Capillary electrophoresis has matured into a highly sensitive and widely applied analytical method over the last forty years. Here we combine text mining and computational chemistry to paint, with... Show moreCapillary electrophoresis has matured into a highly sensitive and widely applied analytical method over the last forty years. Here we combine text mining and computational chemistry to paint, with very broad strokes, the applicability and trends in the scientific literature on capillary electrophoresis, simulta-neously demonstrating that this is not only possible, but reveal both expected and unexpected details of this history. All software and data are freely available on GitHub (https://github.com/ReinV/SCOPE) and OSF (https://osf.io/e56zt/). (c) 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Show less
We have explored the history of the field of capillary electrophoresis using bibliometric methods. The analysis shows that 416 prolific researchers are connected in a single, large, co-authorship... Show moreWe have explored the history of the field of capillary electrophoresis using bibliometric methods. The analysis shows that 416 prolific researchers are connected in a single, large, co-authorship network based on publications on capillary electrophoresis between 1980 and 2021, with a few pioneers having remained active throughout much of this time period. Looking at research topics revealed electro-chemistry, sensors, nanotechnology and metabolomics as 'hot' topics, with fundamental method development being more 'mature', and reveal that capillary electrophoresis technology have matured over a 30-year time period, with research efforts moving from separations to quantitative measurements to biomedical applications. The citation patterns showed the strongest coupling between journals of similar scope. Interactive versions of the bibliometric network visualizations are available on-line at https://tinyurl.com/2z7q7wcx (researcher co-authorship network), https://tinyurl.com/2jmhsgxx (research topic network) and https://tinyurl.com/2lnfzzgn (journal bibliographic coupling citation network).(c) 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Show less
Power, R.C.; Henry, A.G.; Moosmann, J.; Beckmann, F.; Temming, H.; Roberts, A.; Le Cabec, A. 2022
Purpose: Dental calculus forms on teeth during the life of an individual and its investigation can yield information about diet, health status, and environmental pollution. Currently, the... Show morePurpose: Dental calculus forms on teeth during the life of an individual and its investigation can yield information about diet, health status, and environmental pollution. Currently, the analytical techniques used to visualize the internal structure of human dental calculus and entrapped inclusions are limited and require destructive sampling, which cannot always be justified.Approach: We used propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SR-μCT) to non-destructively examine the internal organization of dental calculus, including its microstructure and entrapped inclusions, on both modern and archeological samples.Results: The virtual histological exploration of the samples shows that PPC-SR-μCT is a powerful approach to visualize the internal organization of dental calculus. We identified several important features, including previously undetected negative imprints of enamel and dentine growth markers (perikymata and periradicular bands, respectively), the non-contiguous structure of calculus layers with multiple voids, and entrapped plant remains.Conclusions: PPC-SR-μCT is an effective technique to explore dental calculus structural organization, and is especially powerful for enabling the identification of inclusions. The non-destructive nature of synchrotron tomography helps protect samples for future research. However, the irregular layers and frequent voids reveal a high heterogeneity and variability within calculus, with implications for research focusing on inclusions. Show less
Su, R.S.; Cornelissen, S.A.P.; Sluijs, M. van der; Es, A.C.G.M. van; Zwam, W.H. van; Dippel, D.W.J.; ... ; Walsum, T. van 2021
The Thrombolysis in Cerebral Infarction (TICI) score is an important metric for reperfusion therapy assessment in acute ischemic stroke. It is commonly used as a technical outcome measure after... Show moreThe Thrombolysis in Cerebral Infarction (TICI) score is an important metric for reperfusion therapy assessment in acute ischemic stroke. It is commonly used as a technical outcome measure after endovascular treatment (EVT). Existing TICI scores are defined in coarse ordinal grades based on visual inspection, leading to inter- and intra-observer variation. In this work, we present autoTICI, an automatic and quantitative TICI scoring method. First, each digital subtraction angiography (DSA) acquisition is separated into four phases (non-contrast, arterial, parenchymal and venous phase) using a multi-path convolutional neural network (CNN), which exploits spatio-temporal features. The network also incorporates sequence level label dependencies in the form of a state-transition matrix. Next, a minimum intensity map (MINIP) is computed using the motion corrected arterial and parenchymal frames. On the MINIP image, vessel, perfusion and background pixels are segmented. Finally, we quantify the autoTICI score as the ratio of reperfused pixels after EVT. On a routinely acquired multi-center dataset, the proposed autoTICI shows good correlation with the extended TICI (eTICI) reference with an average area under the curve (AUC) score of 0.81. The AUC score is 0.90 with respect to the dichotomized eTICI. In terms of clinical outcome prediction, we demonstrate that autoTICI is overall comparable to eTICI. Show less
