Objectives To investigate the prevalence of axial spondyloarthritis (axSpA) in patients with chronic back pain (CBP) of less than 2 years (2y) duration referred to the rheumatologist, the... Show moreObjectives To investigate the prevalence of axial spondyloarthritis (axSpA) in patients with chronic back pain (CBP) of less than 2 years (2y) duration referred to the rheumatologist, the development of diagnosis over time, and patient characteristics of those developing definite (d-)axSpA over 2y. Methods We analysed the 2y data from SPondyloArthritis Caught Early, a European cohort of patients (<45 years) with CBP (>= 3 months, <= 2y) of unknown origin. The diagnostic workup comprised evaluation of clinical SpA features, acute phase reactants, HLA-B27, radiographs and MRI (sacroiliac joints and spine), with repeated assessments. At each visit (baseline, 3 months, 1y and 2y), rheumatologists reported a diagnosis of axSpA or non-axSpA with level of confidence (LoC; 0-not confident at all to 10-very confident). Main outcome: axSpA diagnosis with LoC >= 7 (d-axSpA) at 2y. Results In 552 patients with CBP, d-axSpA was diagnosed in 175 (32%) at baseline and 165 (30%) at 2y. Baseline diagnosis remained rather stable: at 2y, baseline d-axSpA was revised in 5% of patients, while 8% 'gained' d-axSpA. Diagnostic uncertainty persisted in 30%. HLA-B27+ and baseline sacroiliitis imaging discriminated best 2y-d-axSpA versus 2y-d-non-axSpA patients. Good response to non-steroidal anti-inflammatory drugs and MRI-sacroiliitis most frequently developed over follow-up in patients with a new d-axSpA diagnosis. Of the patients who developed MRI-sacroiliitis, 7/8 were HLA-B27+ and 5/8 male. Conclusion A diagnosis of d-axSpA can be reliably made in nearly one-third of patients with CBP referred to the rheumatologist, but diagnostic uncertainty may persist in 5%-30% after 2y. Repeated assessments yield is modest, but repeating MRI may be worthwhile in male HLA-B27+ patients. Show less
Background: Recent advances in data-driven computational approaches have been helpful in devising tools to objectively diagnose psychiatric disorders. However, current machine learning studies... Show moreBackground: Recent advances in data-driven computational approaches have been helpful in devising tools to objectively diagnose psychiatric disorders. However, current machine learning studies limited to small homogeneous samples, different methodologies, and different imaging collection protocols, limit the ability to directly compare and generalize their results. Here we aimed to classify individuals with PTSD versus controls and assess the generalizability using a large heterogeneous brain datasets from the ENIGMA-PGC PTSD Working group. Methods: We analyzed brain MRI data from 3,477 structural-MRI; 2,495 resting state-fMRI; and 1,952 diffusion-MRI. First, we identified the brain features that best distinguish individuals with PTSD from controls using traditional machine learning methods. Second, we assessed the utility of the denoising variational autoencoder (DVAE) and evaluated its classification performance. Third, we assessed the generalizability and reproducibility of both models using leave-one-site-out cross-validation procedure for each modality. Results: We found lower performance in classifying PTSD vs. controls with data from over 20 sites (60 % test AUC for s-MRI, 59 % for rs-fMRI and 56 % for D-MRI), as compared to other studies run on single-site data. The performance increased when classifying PTSD from HC without trauma history in each modality (75 % AUC). The classification performance remained intact when applying the DVAE framework, which reduced the number of features. Finally, we found that the DVAE framework achieved better generalization to unseen datasets compared with the traditional machine learning frameworks, albeit performance was slightly above chance. Conclusion: These results have the potential to provide a baseline classification performance for PTSD when using large scale neuroimaging datasets. Our findings show that the control group used can heavily affect classification performance. The DVAE framework provided better generalizability for the multi-site data. This may be more significant in clinical practice since the neuroimaging-based diagnostic DVAE classification models are much less site-specific, rendering them more generalizable. Show less
Transport inspectorates are looking for novel methods to identify dangerous behavior, ultimately to reduce risks associated to the movements of people and goods. We explore a data-driven approach... Show moreTransport inspectorates are looking for novel methods to identify dangerous behavior, ultimately to reduce risks associated to the movements of people and goods. We explore a data-driven approach to arrive at smart inspections of vehicles. Inspections are smart when they are performed (1) accurate, (2) automated, (3) fair, and (4) in an interpretable manner. We leverage tools from the network science and machine learning domain to encode the behavioral aspect of vehicle’s behavior. Tools used in this thesis include community detection, link prediction, and assortativity. We explore their applicability and provide technical methods. In the final chapter, we also discuss the matter of fairness in machine learning. Show less
