Background and purpose: Automatic approaches are widely implemented to automate dose optimization in radiotherapy treatment planning. This study systematically investigates how to configure automatic planning in order to create the best possible plans. Materials and methods: Automatic plans were generated using protocol based automatic iterative optimization. Starting from a simple automation protocol which consisted of the constraints for targets and organs at risk (OAR), the performance of the automatic approach was evaluated in terms of target coverage, OAR sparing, conformity, beam complexity, and plan quality. More complex protocols were systematically explored to improve the quality of the automatic plans. The protocols could be improved by adding a dose goal on the outer 2 mm of the PTV, by setting goals on strategically chosen subparts of OARs, by adding goals for conformity, and by limiting the leaf motion. For prostate plans, development of an automated post-optimization procedure was required to achieve precise control over the dose distribution. Automatic and manually optimized plans were compared for 20 head and neck (H&N), 20 prostate, and 20 rectum cancer patients. Results: Based on simple automation protocols, the automatic optimizer was not always able to generate adequate treatment plans. For the improved final configurations for the three sites, the dose was lower in automatic plans compared to the manual plans in 12 out of 13 considered OARs. In blind tests, the automatic plans were preferred in 80% of cases. Conclusions: With adequate, advanced, protocols the automatic planning approach is able to create high-quality treatment plans.
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The huge number of images shared on the Web makes effective cataloguing methods for efficient storage and retrieval procedures specifically tailored on the end-user needs a very demanding and crucial issue. In this paper, we investigate the applicability of Automatic Image Annotation (AIA) for image tagging with a focus on the needs of database expansion for a news broadcasting company. First, we determine the feasibility of using AIA in such a context with the aim of minimizing an extensive retraining whenever a new tag needs to be incorporated in the tag set population. Then, an image annotation tool integrating a Convolutional Neural Network model (AlexNet) for feature extraction and a K-Nearest-Neighbours classifier for tag assignment to images is introduced and tested. The obtained performances are very promising addressing the proposed approach as valuable to tackle the problem of image tagging in the framework of a broadcasting company, whilst not yet optimal for integration in the business process.
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Objective:Acknowledging study limitations in a scientific publication is a crucial element in scientific transparency and progress. However, limitation reporting is often inadequate. Natural language processing (NLP) methods could support automated reporting checks, improving research transparency. In this study, our objective was to develop a dataset and NLP methods to detect and categorize self-acknowledged limitations (e.g., sample size, blinding) reported in randomized controlled trial (RCT) publications.Methods:We created a data model of limitation types in RCT studies and annotated a corpus of 200 full-text RCT publications using this data model. We fine-tuned BERT-based sentence classification models to recognize the limitation sentences and their types. To address the small size of the annotated corpus, we experimented with data augmentation approaches, including Easy Data Augmentation (EDA) and Prompt-Based Data Augmentation (PromDA). We applied the best-performing model to a set of about 12K RCT publications to characterize self-acknowledged limitations at larger scale.Results:Our data model consists of 15 categories and 24 sub-categories (e.g., Population and its sub-category DiagnosticCriteria). We annotated 1090 instances of limitation types in 952 sentences (4.8 limitation sentences and 5.5 limitation types per article). A fine-tuned PubMedBERT model for limitation sentence classification improved upon our earlier model by about 1.5 absolute percentage points in F1 score (0.821 vs. 0.8) with statistical significance (). Our best-performing limitation type classification model, PubMedBERT fine-tuning with PromDA (Output View), achieved an F1 score of 0.7, improving upon the vanilla PubMedBERT model by 2.7 percentage points, with statistical significance ().Conclusion:The model could support automated screening tools which can be used by journals to draw the authors’ attention to reporting issues. Automatic extraction of limitations from RCT publications could benefit peer review and evidence synthesis, and support advanced methods to search and aggregate the evidence from the clinical trial literature.
