Visualisation of Long in Time Dynamic Networks on Large Touch Displays

Any dataset containing information about relationships between entities can be modelled as a network. This network can be static, where the entities/relationships do not change over time, or dynamic, where the entities/relationships change over time. Network data that changes over time, dynamic network data, is a powerful resource when studying many important phenomena, across wide-ranging fields from travel networks to epidemiology.However, it is very difficult to analyse this data, especially if it covers a long period of time (e.g, one month) with respect to its temporal resolution (e.g. seconds). In this thesis, we address the problem of visualising long in time dynamic networks: networks that may not be particularly large in terms of the number of entities or relationships, but are long in terms of the length of time they cover when compared to their temporal resolution.We first introduce Dynamic Network Plaid, a system for the visualisation and analysis of long in time dynamic networks. We design and build for an 84" touch-screen vertically-mounted display as existing work reports positive results for the use of these in a visualisation context, and that they are useful for collaboration. The Plaid integrates multiple views and we prioritise the visualisation of interaction provenance. In this system we also introduce a novel method of time exploration called ‘interactive timeslicing’. This allows the selection and comparison of points that are far apart in time, a feature not offered by existing visualisation systems. The Plaid is validated through an expert user evaluation with three public health researchers.To confirm observations of the expert user evaluation, we then carry out a formal laboratory study with a large touch-screen display to verify our novel method of time navigation against existing animation and small multiples approaches. From this study, we find that interactive timeslicing outperforms animation and small multiples for complex tasks requiring a compari-son between multiple points that are far apart in time. We also find that small multiples is best suited to comparisons of multiple sequential points in time across a time interval.To generalise the results of this experiment, we later run a second formal laboratory study in the same format as the first, but this time using standard-sized displays with indirect mouse input. The second study reaffirms the results of the first, showing that our novel method of time navigation can facilitate the visual comparison of points that are distant in time in a way that existing approaches, small multiples and animation, cannot. The study demonstrates that our previous results generalise across display size and interaction type (touch vs mouse).In this thesis we introduce novel representations and time interaction techniques to improve the visualisation of long in time dynamic networks, and experimentally show that our novel method of time interaction outperforms other popular methods for some task types

DataLev: Mid-air Data Physicalisation Using Acoustic Levitation

Data physicalisation is a technique that encodes data through the geometric and material properties of an artefact, allowing users to engage with data in a more immersive and multi-sensory way. However, current methods of data physicalisation are limited in terms of their reconfgurability and the types of materials that can be used. Acoustophoresis—a method of suspending and manipulating materials using sound waves—ofers a promising solution to these challenges. In this paper, we present DataLev, a design space and platform for creating reconfgurable, multimodal data physicalisations with enriched materiality using acoustophoresis. We demonstrate the capabilities of DataLev through eight examples and evaluate its performance in terms of reconfgurability and materiality. Our work ofers a new approach to data physicalisation, enabling designers to create more dynamic, engaging, and expressive artefacts

Tugging Graphs Faster: Efficiently Modifying Path-Preserving Hierarchies for Browsing Paths

International audienceMany graph visualization systems use graph hierarchies to organize a large input graph into logical components. These approaches detect features globally in the data and place these features inside levels of a hierarchy. However, this feature detection is a global process and does not consider nodes of the graph near a feature of interest. TugGraph is a system for exploring paths and proximity around nodes and subgraphs in a graph. The approach modifies a pre-existing hierarchy in order to see how a node or subgraph of interest extends out into the larger graph. It is guaranteed to create path-preserving hierarchies, so that the abstraction shown is meaningful with respect to the underlying structure of the graph. The system works well on graphs of hundreds of thousands of nodes and millions of edges. TugGraph is able to present views of this proximal information in the context of the entire graph in seconds, and does not require a layout of the full graph as input

Invasive intraductal papillary mucinous neoplasm and pancreatic ductal adenocarcinoma : a comparison in clinicopathology and long-term outcome

