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13. Irinotecan-Induced Toxicity: A Pharmacogenetic Study Beyond UGT1A1

Author

de With, Mirjam, primary, van Doorn, Leni, additional, Kloet, Esmay, additional, van Veggel, Anne, additional, Matic, Maja, additional, de Neijs, Micha J., additional, Oomen - de Hoop, Esther, additional, van Meerten, Esther, additional, van Schaik, Ron H. N., additional, Mathijssen, Ron H. J., additional, and Bins, Sander, additional

Published
2023
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19. Standard set of network outcomes for traumatic spinal cord injury: a consensus-based approach using the Delphi method

Author

van Schaik, Thomas J A, Pouw, Martin H, Curt, Armin, van Nes, Ilse J W, Vos-van der Hulst, Marije, van Hooff, Miranda L, University of Zurich, and van Schaik, Thomas J A

Subjects
Reconstructive and regenerative medicine Radboud Institute for Health Sciences [Radboudumc 10], 2742 Rehabilitation, 2728 Neurology (clinical), Neurology, 2808 Neurology, 610 Medicine & health, 10046 Balgrist University Hospital, Swiss Spinal Cord Injury Center, Neurology (clinical), General Medicine
Abstract

Item does not contain fulltext STUDY DESIGN: Consensus study. OBJECTIVES: The purpose of this study is to define a standardized (network) outcomes set for traumatic spinal cord injury (t-SCI), covering the patient journey from acute to chronic rehabilitation phase, including patient-relevant outcomes, adequate measurement instruments, as well as case-mix and risk factors. SETTING: Acute Spinal Cord Injury (ASCI) Unit Nijmegen, the Netherlands. METHODS: A modified Delphi method was performed, including a multidisciplinary panel of 19 health-care professionals with experience in t-SCI management. Formal consensus was reached after two web-based surveys, a face-to-face meeting, and a final confirmation round (threshold consensus: 70%). RESULTS: In the first two Delphi rounds, 18/19 invited panelists (94.7%) responded and 10 panelists participated in the final meeting. The prefinal set was confirmed by all panelists. The standard set encompasses the three-tiered outcome hierarchy and consists of patient-reported and clinician-reported outcome domains and measurement instruments. Consensus was reached to include survival, degree of health or recovery, time to recovery, and return to normal activities, disutility of care or treatment process, sustainability of health and nature of recurrences, and long-term consequences of therapy. A measurement schedule was defined as well as for proposed casemix and risk factors, including demographics, clinical status, and treatment process. CONCLUSION: A standard set of network outcomes is developed that could be implemented in hospitals and rehabilitation centers involved in the treatment of t-SCI. Using this standard set, comparison of the quality of care is possible and prognostic prediction of outcomes of treatment is feasible, so that each patient receives the right care at the right time in the right place. 01 september 2022

Published
2022

20. Non-invasive investigation of Polychromophilus parasite infections in bat populations in Serbia using bat flies

Author

Branka Bajić, Oskar Werb, Ivana Budinski, Jelena Blagojević, Juliane Schaer, and Jaap van Schaik