The focus of this thesis is on the technical methods which help promote the movement towards Trustworthy AI, specifically within the Inspectorate of the Netherlands.The goal is develop and assess... Show moreThe focus of this thesis is on the technical methods which help promote the movement towards Trustworthy AI, specifically within the Inspectorate of the Netherlands.The goal is develop and assess the technical methods which are required to shift the actions of the Inspectorate to a data-driven paradigm, concretely under a supervised classification framework of machine learning.The aspect of reliability is addressed as a data quality concern, viz. missingness and noise.The aspect of fairness is addressed as a counter to bias in the selection process of inspections.The conclusion is that, whilst no complete solution has yet been suggested, it is possible to address the concerns related to data quality and data bias, culminating in well-performing classification models which are reliable and fair. Show less
Based on recent achievements in phylogenetic studies of the Brassicaceae, a novel infrafamilial classification is proposed that includes major improvements at the subfamilial and supertribal levels... Show moreBased on recent achievements in phylogenetic studies of the Brassicaceae, a novel infrafamilial classification is proposed that includes major improvements at the subfamilial and supertribal levels. Herein, the family is subdivided into two subfamilies, Aethionemoideae (subfam. nov.) and Brassicoideae. The Brassicoideae, with 57 of the 58 tribes of Brassicaceae, are further partitioned into five supertribes, including the previously recognized Brassicodae and the newly established Arabodae, Camelinodae, Heliophilodae, and Hesperodae. Additional tribus-level contributions include descriptions of the newly recognized Arabidopsideae, Asperuginoideae, Hemilophieae, Schrenkielleae, and resurrection of the Chamireae and Subularieae. Further detailed comments on 17 tribes in need of clarifications are provided. Show less
There are long-standing unsolved issues regarding the diagnosis and classification of central disorders of hypersomnolence. These include delineating and identifying phenotypes and unique... Show moreThere are long-standing unsolved issues regarding the diagnosis and classification of central disorders of hypersomnolence. These include delineating and identifying phenotypes and unique conditions (“sui generis”), sleep deprivation’s impact on phenotypes and how to separate sleep deprivation as a trigger from other causes, as well as the association of excessive sleepiness with other disorders. We discuss these issues and present a novel, straightforward classification system with consistent terminology to get out of the impasse and do justice to people with hypersomnolence. Show less
Monitoring the illegal trade of wool fibres of wild vicun~a (Vicugna vicugna) and guanaco (Lama guanicoe) is highly desirable. The high market value of fleece from these camelid species poses a... Show moreMonitoring the illegal trade of wool fibres of wild vicun~a (Vicugna vicugna) and guanaco (Lama guanicoe) is highly desirable. The high market value of fleece from these camelid species poses a threat to their wild populations. A previous study showed that direct analysis in real time time-of-flight mass spectrometry (DART-TOFMS) effectively identifies wool fibres to species. Producing high-resolution data in a short period of time makes DART-TOFMS a reliable identification tool, even though data analysis can still be improved. The present study proposes a novel data analysing pipeline based on Convolutional Neural Networks (CNN), applicable to any kind of DART-TOF MS data. We tested our proposed method on keratin fibres of four camelid species (Vicugna vicugna: n 1⁄4 19; Vicugna pacos: n 1⁄4 20; Lama guanicoe: n 1⁄4 20, and Lama glama: n 1⁄4 20). Analyses showed that selecting 512 ions with the highest relative intensity provides the best resolution and yields 100% accuracy for species identification. Show less
