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3,969 results on '"PERRY, D. A."'

4. A conserved complex lipid signature marks human muscle aging and responds to short-term exercise

Author

Janssens, Georges E., Molenaars, Marte, Herzog, Katharina, Grevendonk, Lotte, Remie, Carlijn M. E., Vervaart, Martin A. T., Elfrink, Hyung L., Wever, Eric J. M., Schomakers, Bauke V., Denis, Simone W., Waterham, Hans R., Pras-Raves, Mia L., van Weeghel, Michel, van Kampen, Antoine H. C., Tammaro, Alessandra, Butter, Loes M., van der Rijt, Sanne, Florquin, Sandrine, Jongejan, Aldo, Moerland, Perry D., Hoeks, Joris, Schrauwen, Patrick, Vaz, Frédéric M., and Houtkooper, Riekelt H.

Published
2024
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7. Response to Intervention in Virtual Classrooms with Beginning Writers

Author

Klein, Perry D., Casola, Madelyn, Dombroski, Jill D., Giese, Christine, Sha, Kristen Wing-Yan, and Thompson, Serena C.

Abstract

During the COVID pandemic, two virtual classes of Grade 1 students learned to write personal narratives in a Response to Intervention framework. Classroom teachers delivered Tier 1 Self-Regulated Strategy Development (SRSD) in personal narrative writing to 67% of students. A research associate provided Tier 2 SRSD instruction in personal narrative writing, with reteaching, support and feedback, and ad hoc remediation of handwriting and spelling, to eight students. Then, because three of the Tier 2 students were frequently absent or disengaged, the research associate delivered Tier 3 individual instruction to them. Students in both Tier 1 and Tier 2 instruction made large, statistically significant gains in text quality. Tier 3 students did not make significant gains. Partial correlations, observations during teaching, and teacher interviews suggest that attendance, spelling level, and discourse knowledge affected learning. Teachers identified strengths and limitations of SRSD, Response to Intervention and the specific materials used. The results indicate that in an online setting, SRSD, delivered in a brief RTI format, is effective for improving written expression for typically developing beginning writers and some struggling writers, but that some struggling writers require additional intervention.

Published
2023
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9. Measuring the usability of appliance controls

Author

Meier, A, Aragon, C, Perry, D, Peffer, T, Pritoni, M, and Granderson, J

Abstract

A “smart” device will remain efficient only as long as the settings and other parameters allow it to be. Thus, the degree of usability is becoming an element of energy efficiency similar to other physical characteristics. We developed and tested a procedure to quantify the usability of thermostats. The procedure assumes that usability can be represented by a user’s ability to accomplish a set of tasks. Thirty one subjects were tested in their ability to accomplish six essential tasks on programmable thermostats. The tests revealed a wide variation in the subjects’ ability to accomplish the same task on different thermostats. Thus it was possible to discern thermostats that were more effective than others. We created a metric based on data that are easy to collect and unambiguous that appears to reflect the usability of a task. Metrics from different tasks can be added and an overall usability “score” calculated. This approach, as well as the metric, can be applied to other devices where poor usability may impede energy-saving behaviour.

Published
2021

10. Real-world trough concentrations and effectiveness of long-acting cabotegravir and rilpivirine: a multicenter prospective observational study in Switzerland

Author

Abela, I, Aebi-Popp, K, Anagnostopoulos, A, Battegay, M, Bernasconi, E, Braun, DL, Bucher, HC, Calmy, A, Cavassini, M, Ciuffi, A, Dollenmaier, G, Egger, M, Elzi, L, Fehr, J, Fellay, J, Furrer, H, Fux, CA, Günthard, HF, Hachfeld, A, Haerry, D, Hasse, B, Hirsch, HH, Hoffmann, M, Hösli, I, Huber, M, Jackson-Perry, D, Kahlert, CR, Kaiser, L, Keiser, O, Klimkait, T, Kouyos, RD, Kovari, H, Kusejko, K, Labhardt, N, Leuzinger, K, Martinez de Tejada, B, Marzolini, C, Metzner, KJ, 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, Thoueille, Paul, Saldanha, Susana Alves, Schaller, Fabian, Choong, Eva, Munting, Aline, Cavassini, Matthias, Braun, Dominique, Günthard, Huldrych F., Kusejko, Katharina, Surial, Bernard, Furrer, Hansjakob, Rauch, Andri, Rougemont, Mathieu, Ustero, Pilar, Calmy, Alexandra, Stöckle, Marcel, Marzolini, Catia, Di Benedetto, Caroline, Bernasconi, Enos, Schmid, Patrick, Piso, Rein Jan, Andre, Pascal, Girardin, François R., Guidi, Monia, Buclin, Thierry, and Decosterd, Laurent A.

