Theoretical arguments and empirical investigations indicate that a high proportion of published findings do not replicate and are likely false. The current position paper provides a broad... Show moreTheoretical arguments and empirical investigations indicate that a high proportion of published findings do not replicate and are likely false. The current position paper provides a broad perspective on scientific error, which may lead to replication failures. This broad perspective focuses on reform history and on opportunities for future reform. We organize our perspective along four main themes: institutional reform, methodological reform, statistical reform and publishing reform. For each theme, we illustrate potential errors by narrating the story of a fictional researcher during the research cycle. We discuss future opportunities for reform. The resulting agenda provides a resource to usher in an era that is marked by a research culture that is less error-prone and a scientific publication landscape with fewer spurious findings. Show less
Zijlker, L.P.; Bakker, M.; Hiel, B. van der; Bruining, A.; Klop, W.M.C.; Zuur, C.L.; ... ; Akkooi, A.C.J. van 2022
Background: Merkel cell carcinoma (MCC) is a cutaneous tumor with a high tendency to metastasize, and a significant proportion of patients have metastases at first presentation. This study aims to... Show moreBackground: Merkel cell carcinoma (MCC) is a cutaneous tumor with a high tendency to metastasize, and a significant proportion of patients have metastases at first presentation. This study aims to determine the value of baseline ultrasound (US) and (18)fluorodeoxyglucose-positron emission tomography/computed tomography ((18)FDG-PET/CT) imaging in both patients with clinically localized MCC (Stage I/II) and patients who present with palpable lymph nodes (Stage III). Methods: This retrospective cohort included 135 MCC patients who underwent baseline US (with fine needle aspiration cytology (FNAC)) and/or FDG-PET/CT imaging between 2015 and 2021. Results: Of the 104 patients with clinically localized disease, 48% were upstaged to Stage III and 3% to Stage IV by imaging or sentinel lymph node biopsy (SLNB). FDG-PET/CT imaging identified regional metastases in 23%, while US with FNAC identified regional metastases in 19%. SLNB was performed in 56 patients, of whom 57% were upstaged to Stage III. Of the 31 patients who presented with palpable lymph nodes, 16% were upstaged to Stage IV by FDG-PET/CT imaging. Conclusion: Baseline imaging frequently upstages Stage I/II MCC patients to Stage III, both by US and FDG-PET/CT, Stage IV disease is rarely identified. Patients who present with palpable nodes are frequently upstaged to Stage IV by FDG-PET/CT imaging. Show less
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log(10) increase (i.e., a similar to 3.5-fold to 5.5... Show moreWe discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log(10) increase (i.e., a similar to 3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination. with increased transmissibility and an unfamiliar molecular mechanism of virulence. Show less
Van den Akker, O.R.; Weston, S.; Campbell, L.; Chopik, B.; Damian, R.; Davis-Kean, P.; ... ; Bakker, M. 2021
Imaging pulmonary fissures by CT provides useful information on diagnosis of pulmonary diseases. Automatic segmentation of fissures is a challenging task due to the variable appearance of fissures,... Show moreImaging pulmonary fissures by CT provides useful information on diagnosis of pulmonary diseases. Automatic segmentation of fissures is a challenging task due to the variable appearance of fissures, such as inhomogeneous intensities, pathological deformation and imaging noise. To overcome these challenges, we propose an anisotropic differential operator called directional derivative of plate (DDoP) filter to probe the presence of fissure objects in 3D space by modeling the profile of a fissure patch with three parallel plates. To reduce the huge computation burden of dense matching with rotated DDoP kernels, a family of spherical harmonics are particularly utilized for acceleration. Additionally, a two-stage post-processing scheme is introduced to segment fissures. The performance of our method was verified in experiments using 55 scans from the publicly available LOLA11 dataset and 50 low-dose CT scans of lung cancer patients from the VIA-ELCAP database. Our method showed superior performance compared to the derivative of sticks (DoS) method and the Hessian-based method in terms of median and mean F-1 - score. The median F-1 - score for DDoP, DoS-based and Hessian-based methods on the LOLA11 dataset was 0.899, 0.848 and 0.843, respectively, and the mean F-1 - score was 0.858 +/- 0.103, 0.781 +/- 0.165 and 0.747 +/- 0.239, respectively. (C) 2020 Elsevier B.V. All rights reserved. Show less
Zoest, R.A. van; Law, M.; Sabin, C.A.; Vaartjes, I.; Valk, M. van der; Arends, J.E.; ... ; Elst-Laurijssen, D.H. 2019