This dissertation examines how in eighteenth-century Europe, naturalists sought to study, grasp and capture the world of fish. Working on the intersection of the history of science and book history... Show moreThis dissertation examines how in eighteenth-century Europe, naturalists sought to study, grasp and capture the world of fish. Working on the intersection of the history of science and book history, this research aims to shed light on how naturalists came to present themselves as authorities in an emerging field. It does so by focussing on a set of ‘fish books’, i.e., natural historical works that describe and depict fish. The first is Francis Willughby and John Ray’s "Historia piscium" (Oxford, 1686); the second Peter Artedi’s "Ichthyologia sive opera omnia de piscibus" (Leiden, 1738), and the third Marcus Élieser Bloch’s twelve volume series "Allgemeine Naturgeschichte der Fische" (Berlin, 1782–1795). These works are analysed alongside correspondences, manuscripts and natural historical collections. Together, these sources show that the development of the study of fish in this period can be best be understood as a process of continuous demarcation. This dissertation argues that the study of fish was subject to recurrent debates on subject, method and practitioner, and that such discussions were of both epistemological and social nature. In presenting their fish books, naturalists leveraged such discussions as to secure a place for themselves in the capricious environment of early modern natural history. Show less
It has been argued that the Internet presents numerous new opportunities for crime, including homicide. So far, empirical scholarly research in this domain is rather limited. In order to discover... Show moreIt has been argued that the Internet presents numerous new opportunities for crime, including homicide. So far, empirical scholarly research in this domain is rather limited. In order to discover how perpetrators have used the Internet in the homicides they have committed, we conducted an international newspaper search (2006–2017). Based on this analysis, we identify five distinct types of Internet use in homicides, namely Internet as an encyclopedia, Internet as a platform, Internet as a trigger, Internet as a market place, and Internet as a meeting place. Our findings indicate that these types do not significantly differ from key characteristics of homicides in general to the degree that they constitute unique forms of homicide. Rather, Internet-related homicides constitute a replication, or facilitation of already existing forms of homicide assisted through new technological means. Show less
Mastboom, M.J.L.; Verspoor, F.G.M.; Hanff, D.F.; Gademan, M.G.J.; Dijkstra, P.D.S.; Schreuder, H.W.B.; ... ; Sande, M.A.J. van de 2018
We propose a novel classification method that integrates into existing agile software development practices by collecting data records generated by software and tools used in the development... Show moreWe propose a novel classification method that integrates into existing agile software development practices by collecting data records generated by software and tools used in the development process. We extract features from the collected data and create visualizations that provide insights, and feed the data into a prediction framework consisting of a deep neural network. The features and results are validated against conceptual frameworks that model the development methodologies as similar processes in other contexts. Initial results show that the visualization and prediction techniques provide promising outcomes that may help development teams and management gain better understanding of past events and future risks. Show less
De belangrijkste resultaten van dit proefschrift: de ASAS classificatie criteria voor axSpA blijken robuust en zijn goed toepasbaar in een setting waarbij de waarschijnlijkheid op axSpA lager is... Show moreDe belangrijkste resultaten van dit proefschrift: de ASAS classificatie criteria voor axSpA blijken robuust en zijn goed toepasbaar in een setting waarbij de waarschijnlijkheid op axSpA lager is dan waarin de criteria ontwikkeld zijn. Daarnaast is er op basis van bevindingen in dit proefschrift een belangrijke aanpassing doorgevoerd in een hulpmiddel dat reumatologen begeleidt in het diagnostische proces van (vroege) axSpA. Tevens is het MRI protocol van het SPACE cohort aangepast nadat de toegevoegde waarde van het toedienen van een contrastvloeistof bij het maken van MRI’s nihil bleek te zijn, met als resultaat dat er sinds april 2012 geen MRI’s meer worden gemaakt met de toediening van gadolinium. Dit proefschrift biedt ook adequate handvatten voor verder onderzoek naar de optimale definitie van een positieve MRI. Bovendien worden discrepanties aangaande de beoordeling door verschillende soorten lezers van afwijkingen in de rug (op röntgenfoto’s en MRI’s) aan het licht gebracht waardoor de vraag naar voren komt of training in het onderscheiden van axSpA afwijkingen en afwijkingen die niet gerelateerd zijn aan axSpA van potentiële belang is op de betrouwbaarheid van het beoordelen van afwijkingen in de rug. De onderzoeken in dit proefschrift leveren een bijdrage aan betere herkenning en behandeling van axSpA. Show less
This work comprises a linguistic survey of the Ancient North Arabian (ANA) epigraphic material from Taymāʾ, conventionally known as Taymanitic (Macdonald 2000: 28-9). A grammatical sketch, based on... Show moreThis work comprises a linguistic survey of the Ancient North Arabian (ANA) epigraphic material from Taymāʾ, conventionally known as Taymanitic (Macdonald 2000: 28-9). A grammatical sketch, based on the linguistic features in the Taymanitic corpus is presented, followed by a discussion of the linguistic features of Taymanitic that are relevant to its linguistic classification. Two appendices follow: a compilation of all previously published inscriptions with grammatical content, and a glossary Show less