Published
2024
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11. Making Energy Savings Easier: Usability Metrics for Thermostats

Author

Perry, D, Pritoni, M, Aragon, C, Meier, A, and Peffer, T

Subjects
Information Systems, Library and Information Studies
Abstract

U.S. residential thermostats control approximately 9% of the nation’s energy use. Many building codes now require programmable thermostats (PTs) because of their assumed energy savings. However, several recent field studies have shown no significant savings or even higher energy use in households using PTs compared to those using non-PTs. These studies point to usability problems that lead to incorrect use and wasted energy. However, the lack of clear, consistent metrics has hampered the acceptance of usability concerns by thermostat manufacturers. Thus there is a need for metrics specific to PTs that manufacturers can use to evaluate their products.In this paper, we report on the results of a usability study conducted on five commercially available PTs and the development of four new metrics suitable for use in evaluating thermostat usability. Our study confirmed usability deficits in the current generation of PTs and showed the metrics are correlated with each other as well as agreeing with the qualitative results of the study.

Published
2021

13. CRB1 is required for recycling by RAB11A+ vesicles in human retinal organoids

Author

Buck, Thilo M., Quinn, Peter M.J., Pellissier, Lucie P., Mulder, Aat A., Jongejan, Aldo, Lu, Xuefei, Boon, Nanda, Koot, Daniëlle, Almushattat, Hind, Arendzen, Christiaan H., Vos, Rogier M., Bradley, Edward J., Freund, Christian, Mikkers, Harald M.M., Boon, Camiel J.F., Moerland, Perry D., Baas, Frank, Koster, Abraham J., Neefjes, Jacques, Berlin, Ilana, Jost, Carolina R., and Wijnholds, Jan

Published
2023
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14. Viral suppression and retention in HIV care during the postpartum period among women living with HIV: a longitudinal multicenter cohort study

Author

Abela, I., Aebi-Popp, K., Anagnostopoulos, A., Battegay, M., Baumann, M., Bernasconi, E., Braun, D.L., Bucher, H.C., Calmy, A., Cavassini, M., Ciuffi, A., Crisinel, P.A., Darling, K., Duppenthaler, A., Dollenmaier, G., Egger, M., Elzi, L., Fehr, J., Fellay, J., Francini, K., 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., Kapfhammer, E., Keiser, O., Klimkait, T., Kohns, M., Kottanattu, L., Kouyos, R.D., Kovari, H., Kusejko, K., Labhardt, N., Martinez de Tejada, B., Marzolini, C., Metzner, K.J., Müller, N., Nemeth, J., Nicca, D., Notter, J., Paioni, P., Pantaleo, G., Perreau, M., Polli, Ch, Rauch, A., Salazar-Vizcaya, L., Schmid, P., Speck, R., Stöckle, M., Tarr, P., Thanh Lecompte, M., Trkola, A., Wagner, N., Wandeler, G., Weisser, M., Yerly, S., Paioni, Paolo, Aebi-Popp, Karoline, Martinez de Tejada, Begoña, Rudin, Christoph, Bernasconi, Enos, Braun, Dominique L., Kouyos, Roger, Wagner, Noémie, Crisinel, Pierre Alex, Güsewell, Sabine, Darling, Katharine E.A., Duppenthaler, Andrea, Baumann, Marc, Polli, Christian, Fischer, Tina, and Kahlert, Christian R.

Published
2023
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15. SMG1, a nonsense‐mediated mRNA decay (NMD) regulator, as a candidate therapeutic target in multiple myeloma

Author

Alexander C. Leeksma, Ingrid A. M. Derks, Brett Garrick, Aldo Jongejan, Martino Colombo, Timon Bloedjes, Torsten Trowe, Jim C. Leisten, Michelle Howarth, Mehnaz Malek, Deborah S. Mortensen, Kate Blease, Mathew C. Groza, Rama Krishna Narla, Remco Loos, Marie‐José Kersten, Perry D. Moerland, Jeroen E. J. Guikema, Arnon P. Kater, Eric Eldering, and Ellen H. Filvaroff

