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1. Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

Author

Joeres, M., Maksimov, P., Höper, D., Calvelage, S., Calero-Bernal, R., Fernández-Escobar, M., Koudela, B., Blaga, R., Vrhovec, M. Globokar, Stollberg, K., Bier, N., Sotiraki, S., Sroka, J., Piotrowska, W., Kodym, P., Basso, W., Conraths, F. J., Mercier, A., Galal, L., Dardé, M. L., Balea, A., Spano, F., Schulze, C., Peters, M., Scuda, N., Lundén, A., Davidson, R. K., Terland, R., Waap, H., de Bruin, E., Vatta, P., Caccio, S., Ortega-Mora, L. M., Jokelainen, P., and Schares, G.

Published
2023
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2. Combining one-session treatment with a homework program including app-based technology to enhance the treatment of childhood specific phobias: A study protocol of a multicenter pragmatic randomized controlled trial

Author

Klein, A.M., Hagen, A., Rahemenia, J., de Gier, E., Rapee, R.M., Nauta, M., de Bruin, E., Biesters, J., van Rijswijk, L., Bexkens, A., Baartmans, J.M.D., Mobach, L., Zimmermann, R., Krause, K., Bögels, S.M., Ollendick, T.H., and Schneider, S.

Published
2024
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3. Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling

