnörr, P.P., van Veen, R., van Vliet-Klein Gunnewiek, W.H.G., and Witte, E.C.M.

Abstract

Currently, real-world data on doravirine are scarce. In a national prospective cohort, we assessed the effectiveness and tolerability of switching to doravirine-based antiretroviral therapy (ART) in people with HIV.

Published
2024
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14. On the Quantization of the Higher Spin Fields

Author

Wagenaar, J. W. and Rijken, T. A.

Subjects
High Energy Physics - Theory
Abstract

In this article we quantize (massive) higher spin ($1\leq j\leq2$) fields by means of Dirac's Constrained Hamilton procedure both in the situation were they are totally free and were they are coupled to (an) auxiliary field(s). A full constraint analysis and quantization is presented by determining and discussing all constraints and Lagrange multipliers and by giving all equal times (anti) commutation relations. Also we construct the relevant propagators. In the free case we obtain the well-known propagators and show that they are not covariant, which is also well known. In the coupled case we do obtain covariant propagators (in the spin-3/2 case this requires $b=0$) and show that they have a smooth massless limit connecting perfectly to the massless case (with auxiliary fields). We notice that in our system of the spin-3/2 and spin-2 case the massive propagators coupled to conserved currents only have a smooth limit to the pure massless spin-propagator, when there are ghosts in the massive case., Comment: 25 pages

Published
2009
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15. Pion-Nucleon Scattering in Kadyshevsky Formalism: II Baryon Exchange Sector

Author

Wagenaar, J. W. and Rijken, T. A.

Subjects
Nuclear Theory
Abstract

In this paper, which is the second part in a series of two, we construct tree level baryon exchange and resonance amplitudes for $\pi N$ / $MB$-scattering in the framework of the Kadyshevsky formalism. We use this formalism to formally implement absolute pair suppression, where we make use of the method of Takahashi and Umezawa. The resulting amplitudes are Lorentz invariant and causal. We continue studying the frame dependence of the Kadyshevsky integral equation using the method of Gross and Jackiw. The invariant amplitudes, including those for meson exchange, are linked to the phase-shifts using the partial wave basis., Comment: 49 pages

Published
2009
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16. Pion-Nucleon Scattering in Kadyshevsky Formalism: I Meson Exchange Sector

Author

Wagenaar, J. W. and Rijken, T. A.

Subjects
Nuclear Theory
Abstract

In a series of two papers we present the theoretical results of $\pi N$/meson-baryon scattering in the Kadyshevsky formalism. In this paper the results are given for meson exchange diagrams. On the formal side we show, by means of an example, how general couplings, i.e. couplings containing multiple derivatives and/or higher spin fields, should be treated. We do this by introducing and applying the Takahashi-Umezawa and the Gross-Jackiw method. For practical purposes we introduce the $\bar{P}$ method. We also show how the Takashashi-Umezawa method can be derived using the theory of Bogoliubov and collaborators and the Gross-Jackiw method is also used to study the $n$-dependence of the Kadyshevsky integral equation. Last but not least we present the second quantization procedure of the quasi particle in Kadyshevsky formalism., Comment: 29 pages

Published
2009
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17. Pion-Nucleon Scattering in Kadyshevsky Formalism and Higher Spin Field Quantization

Author

Wagenaar, J. W.

Subjects
Nuclear Theory
Abstract

This thesis contains two parts. The first part deals with pion-nucleon/meson-baryon scattering in the Kadyshevsky formalism. This formalism is introduced and discussed. Problems may arise when derivative couplings and/or higher spin fields are used, especially when compared to the results in the Feynman formalism: unwanted contact terms pop-up. These terms are cancelled using the Gross and Jackiw or Takahashi and Umezawa method. The final results in both formalisms are therefore equal, causal and covariant. Formal incorporation of pair suppression in the baryon exchange sector is achieved using a method based on the Takahashi and Umezawa method. For the resulting tree level amplitudes, we have shown, to our knowledge for the first time, that they are causal, covariant and n-independent. Moreover, the amplitudes are just a factor 1/2 of the usual Feynman expressions. The amplitudes contain only posititve energy initial and final states, although it should be mentioned that negative energy is present inside an amplitude via the Delta propagator. The second part of this thesis deals with higher spin field quantization in the framework of Dirac's Constraint analysis. A full constraint analysis and quantization procedure is presented for the free spin 1,3/2 and 2 case and for the situation where these fields are coupled to auxiliary fields. The constructed propagators in the former case are shown to be non-covariant, as is well-known. Therefore, auxiliary fields coupled to gauge conditions of the free case are introduced in the Lagrangian. Now, the resulting propagators are covariant., Comment: 189 pages

