Anchoring fins of fully covered self-expandable metal stents affect pull-out force and stent migration.

BACKGROUND AND AIMS: Stent migration and subsequent adverse events are frequently observed in the use of fully covered self-expandable metal stents (FCSEMSs) for distal biliary stenosis. In this study, we identified predictors for stent migration based on biomechanical stent characteristics and associated these findings with clinical outcomes. METHODS: The migration resistance of FCSEMSs was quantified by measuring the pull-out force. We analyzed a single-center retrospective cohort of 178 FCSEMSs for treatment success and adverse events occurring during 180 days of follow-up. RESULTS: Biomechanical measurements revealed a 4-fold higher migration resistance of FCSEMSs with anchoring fins (AF-FCSEMSs; Fmax = 14.2 ± .1 N) compared with FCSEMSs with flared ends (FE-FCSEMSs; Fmax = 3.8 ± 1.0 N; P < .0001). Clinically, AF-FCSEMSs showed lower rates of migration compared with FE-FCSEMSs (5% vs 34%, P < .0001). Unscheduled ERCP procedures because of stent dysfunction were less frequent in the AF group compared with the FE group (15% vs 29%, P = .046). Cholangitis because of stent dysfunction was observed in 5% of the AF group compared with 19% in the FE group (P = .02). Stent patency rates at 1, 3, and 6 months were higher in the AF group (96%, 90%, and 80%, respectively) compared with the FE group (90%, 74%, and 66%; log-rank test: P = .03). CONCLUSIONS: The pull-out force as a biomechanical stent property predicts the migration resistance of FCSEMSs in distal biliary stenosis and may thus be used to classify stents for this application. AF-FCSEMSs showed a significantly lower rate of migration and adverse events compared with FE-FCSEMSs.

Changing Aesthetics in Biomolecular Graphics.

Aesthetics for the visualization of biomolecular structures have evolved over the years according to technological advances, user needs, and modes of dissemination. In this article, we explore the goals, challenges, and solutions that have shaped the current landscape of biomolecular imagery from the overlapping perspectives of computer science, structural biology, and biomedical illustration. We discuss changing approaches to rendering, color, human-computer interface, and narrative in the development and presentation of biomolecular graphics. With this historical perspective on the evolving styles and trends in each of these areas, we identify opportunities and challenges for future aesthetics in biomolecular graphics that encourage continued collaboration from multiple intersecting fields.

ScrollyVis: Interactive Visual Authoring of Guided Dynamic Narratives for Scientific Scrollytelling.

Visual stories are an effective and powerful tool to convey specific information to a diverse public. Scrollytelling is a recent visual storytelling technique extensively used on the web, where content appears or changes as users scroll up or down a page. By employing the familiar gesture of scrolling as its primary interaction mechanism, it provides users with a sense of control, exploration and discoverability while still offering a simple and intuitive interface. In this article, we present a novel approach for authoring, editing, and presenting data-driven scientific narratives using scrollytelling. Our method flexibly integrates common sources such as images, text, and video, but also supports more specialized visualization techniques such as interactive maps as well as scalar field and mesh data visualizations. We show that scrolling navigation can be used to traverse dynamic narratives and demonstrate how it can be combined with interactive parameter exploration. The resulting system consists of an extensible web-based authoring tool capable of exporting stand-alone stories that can be hosted on any web server. We demonstrate the power and utility of our approach with case studies from several diverse scientific fields and with a user study including 12 participants of diverse professional backgrounds. Furthermore, an expert in creating interactive articles assessed the usefulness of our approach and the quality of the created stories.

Spatial heterogeneity and differential treatment response of acute myeloid leukemia and relapsed/refractory extramedullary disease after allogeneic hematopoietic cell transplantation.

