Quantitative Super-Resolution Microscopy

Super-Resolution Microscopy is an optical fluorescence technique. In this thesis we focus on single molecule super-resolution, where the position of single molecules is determined. Typically these molecules can be localized with a 10 to 30nm precision. This technique is applied in four different studies. To determine the spatial distribution of Ras-protein in live cells, Ripley's analysis is used on localization data to quantify size an diffusion parameters of nanodomains. Particle image correlation spectroscopy (PICS) is a second order spatial distribution analysis to determine diffusion properties of single molecule populations. A mathematical framework to correct the data when applied on 3D diffusion is presented in the second chapter. In the fourth chapter the uptake of alpha-synuclein aggregates by the cells is observed using super-resolution microscopy. Their partial degradation was followed and showed the importance of the lysosome-dependent mechanism for protecting cells from exposure to potentially toxic a-synuclein. In the fifth chapter we correlate the number of vinculin proteins in a focal adhesion protein complex, to the local force generated by the cell via this complex. A method was developed to determine the local stoichiometry of molecules by their correlated distances as obtained from SMLM. Biological and Soft Matter Physic

Porting a visualization package from IRIX to NT : what will I get, what will I pay?

We discuss our experiences in porting a moderately large scientific visualization environment from IRIX to NT~4.0. Two porting strategies have been taken: a port via a POSIX emulation layer and a native NT port. POSIX compliant code can be ported to NT with relatively little effort if the code adheres to general accepted programming principles, such as modularity and encapsulation. The performance of a modern 3D Wintel machine is quite satisfactory for a variety of scientific desktop tasks. We have compared the performance of a 2 CPU Dell OptiPlex with FireGL 4000 graphics option to various SGI desktop workstations

Microplastics: a review of policies and responses

Although (micro)plastic contamination is a worldwide concern, most scientific literature only restates that issue rather than presenting strategies to cope with it. This critical review assembles the current knowledge on policies and responses to tackle plastic pollution, including peer-reviewed scientific literature, gray literature and relevant reports to provide: (1) a timeline of policies directly or indirectly addressing microplastics; (2) the most up-to-date upstream responses to prevent microplastics pollution, such as circular economy, behavioral change, development of bio-based polymers and market-based instruments as well as source-specific strategies, focusing on the clothing industry, tire and road wear particles, antifouling paints and recreational activities; (3) a set of downstream responses tackling microplastics, such as waste to energy, degradation, water treatment plants and litter clean-up strategies; and examples of (4) multifaceted responses focused on both mitigating and preventing microplastics pollution, e.g., approaches implemented in fisheries and aquaculture facilities. Preventive strategies and multifaceted responses are postulated as pivotal to handling the exacerbated release of microplastics in the environment, while downstream responses stand out as auxiliary strategies to the chief upstream responses. The information gathered here bridges the knowledge gaps on (micro)plastic pollution by providing a synthesized baseline material for further studies addressing this environmental issue

Imaging the lipid bilayer of giant unilamellar vesicles using red-to-blue light upconversion

Red-to-blue triplet–triplet annihilation upconversion was obtained in giant unilamellar vesicles. The upconverted light was homogeneously distributed across the membrane and could be utilized for the imaging of individual giant vesicles in three dimensions. These results show the great potential of TTA-UC for imaging applications under anoxic conditions

Spatial interplay of lymphocytes and fibroblasts in estrogen receptor-positive HER2-negative breast cancer

In estrogen-receptor-positive, HER2-negative (ER+HER2−) breast cancer, higher levels of tumor infiltrating lymphocytes (TILs) are often associated with a poor prognosis and this phenomenon is still poorly understood. Fibroblasts represent one of the most frequent cells in breast cancer and harbor immunomodulatory capabilities. Here, we evaluate the molecular and clinical impact of the spatial patterns of TILs and fibroblast in ER+HER2− breast cancer. We used a deep neural network to locate and identify tumor, TILs, and fibroblasts on hematoxylin and eosin-stained slides from 179 ER+HER2− breast tumors (ICGC cohort) together with a new density estimation analysis to measure the spatial patterns. We clustered tumors based on their spatial patterns and gene set enrichment analysis was performed to study their molecular characteristics. We independently assessed the spatial patterns in a second cohort of ER+HER2− breast cancer (N = 630, METABRIC) and studied their prognostic value. The spatial integration of fibroblasts, TILs, and tumor cells leads to a new reproducible spatial classification of ER+HER2− breast cancer and is linked to inflammation, fibroblast meddling, or immunosuppression. ER+HER2− patients with high TIL did not have a significant improved overall survival (HR = 0.76, P = 0.212), except when they had received chemotherapy (HR = 0.447). A poorer survival was observed for patients with high fibroblasts that did not show a high level of TILs (HR = 1.661, P = 0.0303). Especially spatial mixing of fibroblasts and TILs was associated with a good prognosis (HR = 0.464, P = 0.013). Our findings demonstrate a reproducible pipeline for the spatial profiling of TILs and fibroblasts in ER+HER2− breast cancer and suggest that this spatial interplay holds a decisive role in their cancer-immune interactions