Author

Hobor, S, Al Bakir, M, Hiley, C, Skrzypski, M, Frankell, A, Bakker, B, Watkins, T, Markovets, A, Dry, J, Brown, A, van der Aart, J, van den Bos, H, Spierings, D, Oukrif, D, Novelli, M, Chakrabarti, T, Rabinowitz, A, Ait Hassou, L, Litiere, S, Kerr, D, Tan, L, Kelly, G, Moore, D, Renshaw, M, Venkatesan, S, Hill, W, Huebner, A, Martinez-Ruiz, C, Black, J, Wu, W, Angelova, M, Mcgranahan, N, Downward, J, Chmielecki, J, Barrett, C, Litchfield, K, Chew, S, Blakely, C, de Bruin, E, Foijer, F, Vousden, K, Bivona, T, Lester, J, Bajaj, A, Nakas, A, Sodha-Ramdeen, A, Tufail, M, Scotland, M, Boyles, R, Rathinam, S, Wilson, C, Marrone, D, Dulloo, S, Fennell, D, Matharu, G, Shaw, J, Boleti, E, Cheyne, H, Khalil, M, Richardson, S, Cruickshank, T, Price, G, Kerr, K, Benafif, S, French, J, Gilbert, K, Naidu, B, Patel, A, Osman, A, Enstone, C, Langman, G, Shackleford, H, Djearaman, M, Kadiri, S, Middleton, G, Leek, A, Hodgkinson, J, Totton, N, Montero, A, Smith, E, Fontaine, E, Granato, F, Paiva-Correia, A, Novasio, J, Rammohan, K, Joseph, L, Bishop, P, Shah, R, Moss, S, Joshi, V, Crosbie, P, Brown, K, Carter, M, Chaturvedi, A, Oliveira, P, Lindsay, C, Blackhall, F, Krebs, M, Summers, Y, Clipson, A, Tugwood, J, Kerr, A, Rothwell, D, Dive, C, Aerts, H, Schwarz, R, Kaufmann, T, Wilson, G, Rosenthal, R, Van Loo, P, Birkbak, N, Szallasi, Z, Kisistok, J, Sokac, M, Salgado, R, Diossy, M, Demeulemeester, J, Bunkum, A, Dwornik, A, Magness, A, Rowan, A, Karamani, A, Toncheva, A, Chain, B, Castignani, C, Bailey, C, Abbosh, C, Puttick, C, Weeden, C, Lee, C, Richard, C, Naceur-Lombardelli, C, Pearce, D, Karagianni, D, Biswas, D, Levi, D, Larose Cadieux, E, Lim, E, Colliver, E, Nye, E, Galvez-Cancino, F, Gimeno-Valiente, F, Kassiotis, G, Stavrou, G, Mastrokalos, G, Lowe, H, Matos, I, Noorani, I, Goldman, J, Reading, J, Rane, J, Nicod, J, Hartley, J, Peggs, K, Enfield, K, Selvaraju, K, Thol, K, Ng, K, Chen, K, Dijkstra, K, Grigoriadis, K, Thakkar, K, Ensell, L, Shah, M, Litovchenko, M, Jamal-Hanjani, M, Werner Sunderland, M, Huska, M, Hill, M, Dietzen, M, Leung, M, Escudero, M, Tanic, M, Sivakumar, M, Chervova, O, Lucas, O, Pich, O, Al-Sawaf, O, Prymas, P, Hobson, P, Pawlik, P, Stone, R, Bentham, R, Vendramin, R, Saghafinia, S, Gamble, S, Veeriah, S, Ung, S, Quezada, S, Vanloo, S, Hessey, S, Ward, S, Harries, S, Boeing, S, Beck, S, Bola, S, Karasaki, T, Denner, T, Marafioti, T, Jones, T, Spanswick, V, Barbe, V, Lu, W, Liu, W, Wu, Y, Naito, Y, Ramsden, Z, Veiga, C, Royle, G, Collins-Fekete, C, Fraioli, F, Ashford, P, Forster, M, Lee, S, Borg, E, Falzon, M, Papadatos-Pastos, D, Wilson, J, Ahmad, T, Procter, A, Ahmed, A, Taylor, M, Nair, A, Lawrence, D, Patrini, D, Navani, N, Thakrar, R, Janes, S, Martinoni Hoogenboom, E, Monk, F, Holding, J, Choudhary, J, Bhakhri, K, Scarci, M, Gorman, P, Khiroya, R, Stephens, R, Wong, Y, Kaplar, Z, Bandula, S, Hackshaw, A, Hacker, A, Sharp, A, Smith, S, Kaur Dhanda, H, Pilotti, C, Leslie, R, Grapa, A, Zhang, H, Abduljabbar, K, Pan, X, Yuan, Y, Chuter, D, Mackenzie, M, Chee, S, Alzetani, A, Cave, J, Richards, J, De Sousa, P, Jordan, S, Rice, A, Raubenheimer, H, Bhayani, H, Ambrose, L, Devaraj, A, Chavan, H, Begum, S, Buderi, S, Kaniu, D, Malima, M, Booth, S, Nicholson, A, Fernandes, N, Shah, P, Proli, C, Hewish, M, Danson, S, Shackcloth, M, Robinson, L, Russell, P, Blyth, K, Kidd, A, Dick, C, Le Quesne, J, Kirk, A, Asif, M, Bilancia, R, Kostoulas, N, Thomas, M, Hynds, R, Kanu, N, Zaccaria, S, Gronroos, E, Swanton, C, Hobor S., Al Bakir M., Hiley C. T., Skrzypski M., Frankell A. M., Bakker B., Watkins T. B. K., Markovets A., Dry J. R., Brown A. P., van der Aart J., van den Bos H., Spierings D., Oukrif D., Novelli M., Chakrabarti T., Rabinowitz A. H., Ait Hassou L., Litiere S., Kerr D. L., Tan L., Kelly G., Moore D. A., Renshaw M. J., Venkatesan S., Hill W., Huebner A., Martinez-Ruiz C., Black J. R. M., Wu W., Angelova M., McGranahan N., Downward J., Chmielecki J., Barrett C., Litchfield K., Chew S. K., Blakely C. M., de Bruin E. C., Foijer F., Vousden K. H., Bivona T. G., Lester J. F., Bajaj A., Nakas A., Sodha-Ramdeen A., Tufail M., Scotland M., Boyles R., Rathinam S., Wilson C., Marrone D., Dulloo S., Fennell D. A., Matharu G., Shaw J. A., Boleti E., Cheyne H., Khalil M., Richardson S., Cruickshank T., Price G., Kerr K. M., Benafif S., French J., Gilbert K., Naidu B., Patel A. J., Osman A., Enstone C., Langman G., Shackleford H., Djearaman M., Kadiri S., Middleton G., Leek A., Hodgkinson J. D., Totton N., Montero A., Smith E., Fontaine E., Granato F., Paiva-Correia A., Novasio J., Rammohan K., Joseph L., Bishop P., Shah R., Moss S., Joshi V., Crosbie P. A. J., Brown K. D., Carter M., Chaturvedi A., Oliveira P., Lindsay C. R., Blackhall F. H., Krebs M. G., Summers Y., Clipson A., Tugwood J., Kerr A., Rothwell D. G., Dive