Subjects
cancer, MM, NMD, SMG1, therapy, UPR, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Early data suggested that CC‐115, a clinical molecule, already known to inhibit the mammalian target of rapamycin kinase (TORK) and DNA‐dependent protein kinase (DNA‐PK) may have additional targets beyond TORK and DNA‐PK. Therefore, we aimed to identify such target(s) and investigate a potential therapeutic applicability. Functional profiling of 141 cancer cell lines revealed inhibition of kinase suppressor of morphogenesis in genitalia 1 (SMG1), a key regulator of the RNA degradation mechanism nonsense‐mediated mRNA decay (NMD), as an additional target of CC‐115. CC‐115 treatment showed a dose‐dependent increase of SMG1‐mediated NMD transcripts. A subset of cell lines, including multiple myeloma (MM) cell lines sensitive to the endoplasmic reticulum stress‐inducing compound thapsigargin, were highly susceptible to SMG1 inhibition. CC‐115 caused the induction of UPR transcripts and cell death by mitochondrial apoptosis, requiring the presence of BAX/BAK and caspase activity. Superior antitumor activity of CC‐115 over TORK inhibitors in primary human MM cells and three xenograft mouse models appeared to be via inhibition of SMG1. Our data support further development of SMG1 inhibitors as possible therapeutics in MM.

Published
2023
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16. Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods

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., Martinez de Tejada, B., 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., Otte, Fabian, Zhang, Yuepeng, Spagnuolo, Julian, Thielen, Alexander, Däumer, Martin, Wiethe, Carsten, Stoeckle, Marcel, Kusejko, Katharina, Klein, Florian, Metzner, Karin J., and Klimkait, Thomas

Published
2023
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17. 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., 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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19. Roles of ventral versus dorsal pathways in language production: An awake language mapping study

Author

Ries, SK, Piai, V, Perry, D, Griffin, S, Jordan, K, Henry, R, Knight, RT, and Berger, MS

Subjects
Biological Psychology, Cognitive and Computational Psychology, Psychology, Neurosciences, Clinical Research, Adult, Cerebral Cortex, Connectome, Electric Stimulation, Female, Humans, Male, Middle Aged, Neural Pathways, Semantics, Wakefulness, Medical and Health Sciences, Psychology and Cognitive Sciences, Language, Communication and Culture, Experimental Psychology, Biomedical and clinical sciences, Language, communication and culture
Abstract

Human language is organized along two main processing streams connecting posterior temporal cortex and inferior frontal cortex in the left hemisphere, travelling dorsal and ventral to the Sylvian fissure. Some views propose a dorsal motor versus ventral semantic division. Others propose division by combinatorial mechanism, with the dorsal stream responsible for combining elements into a sequence and the ventral stream for forming semantic dependencies independent of sequential order. We acquired data from direct cortical stimulation in the left hemisphere in 17 neurosurgical patients and subcortical resection in a subset of 10 patients as part of awake language mapping. Two language tasks were employed: a sentence generation (SG) task tested the ability to form sequential and semantic dependencies, and a picture-word interference (PWI) task manipulated semantic interference. Results show increased error rates in the SG versus PWI task during subcortical testing in the dorsal stream territory, and high error rates in both tasks in the ventral stream territory. Connectivity maps derived from diffusion imaging and seeded in the tumor sites show that patients with more errors in the SG than in the PWI task had tumor locations associated with a dorsal stream connectivity pattern. Patients with the opposite pattern of results had tumor locations associated with a more ventral stream connectivity pattern. These findings provide initial evidence using fiber tract disruption with electrical stimulation that the dorsal pathways are critical for organizing words in a sequence necessary for sentence generation, and the ventral pathways are critical for processing semantic dependencies.

Published
2019

20. A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike

Author

Mathieu Claireaux, Tom G. Caniels, Marlon de Gast, Julianna Han, Denise Guerra, Gius Kerster, Barbera D. C. van Schaik, Aldo Jongejan, Angela I. Schriek, Marloes Grobben, Philip J. M. Brouwer, Karlijn van der Straten, Yoann Aldon, Joan Capella-Pujol, Jonne L. Snitselaar, Wouter Olijhoek, Aafke Aartse, Mitch Brinkkemper, Ilja Bontjer, Judith A. Burger, Meliawati Poniman, Tom P. L. Bijl, Jonathan L. Torres, Jeffrey Copps, Isabel Cuella Martin, Steven W. de Taeye, Godelieve J. de Bree, Andrew B. Ward, Kwinten Sliepen, Antoine H. C. van Kampen, Perry D. Moerland, Rogier W. Sanders, and Marit J. van Gils

Subjects
Science
Abstract

To fully understand the potential shortcomings of SARS-CoV-2 vaccination, it is necessary to delineate the properties of the antibodies elicited, during immunization, and also infection. Through investigation of the SARS-CoV-2 spike-reactive B cell repertoire, authors identify following infection, a subset of B cells enriched and almost exclusively target a non-neutralizing S2 epitope present in aberrant forms.