Subjects
Infectious Diseases, Parasitology
Abstract

Background Haemosporidian parasites of the genus Polychromophilus infect bats worldwide. They are vectored by obligate ectoparasitic bat flies of the family Nycteribiidae. Despite their global distribution, only five Polychromophilus morphospecies have been described to date. The two predominant species, Polychromophilus melanipherus and Polychromophilus murinus, are broadly distributed and mainly infect miniopterid and vespertilionid bats, respectively. In areas where species from different bat families aggregate together, the infection dynamics and ability of either Polychromophilus species to infect other host families is poorly characterized. Methods We collected 215 bat flies from two bat species, Miniopterus schreibersii and Rhinolophus ferrumequinum, which sometimes form mixed clusters in Serbia. Miniopterus schreibersii is known to be frequently infected with P. melanipherus, whereas R. ferrumequinum has been observed to be incidentally infected with both Polychromophilus species. All flies were screened for Polychromophilus infections using a PCR targeting the haemosporidian cytb gene. Positive samples were subsequently sequenced for 579 bp of cytochrome b (cytb) and 945 bp of cytochrome oxidase subunit 1 (cox1). Results Polychromophilus melanipherus DNA was detected at six out of nine sampling locations and in all three examined bat fly species collected from M. schreibersii (Nycteribia schmidlii, n = 21; Penicillidia conspicua, n = 8; Penicillidia dufourii, n = 3). Four and five haplotypes were found for cytb and cox1, respectively. Evidence for multiple Polychromophilus haplotypes was found in 15 individual flies. These results point to a high diversity of P. melanipherus parasites in Miniopterus hosts and efficient transmission throughout the study area. A single Phthiridium biarticulatum bat fly collected from R. ferrumequinum screened positive for P. melanipherus, but only yielded a partial cox1 sequence fragment. Nevertheless, this result suggests that secondary hosts (both bat and fly species) are regularly confronted with this parasite. Conclusions The results of this study provide new insights into the prevalence and distribution of Polychromophilus parasites in European bats and their nycteribiid vectors. The use of bat flies for the non-invasive investigation of Polychromophilus infections in bat populations has proven to be efficient and thus represents an alternative for large-scale studies of infections in bat populations without the need to invasively collect blood from bats. Graphical Abstract

Published
2023

21. Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data

Author

Siu Fung Stanley Ho, Nicole Wheeler, Andrew D. Millard, and Willem van Schaik

Subjects
Microbiology (medical), education.field_of_study, Contig, Computer science, Shotgun sequencing, Population, Benchmarking, Computational biology, Genome, Microbiology, Metagenomics, RefSeq, Alpha diversity, education
Abstract

Background The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research. Methods Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool’s output. Results VIBRANT and VirSorter2 achieved the highest F1 scores (0.93) in the RefSeq artificial contigs dataset, with several other tools also performing well. Kraken2 had the highest F1 score (0.86) in the mock community benchmark by a large margin (0.3 higher than DeepVirFinder in second place), mainly due to its high precision (0.96). Generally, k-mer-based tools performed better than reference similarity tools and gene-based methods. Several tools, most notably PPR-Meta, called a high number of false positives in the randomly shuffled sequences. When analysing the diversity of the genomes that each tool predicted from a virome set, most tools produced a viral genome set that had similar alpha- and beta-diversity patterns to the original population, with Seeker being a notable exception. Conclusions This study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools. We highlight that the choice of tool for identification of phages in metagenomic datasets, as well as their parameters, can bias the results and provide pointers for different use case scenarios. We have also made our benchmarking dataset available for download in order to facilitate future comparisons of phage identification tools.

Published
2023

22. Neural network based integration of assays to assess pathogenic potential

Author

Mohammed Eslami, Yi-Pei Chen, Ainsley C. Nicholson, Mark Weston, Melissa Bell, John R. McQuiston, James Samuel, Erin J. van Schaik, and Paul de Figueiredo

Subjects
Multidisciplinary
Abstract

Limited data significantly hinders our capability of biothreat assessment of novel bacterial strains. Integration of data from additional sources that can provide context about the strain can address this challenge. Datasets from different sources, however, are generated with a specific objective and which makes integration challenging. Here, we developed a deep learning-based approach called the neural network embedding model (NNEM) that integrates data from conventional assays designed to classify species with new assays that interrogate hallmarks of pathogenicity for biothreat assessment. We used a dataset of metabolic characteristics from a de-identified set of known bacterial strains that the Special Bacteriology Reference Laboratory (SBRL) of the Centers for Disease Control and Prevention (CDC) has curated for use in species identification. The NNEM transformed results from SBRL assays into vectors to supplement unrelated pathogenicity assays from de-identified microbes. The enrichment resulted in a significant improvement in accuracy of 9% for biothreat. Importantly, the dataset used in our analysis is large, but noisy. Therefore, the performance of our system is expected to improve as additional types of pathogenicity assays are developed and deployed. The proposed NNEM strategy thus provides a generalizable framework for enrichment of datasets with previously collected assays indicative of species.