C., Aerts H. J. W. L., Schwarz R. F., Kaufmann T. L., Wilson G. A., Rosenthal R., Van Loo P., Birkbak N. J., Szallasi Z., Kisistok J., Sokac M., Salgado R., Diossy M., Demeulemeester J., Bunkum A., Dwornik A., Magness A., Rowan A. J., Karamani A., Toncheva A., Chain B., Castignani C., Bailey C., Abbosh C., Puttick C., Weeden C. E., Lee C., Richard C., Naceur-Lombardelli C., Pearce D. R., Karagianni D., Biswas D., Levi D., Larose Cadieux E., Lim E. L., Colliver E., Nye E., Galvez-Cancino F., Gimeno-Valiente F., Kassiotis G., Stavrou G., Mastrokalos G. -T., Lowe H. L., Matos I. G., Noorani I., Goldman J., Reading J. L., Rane J. K., Nicod J., Hartley J. A., Peggs K. S., Enfield K. S. S., Selvaraju K., Thol K., Ng K. W., Chen K., Dijkstra K., Grigoriadis K., Thakkar K., Ensell L., Shah M., Litovchenko M., Jamal-Hanjani M., Werner Sunderland M., Huska M. R., Hill M. S., Dietzen M., Leung M. M., Escudero M., Tanic M., Sivakumar M., Chervova O., Lucas O., Pich O., Al-Sawaf O., Prymas P., Hobson P., Pawlik P., Stone R. K., Bentham R., Vendramin R., Saghafinia S., Gamble S., Veeriah S., Ung S. K. A., Quezada S. A., Vanloo S., Hessey S., Ward S., Harries S., Boeing S., Beck S., Bola S. K., Karasaki T., Denner T., Marafioti T., Jones T. P., Spanswick V., Barbe V., Lu W. -T., Liu W. K., Wu Y., Naito Y., Ramsden Z., Veiga C., Royle G., Collins-Fekete C. -A., Fraioli F., Ashford P., Forster M. D., Lee S. M., Borg E., Falzon M., Papadatos-Pastos D., Wilson J., Ahmad T., Procter A. J., Ahmed A., Taylor M. N., Nair A., Lawrence D., Patrini D., Navani N., Thakrar R. M., Janes S. M., Martinoni Hoogenboom E., Monk F., Holding J. W., Choudhary J., Bhakhri K., Scarci M., Gorman P., Khiroya R., Stephens R. C. M., Wong Y. N. S., Kaplar Z., Bandula S., Hackshaw A., Hacker A. -M., Sharp A., Smith S., Kaur Dhanda H., Pilotti C., Leslie R., Grapa A., Zhang H., AbdulJabbar K., Pan X., Yuan Y., Chuter D., MacKenzie M., Chee S., Alzetani A., Cave J., Richards J., Lim E., De Sousa P., Jordan S., Rice A., Raubenheimer H., Bhayani H., Ambrose L., Devaraj A., Chavan H., Begum S., Buderi S. I., Kaniu D., Malima M., Booth S., Nicholson A. G., Fernandes N., Shah P., Proli C., Hewish M., Danson S., Shackcloth M. J., Robinson L., Russell P., Blyth K. G., Kidd A., Dick C., Le Quesne J., Kirk A., Asif M., Bilancia R., Kostoulas N., Thomas M., Hynds R. E., Kanu N., Zaccaria S., Gronroos E., Swanton C., Hobor, S, Al Bakir, M, Hiley, C, Skrzypski, M, Frankell, A, Bakker, B, Watkins, T, Markovets, A, Dry, J, Brown, A, van der Aart, J, van den Bos, H, Spierings, D, Oukrif, D, Novelli, M, Chakrabarti, T, Rabinowitz, A, Ait Hassou, L, Litiere, S, Kerr, D, Tan, L, Kelly, G, Moore, D, Renshaw, M, Venkatesan, S, Hill, W, Huebner, A, Martinez-Ruiz, C, Black, J, Wu, W, Angelova, M, Mcgranahan, N, Downward, J, Chmielecki, J, Barrett, C, Litchfield, K, Chew, S, Blakely, C, de Bruin, E, Foijer, F, Vousden, K, Bivona, T, Lester, J, Bajaj, A, Nakas, A, Sodha-Ramdeen, A, Tufail, M, Scotland, M, Boyles, R, Rathinam, S, Wilson, C, Marrone, D, Dulloo, S, Fennell, D, Matharu, G, Shaw, J, Boleti, E, Cheyne, H, Khalil, M, Richardson, S, Cruickshank, T, Price, G, Kerr, K, Benafif, S, French, J, Gilbert, K, Naidu, B, Patel, A, Osman, A, Enstone, C, Langman, G, Shackleford, H, Djearaman, M, Kadiri, S, Middleton, G, Leek, A, Hodgkinson, J, Totton, N, Montero, A, Smith, E, Fontaine, E, Granato, F, Paiva-Correia, A, Novasio, J, Rammohan, K, Joseph, L, Bishop, P, Shah, R, Moss, S, Joshi, V, Crosbie, P, Brown, K, Carter, M, Chaturvedi, A, Oliveira, P, Lindsay, C, Blackhall, F, Krebs, M, Summers, Y, Clipson, A, Tugwood, J, Kerr, A, Rothwell, D, Dive, C, Aerts, H, Schwarz, R, Kaufmann, T, Wilson, G, Rosenthal, R, Van Loo, P, Birkbak, N, Szallasi, Z, Kisistok, J, Sokac, M, Salgado, R, Diossy, M, Demeulemeester, J, Bunkum, A, Dwornik, A, Magness, A, Rowan, A, Karamani, A, Toncheva, A, Chain, B, Castignani, C, Bailey, C, Abbosh, C, Puttick, C, Weeden, C, Lee, C, Richard, C, Naceur-Lombardelli, C, Pearce, D, Karagianni, D, Biswas, D, Levi, D, Larose Cadieux, E, Lim, E, Colliver, E, Nye, E, Galvez-Cancino, F, Gimeno-Valiente, F, Kassiotis, G, Stavrou, G, Mastrokalos, G, Lowe, H, Matos, I, Noorani, I, Goldman, J, Reading, J, Rane, J, Nicod, J, Hartley, J, Peggs, K, Enfield, K, Selvaraju, K, Thol, K, Ng, K, Chen, K, Dijkstra, K, Grigoriadis, K, Thakkar, K, Ensell, L, Shah, M, Litovchenko, M, Jamal-Hanjani, M, Werner Sunderland, M, Huska, M, Hill, M, Dietzen, M, Leung, M, Escudero, M, Tanic, M, Sivakumar, M, Chervova, O, Lucas, O, Pich, O, Al-Sawaf, O, Prymas, P, Hobson, P, Pawlik, P, Stone, R, Bentham, R, Vendramin, R, Saghafinia, S, Gamble, S, Veeriah, S, Ung, S, Quezada, S, Vanloo, S, Hessey, S, Ward, S, Harries, S, Boeing, S, Beck, S, Bola, S, Karasaki, T, Denner, T, Marafioti, T, Jones, T, Spanswick, V, Barbe, V, Lu, W, Liu, W, Wu, Y, Naito, Y, Ramsden, Z, Veiga, C, Royle, G, Collins-Fekete, C, Fraioli, F, Ashford, P, Forster, M, Lee, S, Borg, E, Falzon, M, Papadatos-Pastos, D, Wilson, J, Ahmad, T, Procter, A, Ahmed, A, Taylor, M, Nair, A, Lawrence, D, Patrini, D, Navani, N, Thakrar, R, Janes, S, Martinoni