Published
2022
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21. Ion Implantation for Deterministic Single Atom Devices

Author

Pacheco, J. L., Singh, M., Perry, D. L., Wendt, J. R., Eyck, G. Ten, Manginell, R. P., Pluym, T., Luhman, D. R., Lilly, M. P., Carroll, M. S., and Bielejec, E.

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

We demonstrate a capability of deterministic doping at the single atom level using a combination of direct write focused ion beam and solid-state ion detectors. The focused ion beam system can position a single ion to within 35 nm of a targeted location and the detection system is sensitive to single low energy heavy ions. This platform can be used to deterministically fabricate single atom devices in materials where the nanostructure and ion detectors can be integrated, including donor-based qubits in Si and color centers in diamond.

Published
2017
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22. Electroforming-Free TaOx Memristors using Focused Ion Beam Irradiations

Author

Pacheco, J. L., Perry, D. L., Hughart, D. R., Marinella, M., and Bielejec, E.

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

We demonstrate creation of electroforming-free TaOx memristive devices using focused ion beam irradiations to locally define conductive filaments in TaOx films. Electrical characterization shows that these irradiations directly create fully functional memristors without the need for electroforming. Ion beam forming of conductive filaments combined with state-of-the-art nano-patterning presents a CMOS compatible approach to wafer level fabrication of fully formed and operational memristors.

Published
2017
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23. A bright nanowire single photon source based on SiV centers in diamond

Author

Marseglia, L., Saha, K., Ajoy, A., Schröder, T., Englund, D., Jelezko, F., Walsworth, R., Pacheco, J. L., Perry, D. L., Bielejec, E. S., and Cappellaro, P.

Subjects
Physics - Applied Physics, Quantum Physics
Abstract

The practical implementation of many quantum technologies relies on the development of robust and bright single photon sources that operate at room temperature. The negatively charged silicon-vacancy (SiV-) color center in diamond is a possible candidate for such a single photon source. However, due to the high refraction index mismatch to air, color centers in diamond typically exhibit low photon out-coupling. An additional shortcoming is due to the random localization of native defects in the diamond sample. Here we demonstrate deterministic implantation of Si ions with high conversion efficiency to single SiV- centers, targeted to fabricated nanowires. The co-localization of single SiV- centers with the nanostructures yields a ten times higher light coupling efficiency than for single SiV- centers in bulk diamond. This enhanced photon out-coupling, together with the intrinsic scalability of the SiV- creation method, enables a new class of devices for integrated photonics and quantum science., Comment: 15 pages, 5 figures

Published
2017
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27. The Clinical Impact of Implementation of a Multidisciplinary Endocarditis Team

Author

El-Dalati, Sami, Cronin, Daniel, Riddell, James, IV, Shea, Michael, Weinberg, Richard L., Washer, Laraine, Stoneman, Emily, Perry, D. Alexander, Bradley, Suzanne, Burke, James, Murali, Sadhana, Fagan, Christopher, Chanderraj, Rishi, Christine, Paul, Patel, Twisha, Ressler, Kirra, Fukuhara, Shinichi, Romano, Matthew, Yang, Bo, and Deeb, George Michael

Published
2022
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29. A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike

Author

Claireaux, Mathieu, Caniels, Tom G., de Gast, Marlon, Han, Julianna, Guerra, Denise, Kerster, Gius, van Schaik, Barbera D. C., Jongejan, Aldo, Schriek, Angela I., Grobben, Marloes, Brouwer, Philip J. M., van der Straten, Karlijn, Aldon, Yoann, Capella-Pujol, Joan, Snitselaar, Jonne L., Olijhoek, Wouter, Aartse, Aafke, Brinkkemper, Mitch, Bontjer, Ilja, Burger, Judith A., Poniman, Meliawati, Bijl, Tom P. L., Torres, Jonathan L., Copps, Jeffrey, Martin, Isabel Cuella, de Taeye, Steven W., de Bree, Godelieve J., Ward, Andrew B., Sliepen, Kwinten, van Kampen, Antoine H. C., Moerland, Perry D., Sanders, Rogier W., and van Gils, Marit J.