Published
2023

23. Dutch Pharmacogenetics Working Group (DPWG) guideline for the gene-drug interaction between CYP2D6, CYP3A4 and CYP1A2 and antipsychotics

Author

Beunk, Lianne, primary, Nijenhuis, Marga, additional, Soree, Bianca, additional, de Boer-Veger, Nienke J., additional, Buunk, Anne-Marie, additional, Guchelaar, Henk Jan, additional, Houwink, Elisa J. F., additional, Risselada, Arne, additional, Rongen, Gerard A. P. J. M., additional, van Schaik, Ron H. N., additional, Swen, Jesse J., additional, Touw, Daan, additional, van Westrhenen, Roos, additional, Deneer, Vera H. M., additional, and van der Weide, Jan, additional

Published
2023
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24. Addition of the FTD Module to the Neuropsychiatric Inventory improves classification of frontotemporal dementia spectrum disorders

Author

Jiskoot, Lize C., primary, Russell, Lucy L., additional, Greaves, Caroline V., additional, van Schaik, Esther, additional, van den Berg, Esther, additional, Poos, Jackie M., additional, de Boer, Liset, additional, Donker Kaat, Laura, additional, Seelaar, Harro, additional, Pijnenburg, Yolande A. L., additional, van Swieten, John C., additional, and Rohrer, Jonathan D., additional

Published
2023
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25. Correction: Dutch Pharmacogenetics Working Group (DPWG) guideline for the gene–drug interaction between UGT1A1 and irinotecan

Author

Hulshof, Emma C., primary, Deenen, Maarten J., additional, Nijenhuis, Marga, additional, Soree, Bianca, additional, de Boer-Veger, Nienke J., additional, Buunk, Anne-Marie, additional, Houwink, Elisa J. F., additional, Risselada, Arne, additional, Rongen, Gerard A. P. J. M., additional, van Schaik, Ron H. N., additional, Touw, Daan J., additional, van der Weide, Jan, additional, van Westrhenen, Roos, additional, Deneer, Vera H. M., additional, Guchelaar, Henk-Jan, additional, and Swen, Jesse J., additional

Published
2023
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27. Correction: Dutch Pharmacogenetics Working Group (DPWG) guideline for the gene–drug interaction between UGT1A1 and irinotecan

Author

Emma C. Hulshof, Maarten J. Deenen, Marga Nijenhuis, Bianca Soree, Nienke J. de Boer-Veger, Anne-Marie Buunk, Elisa J. F. Houwink, Arne Risselada, Gerard A. P. J. M. Rongen, Ron H. N. van Schaik, Daan J. Touw, Jan van der Weide, Roos van Westrhenen, Vera H. M. Deneer, Henk-Jan Guchelaar, and Jesse J. Swen

Subjects
Genetics, Genetics (clinical)
Published
2023

28. Dutch pharmacogenetics working group (DPWG) guideline for the gene-drug interaction of CYP2D6 and COMT with atomoxetine and methylphenidate

Author

Nijenhuis, Marga, primary, Soree, Bianca, additional, Jama, Wafa O. M., additional, de Boer-Veger, Nienke J., additional, Buunk, Anne Marie, additional, Guchelaar, Henk-Jan, additional, Houwink, Elisa J. F., additional, Rongen, Gerard A., additional, van Schaik, Ron H. N., additional, Swen, Jesse J., additional, Touw, Daan, additional, van der Weide, Jan, additional, van Westrhenen, Roos, additional, Deneer, Vera H. M., additional, and Risselada, Arne, additional

Published
2022
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29. Dutch pharmacogenetics working group (DPWG) guideline for the gene–drug interaction between UGT1A1 and irinotecan

Author

Hulshof, Emma C., primary, Deenen, Maarten J., additional, Nijenhuis, Marga, additional, Soree, Bianca, additional, de Boer-Veger, Nienke J., additional, Buunk, Anne-Marie, additional, Houwink, Elisa J. F., additional, Risselada, Arne, additional, Rongen, Gerard A. P. J. M., additional, van Schaik, Ron H. N., additional, Touw, Daan J., additional, van der Weide, Jan, additional, van Westrhenen, Roos, additional, Deneer, Vera H. M., additional, Guchelaar, Henk-Jan, additional, and Swen, Jesse J., additional

