Time-resolved analysis of cell colony growth in vitro after irradiation

Here I developed a novel method to investigate the growth of cell colonies in vitro. The method is inspired by and augments the standard in vitro clonogenic assay (IVCA). While the field of application is radiobiological research, the approach can be applied to any domain where colony growth of adherent cells is of interest. The method utilizes high numbers of time-resolved microscopy image series and hence requires largely automated image data acquisition, image processing, quantitative data extraction and single-colony growth characterization. I designed a multi-step analysis framework to implement these steps. This contrasts with traditional approaches relying on visual examination of cell culture containers and manual classification of cell colonies. This new approach allows yet unattained insights into growth behaviors and growth rates of large numbers of individual cell colonies. In applying the new method to five different cell lines (H3122, H460, RENCA, SAT, UTSCC-5) in different experimental settings, the following main results were found: a) For some of the cell lines, the initial seeding density influences the growth dynamics of the resulting colonies in densities commonly used in standard experiments. b) Pre-experimental cell culture conditions influence the growth dynamics in two tested cell lines (SAT, UTSCC-5) without irradiation. c) Exponential growth rates of two tested cell lines (H3122, RENCA) are normally distributed independent of irradiation dose, but the average growth rate decreases linearly across commonly used doses. d) Some colonies growing from photon-irradiated cells exhibit a distinct delayed abortive growth behavior, as observed for the two analysed cell lines (H3122, RENCA). The frequency of this behavior increases with increasing dose. e) Survival rates, as traditionally determined via the standard IVCA, clearly depend on experimental readout choices, namely the time of readout and the size threshold used to score survival of colonies. My analysis indicates that this dependence emerges from observations c) and d). f) The observed influence of readout choices propagates into relative biological effectiveness quantification for carbon irradiation for three examined cell lines (H460, RENCA, UTSCC-5). Hence, I demonstrate that the presented method can be used to inform experimental design decisions in standard IVCA experiments, to perform robustness analyses on these assays, and to find distinct types of growth behavior. Still, the application in its current form is limited to adherently growing cell lines forming contiguous colonies. In addition, due to the multi-step procedure,some underlying assumptions and methodological decisions need to be made which potentially influence the resulting findings. I discuss these aspects in a dedicated chapter. In future work, potential extensions and combinations with quantitative single-cell analysis methods such as FACS, fluorescent live-cell imaging or single cell omics methods can make this method a cornerstone application to build on in order to understand not only how, but also why colonies grow the way they do. In conclusion, the presented method elucidates colony growth in unprecedented detail. The presented results showcase the potential relevance of these details. However, to establish this method as a standard tool for applied research, a unified analysis framework is necessary to standardize the methodological aspects, from image acquisition to colony growth type classification

Relating the permeability of quartz sands to their grain size and spectral induced polarization characteristics

Recently, Revil & Florsch proposed a novel mechanistic model based on the polarization of the Stern layer relating the permeability of granular media to their spectral induced polarization (SIP) characteristics based on the formation of polarized cells around individual grains. To explore the practical validity of this model, we compare it to pertinent laboratory measurements on samples of quartz sands with a wide range of granulometric characteristics. In particular, we measure the hydraulic and SIP characteristics of all samples both in their loose, non-compacted and compacted states, which might allow for the detection of polarization processes that are independent of the grain size. We first verify the underlying grain size/permeability relationship upon which the model of Revil & Florsch is based and then proceed to compare the observed and predicted permeability values for our samples by substituting the grain size characteristics by corresponding SIP parameters, notably the so-called Cole-Cole time constant. In doing so, we also asses the quantitative impact of an observed shift in the Cole-Cole time constant related to textural variations in the samples and observe that changes related to the compaction of the samples are not relevant for the corresponding permeability predictions. We find that the proposed model does indeed provide an adequate prediction of the overall trend of the observed permeability values, but underestimates their actual values by approximately one order-of-magnitude. This discrepancy in turn points to the potential importance of phenomena, which are currently not accounted for in the model and which tend to reduce the characteristic size of the prevailing polarization cells compared to the considered model, such as, for example, membrane polarization, contacts of double-layers of neighbouring grains, and incorrect estimation of the size of the polarized cells because of the irregularity of natural sand grain

The Dirichlet problem for the Jacobian equation in critical and supercritical Sobolev spaces

We study existence and regularity of solutions to the Dirichlet problem for the prescribed Jacobian equation, $\det Du = f$, where $f$ is integrable and bounded away from zero. In particular, we take $f\in L^p$, where $p > 1$, or in $L\log L$. We prove that for a Baire-generic $f$ in either space there are no solutions with the expected regularity.Comment: 14 page

