Single-cell analysis of cell competition using quantitative microscopy and machine learning

Cell competition is a widely conserved, fundamental biological quality control mechanism. The cell competition assay of MDCK wild-type versus mutant MDCK Scribble-knockdown (ScribKD) relies on a mechanical mechanism of competition, which posits that the emergence of compressing stresses within the tissue at high confluency drive the competitive outcome. According to this mechanism, proliferating wild-type cells out-compete mutant ScribKD cells, resulting in their apoptosis and apical extrusion. Previous studies show that there is an increased division rate of wild-type cells in neighbourhoods with high numbers of ScribKD cells, but what still remains a mystery is whether this is a cause or consequence of increased apoptosis in the “loser” cell population. This project also interrogated the competitive assay of wild-type versus RasV12 , which is hypothesized to operate on a biochemical mechanism and results in the apical extrusion (but not apoptosis) of the loser RasV12 population. For both these mechanisms of competition it is still unknown which population of cells are driving the winner/loser outcome. Is the winner cell proliferation prompting the loser cell demise? Or is an autonomous loser elimination prompting a subsequent winner cell proliferation? In my research, I have employed multi-modal, time-lapse microscopy to image competition assays continuously for several days. These data were then segmented into wild-type or mutant instances using a Convolutional Neural Network (CNN) that can differentiate between the cell types, after which they were tracked across cellular generations using a Bayesian multi-object tracker. A conjugate analysis of fluorescent cell-cycle indicator probes was then utilised to automatically identify key time points of cellular fate commitment using deep-learning image classification. A spatio-temporal analysis was then conducted in order to quantify any correlation between wild-type proliferation and mutant cell demise. For the case of wild-type versus ScribKD , there was no clear evidence for the wild-type cells mitoses directly impacting upon the ScribKD cell apoptotic elimination. Instead, a subsequent analysis found that a more subtle mechanism of pre-emptive, local density increases around the apoptosis site appeared to be determining the eventual ScribKD fate. On the other hand, there was clear evidence of a direct impact of wild-type mitoses on the subsequent apical extrusion and competitive elimination of RasV12 cells. Both of these conclusions agree with the prevailing classification of cell competition types: mechanical interactions are more diffuse and occur over a larger spatio-temporal domain, whereas biochemical interactions are constrained to nearest neighbour cells. The hypothesized density-dependency of ScribKD elimination was further quantified on a single-cell scale by these analyses, as well as a potential new understanding of RasV12 extrusion. Most interestingly, it appears that there is a clear biophysical mechanism to the elimination in the biochemical RasV12 cell competition. This suggests that perhaps a new semantic approach is needed in the field of cell competition in order to accurately classify different mechanisms of elimination

Assessing Remedial Course Transitional Intervention Effectiveness for First Generation College Students

First generation college students experience a more challenging transition to collegiate success than their peers. As institutions feel the pressure to fulfill their enrollment goals, the doors of opportunity are being widened which includes an increase in first generation college students This study focuses on how the remedial course intervention affects student confidence levels in key college success indicators after their first semester of college level coursework. A survey is used to determine variations between first generation students who were exposed to this form of intervention, and those who were not. The findings point to a need for expanded conversation on intervention methodology to better frame a holistic model of success for today’s incoming student

Virucidal activity of 70% Ethanol vs Enveloped and Non-Enveloped Viruses

Viruses contain genetic material packaged in a protein coat called the capsid. For some viruses, the capsid is surrounded by an envelope composed of a lipid bilayer derived from the host cell membrane (Figure 2). Virus structure determines the stability characteristics of the virus particle, such as resistance to chemical or physical inactivation (Lucas, 2010). To maintain a safe environment at the Institute for Antiviral Research, it is important to understand which viruses are resistant to which chemicals. Thus, the objective of this experiment was to test survival of the viruses listed in table 1, when exposed to various chemicals. Neutral red dye is routinely used in antiviral assays and 70% ethanol is common disinfectant used. MEM & H2O were used as negative controls. Mt. Dew was also tested because we thought it would be fun

An agent-based modeling template for a cohort of veterans with diabetic retinopathy