Published
2022
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31. Osteopontin associates with brain TRM-cell transcriptome and compartmentalization in donors with and without multiple sclerosis

Author

Cheng-Chih Hsiao, Hendrik J. Engelenburg, Aldo Jongejan, Jing Zhu, Baohong Zhang, Michael Mingueneau, Perry D. Moerland, Inge Huitinga, Joost Smolders, and Jörg Hamann

Subjects
Neuroscience, Molecular neuroscience, Omics, Transcriptomics, Science
Abstract

Summary: The human brain is populated by perivascular T cells with a tissue-resident memory T (TRM)-cell phenotype, which in multiple sclerosis (MS) associate with lesions. We investigated the transcriptional and functional profile of freshly isolated T cells from white and gray matter. RNA sequencing of CD8+ and CD4+ CD69+ T cells revealed TRM-cell signatures. Notably, gene expression hardly differed between lesional and normal-appearing white matter T cells in MS brains. Genes up-regulated in brain TRM cells were MS4A1 (CD20) and SPP1 (osteopontin, OPN). OPN is also abundantly expressed by microglia and has been shown to inhibit T cell activity. In line with their parenchymal localization and the increased presence of OPN in active MS lesions, we noticed a reduced production of inflammatory cytokines IL-2, TNF, and IFNγ by lesion-derived CD8+ and CD4+ T cells ex vivo. Our study reports traits of brain TRM cells and reveals their tight control in MS lesions.

Published
2023
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34. Silicon Quantum Dots with Counted Antimony Donor Implants

Author

Singh, M., Pacheco, J. L., Perry, D., Garratt, E., Eyck, G. Ten, Bishop, N. C., Wendt, J. R., Manginell, R. P., Dominguez, J., Pluym, T., Luhman, D. R., Bielejec, E., Lilly, M. P., and Carroll, M. S.

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Deterministic control over the location and number of donors is crucial to donor spin quantum bits (qubits) in semiconductor based quantum computing. In this work, a focused ion beam is used to implant antimony donors close to quantum dots. Ion detectors are integrated next to the quantum dots to sense the implants. The numbers of donors implanted can be counted to a precision of a single ion. In low-temperature transport measurements, regular coulomb blockade is observed from the quantum dots. Charge offsets indicative of donor ionization are also observed in devices with counted donor implants.

Published
2015

35. A test of optimal laser impulsion for controlling population within the $N_s=1$, $N_r=5$ polyad of $^{12}C_2H_2$

Author

Santos, L., Iacobellis, N., Herman, M., Perry, D. S., Desouter-Lecomte, M., and Vaeck, N.

Subjects
Quantum Physics
Abstract

Optimal control theory has been employed to populate separately two dark states of the acetylene polyad $N_s=1$, $N_r=5$ by indirect coupling via the ground state. Relevant level energies and transition dipole moments are extracted from the experimental literature. The optimal pulses are rather simple. The evolution of the populations is shown for the duration of the control process and also for the field free-evolution that follows the control. One of the dark states appears to be a potential target for realistic experimental investigation because the average population of the Rabi oscillation remains high and decoherence is expected to be weak., Comment: 28 pages, 5 figures

Published
2015
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36. Candidate Plasma Biomarkers to Detect Anthracycline‐Related Cardiomyopathy in Childhood Cancer Survivors: A Case Control Study in the Dutch Childhood Cancer Survivor Study

Author

Jan M. Leerink, Elizabeth A. M. Feijen, Perry D. Moerland, Esmee C. de Baat, Remy Merkx, Helena J. H. van der Pal, Wim J. E. Tissing, Marloes Louwerens, Marry M. van den Heuvel‐Eibrink, A. Birgitta Versluys, Folkert W. Asselbergs, Arjan Sammani, Arco J. Teske, Elvira C. van Dalen, Margriet van der Heiden‐van der Loo, Eline van Dulmen‐den Broeder, Andrica C. H. de Vries, Livia Kapusta, Jacqueline Loonen, Yigal M. Pinto, Leontien C. M. Kremer, Annelies M. C. Mavinkurve‐Groothuis, and Wouter E. M. Kok

Subjects
anthracycline‐related cardiomyopathy, biomarkers, cancer therapy–related cardiac dysfunction, cardio‐oncology, chemokine ligands, childhood cancer survivors, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Background Plasma biomarkers may aid in the detection of anthracycline‐related cardiomyopathy (ACMP). However, the currently available biomarkers have limited diagnostic value in long‐term childhood cancer survivors. This study sought to identify diagnostic plasma biomarkers for ACMP in childhood cancer survivors. Methods and Results We measured 275 plasma proteins in 28 ACMP cases with left ventricular ejection fraction

Published
2022
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38. A Conserved Mito-Cytosolic Translational Balance Links Two Longevity Pathways

Author

Molenaars, Marte, Janssens, Georges E., Williams, Evan G., Jongejan, Aldo, Lan, Jiayi, Rabot, Sylvie, Joly, Fatima, Moerland, Perry D., Schomakers, Bauke V., Lezzerini, Marco, Liu, Yasmine J., McCormick, Mark A., Kennedy, Brian K., van Weeghel, Michel, van Kampen, Antoine H.C., Aebersold, Ruedi, MacInnes, Alyson W., and Houtkooper, Riekelt H.