Although extramedullary manifestations (EMs) are frequent in patients with acute myeloid leukemia (AML), they are often not detected during clinical workup and neither imaging- nor molecularly based diagnostic strategies are established to reveal their existence. Still, the detection of EM is essential for therapeutic decision-making, as EM present with aggressive and resistant disease and since mutational profiling might render patients within a different risk category, requiring personalized therapeutic strategies. Here, we report the case of an AML patient presenting with AML bone marrow (BM) infiltration and molecularly distinct EM at time of diagnosis followed by multiple EM relapses while undergoing several intensive chemotherapies including allogeneic hematopoietic cell transplantations (alloHCTs). 18Fluorodesoxy-glucose positron emission tomography (18FDG-PET)-imaging revealed EM sites in the mediastinum, duodenum, skin, and in retroperitoneal tissue, whereas recurrent BM biopsies showed continuous cytomorphologic and cytogenetic remission after alloHCT. To investigate the molecular background of the aggressive character of extramedullary disease and its differential treatment response, we performed amplicon-based next generation sequencing. An exon 4 (c.497_498insGA) frameshift RUNX1 mutation was exclusively found in all of the patient's EM sites, but not in the BM or in peripheral blood samples at time of EM reoccurrence. In addition, we detected an exon 13 (c.3306G>T) ASXL1 point mutation only in the retroperitoneal tumor tissue at the time of the fourth relapse. In contrast to the patient's intermediate-risk BM AML at diagnosis according to ELN2017, EM sites showed molecular adverse-risk features implicating intensified strategies like cellular therapies. Notably, disease relapse could only be detected by imaging throughout the course of disease. This case demonstrates both the necessity of continuous molecular profiling of EM to reveal differential molecular composition of EM and BM-derived AML, supposedly leading to divergent susceptibility to established therapies, as well as recurrent 18FDG-PET-imaging for detecting residual disease and assessment of treatment response in case of EM AML.

Considering best practices in color palettes for molecular visualizations.

Biomedical illustration and visualization techniques provide a window into complex molecular worlds that are difficult to capture through experimental means alone. Biomedical illustrators frequently employ color to help tell a molecular story, e.g., to identify key molecules in a signaling pathway. Currently, color use for molecules is largely arbitrary and often chosen based on the client, cultural factors, or personal taste. The study of molecular dynamics is relatively young, and some stakeholders argue that color use guidelines would throttle the growth of the field. Instead, content authors have ample creative freedom to choose an aesthetic that, e.g., supports the story they want to tell. However, such creative freedom comes at a price. The color design process is challenging, particularly for those without a background in color theory. The result is a semantically inconsistent color space that reduces the interpretability and effectiveness of molecular visualizations as a whole. Our contribution in this paper is threefold. We first discuss some of the factors that contribute to this array of color palettes. Second, we provide a brief sampling of color palettes used in both industry and research sectors. Lastly, we suggest considerations for developing best practices around color palettes applied to molecular visualization.

Structure of the Yeast Cell Wall Integrity Sensor Wsc1 Reveals an Essential Role of Surface-Exposed Aromatic Clusters.

In the yeast Saccharomyces cerevisiae and other ascomycetes, the maintenance of cell wall integrity is governed by a family of plasma-membrane spanning sensors that include the Wsc-type proteins. These cell wall proteins apparently sense stress-induced mechanical forces at the cell surface and target the cell wall integrity (CWI) signaling pathway, but the structural base for their sensor function is yet unknown. Here, we solved a high-resolution crystal structure of the extracellular cysteine-rich domain (CRD) of yeast Wsc1, which shows the characteristic PAN/Apple domain fold with two of the four Wsc1 disulfide bridges being conserved in other PAN domain cores. Given the general function of PAN domains in mediating protein-protein and protein-carbohydrate interactions, this finding underpins the importance of Wsc domains in conferring sensing and localization functions. Our Wsc1 CRD structure reveals an unusually high number of surface-exposed aromatic residues that are conserved in other fungal CRDs, and can be arranged into three solvent-exposed clusters. Mutational analysis demonstrates that two of the aromatic clusters are required for conferring S. cerevisiae Wsc1-dependent resistance to the glucan synthase inhibitor caspofungin, and the chitin-binding agents Congo red and Calcofluor white. These findings suggest an essential role of surface-exposed aromatic clusters in fungal Wsc-type sensors that might include an involvement in stress-induced sensor-clustering required to elicit appropriate cellular responses via the downstream CWI pathway.

Detecting drug resistance in pancreatic cancer organoids guides optimized chemotherapy treatment.