BACKGROUNDAgent-based models are valuable for examining systems where large numbers of discrete individuals interact with each other, or with some environment. Diabetic Veterans seeking eye care at a Veterans Administration hospital represent one such cohort.OBJECTIVEThe objective of this study was to develop an agent-based template to be used as a model for a patient with diabetic retinopathy (DR). This template may be replicated arbitrarily many times in order to generate a large cohort which is representative of a real-world population, upon which in-silico experimentation may be conducted.METHODSAgent-based template development was performed in java-based computer simulation suite AnyLogic Professional 6.6. The model was informed by medical data abstracted from 535 patient records representing a retrospective cohort of current patients of the VA St. Louis Healthcare System Eye clinic. Logistic regression was performed to determine the predictors associated with advancing stages of DR. Predicted probabilities obtained from logistic regression were used to generate the stage of DR in the simulated cohort.RESULTSThe simulated cohort of DR patients exhibited no significant deviation from the test population of real-world patients in proportion of stage of DR, duration of diabetes mellitus (DM), or the other abstracted predictors. Simulated patients after 10 years were significantly more likely to exhibit proliferative DR (PCONCLUSIONSAgent-based modeling is an emerging platform, capable of simulating large cohorts of individuals based on manageable data abstraction efforts. The modeling method described may be useful in simulating many different conditions where course of disease is described in categorical stages

Does detection range matter for inferring social networks in a benthic shark using acoustic telemetry?

Accurately estimating contacts between animals can be critical in ecological studies such as examining social structure, predator–prey interactions or transmission of information and disease. While biotelemetry has been used successfully for such studies in terrestrial systems, it is still under development in the aquatic environment. Acoustic telemetry represents an attractive tool to investigate spatio-temporal behaviour of marine fish and has recently been suggested for monitoring underwater animal interactions. To evaluate the effectiveness of acoustic telemetry in recording interindividual contacts, we compared co-occurrence matrices deduced from three types of acoustic receivers varying in detection range in a benthic shark species. Our results demonstrate that (i) associations produced by acoustic receivers with a large detection range (i.e. Vemco VR2W) were significantly different from those produced by receivers with smaller ranges (i.e. Sonotronics miniSUR receivers and proximity loggers) and (ii) the position of individuals within their network, or centrality, also differed. These findings suggest that acoustic receivers with a large detection range may not be the best option to represent true social networks in the case of a benthic marine animal. While acoustic receivers are increasingly used by marine ecologists, we recommend users first evaluate the influence of detection range to depict accurate individual interactions before using these receivers for social or predator–prey studies. We also advocate for combining multiple receiver types depending on the ecological question being asked and the development of multi-sensor tags or testing of new automated proximity loggers, such as the Encounternet system, to improve the precision and accuracy of social and predator–prey interaction studies

Impedance-based sensor for potassium ions.

A conductometric sensor for potassium ions in solution is presented. Interdigitated, planar gold electrodes were coated with a potassium-selective polymer membrane composed of a poly(vinyl chloride) matrix with about 65 wt% of plasticiser and 2-5 wt% of a potassium-selective ionophore. The impedance of the membrane was measured, using the electrodes as a transducer, and related to the concentration of potassium in a sample solution in contact with the membrane. Sensitivity was optimised by varying the sensor components, and selectivity for potassium over sodium was also shown. The resulting devices are compact, miniature, robust sensors which, by means of impedance measurements, eliminate the need for a reference electrode. The sensor was tested for potassium concentration changes of 2 mM across the clinically relevant range of 2.7-18.7 mM.Henslow Fellowship, Darwin College, Cambridge L'Oreal -UNESCO UK & Ireland Fellowship For Women In Scienc

Lattice congruences of the weak order

We study the congruence lattice of the poset of regions of a hyperplane arrangement, with particular emphasis on the weak order on a finite Coxeter group. Our starting point is a theorem from a previous paper which gives a geometric description of the poset of join-irreducibles of the congruence lattice of the poset of regions in terms of certain polyhedral decompositions of the hyperplanes. For a finite Coxeter system (W,S) and a subset K of S, let \eta_K:w \mapsto w_K be the projection onto the parabolic subgroup W_K. We show that the fibers of \eta_K constitute the smallest lattice congruence with 1\equiv s for every s\in(S-K). We give an algorithm for determining the congruence lattice of the weak order for any finite Coxeter group and for a finite Coxeter group of type A or B we define a directed graph on subsets or signed subsets such that the transitive closure of the directed graph is the poset of join-irreducibles of the congruence lattice of the weak order.Comment: 26 pages, 4 figure

Game-Based Design for Inclusive and Accessible Digital Exhibits

Imagining the future of libraries and especially of digital exhibits cannot be completed without exploring the role games can play in the future of collection curation. Besides their popularity, games facilitate and inform our understanding through interactive engagement, and have been shown to serve as alternative modes for designing learning experiences and environments. We adopt such a perspective as we look into the ways gaming can inform the design of digital exhibits and help make digital collections more accessible and inclusive to a wider audience