Stressor: An R Package for Benchmarking Machine Learning Models

Many discipline specific researchers need a way to quickly compare the accuracy of their predictive models to other alternatives. However, many of these researchers are not experienced with multiple programming languages. Python has recently been the leader in machine learning functionality, which includes the PyCaret library that allows users to develop high-performing machine learning models with only a few lines of code. The goal of the stressor package is to help users of the R programming language access the advantages of PyCaret without having to learn Python. This allows the user to leverage R’s powerful data analysis workflows, while simultaneously leveraging Python’s powerful machine learning functionality. stressor also implements a series of synthetic data set generation functions that create data sets where users can test ideas with models they create and/or use. These data sets can be paired with various forms of accuracy comparison to stress-test the models predictive capacity. This thesis illustrates this stress-test workflow on both real and synthetic data, illustrating stressor’s utility and ease of use

The development and impact of an endoscopic non-technical skills (ENTS) behavioural marker system

Background: Non-technical skills (NTS) are crucial to effective team working in endoscopy. Training in NTS has been shown to improve team performance and patient outcomes. As such, NTS training and assessment are now considered essential components of the endoscopy quality assurance process. Across the literature, other specialties have achieved this through development of behavioural marker systems (BMS). BMS provide a framework for assessing, training and measuring the NTS relevant to healthcare individuals and team. This article describes the development and impact of a novel BMS for endoscopy: the endoscopic non-technical skills (ENTS) system. Methods: The initial NTS taxonomy for endoscopy was created through a combination of literature review, staff focus groups and semi-structured interviews, incorporating the critical decision method. Framework analysis was conducted with three individual coders and generated a skills list which formed the preliminary taxonomy. Video observation of Bowel Cancer Screening endoscopists was used to identify exemplar behaviours which were mapped to relevant skills in the NTS taxonomy. Behavioural descriptors, derived from video data, were added to form the basis of the ENTS system. Results: A taxonomy of 33 skills in 14 separate categories were identified through framework analysis. Following video analysis and behaviour mapping, 4 overarching categories and 13 behavioural elements were identified which formed the ENTS framework. The endoscopy (directly observed procedural skills) 4-point rating scale was added to create the final ENTS system. Since its development in 2010, the ENTS system has been validated in the assessment of endoscopy for trainees nationally. ENTS informs a number of training initiatives, including a national strategy to improve NTS for all endoscopists. Conclusions: The ENTS system is a clinically relevant tool, validated for use in trainee assessment. The use of ENTS will be important to the future of training and quality assurance in endoscopy

Pre-clinical evaluation of advanced nerve guide conduits using a novel 3D in vitro testing model

Autografts are the current gold standard for large peripheral nerve defects in clinics despite the frequentlyoccurring side effects like donor site morbidity. Hollow nerve guidance conduits (NGC) are proposed alternatives toautografts, but failed to bridge gaps exceeding 3 cm in humans. Internal NGC guidance cues like microfibresare believed to enhance hollow NGCs by giving additional physical support for directed regeneration of Schwann cellsand axons. In this study, we report a new 3D in vitro model that allows the evaluation of different intraluminal fibrescaffolds inside a complete NGC. The performance of electrospun polycaprolactone (PCL) microfibres inside 5 mmlong polyethylene glycol (PEG) conduits were investigated in neuronal cell and dorsal root ganglion (DRG) cultures invitro. Z-stack confocal microscopy revealed the aligned orientation of neuronal cells along the fibres throughout thewhole NGC length and depth. The number of living cells in the centre of the scaffold was not significantly different tothe tissue culture plastic (TCP) control. For ex vivo analysis, DRGs were placed on top of fibre-filled NGCs to simulatethe proximal nerve stump. In 21 days of culture, Schwann cells and axons infiltrated the conduits along the microfibreswith 2.2 ± 0.37 mm and 2.1 ± 0.33 mm, respectively. We conclude that this in vitro model can help define internal NGCscaffolds in the future by comparing different fibre materials, composites and dimensions in one setup prior to animaltesting