Published
2020
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39. Infiltrative classical monocyte-derived andSPP1lipid-associated macrophages mediate inflammation and fibrosis in ANCA-associated glomerulonephritis

Author

Vegting, Yosta, primary, Jongejan, Aldo, additional, Neele, Annette E, additional, Claessen, Nike, additional, Sela, Gal, additional, Prange, Koen H M, additional, Kers, Jesper, additional, Roelofs, Joris J T H, additional, van der Heijden, Joost W, additional, de Boer, Onno J, additional, Remmerswaal, Ester B M, additional, Vogt, Liffert, additional, Bemelman, Frederike J, additional, de Winther, Menno P J, additional, Moerland, Perry D, additional, and Hilhorst, Marc L, additional

Published
2024
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40. Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer

Author

Maryam Soleimani Dodaran, Simone Borgoni, Emre Sofyalı, Pernette J. Verschure, Stefan Wiemann, Perry D. Moerland, and Antoine H. C. van Kampen

Subjects
Breast cancer, DNA methylation, Endocrine therapy, Resistance, Survival, T47D, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Estrogen receptor (ER) positive breast cancer is often effectively treated with drugs that inhibit ER signaling, i.e., tamoxifen (TAM) and aromatase inhibitors (AIs). However, 30% of ER+ breast cancer patients develop resistance to therapy leading to tumour recurrence. Changes in the methylation profile have been implicated as one of the mechanisms through which therapy resistance develops. Therefore, we aimed to identify methylation loci associated with endocrine therapy resistance. Methods We used genome-wide DNA methylation profiles of primary ER+/HER2- tumours from The Cancer Genome Atlas in combination with curated data on survival and treatment to predict development of endocrine resistance. Association of individual DNA methylation markers with survival was assessed using Cox proportional hazards models in a cohort of ER+/HER2- tumours (N = 552) and two sub-cohorts corresponding to the endocrine treatment (AI or TAM) that patients received (N = 210 and N = 172, respectively). We also identified multivariable methylation signatures associated with survival using Cox proportional hazards models with elastic net regularization. Individual markers and multivariable signatures were compared with DNA methylation profiles generated in a time course experiment using the T47D ER+ breast cancer cell line treated with tamoxifen or deprived from estrogen. Results We identified 134, 5 and 1 CpGs for which DNA methylation is significantly associated with survival in the ER+/HER2-, TAM and AI cohorts respectively. Multi-locus signatures consisted of 203, 36 and 178 CpGs and showed a large overlap with the corresponding single-locus signatures. The methylation signatures were associated with survival independently of tumour stage, age, AI treatment, and luminal status. The single-locus signature for the TAM cohort was conserved among the loci that were differentially methylated in endocrine-resistant T47D cells. Similarly, multi-locus signatures for the ER+/HER2- and AI cohorts were conserved in endocrine-resistant T47D cells. Also at the gene set level, several sets related to endocrine therapy and resistance were enriched in both survival and T47D signatures. Conclusions We identified individual and multivariable DNA methylation markers associated with therapy resistance independently of luminal status. Our results suggest that these markers identified from primary tumours prior to endocrine treatment are associated with development of endocrine resistance.

Published
2020
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41. Amyloid in dementia associated with familial FTLD: not an innocent bystander

Author

Naasan, G, Rabinovici, GD, Ghosh, P, Elofson, JD, Miller, BL, Coppola, G, Karydas, A, Fong, J, Perry, D, Lee, SE, Yokoyama, JS, Seeley, WW, Kramer, JH, Weiner, MW, Schuff, N, Jagust, WJ, Grinberg, LT, Pribadi, M, Yang, Z, Sears, R, Klein, E, Wojta, K, and Rosen, HJ

Subjects
Clinical Sciences, Psychology, Cognitive Sciences, Experimental Psychology, Neurosciences, Biological psychology, Clinical and health psychology
Abstract

Patients with frontotemporal lobar degeneration (FTLD) can show superimposed amyloid pathology, though the impact of amyloid on the clinical presentation of FTLD is not well characterized. This cross-sectional case–control study compared clinical features, fluorodeoxyglucose-positron emission tomography metabolism and gray matter volume loss in 30 patients with familial FTLD in whom amyloid status was confirmed with autopsy or Pittsburgh compound B-PET. Compared to the amyloid-negative patients, the amyloid-positive patients performed significantly worse on several cognitive tests and showed hypometabolism and volume loss in more temporoparietal regions. Our results suggest that in FTLD amyloid positivity is associated with a more Alzheimer’s disease-like pattern of neurodegeneration.