Published
2022
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30. Efficacy of belimumab combined with rituximab in severe systemic lupus erythematosus: study protocol for the phase 3, multicenter, randomized, open-label Synbiose 2 trial

Author

van Schaik, Mieke, primary, Arends, Eline J., additional, Soonawala, Darius, additional, van Ommen, Ellen, additional, de Leeuw, Karina, additional, Limper, Maarten, additional, van Paassen, Pieter, additional, Huizinga, Tom W. J., additional, Toes, René E. M., additional, van Kooten, Cees, additional, Rotmans, Joris I., additional, Rabelink, Ton J., additional, and Teng, Y. K. Onno, additional

Published
2022
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31. Identification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein

Author

Jelle van Schooten, Elinaz Farokhi, Anna Schorcht, Tom L. G. M. van den Kerkhof, Hongmei Gao, Patricia van der Woude, Judith A. Burger, Tim G. Rijkhold Meesters, Tom Bijl, Riham Ghalaiyini, Hannah L. Turner, Jessica Dorning, Barbera D. C. van Schaik, Antoine H. C. van Kampen, Celia C. Labranche, Robyn L. Stanfield, Devin Sok, David C. Montefiori, Dennis R. Burton, Michael S. Seaman, Gabriel Ozorowski, Ian A. Wilson, Rogier W. Sanders, Andrew B. Ward, Marit J. van Gils, Graduate School, AII - Infectious diseases, Medical Microbiology and Infection Prevention, Epidemiology and Data Science, APH - Methodology, and APH - Personalized Medicine

Subjects
Binding Sites, Multidisciplinary, Cryoelectron Microscopy, General Physics and Astronomy, HIV Infections, General Chemistry, HIV Antibodies, Antibodies, Neutralizing, Complementarity Determining Regions, General Biochemistry, Genetics and Molecular Biology, CD4 Antigens, HIV-1, Humans, Antigens, Viral, Broadly Neutralizing Antibodies, Glycoproteins
Abstract

A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3). Here, we describe three IOMA-class NAbs, ACS101-103, with up to 37% breadth, that share many characteristics with IOMA, including an average-length CDRL3. Cryo-electron microscopy revealed that ACS101 shares interactions with those observed with other VH1-2 and VH1-46-class bNAbs, but exhibits a unique binding mode to residues in loop D. Analysis of longitudinal sequences from the patient suggests that a transmitter/founder-virus lacking the N276 glycan might have initiated the development of these NAbs. Together these data strengthen the rationale for germline-targeting vaccination strategies to induce IOMA-class bNAbs and provide a wealth of sequence and structural information to support such strategies.

Published
2022

32. Dutch pharmacogenetics working group guideline for the gene-drug interaction of ABCG2, HLA-B and Allopurinol, and MTHFR, folic acid and methotrexate

Author

van der Pol, Karel H., primary, Nijenhuis, Marga, additional, Soree, Bianca, additional, de Boer-Veger, Nienke J., additional, Buunk, Anne Marie, additional, Guchelaar, Henk-Jan, additional, Risselada, Arne, additional, van Schaik, Ron H. N., additional, Swen, Jesse J., additional, Touw, Daan, additional, van der Weide, Jan, additional, van Westrhenen, Roos, additional, Deneer, Vera H. M., additional, Houwink, Elisa J. F., additional, and Rongen, Gerard A., additional

Published
2022
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34. Effect of an exercise intervention on global cognition after transient ischemic attack or minor stroke: the MoveIT randomized controlled trial

Author

Deijle, Inger A., primary, Hemmes, Roelofjan, additional, Boss, H. Myrthe, additional, de Melker, Edwin C., additional, van den Berg, Bob T. J., additional, Kwakkel, Gert, additional, van Wegen, Erwin, additional, Bosboom, Wendy M., additional, Weinstein, Henry C., additional, van Schaik, Sander M., additional, and Van den Berg-Vos, Renske M., additional

