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4. Wild Bird Densities and Landscape Variables Predict Spatial Patterns in HPAI Outbreak Risk across The Netherlands

Author

Schreuder, J., de Knegt, Henjo, Velkers, F.C., Elbers, A.R.W., Stahl, Julia, Slaterus, Roy, Stegeman, Arjan, de Boer, Fred, Schreuder, J., de Knegt, Henjo, Velkers, F.C., Elbers, A.R.W., Stahl, Julia, Slaterus, Roy, Stegeman, Arjan, and de Boer, Fred

Abstract

Highly pathogenic avian influenza viruses’ (HPAIVs) transmission from wild birds to poultry occurs globally, threatening animal and public health. To predict the HPAI outbreak risk in relation to wild bird densities and land cover variables, we performed a case‐control study of 26 HPAI outbreaks (cases) on Dutch poultry farms, each matched with four comparable controls. We trained machine learning classifiers to predict outbreak risk with predictors analyzed at different spatial scales. Of the 20 best explaining predictors, 17 consisted of densities of water‐associated bird species, 2 of birds of prey, and 1 represented the surrounding landscape, i.e., agricultural cover. The spatial distribution of mallard (Anas platyrhynchos) contributed most to risk prediction, followed by mute swan (Cygnus olor), common kestrel (Falco tinnunculus) and brant goose (Branta bernicla). The model successfully distinguished cases from controls, with an area under the receiver operating characteristic curve of 0.92, indicating accurate prediction of HPAI outbreak risk despite the limited numbers of cases. Different classification algorithms led to similar predictions, demonstrating robustness of the risk maps. These analyses and risk maps facilitate insights into the role of wild bird species and support prioritization of areas for surveillance, biosecurity measures and establishments of new poultry farms to reduce HPAI outbreak risks.

Published
2022

5. Monitoring der Pulmonalzirkulation

Author

Versprille, A., Jansen, J. R. C., Schreuder, J. J., Bergmann, H., editor, Brückner, J. B., editor, Gemperle, M., editor, Henschel, W. F., editor, Mayrhofer, O., editor, Meßmer, K., editor, Peter, K., editor, and Versprille, Adriaan, editor

Published
1992
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10. Blockade of the co-inhibitory molecule PD-1 unleashes ILC2-dependent antitumor immunity in melanoma

Author

Jacquelot, N, Seillet, C, Wang, M, Pizzolla, A, Liao, Y, Hediyeh-zadeh, S, Grisaru-Tal, S, Louis, C, Huang, Q, Schreuder, J, Souza-Fonseca-Guimaraes, F, de Graaf, CA, Thia, K, Macdonald, S, Camilleri, M, Luong, K, Zhang, S, Chopin, M, Molden-Hauer, T, Nutt, SL, Umansky, V, Ciric, B, Groom, JR, Foster, PS, Hansbro, PM, McKenzie, ANJ, Gray, DHD, Behren, A, Cebon, J, Vivier, E, Wicks, IP, Trapani, JA, Munitz, A, Davis, MJ, Shi, W, Neeson, PJ, Belz, GT, Jacquelot, N, Seillet, C, Wang, M, Pizzolla, A, Liao, Y, Hediyeh-zadeh, S, Grisaru-Tal, S, Louis, C, Huang, Q, Schreuder, J, Souza-Fonseca-Guimaraes, F, de Graaf, CA, Thia, K, Macdonald, S, Camilleri, M, Luong, K, Zhang, S, Chopin, M, Molden-Hauer, T, Nutt, SL, Umansky, V, Ciric, B, Groom, JR, Foster, PS, Hansbro, PM, McKenzie, ANJ, Gray, DHD, Behren, A, Cebon, J, Vivier, E, Wicks, IP, Trapani, JA, Munitz, A, Davis, MJ, Shi, W, Neeson, PJ, and Belz, GT

Abstract

Group 2 innate lymphoid cells (ILC2s) are essential to maintain tissue homeostasis. In cancer, ILC2s can harbor both pro-tumorigenic and anti-tumorigenic functions, but we know little about their underlying mechanisms or whether they could be clinically relevant or targeted to improve patient outcomes. Here, we found that high ILC2 infiltration in human melanoma was associated with a good clinical prognosis. ILC2s are critical producers of the cytokine granulocyte-macrophage colony-stimulating factor, which coordinates the recruitment and activation of eosinophils to enhance antitumor responses. Tumor-infiltrating ILC2s expressed programmed cell death protein-1, which limited their intratumoral accumulation, proliferation and antitumor effector functions. This inhibition could be overcome in vivo by combining interleukin-33-driven ILC2 activation with programmed cell death protein-1 blockade to significantly increase antitumor responses. Together, our results identified ILC2s as a critical immune cell type involved in melanoma immunity and revealed a potential synergistic approach to harness ILC2 function for antitumor immunotherapies.