The taxonomist - an endangered race : a practical proposal for its survival

Background: Taxonomy or biological systematics is the basic scientific discipline of biology, postulating hypotheses of identity and relationships, on which all other natural sciences dealing with organisms relies. However, the scientific contributions of taxonomists have been largely neglected when using species names in scientific publications by not citing the authority on which they are based. Discussion: Consequences of this neglect is reduced recognition of the importance of taxonomy, which in turn results in diminished funding, lower interest from journals in publishing taxonomic research, and a reduced number of young scientists entering the field. This has lead to the so-called taxonomic impediment at a time when biodiversity studies are of critical importance. Here we emphasize a practical and obvious solution to this dilemma. We propose that whenever a species name is used, the author(s) of the species hypothesis be included and the original literature source cited, including taxonomic revisions and identification literature - nothing more than what is done for every other hypothesis or assumption included in a scientific publication. In addition, we postulate that journals primarily publishing taxonomic studies should be indexed in ISISM. Summary: The proposal outlined above would make visible the true contribution of taxonomists within the scientific community, and would provide a more accurate assessment for funding agencies impact and importance of taxonomy, and help in the recruitment of young scientists into the field, thus helping to alleviate the taxonomic impediment. In addition, it would also make much of the biological literature more robust by reducing or alleviating taxonomic uncertainty. Keywords: Taxonomy crisis; taxonomic impediment; impact factor; original species description; citation index; systematic

A Curriculum Mining Method for Clustering Study Modules and Assessing their Uniqueness

Curriculum development can pursue several pedagogical goals. One is to design a curriculum that is attractive in comparison with other competing universities. To contribute to such a comparative assessment and, thereby, to the targeted development of curricula, the idea of a curriculum mining method is presented. Here, study modules are divided into homogeneous groups by means of a document clustering procedure. The generated knowledge improves the comparative assessment of curricula in two ways: First, depending on the context, it can be used to assess either the extent of the uniqueness of a module or its consecutiveness with other modules. Second, by supplementing the modules with metadata (e.g., region), a competitive analysis is provided in terms of modules offered by competing institutions. An exemplary case study demonstrates how this improves the evaluation of a specific IS curriculum. In conclusion, the current limitations and next steps of the research project are summarized

Robotic Process Flexibilization in the Term of Crisis: A Case Study of Robotic Process Automation in a Public Health Department

Due to the pandemic, institutions of the health sector, especially public health departments, are facing major challenges in managing their processes. In a constantly changing environment, new and existing processes have to be adopted or implemented in the shortest possible time, while the process volumes to be managed are constantly increasing. In our article, we use a case study to show how the concept of “flexibility by design” can be influenced by RPA in the sensitive environment of healthcare and how exactly flexibility in process execution can be achieved with it. As a result, we show that RPA can positively implement or enable three of the six realization options from the concept. In addition, the concept was supplemented by two aggregated theoretical dimensions, namely “Response” and “Range,” which summarize the supporting conditions for a process flexibilization with RPA. In the article, we thereby show how exactly RPA can complement existing processes in a healthcare environment and thus, serve to subsequently make rigid process models more flexible

Saliency on a chip: a digital approach with an FPGA

Selective-visual-attention algorithms have been successfully implemented in analog VLSI circuits.1 However, in addition to the usual issues of analog VLSI—such as the need to fi ne-tune a large number of biases— these implementations lack the spatial resolution and pre-processing capabilities to be truly useful for image-processing applications. Here we take an alternative approach and implement a neuro-mimetic algorithm for selective visual attention in digital hardware

Subcorneal Pustular Dermatosis with Temporary Autoimmune Features during COVID-19 Pandemic

Subcorneal pustular dermatosis, Sneddon-Wilkinson, is an uncommon neutrophilic dermatosis of unknown etiology. We report on a 51-year-old woman who presented with multiple superficial erythematous erosions surrounded by annular arranged sterile pustules concentrated on the trunk, the neck, and the proximal extremities during the coronavirus disease-19 pandemic. Larges pustules and flaccid bullae showed a hypopyon. There were no fever and no pruritus, general health was unaffected. Laboratory investigations revealed leukocytosis, neutrophilia, lymphopenia, and increased C-reactive protein. Initially, antinuclear antibodies, pemphigoid antibodies, and antibodies to BP 230 were positive, but negative 5 days later. Nasopharyngeal swabs were negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA tested by real-time reverse-transcriptase-polymerase chain reaction. A diagnostic skin biopsy showed epidermal spongiotic vesiculation and subcorneal pustulation with acantholysis and an inflammatory infiltrate composed of neutrophils and lymphocytes. The confirmed diagnosis was subcorneal pustular dermatosis Sneddon-Wilkinson. She was treated by dapsone and corticosteroids with the latter tempered down. Clinical response was rapid. We suggest that the autoimmune features seen on admission may be due to an undefined viral infection, but not SARS-CoV-2

Multidimensional flow mapping for proportional valves

Inverse, multidimensional input-output flow mapping is very important for use of valves in precision motion control applications. Due to the highly nonlinear characteristic and uncertain model structure of the cartridge valves, it is hard to formulate the modelling of their flow mappings into simple parameter estimation problems. This contribution conducts a comprehensive analysis and validation of three- and four-dimensional input-output-mapping approaches for a proportional pilot operated seat valves. Therefore, a virtual and a physical test-rig setup are utilized for initial measurement, implementation and assessment. After modeling and validating the valve under consideration, as a function of flow, pressure and temperature different mapping methods are investigated. More specifically, state of the art approaches, deep-learning methods and a newly developed approach (extPoly) are examined. Especially ANNs and Polynomials show reasonable approximation results even for more than two inputs. However, the results are strongly dependent on the structure and distribution of the input data points. Besides identification effort, the invertibility was investigated