Drug combination therapies for cancer treatment show high efficacy but often induce severe side effects, resulting in dose or cycle number reduction. We investigated the impact of neoadjuvant chemotherapy (neoCTx) adaptions on treatment outcome in 59 patients with pancreatic ductal adenocarcinoma (PDAC). Resections with tumor-free margins were significantly more frequent when full-dose neoCTx was applied. We determined if patient-derived organoids (PDOs) can be used to personalize poly-chemotherapy regimens by pharmacotyping of treatment-naïve and post-neoCTx PDAC PDOs. Five out of ten CTx-naïve PDO lines exhibited a differential response to either the FOLFIRINOX or the Gem/Pac regimen. NeoCTx PDOs showed a poor response to the neoadjuvant regimen that had been administered to the respective patient in 30% of cases. No significant difference in PDO response was noted when comparing modified treatments in which the least effective single drug was removed from the complete regimen. Drug testing of CTx-naïve PDAC PDOs and neoCTx PDOs may be useful to guide neoadjuvant and adjuvant regimen selection, respectively. Personalizing poly-chemotherapy regimens by omitting substances with low efficacy could potentially result in less severe side effects, thereby increasing the fraction of patients receiving a full course of neoadjuvant treatment. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Macroscopic, histologic, and clinical assessment of acute graft-versus-host disease of the upper gastrointestinal tract within 6 weeks after allogeneic hematopoietic cell transplantation.

Acute graft-versus-host-disease (aGVHD) is the main cause of morbidity and nonrelapse mortality (NRM) following allogeneic hematopoietic cell transplantation (alloHCT). Nausea, vomiting, and anorexia after alloHCT can be early signs of aGVHD of the gastrointestinal tract (GIT) but may also reflect lasting mucosal damage or side effects of drugs. If upper GIT aGVHD is suspected, upper endoscopic evaluation and histological examination are crucial. Still, the interpretation of clinical symptoms, macroscopical alterations, and histological findings can be challenging. Therefore, we conducted a retrospective analysis on single-center data from 174 patients with suspected aGVHD of the upper GIT who underwent upper endoscopy within the first 6 weeks after alloHCT, to study the distribution of aGVHD-related histological findings in relation to clinical symptoms and macroscopic findings and to correlate the severity of changes with data on relapse and NRM. Our data suggest that biopsies of the duodenum reveal the severity of upper GIT aGVHD most accurately. While the histological grading correlated weakly with the severity of macroscopic changes, we found a tight correlation between histological and clinical grades of upper GIT aGVHD (p < 0.001). Although correlation of histological grading of upper GIT aGVHD with the risk for NRM missed statistical significance (HR 1.53, Lerner ≥1° versus <1º, p = 0.13), overall clinical aGVHD severity correlated with NRM (HR 4.3, IIIº-IVº versus 0-Iº, p < 0.01). In conclusion, biopsies from the duodenum are most sensitive in excluding aGVHD in patients with normal macroscopic findings at esophagogastroduodenoscopy. Clinical grading of aGVHD predicts NRM better than histological grading.

Finding haplotypic signatures in proteins.

BACKGROUND: The nonrandom distribution of alleles of common genomic variants produces haplotypes, which are fundamental in medical and population genetic studies. Consequently, protein-coding genes with different co-occurring sets of alleles can encode different amino acid sequences: protein haplotypes. These protein haplotypes are present in biological samples and detectable by mass spectrometry, but they are not accounted for in proteomic searches. Consequently, the impact of haplotypic variation on the results of proteomic searches and the discoverability of peptides specific to haplotypes remain unknown. FINDINGS: Here, we study how common genetic haplotypes influence the proteomic search space and investigate the possibility to match peptides containing multiple amino acid substitutions to a publicly available data set of mass spectra. We found that for 12.42% of the discoverable amino acid substitutions encoded by common haplotypes, 2 or more substitutions may co-occur in the same peptide after tryptic digestion of the protein haplotypes. We identified 352 spectra that matched to such multivariant peptides, and out of the 4,582 amino acid substitutions identified, 6.37% were covered by multivariant peptides. However, the evaluation of the reliability of these matches remains challenging, suggesting that refined error rate estimation procedures are needed for such complex proteomic searches. CONCLUSIONS: As these procedures become available and the ability to analyze protein haplotypes increases, we anticipate that proteomics will provide new information on the consequences of common variation, across tissues and time.

Semantic Snapping for Guided Multi-View Visualization Design.