Published
2021

11. Phyloseq R object accompanying the paper Temporal Dynamics Cloacal Microbiota 16S metataxonomics

Author

Bossers, A., Schreuder, J., Bossers, A., and Schreuder, J.

Abstract

This ready to load phyloseq R S4 object contains the ASV table, taxonomy table and sample metadata. This data was build using the DaDa2 (version 1.6.0) and phyloseq (version 1.223) R packages using our raw MiSeq PE300 sequencing data deposited at NCBI-SRA under BioProject: PRJNA673103. Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 % and 4.4 % of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable

Published
2021

12. An observational field study of the cloacal microbiota in adult laying hens with and without access to an outdoor range

Author

FAH veterinaire epidemiologie, dFAH I&I, FAH GZ pluimvee, dFAH AVR, Schreuder, J., Velkers, F.C., Bouwstra, Ruth, Beerens, Nancy, Stegeman, J.A., de Boer, Fred, van Hooft, Pim, Elbers, Armin, Bossers, Alex, Jurburg, Stephanie D, FAH veterinaire epidemiologie, dFAH I&I, FAH GZ pluimvee, dFAH AVR, Schreuder, J., Velkers, F.C., Bouwstra, Ruth, Beerens, Nancy, Stegeman, J.A., de Boer, Fred, van Hooft, Pim, Elbers, Armin, Bossers, Alex, and Jurburg, Stephanie D

Published
2020

23. Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer (vol 10, 766, 2019)

Author

Merino, D, Weber, TS, Serrano, A, Vaillant, F, Liu, K, Pal, B, Di Stefano, L, Schreuder, J, Lin, D, Chen, Y, Asselin-Labat, ML, Schumacher, TN, Cameron, D, Smyth, GK, Papenfuss, AT, Lindeman, GJ, Visvader, JE, Naik, SH, Merino, D, Weber, TS, Serrano, A, Vaillant, F, Liu, K, Pal, B, Di Stefano, L, Schreuder, J, Lin, D, Chen, Y, Asselin-Labat, ML, Schumacher, TN, Cameron, D, Smyth, GK, Papenfuss, AT, Lindeman, GJ, Visvader, JE, and Naik, SH

Abstract

The original version of this Article contained an error in Fig. 4. In the left histogram of the right panel of Fig. 4d, several data points were inadvertently deleted from the histogram during the production process. This error has been corrected in both the PDF and HTML versions of the Article. The original, incorrect version of Fig. 4 is presented in the accompanying Publisher Correction.

Published
2019

24. Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer

Author

Merino, D, Weber, TS, Serrano, A, Vaillant, F, Liu, K, Pal, B, Di Stefano, L, Schreuder, J, Lin, D, Chen, Y, Asselin-Labat, ML, Schumacher, TN, Cameron, D, Smyth, GK, Papenfuss, AT, Lindeman, GJ, Visvader, JE, Naik, SH, Merino, D, Weber, TS, Serrano, A, Vaillant, F, Liu, K, Pal, B, Di Stefano, L, Schreuder, J, Lin, D, Chen, Y, Asselin-Labat, ML, Schumacher, TN, Cameron, D, Smyth, GK, Papenfuss, AT, Lindeman, GJ, Visvader, JE, and Naik, SH

Abstract

Primary triple negative breast cancers (TNBC) are prone to dissemination but sub-clonal relationships between tumors and resulting metastases are poorly understood. Here we use cellular barcoding of two treatment-naïve TNBC patient-derived xenografts (PDXs) to track the spatio-temporal fate of thousands of barcoded clones in primary tumors, and their metastases. Tumor resection had a major impact on reducing clonal diversity in secondary sites, indicating that most disseminated tumor cells lacked the capacity to 'seed', hence originated from 'shedders' that did not persist. The few clones that continued to grow after resection i.e. 'seeders', did not correlate in frequency with their parental clones in primary tumors. Cisplatin treatment of one BRCA1-mutated PDX model to non-palpable levels had a surprisingly minor impact on clonal diversity in the relapsed tumor yet purged 50% of distal clones. Therefore, clonal features of shedding, seeding and drug resistance are important factors to consider for the design of therapeutic strategies.