The Development of Practice Recommendations for Drug-Disease Interactions by Literature Review and Expert Opinion

Background: Drug-disease interactions negatively affect the benefit/risk ratio of drugs for specific populations. In these conditions drugs should be avoided, adjusted, or accompanied by extra monitoring. The motivation for many drug-disease interactions in the Summary of Product Characteristics (SmPC) is sometimes insufficiently supported by (accessible) evidence. As a consequence the translation of SmPC to clinical practice may lead to non-specific recommendations. For the translation of this information to the real world, it is necessary to evaluate the available knowledge about drug-disease interactions, and to formulate specific recommendations for prescribers and pharmacists. The aim of this paper is to describe a standardized method how to develop practice recommendations for drug-disease interactions by literature review and expert opinion. Methods: The development of recommendations for drug-disease interactions will follow a six-step plan involving a multidisciplinary expert panel (1). The scope of the drug-disease interaction will be specified by defining the disease and by describing relevant effects of this drug-disease interaction. Drugs possibly involved in this drug-disease interaction are selected by checking the official product information, literature, and expert opinion (2). Evidence will be collected from the official product information, guidelines, handbooks, and primary literature (3). Study characteristics and outcomes will be evaluated and presented in standardized reports, including preliminary conclusions on the clinical relevance and practice recommendations (4). The multidisciplinary expert panel will discuss the reports and will either adopt or adjust the conclusions (5). Practice recommendations will be integrated in clinical decision support systems and published (6). The results of the evaluated drug-disease interactions will remain up-to-date by screening new risk information, periodic literature review, and (re)assessments initiated by health care providers. Actionable Recommendations: The practice recommendations will result in advices for specific DDSI. The content and considerations of these DDSIs will be published and implemented in all Clinical Decision Support Systems in the Netherlands. Discussion: The recommendations result in professional guidance in the context of individual patient care. The professional will be supported in the decision making in concerning pharmacotherapy for the treatment of a medical problem, and the clinical risks of the proposed medication in combination with specific diseases

Standard set of health outcome measures for older persons

Background: The International Consortium for Health Outcomes Measurement (ICHOM) was founded in 2012 to propose consensus-based measurement tools and documentation for different conditions and populations.This article describes how the ICHOM Older Person Working Group followed a consensus-driven modified Delphi technique to develop multiple global outcome measures in older persons. The standard set of outcome measures developed by this group will support the ability of healthcare systems to improve their care pathways and quality of care. An additional benefit will be the opportunity to compare variations in outcomes which encourages and supports learning between different health care systems that drives quality improvement. These outcome measures were not developed for use in research. They are aimed at non researchers in healthcare provision and those who pay for these services. Methods: A modified Delphi technique utilising a value based healthcare framework was applied by an international panel to arrive at consensus decisions.To inform the panel meetings, information was sought from literature reviews, longitudinal ageing surveys and a focus group. Results: The outcome measures developed and recommended were participation in decision making, autonomy and control, mood and emotional health, loneliness and isolation, pain, activities of daily living, frailty, time spent in hospital, overall survival, carer burden, polypharmacy, falls and place of death mapped to a three tier value based healthcare framework. Conclusions: The first global health standard set of outcome measures in older persons has been developed to enable health care systems improve the quality of care provided to older persons

Low-risk susceptibility alleles in 40 human breast cancer cell lines

Background: Low-risk breast cancer susceptibility alleles or SNPs confer only modest breast cancer risks ranging from just over 1.0 to 1.3 fold. Yet, they are common among most populations and therefore are involved in the development of essentially all breast cancers. The mechanism by which the low-risk SNPs confer breast cancer risks is currently unclear. The breast cancer association consortium BCAC has hypothesized that the low-risk SNPs modulate expression levels of nearby located genes. Methods: Genotypes of five low-risk SNPs were determined for 40 human breast cancer cell lines, by direct sequencing of PCR-amplified genomic templates. We have analyzed expression of the four genes that are located nearby the low-risk SNPs, by using real-time RT-PCR and Human Exon microarrays. Results: The SNP genotypes and additional phenotypic data on the breast cancer cell lines are presented. We did not detect any effect of the SNP genotypes on expression levels of the nearby-located genes MAP3K1, FGFR2, TNRC9 and LSP1. Conclusion: The SNP genotypes provide a base line for functional studies in a well-characterized cohort of 40 human breast cancer cell lines. Our expression analyses suggest that a putative disease mechanism through gene expression modulation is not operative in breast cancer cell lines