Visual information displays are typically composed of multiple visualizations that are used to facilitate an understanding of the underlying data. A common example are dashboards, which are frequently used in domains such as finance, process monitoring and business intelligence. However, users may not be aware of existing guidelines and lack expert design knowledge when composing such multi-view visualizations. In this paper, we present semantic snapping, an approach to help non-expert users design effective multi-view visualizations from sets of pre-existing views. When a particular view is placed on a canvas, it is "aligned" with the remaining views-not with respect to its geometric layout, but based on aspects of the visual encoding itself, such as how data dimensions are mapped to channels. Our method uses an on-the-fly procedure to detect and suggest resolutions for conflicting, misleading, or ambiguous designs, as well as to provide suggestions for alternative presentations. With this approach, users can be guided to avoid common pitfalls encountered when composing visualizations. Our provided examples and case studies demonstrate the usefulness and validity of our approach.

Integrated Dual Analysis of Quantitative and Qualitative High-Dimensional Data.

The Dual Analysis framework is a powerful enabling technology for the exploration of high dimensional quantitative data by treating data dimensions as first-class objects that can be explored in tandem with data values. In this article, we extend the Dual Analysis framework through the joint treatment of quantitative (numerical) and qualitative (categorical) dimensions. Computing common measures for all dimensions allows us to visualize both quantitative and qualitative dimensions in the same view. This enables a natural joint treatment of mixed data during interactive visual exploration and analysis. Several measures of variation for nominal qualitative data can also be applied to ordinal qualitative and quantitative data. For example, instead of measuring variability from a mean or median, other measures assess inter-data variation or average variation from a mode. In this work, we demonstrate how these measures can be integrated into the Dual Analysis framework to explore and generate hypotheses about high-dimensional mixed data. A medical case study using clinical routine data of patients suffering from Cerebral Small Vessel Disease (CSVD), conducted with a senior neurologist and a medical student, shows that a joint Dual Analysis approach for quantitative and qualitative data can rapidly lead to new insights based on which new hypotheses may be generated.

DimLift: Interactive Hierarchical Data Exploration Through Dimensional Bundling.

The identification of interesting patterns and relationships is essential to exploratory data analysis. This becomes increasingly difficult in high dimensional datasets. While dimensionality reduction techniques can be utilized to reduce the analysis space, these may unintentionally bury key dimensions within a larger grouping and obfuscate meaningful patterns. With this work we introduce DimLift, a novel visual analysis method for creating and interacting with dimensional bundles. Generated through an iterative dimensionality reduction or user-driven approach, dimensional bundles are expressive groups of dimensions that contribute similarly to the variance of a dataset. Interactive exploration and reconstruction methods via a layered parallel coordinates plot allow users to lift interesting and subtle relationships to the surface, even in complex scenarios of missing and mixed data types. We exemplify the power of this technique in an expert case study on clinical cohort data alongside two additional case examples from nutrition and ecology.

Vis-a-Vis: Visual Exploration of Visualization Source Code Evolution.

Developing an algorithm for a visualization prototype often involves the direct comparison of different development stages and design decisions, and even minor modifications may dramatically affect the results. While existing development tools provide visualizations for gaining general insight into performance and structural aspects of the source code, they neglect the central importance of result images unique to graphical algorithms. In this article, we present a novel approach that enables visualization programmers to simultaneously explore the evolution of their algorithm during the development phase together with its corresponding visual outcomes by providing an automatically updating meta visualization. Our interactive system allows for the direct comparison of all development states on both the visual and the source code level, by providing easy to use navigation and comparison tools. The on-the-fly construction of difference images, source code differences, and a visual representation of the source code structure further enhance the user's insight into the states' interconnected changes over time. Our solution is accessible via a web-based interface that provides GPU-accelerated live execution of C++ and GLSL code, as well as supporting a domain-specific programming language for scientific visualization.

SplitStreams: A Visual Metaphor for Evolving Hierarchies.