Background: The resections for both pre-malignant and invasive intraductal papillary mucinous neoplasm (inv-IPMN) have increased the last decades. Long term outcome, and the impact of adjuvant chemotherapy, non-regional lymph node status and recurrence pattern on overall survival (OS) is known for conventional pancreatic ductal adenocarcinoma (PDAC), but not so for inv-IPMN. Aims: I) Investigate differences and similarities in clinicopathology and overall survival between patients resected for inv-IPMN and PDAC. II) Elucidate whether the raised numbers of pancreatic resections for inv-IPMN in combination with the improvement in OS recent years have influenced outcome. III) Assess the prognostic significance of para-aortal lymph node (PALN) involvement in patients resected for inv-IPMN and PDAC in the pancreatic head. IV) Explore the impact of adjuvant chemotherapy and spatio-temporal recurrence pattern on overall survival for inv-IPMN compared with PDAC. Methods: All studies were retrospective observational studies of consecutive patients ≥ 18 years of age resected for inv-IPMN and PDAC. Study I-III were single-centre studies of in total 515 patients resected at Karolinska University Hospital between 2009-2018, Study IV was a national multi-centre study of patients resected in Sweden between 2010–2019. Clinicopathological variables were analysed in multivariable Cox regression models. Outcome was assessed by calculating two- or three-year OS rate and estimating OS using the Kaplan-Meier model. Survival functions were compared with log-rank test. In study I were clinicopathological variables also analysed in multivariable logistic regression models. Study II only comprised patients with PDAC or inv-IPMN in the pancreatic head who underwent partial or total pancreatoduodenectomy including PALN resection. In study III, that only included patients residing in the Stockholm area, different initial recurrence sites and time frames as well as predictors for death including the impact of adjuvant chemotherapy were assessed with multivariable logistic and Cox regressions. In study IV, clinicopathological variables were retrieved from the Swedish national pancreatic and periampullary cancer registry. The effect on death was assessed in two multivariable Cox regression models, one for patients resected 2010-2015, one for patients resected 2016-2019. Results: In study I, 513 patients were included, 122 inv-IPMN and 391 PDAC. The proportion resected inv-IPMN and two-year OS increased during the study period. In Kaplan-Meier survival analysis, inv-IPMN had more favourable median OS compared to PDAC. In multivariable Cox Regression analysis, tumour type was not a predictor for death. In study II, 403 patients were included, 89 inv-IPMN and 314 PDAC. PALN were metastatic in 16% and there was no difference between the groups. N0- and N2-stage were present in 16% and 53% respectively for patients with inv-IPMN compared to 6% and 65% respectively for patients with PDAC (p=0.007). Median OS was 12.7 and 22.7 months in the presence or absence of PALN metastases respectively (p<0.001), and similar in N2-stage regardless the presence of PALN status. PALN status was not an independent prognostic factor. In study III, 396 patients were included, 92 inv-IPMN and 304 PDAC. Both recurrence rate and death rate within three-years were lower for inv-IPMN compared to PDAC. The most common recurrence patterns were multi-site (25%), single-site liver (21%) and single-site locoregional (10%) recurrence. The most important predictors for death were multi-site, single-site peritoneal and single-site liver recurrence. These predictors were less common in inv-IPMN compared to PDAC. Adjuvant chemotherapy had similar effect in the two groups. In study IV, 1909 patients were included, 293 inv-IPMN and 1616 PDAC. Tumour type was an independent predictor for death in the 2016-2019 cohort, but not in the 2010-2015 cohort. In Kaplan-Meier survival analysis, inv-IPMN was associated with longer median OS in stage N0-1 and in stage M0 compared to PDAC. However, in stage T2-4 and stage N2 median OS was similar, whereas median OS in stage M1 was even shorter for inv-IPMN compared to PDAC. Conclusions: Inv-IPMN seemed to have favourable survival outcome compared to PDAC in lower stages, and similar to worse in higher. Outcome was dependent on the combination of a pronounced increase in resected inv-IPMN and a concurrent hazard reduction for death within 2 years during the study period. PALN status is not an independent risk factor for death and does not influence survival in N2-staged disease. The M1-stage for PALN positivity may therefore need reconsideration. Resected inv-IPMN exhibited a less aggressive recurrence pattern than PDAC that translated into a more favourable overall survival

LightGuider: Guiding Interactive Lighting Design using Suggestions, Provenance, and Quality Visualization