Hoogenboom, E, Monk, F, Holding, J, Choudhary, J, Bhakhri, K, Scarci, M, Gorman, P, Khiroya, R, Stephens, R, Wong, Y, Kaplar, Z, Bandula, S, Hackshaw, A, Hacker, A, Sharp, A, Smith, S, Kaur Dhanda, H, Pilotti, C, Leslie, R, Grapa, A, Zhang, H, Abduljabbar, K, Pan, X, Yuan, Y, Chuter, D, Mackenzie, M, Chee, S, Alzetani, A, Cave, J, Richards, J, De Sousa, P, Jordan, S, Rice, A, Raubenheimer, H, Bhayani, H, Ambrose, L, Devaraj, A, Chavan, H, Begum, S, Buderi, S, Kaniu, D, Malima, M, Booth, S, Nicholson, A, Fernandes, N, Shah, P, Proli, C, Hewish, M, Danson, S, Shackcloth, M, Robinson, L, Russell, P, Blyth, K, Kidd, A, Dick, C, Le Quesne, J, Kirk, A, Asif, M, Bilancia, R, Kostoulas, N, Thomas, M, Hynds, R, Kanu, N, Zaccaria, S, Gronroos, E, Swanton, C, Hobor S., Al Bakir M., Hiley C. T., Skrzypski M., Frankell A. M., Bakker B., Watkins T. B. K., Markovets A., Dry J. R., Brown A. P., van der Aart J., van den Bos H., Spierings D., Oukrif D., Novelli M., Chakrabarti T., Rabinowitz A. H., Ait Hassou L., Litiere S., Kerr D. L., Tan L., Kelly G., Moore D. A., Renshaw M. J., Venkatesan S., Hill W., Huebner A., Martinez-Ruiz C., Black J. R. M., Wu W., Angelova M., McGranahan N., Downward J., Chmielecki J., Barrett C., Litchfield K., Chew S. K., Blakely C. M., de Bruin E. C., Foijer F., Vousden K. H., Bivona T. G., Lester J. F., Bajaj A., Nakas A., Sodha-Ramdeen A., Tufail M., Scotland M., Boyles R., Rathinam S., Wilson C., Marrone D., Dulloo S., Fennell D. A., Matharu G., Shaw J. A., Boleti E., Cheyne H., Khalil M., Richardson S., Cruickshank T., Price G., Kerr K. M., Benafif S., French J., Gilbert K., Naidu B., Patel A. J., Osman A., Enstone C., Langman G., Shackleford H., Djearaman M., Kadiri S., Middleton G., Leek A., Hodgkinson J. D., Totton N., Montero A., Smith E., Fontaine E., Granato F., Paiva-Correia A., Novasio J., Rammohan K., Joseph L., Bishop P., Shah R., Moss S., Joshi V., Crosbie P. A. J., Brown K. D., Carter M., Chaturvedi A., Oliveira P., Lindsay C. R., Blackhall F. H., Krebs M. G., Summers Y., Clipson A., Tugwood J., Kerr A., Rothwell D. G., Dive C., Aerts H. J. W. L., Schwarz R. F., Kaufmann T. L., Wilson G. A., Rosenthal R., Van Loo P., Birkbak N. J., Szallasi Z., Kisistok J., Sokac M., Salgado R., Diossy M., Demeulemeester J., Bunkum A., Dwornik A., Magness A., Rowan A. J., Karamani A., Toncheva A., Chain B., Castignani C., Bailey C., Abbosh C., Puttick C., Weeden C. E., Lee C., Richard C., Naceur-Lombardelli C., Pearce D. R., Karagianni D., Biswas D., Levi D., Larose Cadieux E., Lim E. L., Colliver E., Nye E., Galvez-Cancino F., Gimeno-Valiente F., Kassiotis G., Stavrou G., Mastrokalos G. -T., Lowe H. L., Matos I. G., Noorani I., Goldman J., Reading J. L., Rane J. K., Nicod J., Hartley J. A., Peggs K. S., Enfield K. S. S., Selvaraju K., Thol K., Ng K. W., Chen K., Dijkstra K., Grigoriadis K., Thakkar K., Ensell L., Shah M., Litovchenko M., Jamal-Hanjani M., Werner Sunderland M., Huska M. R., Hill M. S., Dietzen M., Leung M. M., Escudero M., Tanic M., Sivakumar M., Chervova O., Lucas O., Pich O., Al-Sawaf O., Prymas P., Hobson P., Pawlik P., Stone R. K., Bentham R., Vendramin R., Saghafinia S., Gamble S., Veeriah S., Ung S. K. A., Quezada S. A., Vanloo S., Hessey S., Ward S., Harries S., Boeing S., Beck S., Bola S. K., Karasaki T., Denner T., Marafioti T., Jones T. P., Spanswick V., Barbe V., Lu W. -T., Liu W. K., Wu Y., Naito Y., Ramsden Z., Veiga C., Royle G., Collins-Fekete C. -A., Fraioli F., Ashford P., Forster M. D., Lee S. M., Borg E., Falzon M., Papadatos-Pastos D., Wilson J., Ahmad T., Procter A. J., Ahmed A., Taylor M. N., Nair A., Lawrence D., Patrini D., Navani N., Thakrar R. M., Janes S. M., Martinoni Hoogenboom E., Monk F., Holding J. W., Choudhary J., Bhakhri K., Scarci M., Gorman P., Khiroya R., Stephens R. C. M., Wong Y. N. S., Kaplar Z., Bandula S., Hackshaw A., Hacker A. -M., Sharp A., Smith S., Kaur Dhanda H., Pilotti C., Leslie R., Grapa A., Zhang H., AbdulJabbar K., Pan X., Yuan Y., Chuter D., MacKenzie M., Chee S., Alzetani A., Cave J., Richards J., Lim E., De Sousa P., Jordan S., Rice A., Raubenheimer H., Bhayani H., Ambrose L., Devaraj A., Chavan H., Begum S., Buderi S. I., Kaniu D., Malima M., Booth S., Nicholson A. G., Fernandes N., Shah P., Proli C., Hewish M., Danson S., Shackcloth M. J., Robinson L., Russell P., Blyth K. G., Kidd A., Dick C., Le Quesne J., Kirk A., Asif M., Bilancia R., Kostoulas N., Thomas M., Hynds R. E., Kanu N., Zaccaria S., Gronroos E., and Swanton C.