The visualization of hierarchically structured data over time is an ongoing challenge and several approaches exist trying to solve it. Techniques such as animated or juxtaposed tree visualizations are not capable of providing a good overview of the time series and lack expressiveness in conveying changes over time. Nested streamgraphs provide a better understanding of the data evolution, but lack the clear outline of hierarchical structures at a given timestep. Furthermore, these approaches are often limited to static hierarchies or exclude complex hierarchical changes in the data, limiting their use cases. We propose a novel visual metaphor capable of providing a static overview of all hierarchical changes over time, as well as clearly outlining the hierarchical structure at each individual time step. Our method allows for smooth transitions between treemaps and nested streamgraphs, enabling the exploration of the trade-off between dynamic behavior and hierarchical structure. As our technique handles topological changes of all types, it is suitable for a wide range of applications. We demonstrate the utility of our method on several use cases, evaluate it with a user study, and provide its full source code.

Kin discrimination in social yeast is mediated by cell surface receptors of the Flo11 adhesin family.

Microorganisms have evolved specific cell surface molecules that enable discrimination between cells from the same and from a different kind. Here, we investigate the role of Flo11-type cell surface adhesins from social yeasts in kin discrimination. We measure the adhesion forces mediated by Flo11A-type domains using single-cell force spectroscopy, quantify Flo11A-based cell aggregation in populations and determine the Flo11A-dependent segregation of competing yeast strains in biofilms. We find that Flo11A domains from diverse yeast species confer remarkably strong adhesion forces by establishing homotypic interactions between single cells, leading to efficient cell aggregation and biofilm formation in homogenous populations. Heterotypic interactions between Flo11A domains from different yeast species or Saccharomyces cerevisiae strains confer weak adhesive forces and lead to efficient strain segregation in heterogenous populations, indicating that in social yeasts Flo11A-mediated cell adhesion is a major mechanism for kin discrimination at species and sub-species levels. These findings, together with our structure and mutation analysis of selected Flo11A domains, provide a rationale of how cell surface receptors have evolved in microorganisms to mediate kin discrimination.

EUS-guided stent removal in buried lumen-apposing metal stent syndrome: a case series.

BACKGROUND AND AIMS: Lumen-apposing metal stents (LAMSs) play an increasing role in transgastric and transduodenal drainage of pancreatic fluid collections and allow novel EUS-guided interventions. Alongside the main adverse events of bleeding and occlusion, LAMSs can be overgrown by mucosa, which leads to the inability to visualize the stent in endoscopy. METHODS: We describe a series of 4 cases of buried LAMSs that were removed under EUS guidance for identification of the stent followed by removal with rat-tooth forceps. RESULTS: The median in situ time of the LAMSs in the reported 4 cases was 53 days. All stents could no longer be visualized endoscopically when drainage of necrosis was complete. All 4 buried LAMSs could be identified by EUS and were removed successfully with forceps. In 1 case, balloon dilation of the stent tract was performed before stent removal. No adverse events were observed after the procedure. CONCLUSIONS: Buried stent syndrome is a rare adverse event of LAMSs. Here we describe a safe and effective approach for stent identification and removal without prior mucosal dissection.

Scale-Space Splatting: Reforming Spacetime for Cross-Scale Exploration of Integral Measures in Molecular Dynamics.

Understanding large amounts of spatiotemporal data from particle-based simulations, such as molecular dynamics, often relies on the computation and analysis of aggregate measures. These, however, by virtue of aggregation, hide structural information about the space/time localization of the studied phenomena. This leads to degenerate cases where the measures fail to capture distinct behaviour. In order to drill into these aggregate values, we propose a multi-scale visual exploration technique. Our novel representation, based on partial domain aggregation, enables the construction of a continuous scale-space for discrete datasets and the simultaneous exploration of scales in both space and time. We link these two scale-spaces in a scale-space space-time cube and model linked views as orthogonal slices through this cube, thus enabling the rapid identification of spatio-temporal patterns at multiple scales. To demonstrate the effectiveness of our approach, we showcase an advanced exploration of a protein-ligand simulation.

Towards Advanced Interactive Visualization for Virtual Atlases.