Published
2009

20. External validation of the PAGE-B score for HCC risk prediction in people living with HIV/HBV coinfection

Author

Egger, M., Hoffmann, M., Rauch, A., van der Valk, M., Goorhuis, A., Prins, J. M., van Vugt, M., Wit, F. W.M.N., Cornelissen, M. T.E., Jonges, M., Wolthers, K. C., Zaaijer, H. L., Peters, E. J.G., van Agtmael, M. A., Autar, R. S., Laan, L. M., van den Berge, M., Baas, S., van Arkel, A., Pronk, M. J.H., Alers, W., Nobel, H., Berrevoets, M. A.H., Brouwer, A. E., Rokx, C., Anas, A. A., Bax, H. I., van Gorp, E. C.M., van Nood, E., Nouwen, J. L., Rijnders, B. J.A., Schurink, C. A.M., Slobbe, L., de Vries-Sluijs, T. E.M.S., Bassant, N., van Beek, J. E.A., Vriesde, M., van Zonneveld, L. M., de Groot, J., van Kampen, J. J.A., Koopmans, M. P.G., Rahamat-Langendoen, J. C., Douma, R. A., Schippers, E. F., Gelinck, L. B.S., Mollema, F., Nguyen, T., Groeneveld, P. H.P., Lammers, A. J.J., de Boer, M. G.J., Claas, E. C.J., Brouwer, C. J., Mulder, E., Smit, J. V., van Niekerk, T., Pontesilli, O., van Tienen, C., van Wolfswinkel, M. E., Schippers, J., Kampschreur, L. M., Wagenaar, J., de Regt, M., Schouten, W. E.M., Veenstra, J., Blaauw, H., Knapen, M., Kok, M., Albers, M., de Haan, M., McCall, M., Burger, D., Claassen, M., Hassing, R. J., Verhagen, D. W.M., van Wijk, M., Bakker, M., Postma, D. F., Schenk, H. M., Boonstra, A., de Jonge, H., Niesters, H. G.M., Bruns, A. H.W., Hensgens, M. P.M., Oosterheert, J. J., Verbon, A., Berends, H., Bezemer, D. O., Smit, C., Bergsma, D., Lelivelt, K. J., van de Sande, L., van den Akker, M., Bakker, Y., Bezemer-Goedhart, M., Koster, L. E., Lucas, E. G.A., Schoorl, M. J.C., Witte, E. C.M., Peters, L., Larsen, J. F., Fischer, A. H., Jensen, S. K., Nguyen, D., Garcia, M., Egger, M., Hoffmann, M., Rauch, A., van der Valk, M., Goorhuis, A., Prins, J. M., van Vugt, M., Wit, F. W.M.N., Cornelissen, M. T.E., Jonges, M., Wolthers, K. C., Zaaijer, H. L., Peters, E. J.G., van Agtmael, M. A., Autar, R. S., Laan, L. M., van den Berge, M., Baas, S., van Arkel, A., Pronk, M. J.H., Alers, W., Nobel, H., Berrevoets, M. A.H., Brouwer, A. E., Rokx, C., Anas, A. A., Bax, H. I., van Gorp, E. C.M., van Nood, E., Nouwen, J. L., Rijnders, B. J.A., Schurink, C. A.M., Slobbe, L., de Vries-Sluijs, T. E.M.S., Bassant, N., van Beek, J. E.A., Vriesde, M., van Zonneveld, L. M., de Groot, J., van Kampen, J. J.A., Koopmans, M. P.G., Rahamat-Langendoen, J. C., Douma, R. A., Schippers, E. F., Gelinck, L. B.S., Mollema, F., Nguyen, T., Groeneveld, P. H.P., Lammers, A. J.J., de Boer, M. G.J., Claas, E. C.J., Brouwer, C. J., Mulder, E., Smit, J. V., van Niekerk, T., Pontesilli, O., van Tienen, C., van Wolfswinkel, M. E., Schippers, J., Kampschreur, L. M., Wagenaar, J., de Regt, M., Schouten, W. E.M., Veenstra, J., Blaauw, H., Knapen, M., Kok, M., Albers, M., de Haan, M., McCall, M., Burger, D., Claassen, M., Hassing, R. J., Verhagen, D. W.M., van Wijk, M., Bakker, M., Postma, D. F., Schenk, H. M., Boonstra, A., de Jonge, H., Niesters, H. G.M., Bruns, A. H.W., Hensgens, M. P.M., Oosterheert, J. J., Verbon, A., Berends, H., Bezemer, D. O., Smit, C., Bergsma, D., Lelivelt, K. J., van de Sande, L., van den Akker, M., Bakker, Y., Bezemer-Goedhart, M., Koster, L. E., Lucas, E. G.A., Schoorl, M. J.C., Witte, E. C.M., Peters, L., Larsen, J. F., Fischer, A. H., Jensen, S. K., Nguyen, D., and Garcia, M.