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Retail industry consists of the establishment of selling consumer goods (i.e. technology, pharmaceuticals, food and beverages, apparels and accessories, home improvement etc.) and services (i.e. specialty and movies) to customers through multiple channels of distribution including both the traditional brickand-mortar and online retailing. Managing corporate reputation of retail companies is crucial as it has many advantages, for instance, it has been proven to impact generated revenues (Wang et al., 2016). But, in order to be able to manage corporate reputation, one has to be able to measure it, or, nowadays even better, listen to relevant social signals that are out there on the public web. One of the most extensive and widely used frameworks for measuring corporate reputation is through conducting elaborated surveys with respective stakeholders (Fombrun et al., 2015). This approach is valuable but deemed to be laborious and resource-heavy and will not allow to generate automatic alerts and quick and live insights that are extremely needed in this era of internet. For these purposes a social listening approach is needed that can be tailored to online data such as consumer reviews as the main data source. Online review datasets are a form of electronic Word-of-Mouth (WOM) that, when a data source is picked that is relevant to retail, commonly contain relevant information about customers’ perceptions regarding products (Pookulangara, 2011) and that are massively available. The algorithm that we have built in our application provides retailers with reputation scores for all variables that are deemed to be relevant to retail in the model of Fombrun et al. (2015). Examples of such variables for products and services are high quality, good value, stands behind, and meets customer needs. We propose a new set of subvariables with which these variables can be operationalized for retail in particular. Scores are being calculated using proportions of positive opinion pairs such as <fast, delivery> or <rude, staff> that have been designed per variable. With these important insights extracted, companies can act accordingly and proceed to improve their corporate reputation. It is important to emphasize that, once the design is complete and implemented, all processing can be performed completely automatic and unsupervised. The application makes use of a state of the art aspect-based sentiment analysis (ABSA) framework because of ABSA’s ability to generate sentiment scores for all relevant variables and aspects. Since most online data is in open form and we deliberately want to avoid labelling any data by human experts, the unsupervised aspectator algorithm has been picked. It employs a lexicon to calculate sentiment scores and uses syntactic dependency paths to discover candidate aspects (Bancken et al., 2014). We have applied our approach to a large number of online review datasets that we sampled from a list of 50 top global retailers according to National Retail Federation (2020), including both offline and online operation, and that we scraped from trustpilot, a public website that is well-known to retailers. The algorithm has carefully been evaluated by manually annotating a randomly sampled subset of the datasets for validation purposes by two independent annotators. The Kappa’s score on this subset was 80%.
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Adverse Outcome Pathways (AOPs) are conceptual frameworks that tie an initial perturbation (molecular initiat- ing event) to a phenotypic toxicological manifestation (adverse outcome), through a series of steps (key events). They provide therefore a standardized way to map and organize toxicological mechanistic information. As such, AOPs inform on key events underlying toxicity, thus supporting the development of New Approach Methodologies (NAMs), which aim to reduce the use of animal testing for toxicology purposes. However, the establishment of a novel AOP relies on the gathering of multiple streams of evidence and infor- mation, from available literature to knowledge databases. Often, this information is in the form of free text, also called unstructured text, which is not immediately digestible by a computer. This information is thus both tedious and increasingly time-consuming to process manually with the growing volume of data available. The advance- ment of machine learning provides alternative solutions to this challenge. To extract and organize information from relevant sources, it seems valuable to employ deep learning Natural Language Processing techniques. We review here some of the recent progress in the NLP field, and show how these techniques have already demonstrated value in the biomedical and toxicology areas. We also propose an approach to efficiently and reliably extract and combine relevant toxicological information from text. This data can be used to map underlying mechanisms that lead to toxicological effects and start building quantitative models, in particular AOPs, ultimately allowing animal-free human-based hazard and risk assessment.
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We examined the effects of age on automatic and voluntary motor adjustments in pointing tasks. To this end, young (20–25 years) and middle-aged adults (48–62 years) were instructed to point at a target that could unexpectedly change its location (to the left or right) or its color (to green or red) during the movement. In the location change conditions, participants were asked to either adjust their pointing movement toward the new location (i.e., normal pointing) or in the opposite direction (i.e., anti-pointing). In the color change conditions, participants were instructed to adjust their movement to the left or right depending on the change in color. The results showed that in a large proportion of the anti-pointing trials, participants made two adjustments: an early initial automatic adjustment in the direction of the target shift followed by a late voluntary adjustment toward the opposite direction. It was found that the late voluntary adjustments were delayed for the middle-aged participants relative to the young participants. There were no age differences for the fast automatic adjustment in normal pointing, but the early adjustment in anti-pointing tended to be later in the middle-aged adults. Finally, the difference in the onset of early and late adjustments in anti-pointing adjustments was greater among the middle-aged adults. Hence, this study is the first to show that aging slows down voluntary goal-directed movement control processes to greater extent than the automatic stimulus-driven processes.