The Mbam languages of Cameroon have a unique position in Bantu linguistics. Being in between “narrow” Bantu and “wide” Bantu, they sometimes pattern with the one and sometimes with the other, and... Show moreThe Mbam languages of Cameroon have a unique position in Bantu linguistics. Being in between “narrow” Bantu and “wide” Bantu, they sometimes pattern with the one and sometimes with the other, and as such are a rich motherlode for comparative and historical research. The Mbam languages have another point of interest as well. They have been previously analysed as standard 7 vowel languages (/i,e,ɛ,a,ɔ,o,u/) with Advanced Tongue Root (ATR) harmony. While vowel harmony in African languages has received a lot of attention and study, and the vowel-harmony systems of not a few of the Mbam languages have been studied, most of the previous studies have been on individual languages. This study seeks to analyse and compare the vowel systems of ten Mbam languages as a group: both their vowel inventories and their vowel-harmony systems. Various issues in vowel harmony, such as neutral vowels, directionality in and domains of vowel harmony are discussed. This study also proposes a phonological explanation for the functioning of the complex vowel-harmony systems found in the Mbam languages. Finally this study considers the internal classification of the Mbam languages and their position in the wider linguistic context of the Bantu and Bantoid languages. Show less
Wegdam, W.; Moerland, P.D.; Meijer, D.; Jong Shreyas, M. de; Hoefsloot, H.C.J.; Kenter, G.G.; ... ; Aerts, J.M.F.G. 2012
Hoverflies of the subfamily Microdontinae (Diptera: Syrphidae) have a reputation for causing confusion. Their diversity in shape and size is astonishing: from large, furry-haired species and... Show moreHoverflies of the subfamily Microdontinae (Diptera: Syrphidae) have a reputation for causing confusion. Their diversity in shape and size is astonishing: from large, furry-haired species and convincing wasp-mimics to tiny, unsightly creatures, easily mistaken for something uninteresting. The larvae resemble slugs so much that biologists have described them as molluscs on several occasions. Worldwide, hundreds of species of Microdontinae have been described, but so far there has been no comprehensive attempt to unravel this hotchpotch of names. This thesis examines the phylogenetic relationships of Microdontinae, based on morphological and molecular characters, in order to construct a new classification of the subfamily. A total number of 51 (sub)genera (11 new) are recognized, in which 472 valid species (49 new) are classified, resulting in many new combinations. The newly proposed classification facilitates species level taxonomy. In addition, it should provide a framework for further research on biogeography, (cryptic) speciation and evolution of host specialization. This thesis takes a first shot at some of these subjects by exploring the taxonomy of Neotropical Microdontinae that mimic stingless bees, reviewing and evaluating the associations of these flies with ants, and speculating on their historical biogeography. Show less
The concept of distance is a fundamental notion that forms a basis for the orientation in space. It is related to the scientific measurement process: quantitative measurements result in numerical... Show moreThe concept of distance is a fundamental notion that forms a basis for the orientation in space. It is related to the scientific measurement process: quantitative measurements result in numerical values, and these can be immediately translated into distances. Vice versa, a set of mutual distances defines an abstract Euclidean space. Each system is thereby represented as a point, whose Euclidean distances approximate the original distances as close as possible. If the original distance measures interesting properties, these can be found back as interesting patterns in this space. This idea is applied to complex systems: The act of breathing, the structure and activity of the brain, and dynamical systems and time series in general. In all these situations, optimal transportation distances are used; these measure how much work is needed to transform one probability distribution into another. The reconstructed Euclidean space then permits to apply multivariate statistical methods. In particular, canonical discriminant analysis makes it possible to distinguish between distinct classes of systems, e.g., between healthy and diseased lungs. This offers new diagnostic perspectives in the assessment of lung and brain diseases, and also offers a new approach to numerical bifurcation analysis and to quantify synchronization in dynamical systems. Show less