An atlas is generally defined as a bound collection of tables, charts or illustrations describing a phenomenon. In an anatomical atlas for example, a collection of representative illustrations and text describes anatomy for the purpose of communicating anatomical knowledge. The atlas serves as reference frame for comparing and integrating data from different sources by spatially or semantically relating collections of drawings, imaging data, and/or text. In the field of medical image processing, atlas information is often constructed from a collection of regions of interest, which are based on medical images that are annotated by domain experts. Such an atlas may be employed, for example, for automatic segmentation of medical imaging data. The combination of interactive visualization techniques with atlas information opens up new possibilities for content creation, curation, and navigation in virtual atlases. With interactive visualization of atlas information, students are able to inspect and explore anatomical atlases in ways that were not possible with the traditional method of presenting anatomical atlases in book format, such as viewing the illustrations from other viewpoints. With advanced interaction techniques, it becomes possible to query the data that forms the basis for the atlas, thus empowering researchers to access a wealth of information in new ways. So far, atlas-based visualization has been employed mainly for medical education, as well as biological research. In this survey, we provide an overview of current digital biomedical atlas tasks and applications and summarize relevant visualization techniques. We discuss recent approaches for providing next-generation visual interfaces to navigate atlas data that go beyond common text-based search and hierarchical lists. Finally, we reflect on open challenges and opportunities for the next steps in interactive atlas visualization.

Detectability and structural stability of a liquid fiducial marker in fresh ex vivo pancreas tumour resection specimens on CT and 3T MRI.

PURPOSE: To test the detectability of a liquid fiducial marker injected into ex vivo pancreas tumour tissue on magnetic resonance imaging (MRI) and computed tomography (CT). Furthermore, its injection performance using different needle sizes and its structural stability after fixation in formaldehyde were investigated. METHODS: Liquid fiducial markers with a volume of 20-100 µl were injected into freshly resected pancreas specimens of three patients with suspected adenocarcinoma. X­ray guided injection was performed using different needle sizes (18 G, 22 G, 25 G). The specimens were scanned on MRI and CT with clinical protocols. The markers were segmented on CT by signal thresholding. Marker detectability in MRI was assessed in the registered segmentations. Marker volume on CT was compared to the injected volume as a measure of backflow. RESULTS: Markers with a volume ≥20 µl were detected as hyperintensity on X­ray and CT. On T1- and T2-weighted 3T MRI, marker sizes ranging from 20-100 µl were visible as hypointensity. Since most markers were non-spherical, MRI detectability was poor and their differentiation from hypointensities caused by air cavities or surgical clips was only feasible with a reference CT. Marker backflow was only observed when using an 18-G needle. A volume decrease of 6.6 ± 13.0% was observed after 24 h in formaldehyde and, with the exception of one instance, no wash-out occurred. CONCLUSIONS: The liquid fiducial marker injected in ex vivo pancreatic resection specimen was visible as hyperintensity on kV X­ray and CT and as hypointensity on MRI. The marker's size was stable in formaldehyde. A marker volume of ≥50 µL is recommended in clinically used MRI sequences. In vivo injection is expected to improve the markers sphericity due to persisting metabolism and thereby enhance detectability on MRI.

Utility of fiducial markers for target positioning in proton radiotherapy of oesophageal carcinoma.

BACKGROUND AND PURPOSE: Oesophageal mobility relative to bony anatomy is a major source of geometrical uncertainty in proton radiotherapy of oesophageal carcinoma. To mitigate this uncertainty we investigated the use of implanted fiducial markers for direct target verification in terms of safety, visibility, and stability. MATERIALS AND METHODS: A total of 19 helical gold markers were endoscopically implanted in ten patients. Their placement at the proximal and distal tumour borders was compared to tumour demarcations derived from [18F]Fluorodeoxyglucose positron emission tomography, their visibility quantified via the contrast-to-noise ratio on daily orthogonal X-ray imaging, and their mobility relative to bony anatomy analysed by means of retrospective triangulation. RESULTS: Marker implantation proceeded without complications, but the distal tumour border could not be reached in two patients. Marker locations corresponded reasonably well with metabolic tumour edges (mean: 5.4 mm more distally). Marker visibility was limited but mostly sufficient (mean contrast-to-noise ratio: 1.5), and sixteen markers (84%) remained in situ until the end of treatment. Overall, marker excursions from their planned position were larger than 5(10) mm in 59(17)% of all analysed fractions. On one occasion severe target displacement was only identified via markers and was corrected before treatment delivery. CONCLUSION: Implanted helical gold fiducial markers are a safe and reliable method of providing target-centric positioning verification in proton beam therapy of oesophageal carcinoma.