Abstract

The phenomenon of mixed/heterogenous treatment responses to cancer therapies within an individual patient presents a challenging clinical scenario. Furthermore, the molecular basis of mixed intra-patient tumor responses remains unclear. Here, we show that patients with metastatic lung adenocarcinoma harbouring co-mutations of EGFR and TP53, are more likely to have mixed intra-patient tumor responses to EGFR tyrosine kinase inhibition (TKI), compared to those with an EGFR mutation alone. The combined presence of whole genome doubling (WGD) and TP53 co-mutations leads to increased genome instability and genomic copy number aberrations in genes implicated in EGFR TKI resistance. Using mouse models and an in vitro isogenic p53-mutant model system, we provide evidence that WGD provides diverse routes to drug resistance by increasing the probability of acquiring copy-number gains or losses relative to non-WGD cells. These data provide a molecular basis for mixed tumor responses to targeted therapy, within an individual patient, with implications for therapeutic strategies.

Published
2024

5. Nurse‐Led Physical Screening of Patients With Substance Use Disorders: A Cross‐Sectional Study.

Author

Middeldorp, J. F. M., Krijnen‐de Bruin, E., Buwalda, V. J. A., Goudriaan, A. E., and Meijel, B.

Subjects
*PATIENT experience, *MENTAL illness, *PATIENTS' attitudes, *HEALTH behavior, *SMOKING
Abstract

ABSTRACT Introduction Aim Method Results Implications for Practice Conclusion Somatic comorbidity is the main cause of reduced life expectancy in patients with substance use disorders (SUDs).This study aims to investigate somatic health challenges in patients with SUDs using the USS. Patient self‐management of somatic health and quality of life were also assessed.In our study, a stratified random sample of 136 clients who received treatment at a specialist addiction facility was drawn to investigate their physical health and lifestyle behaviours using the Utrecht Somatic Screening 2.0 (USS 2.0). The sample included three subgroups, that is, patients receiving outpatient treatment through Flexible Assertive Community Treatment (FACT), Heroin‐Assisted Treatment (HAT) and Opioid Replacement Therapy (ORT). Pain, self‐management and quality of life were also measured. Descriptive statistics were used to analyse the data.The findings indicate that many patients experience a large number of somatic health problems, including pain and exhaustion. The most prevalent conditions in this study are cardiovascular disease (25%) and COPD (20%), underweight and poor oral health. Tobacco smoking is prevalent among 88% of patients. Fifty percent of the patients expressed a need for support in managing their physical health.Somatic health care and lifestyle promotion should be tailored to the specific characteristics of patients.Patients with SUDs suffer from poor physical health and show unhealthy lifestyle behaviours, which demand the promotion of tailored somatic health. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

Author

Joeres, M., Maksimov, P., Höper, D., Calvelage, S., Calero-Bernal, R., Fernández-Escobar, M., Koudela, B., Blaga, R., Vrhovec, M. Globokar, Stollberg, K., Bier, N., Sotiraki, S., Sroka, J., Piotrowska, W., Kodym, P., Basso, W., Conraths, F. J., Mercier, A., Galal, L., Dardé, M. L., Balea, A., Spano, F., Schulze, C., Peters, M., Scuda, N., Lundén, A., Davidson, R. K., Terland, R., Waap, H., de Bruin, E., Vatta, P., Caccio, S., Ortega-Mora, L. M., Jokelainen, P., Schares, G., Joeres, M., Maksimov, P., Höper, D., Calvelage, S., Calero-Bernal, R., Fernández-Escobar, M., Koudela, B., Blaga, R., Vrhovec, M. Globokar, Stollberg, K., Bier, N., Sotiraki, S., Sroka, J., Piotrowska, W., Kodym, P., Basso, W., Conraths, F. J., Mercier, A., Galal, L., Dardé, M. L., Balea, A., Spano, F., Schulze, C., Peters, M., Scuda, N., Lundén, A., Davidson, R. K., Terland, R., Waap, H., de Bruin, E., Vatta, P., Caccio, S., Ortega-Mora, L. M., Jokelainen, P., and Schares, G.

Abstract

Purpose: A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains. Methods: T. gondii field isolates were collected from different parts of Europe and assessed by whole genome sequencing (WGS). In comparison to ME49 (a type II reference strain), highly polymorphic regions (HPRs) were identified, showing a considerable number of single nucleotide polymorphisms (SNPs). After confirmation by Sanger sequencing, 18 HPRs were used to design a primer panel for multiplex PCR to establish a multilocus Ion AmpliSeq typing method. Toxoplasma gondii isolates and T. gondii present in clinical samples were typed with the new method. The sensitivity of the method was tested with serially diluted reference DNA samples. Results: Among type II specimens, the method could differentiate the same number of haplotypes as the reference standard, microsatellite (MS) typing. Passages of the same isolates and specimens originating from abortion outbreaks were identified as identical. In addition, seven different genotypes, two atypical and two recombinant specimens were clearly distinguished from each other by the method. Furthermore, almost all SNPs detected by the Ion AmpliSeq method corresponded to those expected based on WGS. By testing serially diluted DNA samples, the method exhibited a similar analytical sensitivity as MS typing. Conclusion: The new method can distinguish different T. gondii genotypes and detect intra-genotype variability among European type II T. gondii strains. Furthermore, with WGS data additional target regions can be added to the method to potentially increase typing resolution.

Published
2024

8. Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method

Author

VPDC pathologie, Dutch Wildlife Health Centre (DWHC), Joeres, M., Maksimov, P., Höper, D., Calvelage, S., Calero-Bernal, R., Fernández-Escobar, M., Koudela, B., Blaga, R., Vrhovec, M. Globokar, Stollberg, K., Bier, N., Sotiraki, S., Sroka, J., Piotrowska, W., Kodym, P., Basso, W., Conraths, F. J., Mercier, A., Galal, L., Dardé, M. L., Balea, A., Spano, F., Schulze, C., Peters, M., Scuda, N., Lundén, A., Davidson, R. K., Terland, R., Waap, H., de Bruin, E., Vatta, P., Caccio, S., Ortega-Mora, L. M., Jokelainen, P., Schares, G., VPDC pathologie, Dutch Wildlife Health Centre (DWHC), Joeres, M., Maksimov, P., Höper, D., Calvelage, S., Calero-Bernal, R., Fernández-Escobar, M., Koudela, B., Blaga, R., Vrhovec, M. Globokar, Stollberg, K., Bier, N., Sotiraki, S., Sroka, J., Piotrowska, W., Kodym, P., Basso, W., Conraths, F. J., Mercier, A., Galal, L., Dardé, M. L., Balea, A., Spano, F., Schulze, C., Peters, M., Scuda, N., Lundén, A., Davidson, R. K., Terland, R., Waap, H., de Bruin, E., Vatta, P., Caccio, S., Ortega-Mora, L. M., Jokelainen, P., and Schares, G.