Abstract

Background & Aims: HBV coinfection is common among people living with HIV (PLWH) and is the most important cause of hepatocellular carcinoma (HCC). While risk prediction tools for HCC have been validated in patients with HBV monoinfection, they have not been evaluated in PLWH. Thus, we performed an external validation of PAGE-B in people with HIV/HBV coinfection. Methods: We included data on PLWH from four European cohorts who were positive for HBsAg and did not have HCC before starting tenofovir. We estimated the predictive performance of PAGE-B for HCC occurrence over 15 years in patients receiving tenofovir-containing antiretroviral therapy. Model discrimination was assessed after multiple imputation using Cox regression with the prognostic index as a covariate, and by calculating Harrell's c-index. Calibration was assessed by comparing our cumulative incidence with the PAGE-B derivation study using Kaplan-Meier curves. Results: In total, 2,963 individuals with HIV/HBV coinfection on tenofovir-containing antiretroviral therapy were included. PAGE-B was <10 in 26.5%, 10–17 in 57.7%, and ≥18 in 15.7% of patients. Within a median follow-up of 9.6 years, HCC occurred in 68 individuals (2.58/1,000 patient-years, 95% CI 2.03–3.27). The regression slope of the prognostic index for developing HCC within 15 years was 0.93 (95% CI 0.61–1.25), and the pooled c-index was 0.77 (range 0.73–0.80), both indicating good model discrimination. The cumulative incidence of HCC was lower in our study compared to the derivation study. A PAGE-B cut-off of <10 had a negative predictive value of 99.4% for the development of HCC within 5 years. Restricting efforts to individuals with a PAGE-B of ≥10 would spare unnecessary HCC screening in 27% of individuals. Conclusions: For individuals with HIV/HBV coinfection, PAGE-B is a valid tool to determine the need for HCC screening. Impact and impl

Published
2023

21. LBI Appreciatie concept-Landbouwakkoord

Author

Geijzendorffer, I., Eekeren, N. van, Keijzer, P., Koopmans, C., Luske, B., Pijlman, J., Prins, U., Timmermans, B., Wagenaar, J.-P., Wit, J. de, Geijzendorffer, I., Eekeren, N. van, Keijzer, P., Koopmans, C., Luske, B., Pijlman, J., Prins, U., Timmermans, B., Wagenaar, J.-P., and Wit, J. de

Abstract

Het LBI is specifiek gevraagd om een appreciatie uit te voeren van de in het concept- Landbouwakkoord (concept-LA) opgenomen afspraken met een specifieke focus op ‘natuurinclusieve kringlooplandbouw’ en de biologische landbouw. In aanvulling op deze opdracht heeft het ministerie van LNV namens het kabinet aan het LBI gevraagd om ook de maatregel: “aanscherping graslandnorm naar bijvoorbeeld 0,40 (t.o.v. graslandnorm 0,25/0,30/0,35)” mee te nemen in deze appreciatie.