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

Author

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

Published
2022
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36. Identification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein

Author

van Schooten, Jelle, primary, Farokhi, Elinaz, additional, Schorcht, Anna, additional, van den Kerkhof, Tom L. G. M., additional, Gao, Hongmei, additional, van der Woude, Patricia, additional, Burger, Judith A., additional, Meesters, Tim G. Rijkhold, additional, Bijl, Tom, additional, Ghalaiyini, Riham, additional, Turner, Hannah L., additional, Dorning, Jessica, additional, van Schaik, Barbera D. C., additional, van Kampen, Antoine H. C., additional, Labranche, Celia C., additional, Stanfield, Robyn L., additional, Sok, Devin, additional, Montefiori, David C., additional, Burton, Dennis R., additional, Seaman, Michael S., additional, Ozorowski, Gabriel, additional, Wilson, Ian A., additional, Sanders, Rogier W., additional, Ward, Andrew B., additional, and van Gils, Marit J., additional

Published
2022
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43. Body mass index at diagnosis of a childhood brain tumor; a reflection of hypothalamic-pituitary dysfunction or lifestyle?

Author

van Roessel, I. M. A. A., primary, van Schaik, J., additional, Meeteren, A. Y. N. Schouten-van, additional, Boot, A. M., additional, der Grinten, H. L. Claahsen-van, additional, Clement, S. C., additional, van Iersel, L., additional, Han, K. S., additional, van Trotsenburg, A. S. P., additional, Vandertop, W. P., additional, Kremer, L. C. M., additional, and van Santen, H. M., additional

Published
2022
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45. The effect of estrogen on brown adipose tissue activity in male rats

Author

W. Sievers, C. Kettle, R. A. Green, L. Van Schaik, M. W. Hale, H. R. Irving, D. R. Whelan, and J. A. Rathner

Subjects
Male, Science (General), Sympathetic Nervous System, QH301-705.5, Estrogens, Thermogenesis, General Medicine, Rodents, Thermoregulation, General Biochemistry, Genetics and Molecular Biology, Rats, Q1-390, Adipose Tissue, Brown, Transwomen, Heart Rate, Medicine, Animals, Biology (General)
Abstract

Objective Centrally administered estrogen can increase sympathetic nerve activity to brown adipose tissue, resulting in thermogenesis. The central thermogenic effects of estrogen have not been investigated in males. Therefore, this study sought to investigate the effects of peripherally and centrally administered estrogen on thermogenesis, heart rate and mean arterial pressure in male rats. Thermogenesis was assessed by monitoring brown adipose tissue temperature. Results Peripherally administered estrogen elicited no significant effect on brown adipose tissue temperature, heart rate or mean arterial pressure. Centrally administered estrogen elicited a coincident increase in both brown adipose tissue and core temperature. Centrally administered estrogen also resulted in a decrease in mean arterial pressure but had no effect on heart rate. With the present data it is not possible to elucidate whether changes in temperature were the result of thermogenic or thermoregulatory mechanisms.

Published
2022

47. Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial

Author

Reyman, Marta, primary, van Houten, Marlies A., additional, Watson, Rebecca L., additional, Chu, Mei Ling J. N., additional, Arp, Kayleigh, additional, de Waal, Wouter J., additional, Schiering, Irene, additional, Plötz, Frans B., additional, Willems, Rob J. L., additional, van Schaik, Willem, additional, Sanders, Elisabeth A. M., additional, and Bogaert, Debby, additional

Published
2022
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48. Review of microplastic sources, transport pathways and correlations with other soil stressors: a journey from agricultural sites into the environment

Author

Lwanga, Esperanza Huerta, primary, Beriot, Nicolas, additional, Corradini, Fabio, additional, Silva, Vera, additional, Yang, Xiaomei, additional, Baartman, Jantiene, additional, Rezaei, Mahrooz, additional, van Schaik, Loes, additional, Riksen, Michel, additional, and Geissen, Violette, additional

Published
2022
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