Published
2019

33. Constructing timetables for sport competitions

Author

Schreuder, J. A. M., Cottle, R. W., editor, Dixon, L. C. W., editor, Korte, B., editor, Todd, M. J., editor, Allgower, E. L., editor, Bartels, R., editor, Chvátal, V., editor, Dennis, J. E., Jr., editor, Eaves, B. C., editor, Fletcher, R., editor, Iri, M., editor, Jeroslow, R. G., editor, Johnson, D. S., editor, Lemarechal, C., editor, Lovasz, L., editor, McLinden, L., editor, Padberg, M. W., editor, Powell, M. J. D., editor, Pulleyblank, W. R., editor, Ritter, K., editor, Sargent, R. W. H., editor, Shanno, D. F., editor, Trotter, L. E., Jr., editor, Tuy, H., editor, Wets, R. J. B., editor, Witzgall, C., editor, Beale, E. M. L., editor, Dantzig, G. B., editor, Kantorovich, L. V., editor, Koopmans, T. C., editor, Tucker, A. W., editor, Wolfe, P., editor, and Rayward-Smith, V. J., editor

Published
1980
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36. Suction Due to Left Ventricular Assist: Implications for Device Control and Management

Author

Reesink, K, Dekker, A, VAN DER NAGEL, T, Beghi, Cesare, Leonardi, F, DE CICCO, G, Botti, P, Lorusso, R, Schreuder, J, VAN DER VEEN, F, and Massen, J.

Subjects
Artificial heart, Hemodynamics, Pulmonary vascular resistance, Shock, Thorax, Biophysics, Suction (medicine), Pulmonary Circulation, Cardiac output, medicine.medical_specialty, medicine.medical_treatment, Biomedical Engineering, Medicine (miscellaneous), Bioengineering, Ventricular Function, Left, Pulmonary artery banding, Biomaterials, Internal medicine, medicine.artery, medicine, Animals, Computer Simulation, Sheep, business.industry, Models, Cardiovascular, General Medicine, equipment and supplies, medicine.anatomical_structure, Ventricular assist device, Anesthesia, Hemorheology, Pulmonary artery, Ventricular pressure, Cardiology, Vascular resistance, Aortic pressure, Heart-Assist Devices, business
Abstract

Left ventricular assist device (LVAD) overpumping is associated with hemolysis, thrombus release, and tissue damage at the pump inlet. However, the impact of LVAD suction on pulmonary circulatory function remains unknown. We investigated LVAD suction as induced by pulmonary artery banding and overpumping in experimental animals and in a computer model. In six sheep, a rotary LVAD was implanted. Before inducing suction, partial support (40-60% of cardiac output) was established and characterized by measuring pressures and flows. In the animals, pulmonary artery occlusion (PAOC) elicited LVAD suction (left ventricular pressure was from -10 to -20 mm Hg) within 5-10 heartbeats. During suction, aortic pressure dropped to 50% and LVAD flow decreased significantly. After releasing the occlusion (20 s), the collapsed state persisted for another 20 s. A similar trend was obtained by simulating PAOC in the computer model. Additional simulations showed that pulmonary vascular resistance (PVR), volume status, and right ventricular (RV) contractility are exponentially related to the persistence of collapse after a suction event. Even modest increases in predisposing factors (elevated PVR, RV dysfunction, hypovolemia) caused sustained hemodynamic collapse lasting in excess of 15 min. Both in selected animals and the computer model, comparable suction-induced collapse was obtained by increasing LVAD speed by about 33%. Attempted compensation by simply decreasing speed was not effective, but temporarily shutting down the LVAD caused rapid reversal of collapse. In conclusion, rotary LVAD suction causes unfavorable conditions for effective unloading. The use of pump interventions appears a promising tool to detect suction and to avoid the associated hemodynamic depression.