This study examined whether computerized dynamic testing by utilizing a robot would lead to different patterns in children's (aged 6-9 years) potential for learning and strategy use when solving... Show moreThis study examined whether computerized dynamic testing by utilizing a robot would lead to different patterns in children's (aged 6-9 years) potential for learning and strategy use when solving series-completion tasks. The robot, in a "Wizard of Oz" setting, provided instructions and prompts during dynamic testing. It was found that a dynamic training resulted in greater accuracy and more correctly placed pieces at the post-test than repeated testing only. Moreover, children who were dynamically trained appeared to use more heuristic strategies at the post-test than their peers who were not trained. In general, observations showed that children were excited to work with the robot. All in all, the study revealed that computerized dynamic testing by means of a robot has much potential in tapping into children's potential for learning and strategy use. The implications of using a robot in educational assessment were stressed further in the discussion. Show less
This study aimed to combine the use of electronic technology and dynamic testing to overcome the limitations of conventional static testing, and adapt more closely to children's individual needs.... Show moreThis study aimed to combine the use of electronic technology and dynamic testing to overcome the limitations of conventional static testing, and adapt more closely to children's individual needs. We investigated the effects of a newly developed computerized series completion test using a dynamic testing approach and its relation to school achievement. The study utilized a pre-test-training post-test control-group design in which 164 children from grade 2 participated. To evaluate the additional effects of dynamic testing beyond the effects of (repeated) static testing of inductive reasoning on a tablet, half of the children were trained using a graduated prompts method, while the other half of the children only practiced solving the series completion task-items. The results showed that training with graduated prompts is effective in increasing the likelihood that children can solve series completion problems accurately. Furthermore, the number of prompts children needed during training, significantly predicted the performances of children on mathematics and technical reading tests. Teacher's judgments regarding their pupils' overall school performance and potential for learning, however, did not correlate significantly with the dynamic post-test score of the series completion test, which seemed to indicate that dynamic testing provides teachers with new information about the learning progress of individuals. Show less
The aim of the current study was to investigate to what extent children’s potential for learning is related to their level of cognitive flexibility. Potential for learning was measured through a... Show moreThe aim of the current study was to investigate to what extent children’s potential for learning is related to their level of cognitive flexibility. Potential for learning was measured through a dynamic testing procedure that aimed to measure how much a child can profit from a training procedure integrated into the testing process, including the amount and type of feedback the children required during this training procedure. The study followed a pre-test–training–post-test control group design. Participants were 153 6–7-year-old children. Half of this group of children were provided with a standardised graduated prompts procedure. The other half of the participants performed a non-inductive cognitive task. Children’s cognitive flexibility was measured through a card sorting test and a test of verbal fluency. Results show that cognitive flexibility was positively related to children’s performance, but only for children in the practice-only condition who received no training. These outcomes suggest that dynamic testing, and more in particular, the graduated prompting procedure, supports children’s cognitive flexibility, thereby giving children with weaker flexibility the opportunity to show more of their cognitive potential as measured through inductive reasoning. Show less
Quik, J.; Bakker, M.; Meent, D. van de; Poikkimäki, M.; Dal Maso, M.; Peijnenburg, W.J.G.M. 2018
The current study investigated developmental trajectories of analogical reasoning performance of 104 7- and 8-year-old children. We employed a microgenetic research method and multilevel analysis... Show moreThe current study investigated developmental trajectories of analogical reasoning performance of 104 7- and 8-year-old children. We employed a microgenetic research method and multilevel analysis to examine the influence of several background variables and experimental treatment on the children’s developmental trajectories. Our participants were divided into two treatment groups: repeated practice alone and repeated practice with training. Each child received an initial working memory assessment and was subsequently asked to solve figural analogies on each of several sessions. We examined children’s analogical problem-solving behavior and their subsequent verbal accounts of their employed solving processes. We also investigated the influence of verbal and visual–spatial working memory capacity and initial variability in strategy use on analogical reasoning development. Results indicated that children in both treatment groups improved but that gains were greater for those who had received training. Training also reduced the influence of children’s initial variability in the use of analogical strategies with the degree of improvement in reasoning largely unrelated to working memory capacity. Findings from this study demonstrate the value of a microgenetic research method and the use of multilevel analysis to examine inter- and intra-individual change in problem-solving processes. Show less
Vogelaar, B.; Bakker, M.; Hoogeveen, L.; Resing, W.C.M. 2017