Spatially-resolved omics-data enable researchers to precisely distinguish cell types in tissue and explore their spatial interactions, enabling deep understanding of tissue functionality. To... Show moreSpatially-resolved omics-data enable researchers to precisely distinguish cell types in tissue and explore their spatial interactions, enabling deep understanding of tissue functionality. To understand what causes or deteriorates a disease and identify related biomarkers, clinical researchers regularly perform large-scale cohort studies, requiring the comparison of such data at cellular level. In such studies, with little a-priori knowledge of what to expect in the data, explorative data analysis is a necessity. Here, we present an interactive visual analysis workflow for the comparison of cohorts of spatially-resolved omics-data. Our workflow allows the comparative analysis of two cohorts based on multiple levels-of-detail, from simple abundance of contained cell types over complex co-localization patterns to individual comparison of complete tissue images. As a result, the workflow enables the identification of cohort-differentiating features, as well as outlier samples at any stage of the workflow. During the development of the workflow, we continuously consulted with domain experts. To show the effectiveness of the workflow, we conducted multiple case studies with domain experts from different application areas and with different data modalities. Show less
Somarakis, A.; Unen, V. van; Koning, F.; Lelieveldt, B.; Hollt, T. 2021
Tissue functionality is determined by the characteristics of tissue-resident cells and their interactions within their microenvironment. Imaging Mass Cytometry offers the opportunity to distinguish... Show moreTissue functionality is determined by the characteristics of tissue-resident cells and their interactions within their microenvironment. Imaging Mass Cytometry offers the opportunity to distinguish cell types with high precision and link them to their spatial location in intact tissues at sub-cellular resolution. This technology produces large amounts of spatially-resolved high-dimensional data, which constitutes a serious challenge for the data analysis. We present an interactive visual analysis workflow for the end-to-end analysis of Imaging Mass Cytometry data that was developed in close collaboration with domain expert partners. We implemented the presented workflow in an interactive visual analysis tool; ImaCytE. Our workflow is designed to allow the user to discriminate cell types according to their protein expression profiles and analyze their cellular microenvironments, aiding in the formulation or verification of hypotheses on tissue architecture and function. Finally, we show the effectiveness of our workflow and ImaCytE through a case study performed by a collaborating specialist. Show less
Inflammatory arthritis comprises a group of diseases in which the immune system attacks the body’s own tissues. Two prevalent types of inflammatory arthritis are rheumatoid arthritis (RA) and... Show moreInflammatory arthritis comprises a group of diseases in which the immune system attacks the body’s own tissues. Two prevalent types of inflammatory arthritis are rheumatoid arthritis (RA) and spondyloarthritis (SpA). Clinical research points to the importance of early diagnosis, as treatment in early disease stages increases chances of better outcome and improved quality of life for patients. To this end, the diagnostic potential of imaging modalities sensitive to local inflammation, such as magnetic resonance imaging (MRI), is of great interest. The goal of this thesis was to develop computer-aided methods for assessment of MRI-detected inflammation with the aim of aiding early diagnosis of inflammatory arthritis. In particular, we focused on the tasks of comparative visualization, automatic quantification, and feature selection. The presented studies showcase the potential of comparative visualization and automatic quantification to overcome the limitations of visual scoring and lay out a fertile ground for future improvements. Additionally, the understanding of the diagnostic role of individual inflammatory features in prediction of RA development is further advanced. Collectively, these findings can help facilitate the use of MRI for early diagnosis of inflammatory arthritis and potentially increase chances of better outcome and quality of life for patients. Show less