LightGuider is a novel guidance-based approach to interactive lighting design, which typically consists of interleaved 3D modeling operations and light transport simulations. Rather than having designers use a trial-and-error approach to match their illumination constraints and aesthetic goals, LightGuider supports the process by simulating potential next modeling steps that can deliver the most significant improvements. LightGuider takes predefined quality criteria and the current focus of the designer into account to visualize suggestions for lighting-design improvements via a specialized provenance tree. This provenance tree integrates snapshot visualizations of how well a design meets the given quality criteria weighted by the designer's preferences. This integration facilitates the analysis of quality improvements over the course of a modeling workflow as well as the comparison of alternative design solutions. We evaluate our approach with three lighting designers to illustrate its usefulness

Spatial and genomic analysis of the glioblastoma tumor microenvironment

Glioblastoma (GBM) is an aggressive brain cancer with devastating outcomes and few effective treatments. Although immunotherapy has shown promise in treating a variety of cancers, it is still unclear if and how it can be effectively used in GBM. Elucidating this will require a better understanding of the mechanistic role of immune cells and their interactions in the GBM tumor microenvironment. This thesis utilizes recent technological developments in cancer genomics and imaging to study the mechanisms underlying immunotherapy and the tumor microenvironment. First, we will provide background on our current understanding of GBM, its immune microenvironment, as well as modern sequencing and imaging methods. Second, we will present a longitudinal study of GBM patients before and after treatment with PD-1 immunotherapy. Only a small fraction of GBM patients respond to this type of therapy, so we perform genomic, transcriptomic, and spatial analyses to compare the molecular features of these rare responders versus non-responders. We show that clinical response to PD-1 immunotherapy in GBM is associated with specific molecular alterations and immune infiltration profiles that reflect the tumor’s clonal evolution during treatment. The most common infiltrating immune cells in GBM are macrophages, which are implicated in a wide variety of pro-tumor and anti-tumor roles. We then focus on this specific immune population by analyzing single-cell expression data from GBM tumors. We identify a novel macrophage subpopulation characterized by expression of the scavenger receptor MARCO, which drives tumor progression in GBM and is altered over the course of PD-1 immunotherapy. Next, we demonstrate that the methods we have developed for GBM are applicable to understanding the tumor microenvironments of other cancers as well. We analyze a cohort of melanoma cases to show that transcriptomic and imaging features can be combined to create a biomarker that stratifies patients into different risk groups. Finally, while most of the image analysis described so far has utilized histopathology, we include two appendices where we demonstrate new ways to process and analyze Magnetic Resonance Imaging (MRI) in GBM

Swimming by spinning: spinning-top type rotations regularize sperm swimming into persistently symmetric paths in 3D

Sperm modulate their flagellar symmetry to navigate through complex physico-chemical environments and achieve reproductive function. Yet it remains elusive how sperm swim forwards despite the inherent asymmetry of several components that constitutes the flagellar engine. Despite the critical importance of symmetry, or the lack of it, on sperm navigation and its physiological state, there is no methodology to date that can robustly detect the symmetry state of the beat in free-swimming sperm in 3D.How does symmetric progressive swimming emerge even for asymmetric beating, and how can beating (a)symmetry be inferred experimentally? Here, we numerically resolve the fluid mechanics of swimming around asymmetrically beating spermatozoa. This reveals that sperm spinning critically regularizes swimming into persistently symmetric paths in 3D, allowing sperm to swim forwards despite any imperfections on the beat. The sperm orientation in three-dimensions, and not the swimming path, can inform the symmetry state of the beat, eliminating the need of tracking the flagellum in 3D. We report a surprising correspondence between the movement of sperm and spinning-top experiments, indicating that the flagellum drives ''spinning-top'' type rotations during sperm swimming, and that this parallel is not a mere analogy. These results may prove essential in future studies on the role of (a)symmetry in spinning and swimming microorganisms and micro-robots, as body orientation detection has been vastly overlooked in favour of swimming path detection. Altogether, sperm rotation may provide a foolproof mechanism for forward propulsion and navigation in nature that would otherwise not be possible for flagella with broken symmetry