Published
2024

9. R-Blocks: an Energy-Efficient, Flexible, and Programmable CGRA

Author

de Bruin, E. (Barry), Vadivel, Kanishkan, Wijtvliet, Mark, Jääskeläinen, Pekka, Corporaal, Henk, de Bruin, E. (Barry), Vadivel, Kanishkan, Wijtvliet, Mark, Jääskeläinen, Pekka, and Corporaal, Henk

Abstract

Emerging data-driven applications in the embedded, e-Health, and internet of things (IoT) domain require complex on-device signal analysis and data reduction to maximize energy efficiency on these energy-constrained devices. Coarse-grained reconfigurable architectures (CGRAs) have been proposed as a good compromise between flexibility and energy efficiency for ultra-low power (ULP) signal processing. Existing CGRAs are often specialized and domain-specific or can only accelerate simple kernels, which makes accelerating complete applications on a CGRA while maintaining high energy efficiency an open issue. Moreover, the lack of instruction set architecture (ISA) standardization across CGRAs makes code generation using current compiler technology a major challenge. This work introduces R-Blocks; a ULP CGRA with HW/SW co-design tool-flow based on the OpenASIP toolset. This CGRA is extremely flexible due to its well-established VLIW-SIMD execution model and support for flexible SIMD-processing, while maintaining an extremely high energy efficiency using software bypassing, optimized instruction delivery, and local scratchpad memories. R-Blocks is synthesized in a commercial 22-nm FD-SOI technology and achieves a full-system energy efficiency of 115 MOPS/mW on a common FFT benchmark, 1.45x higher than a highly tuned embedded RISC-V processor. Comparable energy efficiency is obtained on multiple complex workloads, making R-Blocks a promising acceleration target for general-purpose computing., Emerging data-driven applications in the embedded, e-Health, and internet of things (IoT) domain require complex on-device signal analysis and data reduction to maximize energy efficiency on these energy-constrained devices. Coarse-grained reconfigurable architectures (CGRAs) have been proposed as a good compromise between flexibility and energy efficiency for ultra-low power (ULP) signal processing. Existing CGRAs are often specialized and domain-specific or can only accelerate simple kernels, which makes accelerating complete applications on a CGRA while maintaining high energy efficiency an open issue. Moreover, the lack of instruction set architecture (ISA) standardization across CGRAs makes code generation using current compiler technology a major challenge. This work introduces R-Blocks; a ULP CGRA with HW/SW co-design tool-flow based on the OpenASIP toolset. This CGRA is extremely flexible due to its well-established VLIW-SIMD execution model and support for flexible SIMD-processing, while maintaining an extremely high energy efficiency using software bypassing, optimized instruction delivery, and local scratchpad memories. R-Blocks is synthesized in a commercial 22-nm FD-SOI technology and achieves a full-system energy efficiency of 115 MOPS/mW on a common FFT benchmark, 1.45x higher than a highly tuned embedded RISC-V processor. Comparable energy efficiency is obtained on multiple complex workloads, making R-Blocks a promising acceleration target for general-purpose computing.

Published
2024

12. The increasing complexity of arbovirus serology:An in-depth systematic review on cross-reactivity

Author

Kasbergen, LMR, Nieuwenhuijse, DF, de Bruin, E, Sikkema, RS, Koopmans, MPG, Kasbergen, LMR, Nieuwenhuijse, DF, de Bruin, E, Sikkema, RS, and Koopmans, MPG

Abstract

Diagnosis of arbovirus infection or exposure by antibody testing is becoming increasingly difficult due to global expansion of arboviruses, which induce antibodies that may (cross-)react in serological assays. We provide a systematic review of the current knowledge and knowledge gaps in differential arbovirus serology. The search included Medline, Embase and Web of Science databases and identified 911 publications which were reduced to 102 after exclusion of studies not providing data on possible cross-reactivity or studies that did not meet the inclusion criteria regarding confirmation of virus exposure of reference population sets. Using a scoring system to further assess quality of studies, we show that the majority of the selected papers (N = 102) provides insufficient detail to support conclusions on specificity of serological outcomes with regards to elucidating antibody cross-reactivity. Along with the lack of standardization of assays, metadata such as time of illness onset, vaccination, infection and travel history, age and specificity of serological methods were most frequently missing. Given the critical role of serology for diagnosis and surveillance of arbovirus infections, better standards for reporting, as well as the development of more (standardized) specific serological assays that allow discrimination between exposures to multiple different arboviruses, are a large global unmet need.

Published
2023

18. Prebypass: Software Register File Bypassing for Reduced Interconnection Architectures

Author

Vadivel, Kanishkan, de Bruin, E. (Barry), Jordans, Roel, Corporaal, Henk, Jääskeläinen, Pekka, Fabelo, Himar, Ortega, Samuel, Skavhaug, Amund, Tampere University, Computing Sciences, Electronic Systems, Center for Astronomical Instrumentation, EAISI High Tech Systems, and Center for Care & Cure Technology Eindhoven

Subjects
exposed datapath, LLVM, code generation, TTA, 113 Computer and information sciences
Abstract

Exposed Datapath Architectures (EDPAs) with aggressively pruned data-path connectivity, where not all function units in the design have connections to a centralized register file, are promising solutions for energy-efficient computation. A direct bypassing of data between function units without temporary copies to the register file is a prime optimization for programming such architectures. However, traditional compiler frameworks, such as LLVM, assume function-units connect to register-files and allocate all live variables in register-files. This leads to schedule inefficiencies in terms of instruction-level parallelism and reg-ister accesses in the EDPAs. To address these inefficiencies, we propose Prebypass; a new optimization pass for EDPA compiler backends. Experimental results on an EDPA class of architecture, Transport- Triggered Architecture, show that Prebypass improves the runtime, register reads, and register writes up to 16%, 26 %, and 37 % respectively, when the datapath is extremely pruned. Evaluation in a 28-nm FDSOI technology reveals that Prebypass improves the core-level Energy by 17.5 % over the current heuristic scheduler. acceptedVersion

Published
2022
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26. Mindful parenting in secondary child mental health: Key parenting predictors of treatment seekers and treatment effects

Author

Emerson, L.M., Aktar, E., de Bruin, E., Potharst, E., Bögels, S., Developmental Psychopathology (RICDE, FMG), Ontwikkelingspsychologie (Psychologie, FMG), and Brain and Cognition

Abstract

Objectives Emerging evidence supports the positive effects of mindful parenting as a clinical intervention in the context of child psychopathology; however, previous studies have not considered the specific parenting predictors of improvements in child outcomes. Methods Parents accessing a child and youth secondary mental health care center participated in an 8-week mindful parenting training (n = 89). The effects of the mindful parenting training were assessed on parent-reported child’s psychopathology, parents’ own psychopathology, mindfulness, and parenting factors from pre- to post-intervention, 8-week and 1-year follow-up. Results Multi-level analyses indicated immediate and delayed improvements in most child and parent outcomes. Changes in experiential avoidance in parenting partially predicted improvements in child internalizing problems. In combination with mindful parenting, experiential avoidance in parenting fully accounted for improvements in child attention problems. Changes in parental over-reactivity fully accounted for improvements in child externalizing problems. Conclusions The mindful parenting training successfully improved the targeted (mindful) parenting factors, which in turn predicted improvements across different child outcomes.