The amount of 3D modelling applications in archaeology has increased enourmously over the last decade. 3D recording techniques allow researchers to quickly and accurately document... Show moreThe amount of 3D modelling applications in archaeology has increased enourmously over the last decade. 3D recording techniques allow researchers to quickly and accurately document archaeological evidence, and 3D reconstructions have created new possibilities to communicate the results to a larger public. In this latter case, however, numerous scholars have expressed their concern regarding the ethics of such digital representations, since they give prominence to a crystallized image of the past. The study presented here aims to make a practical contribution to a new understanding and use of 3D reconstructions, namely as “laboratories” to test hypotheses and visualize and evaluate alternative interpretations. In order to do so, an analysis of visual reconstructions of the early and late modern period is presented first, followed by a discussion of current applications of 3D digital reconstructions, with a special focus on cityscapes. Lastly, the implementation of a research-driven, intellectually transparent and GIS-based 3D reconstruction is proposed for the urban site of Koroneia, in Boeotia, Central Greece. With a strong focus on the automation and iteration of the reconstruction process, our 3D visualization provides an intuitive insight into hidden relationships and associations among data, and allows the creation and evaluation of alternative reconstruction hypotheses. Show less
This paper presents a fine-grained overview of the usage behavior and topics of interest of different types of users in Mendeley. The analysis is based on 1.2 million Web of Science indexed... Show moreThis paper presents a fine-grained overview of the usage behavior and topics of interest of different types of users in Mendeley. The analysis is based on 1.2 million Web of Science indexed publications published in 2012. The disciplinary differences in the reading (saving) patterns of different types of Mendeley users are identified and depicted using VOSviewer overlay visualizations. The findings show that compared to other fields, publications from Mathematics & Computer Science have the lowest coverage in Mendeley. Publications from the Social Sciences & Humanities receive on average the highest number of readers in Mendeley. The highest uptake of Mendeley is by students, but this differs across fields. Professors, students, and librarians are mainly active in the Social Sciences & Humanities, a field of science with a relatively low citation density in Web of Science. In contrast, researchers and other professionals are mainly active in fields with a relatively high citation density such as the Biomedical & Health Sciences and the Life & Earth Sciences. In addition, it seems that researchers and professionals are relatively more interested in practical, methodological, and technical oriented topics while professors and students are attracted by the more educational and theoretical oriented topics. These different usage patterns among user types possibly reflect the way in which scholarly publications are used for scientific, educational, or other professional purposes. This information could inform relevant stakeholders, such as researchers, librarians, publishers, funders, and policy makers of the scientific, educational, or professional values of publications. Show less
The project focuses on visualizing Agrobacterium Mediated Transformation (AMT) of host cells by real time microscopy. With new visualization techniques the function of several proteins, which have... Show moreThe project focuses on visualizing Agrobacterium Mediated Transformation (AMT) of host cells by real time microscopy. With new visualization techniques the function of several proteins, which have recently been discovered in our lab to play a role during AMT, are studied. Show less
In this thesis novel statistical methods are developed for the analysis of high dimensional microarray data. In short: Chapter 1 gives an overview of the most important research methods developed... Show moreIn this thesis novel statistical methods are developed for the analysis of high dimensional microarray data. In short: Chapter 1 gives an overview of the most important research methods developed so far. Chapter 2 describes a method for testing association of the expression of gene sets (pathways) with a patient level response variable, which can be continuous or two-valued. Chapter 3 extends the methodology of chapter 2 to survival as a response variable. Chapter 4 presents a goodness-of-fit test for the multinomial regression model, which can be used to extend the methodology of chapter 2 to multi-valued outcomes. Chapter 5 presents a general theoretical framework in for the tests of chapters 2-4 and derives optimality properties for these tests. Chapter 6 presents a method for predicting a response variable from high dimensional data, based on latent variables. Chapter 7 presents a visualization tool for improved presentation of scatterplots with many thousands of dots. Show less