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To study the ways in which compounds can induce adverse effects, toxicologists have been constructing Adverse Outcome Pathways (AOPs). An AOP can be considered as a pragmatic tool to capture and visualize mechanisms underlying different types of toxicity inflicted by any kind of stressor, and describes the interactions between key entities that lead to the adverse outcome on multiple biological levels of organization. The construction or optimization of an AOP is a labor intensive process, which currently depends on the manual search, collection, reviewing and synthesis of available scientific literature. This process could however be largely facilitated using Natural Language Processing (NLP) to extract information contained in scientific literature in a systematic, objective, and rapid manner that would lead to greater accuracy and reproducibility. This would support researchers to invest their expertise in the substantive assessment of the AOPs by replacing the time spent on evidence gathering by a critical review of the data extracted by NLP. As case examples, we selected two frequent adversities observed in the liver: namely, cholestasis and steatosis denoting accumulation of bile and lipid, respectively. We used deep learning language models to recognize entities of interest in text and establish causal relationships between them. We demonstrate how an NLP pipeline combining Named Entity Recognition and a simple rules-based relationship extraction model helps screen compounds related to liver adversities in the literature, but also extract mechanistic information for how such adversities develop, from the molecular to the organismal level. Finally, we provide some perspectives opened by the recent progress in Large Language Models and how these could be used in the future. We propose this work brings two main contributions: 1) a proof-of-concept that NLP can support the extraction of information from text for modern toxicology and 2) a template open-source model for recognition of toxicological entities and extraction of their relationships. All resources are openly accessible via GitHub (https://github.com/ontox-project/en-tox).
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During the past two decades the implementation and adoption of information technology has rapidly increased. As a consequence the way businesses operate has changed dramatically. For example, the amount of data has grown exponentially. Companies are looking for ways to use this data to add value to their business. This has implications for the manner in which (financial) governance needs to be organized. The main purpose of this study is to obtain insight in the changing role of controllers in order to add value to the business by means of data analytics. To answer the research question a literature study was performed to establish a theoretical foundation concerning data analytics and its potential use. Second, nineteen interviews were conducted with controllers, data scientists and academics in the financial domain. Thirdly, a focus group with experts was organized in which additional data were gathered. Based on the literature study and the participants responses it is clear that the challenge of the data explosion consist of converting data into information, knowledge and meaningful insights to support decision-making processes. Performing data analyses enables the controller to support rational decision making to complement the intuitive decision making by (senior) management. In this way, the controller has the opportunity to be in the lead of the information provision within an organization. However, controllers need to have more advanced data science and statistic competences to be able to provide management with effective analysis. Specifically, we found that an important skill regarding statistics is the visualization and communication of statistical analysis. This is needed for controllers in order to grow in their role as business partner..
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Background: Manual muscle mass assessment based on Computed Tomography (CT) scans is recognized as a good marker for malnutrition, sarcopenia, and adverse outcomes. However, manual muscle mass analysis is cumbersome and time consuming. An accurate fully automated method is needed. In this study, we evaluate if manual psoas annotation can be substituted by a fully automatic deep learning-based method.Methods: This study included a cohort of 583 patients with severe aortic valve stenosis planned to undergo Transcatheter Aortic Valve Replacement (TAVR). Psoas muscle area was annotated manually on the CT scan at the height of lumbar vertebra 3 (L3). The deep learning-based method mimics this approach by first determining the L3 level and subsequently segmenting the psoas at that level. The fully automatic approach was evaluated as well as segmentation and slice selection, using average bias 95% limits of agreement, Intraclass Correlation Coefficient (ICC) and within-subject Coefficient of Variation (CV). To evaluate performance of the slice selection visual inspection was performed. To evaluate segmentation Dice index was computed between the manual and automatic segmentations (0 = no overlap, 1 = perfect overlap).Results: Included patients had a mean age of 81 ± 6 and 45% was female. The fully automatic method showed a bias and limits of agreement of -0.69 [-6.60 to 5.23] cm2, an ICC of 0.78 [95% CI: 0.74-0.82] and a within-subject CV of 11.2% [95% CI: 10.2-12.2]. For slice selection, 84% of the selections were on the same vertebra between methods, bias and limits of agreement was 3.4 [-24.5 to 31.4] mm. The Dice index for segmentation was 0.93 ± 0.04, bias and limits of agreement was -0.55 [1.71-2.80] cm2.Conclusion: Fully automatic assessment of psoas muscle area demonstrates accurate performance at the L3 level in CT images. It is a reliable tool that offers great opportunities for analysis in large scale studies and in clinical applications.
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Research into automatic text simplification aims to promote access to information for all members of society. To facilitate generalizability, simplification research often abstracts away from specific use cases, and targets a prototypical reader and an underspecified content creator. In this paper, we consider a real-world use case – simplification technology for use in Dutch municipalities – and identify the needs of the content creators and the target audiences in this scenario. The stakeholders envision a system that (a) assists the human writer without taking over the task; (b) provides diverse outputs, tailored for specific target audiences; and (c) explains the suggestions that it outputs. These requirements call for technology that is characterized by modularity, explainability, and variability. We argue that these are important research directions that require further exploration
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