Published
2007

37. Abstracts of papers

Author

Kleinbloesem, C. H., van Brummelen, P., van de Linde, J. A., Breimer, D. D., Kerremans, A. L. M., Cremers, H. J., Rodrigues de Miranda, J. F., van Ginneken, C. A. M., Gribnau, F. W. J., Schols, M., Mooy, J., van Hooff, M., van Baak, M. A., Rahn, K. H., Soeterboek, A. M., van Thiel, M., Westra, P., Vermeer, G. A., van Rooy, H. H., Pirovano, I. M., Soudijn, W., Lohman, J. J. H. M., Hooymans, P. M., Verhey, M. T. J. M., Pluym, B. F. M., Merkus, F. W. H. M., Thijssen, H. H. W., Baars, L. G., Reijnders, M. J., Wagenvoort, J. H. T., Fieren, M. W. J. A., Goessens, W. H. F., Michel, M. F., Edelbroek, P. M., Zitman, F. G., Schreuder, J. N., Rooymans, H. G. M., de Wolff, F. A., Hekster, Ch. A., Vree, T. B., van Baak, M. A., Jennen, W. H. J., Verstappen, F. T. J., Salemans, J., Lenders, J. W. M., Fennis, J., Thien, Th., Houben, H., Binkhorst, R. A., van 't Laar, A., Koopmans, P. P., van Hees, P. A. M., Hoefnagels, W. H. L., Huysmans, F. T. M., Woittiez, A. J. J., Wenting, G. J., Derkx, F. H. M., Schalekamp, M. A. D. H., Storms, G. E. M. G., Lutterman, J. A., de Nobel, E., van 't Laar, A., Sitsen, J. M. A., de Jong, W., Stuyt, P. M. J., Stalenhoef, A. F. H., Demacker, P. N. M., van 't Laar, A., Oosterhuis, B., Berge, R. J. M.ten, Sauerwein, N. P., Endert, E., Schellekens, P. Th. A., van Boxtel, C. J., Terpstra G. K., Raaijmakers, J. A. M., Wassink, G. A., Kreukniet, J., Bakker, J. C., de Vries-v. Rossen, A., Bleeker, W. K., Ufkes, J. G. R., van Rosevelt, R. F., van Mourik, J. A., Loos, J. A., Brummelhuis, H. G. J., Schalken, J. J., Lammers, J. W. J., Beld, A. J., and van Herwaarden, C. L. A.

Published
1983
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42. Assessment of myocardial performance with ventricular pressure-volume relations: clinical applications in cardiac surgery

Author

Caputo M, Schreuder J, Fino C, Baan J, ALFIERI , OTTAVIO, Caputo, M, Schreuder, J, Fino, C, Baan, J, and Alfieri, Ottavio

Subjects
Heart Diseases, Ventricular Pressure, Humans, Reproducibility of Results, Cardiac Surgical Procedures, Prognosis, Myocardial Contraction, Ventricular Function, Left
Abstract

The assessment of myocardial performance in patients with cardiomyopathy is of vital importance in cardiology and cardiac surgery, especially considering the significant increase in the number of patients treated for congestive heart failure. Left ventricular pressure-volume analysis is a method, which can assess accurately myocardial contractility, separating the systolic and diastolic function at different preload and afterload conditions. This technique can be used for determination of the efficacy of a therapeutic pharmaceutical or surgical intervention, for instance the assessment of ventricular function after coronary revascularization. A few studies using the conductance catheter for the analysis of ventricular pressure-volume relations in the field of cardiac surgery have been published. In our center we started to use this technique to analyze cardiac surgical procedures, like mitral valve reconstruction, aortic valve replacement, myocardial revascularization, left ventricular assist, and surgical left ventricular remodeling. This information will be used to develop a therapeutic strategy, which may optimize surgical indications and improve the peri- and postoperative treatment and the efficacy of that surgical technique. In this short review the possible clinical use in cardiac surgery and the methodology of the pressure-volume loops have been described. Three clinical cases are presented to demonstrate functional information related to the surgical treatment of congestive heart failure patients.

Published
2000

45. Shunting passenger trains : getting ready for departure

Author

Akker, van den, J.M., Baarsma, H., Hurink, J.L., Modelski, M.S., Paulus, J.J., Reijnen, I.C., Roozemond, D.A., Schreuder, J., Bokhove, O., Meinsma, G., Stolk, C.C., Vellekoop, M.H., Stochastic Operations Research, Operations Planning Acc. & Control, and Discrete Algebra and Geometry

Subjects
Hardware_PERFORMANCEANDRELIABILITY
Abstract

In this paper we consider the problem of shunting train units on a railway station. Train units arrive at and depart from the station according to a given train schedule and in between the units may have to be stored at the station. The assignment of arriving to departing train units (called matching) and the scheduling of the movements to realize this matching is called shunting. The goal is to realize the shunting using a minimal number of shunt movements. For a restricted version of this problem an ILP approach has been presented in the literature. In this paper, we consider the general shunting problem and derive a greedy heuristic approach and an exact solution method based on dynamic programming. Both methods are flexible in the sense that they allow the incorporation of practical planning rules and may be extended to cover additional requirements from practice.