Published
2023

28. Monitoring of ticks and their pathogens from companion animals obtained by the 'tekenscanner' application in The Netherlands

Author

Kooyman, F N J, Zweerus, H, Nijsse, E R, Jongejan, F, Wagenaar, J A, Broens, E M, Kooyman, F N J, Zweerus, H, Nijsse, E R, Jongejan, F, Wagenaar, J A, and Broens, E M

Abstract

Ticks are vectors for many pathogens of veterinary and medical interest. In order to monitor ticks and tick-borne pathogens, the "Tekenscanner" (Dutch for Tick scanner), a citizen science project, was launched in The Netherlands. It is a smartphone application for pet-owners to get ticks from their dog or cat, identified and checked for pathogens for free. At the same time, information about the pet and the geographic location of tick infestation becomes available for research. The application was launched in 2018, and the results of the first 6 months after launch of the app were reported. Ticks were identified based on morphology, and DNA was extracted and amplified by a panel of tick-borne pathogen-specific primers. Next, the amplicons were subjected to reverse line blot with specific probes for important pathogens to determine their presence or absence. The present paper describes the results of 2019 and 2020. There were 2260 ticks collected from 871 dogs and 255 cats (26 ticks were from an unknown host) and all pet owners were informed about the results. Four species of ticks were collected: Ixodes ricinus (90.0%), Ixodes hexagonus (7.3%), Dermacentor reticulatus (2.8%) and Rhipicephalus sanguineus (0.1%). Ixodes ricinus was the tick with the most divergent pathogens: Anaplasma sp. (1.3%), Babesia sp. (0.8%), Borrelia spp. (4.8%), Neoehrlichia sp. (3.7%) and Rickettsia helvetica (12.6%). In I. hexagonus, R. helvetica (1.8%) and Babesia sp. (0.6%) were detected and Rickettsia raoultii in D. reticulatus (16.2%). One of the two nymphs of R. sanguineus was co-infected with Borrelia and R. helvetica and the other one was uninfected. The high numbers of different pathogens found in this study suggest that companion animals, by definition synanthropic animals, and their ticks can serve as sentinels for emerging tick-borne pathogens.

Published
2022

29. Monitoring of ticks and their pathogens from companion animals obtained by the 'tekenscanner' application in The Netherlands

Author

Klinische infectiologie en microb. lab., dI&I I&I-4, Afd Centrum voor teken-gebonden ziekten, Kooyman, F N J, Zweerus, H, Nijsse, E R, Jongejan, F, Wagenaar, J A, Broens, E M, Klinische infectiologie en microb. lab., dI&I I&I-4, Afd Centrum voor teken-gebonden ziekten, Kooyman, F N J, Zweerus, H, Nijsse, E R, Jongejan, F, Wagenaar, J A, and Broens, E M

Published
2022

30. Begrazing met waterbuffels levert bijdrage aan graslandbeheer

Author

Timmermans, B., Wagenaar, J.-P., Timmermans, B., and Wagenaar, J.-P.

Abstract

Op de Stoerderij in Son en Breugel (Noord-Brabant, zie kader eind artikel) worden waterbuffels gehouden voor melk- en vleesproductie. Zowel melkbuffels als jong- en vleesvee moeten een groot deel van hun dagelijkse voer halen uit beweiding huis- en veldkavel. Het totale areaal (40 ha) bestaat uit een deel private pacht en een deel dat gepacht wordt van Staats Bosbeheer (SBB). De percelen van SBB hebben afhankelijk van ligging en historisch landgebruik een natuurdoelstelling, met bijbehorende gebruiksvoorwaarden. Voor kruidenrijk grasland en nat schraalland, bestaat dit uit jaarlijks 1 tot 2 maaisneden, eventueel in combinatie met naweiden. De Stoerderij zoekt naar mogelijkheden om de pachtpercelen beter te benutten in de bedrijfsvoering, zonder de gewenste vegetatieontwikkeling in het gedrang te laten komen. Met het oog hierop werd met SBB het gesprek aangegaan. Inzet voor de Stoerderij was het verhogen van zowel kwaliteit als kwantiteit van ruwvoer, in combinatie met het terugdringen van ongewenste soorten (o.a. pitrus en lidrus).

Published
2022

33. Feasibility of imaging in nuclear magnetic resonance force microscopy using Boltzmann polarization.

Author

de Wit, M., Welker, G., Wagenaar, J. J. T., Hoekstra, F. G., and Oosterkamp, T. H.