Published
2016

42. Family history of cancer in relation to the risk of keratinocyte carcinoma plus another type of cancer: a case-control study

Author

Small, J, Flanagan, C, Armeson, K, Perry, D, Marchell, R, Thiers, B, and Alberg, AJ

Abstract

BackgroundA personal history of keratinocyte carcinoma (KC) is associated with increased risk for other malignancies. To assess the role of inherited cancer predisposition we investigated if family history (FH) of skin cancer plus noncutaneous malignancy is associated with the risk of KC plus another type of cancer.MethodsThis clinic-based case-control study of non-Hispanic Caucasians had three age- and gender-matched groups: KC plus another cancer (n=49), KC only (n=50), and cancer-free controls (n=50). Patients were interviewed to assess FH in first-degree relatives of “skin cancer” and “cancer other than skin cancer.” Controls were the referent category for the risk of 1) KC only and 2) KC plus another cancer.ResultsWhen FH was categorized into a four-level variable and evaluated across the 3 study groups, compared to the control group a FH of skin plus noncutaneous malignancy was strongly associated with risk of KC only (OR 9.9; 95% CI 1.7-59.7) and KC plus another cancer (OR 9.8; 95% CI 1.7-57.0). The ORs for FH of skin cancer only were weaker and non-significant for both KC only (OR 4.3) and KC plus another cancer (OR 6.8). FH of noncutaneous malignancy only was null across groups.ConclusionsThe overall pattern of associations, especially the similar associations in patients with KC only and with KC plus another cancer, reinforce the known association between a family and personal history of KC but do not support a link between FH of skin plus noncutaneous malignancy and the KC cancer-prone phenotype.

Published
2016

43. Profiling of microglia nodules in multiple sclerosis reveals propensity for lesion formation

Author

van den Bosch, Aletta M R, van der Poel, Marlijn, Fransen, Nina L, Vincenten, Maria C J, Bobeldijk, Anneleen M, Jongejan, Aldo, Engelenburg, Hendrik J, Moerland, Perry D, Smolders, Joost, Huitinga, Inge, Hamann, Jörg, van den Bosch, Aletta M R, van der Poel, Marlijn, Fransen, Nina L, Vincenten, Maria C J, Bobeldijk, Anneleen M, Jongejan, Aldo, Engelenburg, Hendrik J, Moerland, Perry D, Smolders, Joost, Huitinga, Inge, and Hamann, Jörg

Abstract

Microglia nodules (HLA-DR+ cell clusters) are associated with brain pathology. In this post-mortem study, we investigated whether they represent the first stage of multiple sclerosis (MS) lesion formation. We show that microglia nodules are associated with more severe MS pathology. Compared to microglia nodules in stroke, those in MS show enhanced expression of genes previously found upregulated in MS lesions. Furthermore, genes associated with lipid metabolism, presence of T and B cells, production of immunoglobulins and cytokines, activation of the complement cascade, and metabolic stress are upregulated in microglia nodules in MS. Compared to stroke, they more frequently phagocytose oxidized phospholipids and possess a more tubular mitochondrial network. Strikingly, in MS, some microglia nodules encapsulate partially demyelinated axons. Taken together, we propose that activation of microglia nodules in MS by cytokines and immunoglobulins, together with phagocytosis of oxidized phospholipids, may lead to a microglia phenotype prone to MS lesion formation.

Published
2024

44. Gene-expression profiling of individuals resilient to Alzheimer's disease reveals higher expression of genes related to metallothionein and mitochondrial processes and no changes in the unfolded protein response

Author

de Vries, Luuk E, Jongejan, Aldo, Monteiro Fortes, Jennifer, Balesar, Rawien, Rozemuller, Annemieke J M, Moerland, Perry D, Huitinga, Inge, Swaab, Dick F, Verhaagen, Joost, de Vries, Luuk E, Jongejan, Aldo, Monteiro Fortes, Jennifer, Balesar, Rawien, Rozemuller, Annemieke J M, Moerland, Perry D, Huitinga, Inge, Swaab, Dick F, and Verhaagen, Joost