Published
2008

49. Variation in the human TP53 gene affects old age survival and cancer mortality

Author

van Heemst, D, Mooijaart, S P, Beekman, M, Schreuder, J, de, Craen AJ, Brandt, B W, Slagboom, P E, Westendorp, R G, group, Long Life study, and Preventive Dentistry

Subjects
Aging, medicine.medical_specialty, Arginine, media_common.quotation_subject, Longevity, Biology, Biochemistry, Mice, Endocrinology, Atrophy, Neoplasms, Internal medicine, Genotype, Genetics, medicine, Animals, Humans, Genetic Predisposition to Disease, Prospective cohort study, Molecular Biology, Aged, media_common, Aged, 80 and over, Polymorphism, Genetic, Cancer, Cell Biology, Genes, p53, medicine.disease, Ageing, Apoptosis
Abstract

Longevity may depend on a balance between tumor suppression and tissue renewal mechanisms [Campisi, J., 2003. Cancer and ageing: rival demons? Nat. Rev. Cancer 3 (5), 339-349]. Mice with constitutively activated p53 are almost cancer free but their life span is reduced and accompanied by early tissue atrophy [Tyner et al., 2002. p53 mutant mice that display early ageing-associated phenotypes. Nature 415 (6867) 45-53]. Replacement of arginine (Arg) by proline (Pro) at position 72 of human p53 decreases its apoptotic potential [Dumont et al., 2003. The codon 72 polymorphic variants of p53 have markedly different apoptotic potential. Nat. Genet. 33 (3), 357-365] providing a tool to test for a similar trade-off in humans. Using a formal meta-analysis of the published literature we show that carriers of the TP53 codon 72 Pro/Pro genotype have an increased cancer risk compared to Arg/Arg carriers (p

Published
2005

50. Variation in the SHC1 gene and longevity in humans

Author

Mooijaart, S P, van Heemst, D, Schreuder, J, van Gerwen, S, Beekman, M, Brandt, B W, Slagboom, P Eline, Westendorp, R G, Group, 'Long Life' Study, and Preventive Dentistry

Subjects
Adult, Male, Aging, Candidate gene, Src Homology 2 Domain-Containing, Transforming Protein 1, media_common.quotation_subject, Longevity, Physiology, Biology, Biochemistry, Endocrinology, Gene Frequency, Polymorphism (computer science), Valine, Genetics, Humans, Prospective Studies, Mortality, Molecular Biology, Allele frequency, media_common, Adaptor Proteins, Signal Transducing, Aged, Netherlands, Aged, 80 and over, Polymorphism, Genetic, Mortality rate, Genetic Variation, Cell Biology, SHC1, Survival Analysis, Adaptor Proteins, Vesicular Transport, Shc Signaling Adaptor Proteins, Cohort, Female, Follow-Up Studies
Abstract

Mice in which the p66 SHC specific region of the SHC gene is deleted live 30% longer without apparent disease. These mice have lower levels of oxidative stress and apoptosis, both of which have been linked to old age survival in man. This makes SHC1 an important candidate gene for longevity in humans. We found no variations in the p66 specific region of the SHC1 gene in 30 young and 30 extreme long-lived subjects. Thus in man, no common sequence variations occur in p66 specific region of the SHC1 gene. In two independent cohorts of respectively 730 and 563 subjects aged 85 and over, we tested the only known non-synonymous polymorphism, Met 410 Val, for association with longevity using a prospective follow-up design. In the first cohort, we found increasing valine allele frequency in three strata of increasing age at death (2.8–5.2%). Moreover, compared to Met/Met carriers, mortality rate was a factor of 0.71 (95% CI 0.45–1.13) reduced for Met/Val carriers in the combined cohorts, with similar risk estimates in both cohorts. Low valine allele frequency resulted, however, in low power to detect statistical significance. These data suggest that an association between the Met 410 Val polymorphism and longevity in humans may exist.

Published
2004

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