Subjects
MAGNETIC resonance force microscopy, NUCLEAR spin, BLOCH equations, MAGNETIC fields, PROTONS, MAGNETIC resonance imaging
Abstract

We report on magnetic resonance force microscopy measurements of the Boltzmann polarization of nuclear spins in copper by detecting the frequency shift of a soft cantilever. We use the time-dependent solution of the Bloch equations to derive a concise equation describing the effect of radio-frequent (RF) magnetic fields on both on- and off-resonant spins in high magnetic field gradients. We then apply this theory to saturation experiments performed on a 100 nm thick layer of copper, where we use the higher modes of the cantilever as a source of the RF field. We demonstrate a detection volume sensitivity of only (40 nm) 3 , corresponding to about 1.6 × 10 4 polarized copper nuclear spins. We propose an experiment on protons where, with the appropriate technical improvements, frequency-shift based magnetic resonance imaging with a resolution better than (10 nm) 3 could be possible. Achieving this resolution would make imaging based on the Boltzmann polarization competitive with the more traditional stochastic spin-fluctuation based imaging, with the possibility to work at millikelvin temperatures. [ABSTRACT FROM AUTHOR]

Published
2019
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38. Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household

Author

van den Bunt, G, Fluit, A C, Spaninks, M P, Timmerman, A J, Geurts, Y, Kant, A, Scharringa, J, Mevius, D, Wagenaar, J A, Bonten, M J M, van Pelt, W, Hordijk, J, van den Bunt, G, Fluit, A C, Spaninks, M P, Timmerman, A J, Geurts, Y, Kant, A, Scharringa, J, Mevius, D, Wagenaar, J A, Bonten, M J M, van Pelt, W, and Hordijk, J

Published
2020

39. Faecal carriage, risk factors, acquisition and persistence of ESBL-producing Enterobacteriaceae in dogs and cats and co-carriage with humans belonging to the same household

Author

Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB Zorg, Externen Hematologie, MMB, Epi Infectieziekten, van den Bunt, G, Fluit, A C, Spaninks, M P, Timmerman, A J, Geurts, Y, Kant, A, Scharringa, J, Mevius, D, Wagenaar, J A, Bonten, M J M, van Pelt, W, Hordijk, J, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB Zorg, Externen Hematologie, MMB, Epi Infectieziekten, van den Bunt, G, Fluit, A C, Spaninks, M P, Timmerman, A J, Geurts, Y, Kant, A, Scharringa, J, Mevius, D, Wagenaar, J A, Bonten, M J M, van Pelt, W, and Hordijk, J

Published
2020

41. Productief kruidenrijk grasland biedt kansen : Is kruidenrijk grasland echt beter bestand tegen droogte?

Author

Janssen, P., Wagenaar, J.-P., Eekeren, N. van, Antonissen, H., Janssen, P., Wagenaar, J.-P., Eekeren, N. van, and Antonissen, H.

Abstract

Vanwege de belangstelling voor het introduceren van kruidenrijk grasland is er de afgelopen jaren gekeken naar de teeltaspecten. Productie, samenstelling, bodemkwaliteit en onkruiddruk van een aantal mengsels is op verschillende locaties onder de loep genomen. Resultaten van proeven binnen de POP3-projecten ‘Krachtige Kruiden Overijssel’ en ‘Soortenrijk grasland Limburg’ laten de kansen zien van verschillende graskruidenmengsels.

Published
2020

42. Productief kruidenrijk grasland biedt kans

Author

Janssen, P., Wagenaar, J.-P., Eekeren, N. van, Antonissen, H., Janssen, P., Wagenaar, J.-P., Eekeren, N. van, and Antonissen, H.

Abstract

Vanwege de belangstelling voor het introduceren van kruidenrijk grasland is de afgelopen jaren gekeken naar verschillende teeltaspecten ervan. De productie, samenstelling, bodemkwaliteit en onkruiddruk van een aantal mengsels is op verschillende locaties onder de loep genomen. Resultaten van proeven binnen de POP3-projecten ‘Krachtige Kruiden Overijssel’ en ‘Soortenrijk grasland Limburg’ laten de kansen zien van verschillende graskruidenmengsels.

Published
2020

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