Published
2021

29. Transmission of SARS-CoV-2 within households: a prospective cohort study in the Netherlands and Belgium – Interim results

Author

Verberk, JDM, primary, de Hoog, MLA, additional, Westerhof, I, additional, Van Goethem, S, additional, Lammens, C, additional, Ieven, M, additional, de Bruin, E, additional, Bielicki, J, additional, Coenen, S, additional, van Beek, J, additional, Bonten, M, additional, Goossens, H, additional, and Bruijning-Verhagen, PCJL, additional

Published
2021
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32. 350TiP A phase III trial of capivasertib and fulvestrant versus placebo and fulvestrant in patients with HR+/HER2− breast cancer (CAPItello-291)

Author

Turner, N., primary, Howell, S., additional, Jhaveri, K., additional, Gomez, H., additional, Toi, M., additional, Hu, X., additional, Loibl, S., additional, Rugo, H.S., additional, Ni, P., additional, De Bruin, E., additional, Orbegoso, C.M.A.A., additional, Schiavon, G., additional, Foxley, A., additional, and Oliveira, M., additional

Published
2020
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38. A pilot study assessing reliability and age‐related differences in corticomuscular and intramuscular coherence in ankle dorsiflexors during walking

Author

Gennaro, F. and de Bruin, E. D.

Subjects
Adult, Male, Skeletal Muscle, Pyramidal Tracts, Ageing and Degeneration, Walking, gait, lcsh:Physiology, Gamma Rhythm, Humans, corticomuscular coherence, Muscle, Skeletal, Original Research, Aged, Aged, 80 and over, lcsh:QP1-981, intramuscular coherence, aging, Reproducibility of Results, Electroencephalography, corticospinal control, test–retest, Female, Sensorimotor Cortex, Beta Rhythm, Neuroscience
Abstract

Corticomuscular (CMC) and intramuscular (intraMC) coherence represent measures of corticospinal interaction. Both CMC and intraMC can be assessed during human locomotion tasks, for example, while walking. Corticospinal control of gait can deteriorate during the aging process and CMC and intraMC may represent an important monitoring means. However, it is unclear whether such assessments represent a reliable tool when performed during walking in an ecologically valid scenario and whether age‐related differences may occur. Wireless surface electroencephalography and electromyography were employed in a pilot study with young and old adults during overground walking in two separate sessions. CMC and intraMC analyses were performed in the gathered beta and lower gamma frequencies (i.e., 13–40 Hz). Significant log‐transformed coherence area was tested for intersessions test–retest reliability by determining intraclass correlation coefficient (ICC), yielding to low reliability in CMC in both younger and older adults. intraMC exclusively showed low reliability in the older adults, whereas intraMC in the younger adults revealed similar values as previously reported: test–retest reliability [ICC (95% CI): 0.44 (−0.23, 0.87); SEM: 0.46; MDC: 1.28; MDC%: 103; Hedge's g (95% CI): 0.54 (−0.13, 1.57)]. Significant differences between the age groups were observed in intraMC by either comparing the two groups with the first test [Hedge's g (95% CI): 1.55 (0.85, 2.15); p‐value: .006] or with the retest data [Hedge's g (95% CI): 2.24 (0.73, 3.70); p‐value: .005]. Notwithstanding the small sample size investigated, intraMC seems a moderately reliable assessment in younger adults. The further development and use of this measure in practical settings to infer corticospinal interaction in human locomotion in clinical practice is warranted and should help to refine the analysis. This necessitates involving larger sample sizes as well as including a wider number of lower limb muscles. Moreover, further research seems warranted by the observed differences in modulation mechanisms of corticospinal control of gait as ascertained by intraMC between the age groups., Corticomuscular and intramuscular coherence are widely used nowadays in motor control and movement neurophysiology field, but it is unclear whether these assessments represent reliable tools when performed during walking in an ecologically valid scenario. Corticospinal control of gait can deteriorate during the aging process and corticomuscular or intramuscular coherence may represent an important monitoring strategy, but whether any age‐related differences may occur still needs to be elucidated. We show that neural drive to ankle dorsiflexors during gait in an ecological valid scenario is differently modulated in aging and, in parallel, we confirm previous research showing moderate reliability of intramuscular coherence, but not yet regarding corticomuscular coherence.

Published
2020

40. Mindful2Work unterrichten: Das Trainingshandbuch

Author

de Bruin, E., Formsma, A., Bögels, S., Developmental Psychopathology (RICDE, FMG), and Ontwikkelingspsychologie (Psychologie, FMG)

Abstract

Mindful2Work: beruflichen Stress reduzieren – neue Lebensfreude gewinnen Stress ist ein weitverbreitetes Phänomen und kann sich nachteilig auf die körperliche und geistige Gesundheit auswirken - am Arbeitsplatz und darüber hinaus. Achtsamkeitsmeditation, Yoga und Bewegung haben positive Effekte bei stressbedingten Symptomen, wie die Forschung zeigt. Das Trainingsprogramm Mindful2Work kombiniert diese drei Elemente. In sechs Wochen lernen die Teilnehmenden, wie sie Stress während der Arbeit und im Privatleben reduzieren können, sodass sie sich ruhiger und leistungsfähiger fühlen und ihre Work-Life-Balance spürbar verbessern. Dieses Handbuch erläutert Schritt für Schritt, wie das Training aufgebaut ist, enthält sämtliche Übungen und Meditationen und gibt einen Überblick über die theoretischen Grundlagen, die Ergebnisse der Forschung und die Trainer*innenausbildung. Mindful2Work wurde von den Autorinnen in Zusammenarbeit mit der Universität Amsterdam entwickelt und ist wissenschaftlich evaluiert.