Abstract

Some individuals show a discrepancy between cognition and the amount of neuropathological changes characteristic for Alzheimer's disease (AD). This phenomenon has been referred to as 'resilience'. The molecular and cellular underpinnings of resilience remain poorly understood. To obtain an unbiased understanding of the molecular changes underlying resilience, we investigated global changes in gene expression in the superior frontal gyrus of a cohort of cognitively and pathologically well-defined AD patients, resilient individuals and age-matched controls (n = 11-12 per group). 897 genes were significantly altered between AD and control, 1121 between resilient and control and 6 between resilient and AD. Gene set enrichment analysis (GSEA) revealed that the expression of metallothionein (MT) and of genes related to mitochondrial processes was higher in the resilient donors. Weighted gene co-expression network analysis (WGCNA) identified gene modules related to the unfolded protein response, mitochondrial processes and synaptic signaling to be differentially associated with resilience or dementia. As changes in MT, mitochondria, heat shock proteins and the unfolded protein response (UPR) were the most pronounced changes in the GSEA and/or WGCNA, immunohistochemistry was used to further validate these processes. MT was significantly increased in astrocytes in resilient individuals. A higher proportion of the mitochondrial gene MT-CO1 was detected outside the cell body versus inside the cell body in the resilient compared to the control group and there were higher levels of heat shock protein 70 (HSP70) and X-box-binding protein 1 spliced (XBP1s), two proteins related to heat shock proteins and the UPR, in the AD donors. Finally, we show evidence for putative sex-specific alterations in resilience, including gene expression differences related to autophagy in females compared to males. Taken together, these results show possible mechanisms involving MTs, mitochondrial

Published
2024

45. Profiling of microglia nodules in multiple sclerosis reveals propensity for lesion formation

Author

van den Bosch, Aletta, van der Poel, Marlijn, Fransen, Nina L., Vincenten, Maria C J, Bobeldijk, Anneleen M., Jongejan, Aldo, Engelenburg, Hendrik J, Moerland, Perry D., Smolders, Joost, Huitinga, Inge, Hamann, Jörg, van den Bosch, Aletta, van der Poel, Marlijn, Fransen, Nina L., Vincenten, Maria C J, Bobeldijk, Anneleen M., Jongejan, Aldo, Engelenburg, Hendrik J, Moerland, Perry D., Smolders, Joost, Huitinga, Inge, and Hamann, Jörg

Abstract

Microglia nodules (HLA-DR+ cell clusters) are associated with brain pathology. In this post-mortem study, we investigated whether they represent the first stage of multiple sclerosis (MS) lesion formation. We show that microglia nodules are associated with more severe MS pathology. Compared to microglia nodules in stroke, those in MS show enhanced expression of genes previously found upregulated in MS lesions. Furthermore, genes associated with lipid metabolism, presence of T and B cells, production of immunoglobulins and cytokines, activation of the complement cascade, and metabolic stress are upregulated in microglia nodules in MS. Compared to stroke, they more frequently phagocytose oxidized phospholipids and possess a more tubular mitochondrial network. Strikingly, in MS, some microglia nodules encapsulate partially demyelinated axons. Taken together, we propose that activation of microglia nodules in MS by cytokines and immunoglobulins, together with phagocytosis of oxidized phospholipids, may lead to a microglia phenotype prone to MS lesion formation.

Published
2024

47. Physician perceptions of a multidisciplinary endocarditis team

Author

El-Dalati, Sami, Khurana, Irina, Soper, Nathaniel, Cronin, Daniel, Shea, Michael, Weinberg, Richard L., Riddell, IV, James, Washer, Laraine, Shuman, Emily, Burke, James, Murali, Sadhana, Perry, D. Alexander, Fagan, Christopher, Patel, Twisha, Ressler, Kirra, and Deeb, George Michael

Published
2020
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48. Energy efficiency and the misuse of programmable thermostats: The effectiveness of crowdsourcing for understanding household behavior

Author

Pritoni, M, Meier, AK, Aragon, C, Perry, D, and Peffer, T

Subjects
Survey, User behavior, Energy efficiency, Behavioral and Social Science, Human Geography, Policy and Administration
Abstract

Programmable thermostats are generally sold as energy-saving devices controlling heating and cooling systems, but can lead to energy waste when not operated as designed by the manufacturers. We utilized Amazon Mechanical Turk, an online crowdsourcing service, to investigate thermostat settings and behavior in households. We posted a survey and paid respondents to upload pictures of their thermostats to verify self-reported data. About 40% of programmable thermostat owners did not use programming features and 33% had programming features overridden. Respondents demonstrated numerous misconceptions about how thermostats control home energy use. Moreover, we found that 57% of households were occupied nearly all the time, limiting the potential energy savings. The study revealed flaws in self-reported data, when collected solely from traditional surveys, which raises concerns about the validity of current thermostat-related research using such data. "Ground truth" temperature data could now be available in homes with Internet-connected thermostats. Online crowdsourcing platforms emerge as valuable tools for collecting information that would be difficult or expensive to obtain through other means. Advantages over traditional surveys include low-cost, rapid design-implementation-result cycle, access to diverse population, use of multimedia. Crowdsourcing is more effective than alternative online tools due to easier recruitment process and respondents' reputation system.

Published
2015

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