Published
2020

42. COMMENTARY

Author

de Bruin, E D and Rosenbaum, D

Published
2006

43. BrainWave: an energy-efficient EEG monitoring system - evaluation and trade-offs

Author

de Bruin, E. (Barry), Singh, Kamlesh, Huisken, Jos A., Corporaal, Henk, de Bruin, E. (Barry), Singh, Kamlesh, Huisken, Jos A., and Corporaal, Henk

Abstract

This paper presents the design and evaluation of an energy-efficient seizure detection system for emerging EEG-based monitoring applications, such as non-convulsive epileptic seizure detection and Freezing-of-Gait (FoG) detection. As part of the BrainWave system, a BrainWave processor for flexible and energy-efficient signal processing is designed. The key system design parameters, including algorithmic optimizations, feature offloading and near-Threshold computing are evaluated in this work. The BrainWave processor is evaluated while executing a complex EEG-based epileptic seizure detection algorithm. In a 28-nm FDSOI technology, 325 μJ per classification at 0.9 V and 290 μJ at 0.5 V are achieved using an optimized software-only implementation. By leveraging a Coarse-Grained Reconfigurable Array (CGRA), 160 μJ and 135 μJ are obtained, respectively, while maintaining a high level of flexibility. Near-Threshold computing combined with CGRA acceleration leads to an energy reduction of up to 59%, or 55% including idle-Time overhead.

Published
2020

46. Mindful2work: Effectives Training gegen Stress und Burnout mit Bewegung, Yoga und Achtsahmkeit. Übungsbuch

Author

de Bruin, E., Formsma, A., Bögels, S., Developmental Psychopathology (RICDE, FMG), Ontwikkelingspsychologie (Psychologie, FMG), Brain and Cognition, and Research Institute for Child Development and Education

Abstract

Haben Sie ab und zu das Gefühl, dass Ihnen die Arbeit über den Kopf wächst? Fällt es Ihnen schwer, sich zu konzentrieren und zu motivieren? Leiden Sie an Nacken-, Schulter- oder Rückenschmerzen, schlafen schlecht und kommen aus dem Grübeln nicht mehr heraus? Das Mindful2Work-Training bietet die Chance, in sechs Wochen einen neuen Umgang mit Stress bei der Arbeit (und im Leben überhaupt) zu erlernen. Eine einzigartige Mischung aus Bewegung an der frischen Luft, Yoga-Übungen und Achtsamkeitsmeditation bringt Körper, Geist und Seele wieder ins Gleichgewicht und stärkt die Konzentration. Sie lernen, stressige Situationen besser zu bewältigen und auch in turbulenten Zeiten gut für sich zu sorgen. Sie gewinnen Gelassenheit und das Gefühl, Ihr Leben wieder selbst in der Hand zu haben. Mindful2Work wurde von den Autorinnen in Zusammenarbeit mit der Universität Amsterdam entwickelt und ist wissenschaftlich evaluiert. Geführte Übungen als MP3-Download im Arbor Online-Center gesprochen von Lienhard Valentin Sitzmeditation mit Achtsamkeit auf den Atem – 10 Minuten Bodyscan – 16 Minuten Sitzmeditation mit Achtsamkeit auf Atem und Körper – 8 Minuten Atemraum – 5 Minuten Sitzmeditation mit Achtsamkeit auf Geräusche und Gedanken – 12 Minuten Gehmeditation – 9 Minuten Sitzmeditation mit Achtsamkeit auf eine schwierige Situation – 9 Minuten Freundlichkeitsmeditation – 11 Minuten Bergmeditation – 9 Minuten Alle Meditationen sind über einen Link im Buch zum Download erhältlich.

Published
2019

48. Playing Exergames Facilitates Central Drive to the Ankle Dorsiflexors During Gait in Older Adults; a Quasi-Experimental Investigation

Author

de Bruin, E. D., Patt, N., Ringli, L., and Gennaro, F.

Subjects
body regions, older adults, exergame, central drive, tibialis anterior, foot clearance, Neuroscience, Original Research
Abstract

Purpose: Gait training might be of particular importance to reduce fall risk in older adults. In the present study we explore the hypothesis that video game-based training will increase tibialis anterior (TA) muscle EMG-EMG coherence and relates to functional measures of lower limb control. Methods: We focus on video game-based training performed in standing position, where the subjects have to lift their toes to place their feet on different target zones in order to successfully play the game. This type of training is hypothesized leading to progressive changes in the central motor drive to TA motor neurons and, consequently, improved control of ankle dorsiflexion during gait. Results: Twenty older adults, 79 ± 8 years old, 13 females/7 males, participated. Results showed a significant difference against 0 in the experimental ΔPOST condition in dual-task walking and beta Frequency Of Interest (p = 0.002). Walking under dual task condition showed significant change over time in minimal Toe Clearance for both the left [χ2(2) = 7.46, p = 0.024, n = 20] and right [χ2(2) = 8.87, p = 0.012, n = 20] leg. No change in lower extremity function was detectable. Conclusion: Overall we conclude that the initiation of an exergame-based training in upright standing position improves neural drive to the lower extremities in older adults, effects on minimal Toe Clearance and seems an acceptable form of physical exercise for this group., Frontiers in Aging Neuroscience, 11, ISSN:1663-4365

Published
2019
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50. En nu lekker slapen!: Slaap bij kinderen in de basisschoolleeftijd

Author

de Bruin, E., Hendriks, D., and Developmental Psychopathology (RICDE, FMG)

Abstract

Goed slapen is belangrijk voor een gezonde ontwikkeling. Jonge kinderen zijn voor het reguleren van hun slaap sterk afhankelijk van hun ouders. De manier waarop ouders hun kinderen gezond slaapgedrag aanleren, werkt door tot in de adolescentie. Uit onderzoek blijkt echter dat veel kinderen slaapproblemen ervaren en deze problemen lijken de laatste jaren alleen maar toe te nemen. Slaapproblemen bij jonge kinderen hebben vaak ook grote gevolgen voor het hele gezin. Hoe kunnen we deze problemen voorkomen of zo nodig behandelen?

Published
2018

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