An Improved In Vivo Methodology to Visualise Tumour Induced Changes in Vasculature Using the Chick Chorionic Allantoic Membrane Assay

Background/Aim: Decreasing the vascularity of a tumour has proven to be an effective strategy to suppress tumour growth and metastasis. Anti-angiogenic therapies have revolutionized the treatment of advanced-stage cancers, however there is still demand for further improvement. This necessitates new experimental models that will allow researchers to reliably study aspects of angiogenesis. The aim of this study was to demonstrate an in vivo technique in which the highly vascular and accessible chorioallantoic membrane (CAM) of the chick embryo is used to study tumour-induced changes in the macro and microvessels. Materials and Methods: Two cancer cell lines (human melanoma (C8161) and human prostate cancer (PC3)) were selected as model cells. Human dermal fibroblasts were used as a control. One million cells were labelled with green fluorescent protein and implanted on the CAM of the chick embryo at embryonic development day (EDD) 7 and angiogenesis was evaluated at EDDs 10, 12 and 14. A fluorescently-tagged lectin (lens culinaris agglutinin (LCA)) was injected intravenously into the chick embryo to label endothelial cells. The LCA is known to label the luminal surface of endothelial cells, or dextrans, in the CAM vasculature. Macrovessels were imaged by a hand-held digital microscope and images were processed for quantification. Microvessels were evaluated by confocal microscopy. Tumour invasion was assessed by histological and optical sectioning. Results: Tumour cells (C8161 and PC3) produced quantifiable increases in the total area covered by blood vessels, compared to fibroblasts when assessed by digital microscopy. Tumour invasion could be demonstrated by both histological and optical sectioning. The most significant changes in tumour vasculature observed were in the microvascular structures adjacent to the tumour cells, which showed an increase in the endothelial cell coverage. Additionally, tumour intravasation and tumour thrombus formation could be detected in the areas adjacent to tumour cells. The fragility of tumour blood vessels could be demonstrated when tumour cells seeded on a synthetic scaffold were grown on CAM. Conclusion: We report on a modification to a well-studied CAM in vivo assay, which can be effectively used to study tumour induced changes in macro and microvasculature

Measuring the Quantum State of a Large Angular Momentum

We demonstrate a general method to measure the quantum state of an angular momentum of arbitrary magnitude. The (2F+1) x (2F+1) density matrix is completely determined from a set of Stern-Gerlach measurements with (4F+1) different orientations of the quantization axis. We implement the protocol for laser cooled Cesium atoms in the 6S_{1/2}(F=4) hyperfine ground state and apply it to a variety of test states prepared by optical pumping and Larmor precession. A comparison of input and measured states shows typical reconstruction fidelities of about 0.95.Comment: 4 pages, 6 figures, submitted to PR

Reduced grapevine canopy size post-flowering via mechanical trimming alters ripening and yield of 'Pinot noir'

The degree and time of canopy trimming can alter phenology, rates of increase or decrease in berry components during grape ripening, and may influence yield and its components. The objective of this study was to investigate the extent to which reducing canopy size, by mechanical trimming post-flowering, changed Vitis vinifera L. 'Pinot noir' fruit yield and composition. Vines were mechanically trimmed to three different canopy heights at fruitset: 1000 mm (100 % canopy height), 600 mm (60 % canopy height relative to the control treatment) and 300 mm (30 % canopy height relative to the control treatment). Total soluble solids concentration and content, titratable acidity, pH and fresh berry mass were measured throughout ripening, and yield and leaf area were measured at harvest.Reduced canopy size via trimming to 30 and 60 % of the control treatment height slowed total soluble solids accumulation and in some cases increased titratable acidity and increased pH. The total soluble solids-titratable acidity ratio was therefore reduced throughout ripening by these trimming treatments relative to the full canopy height. Trimming to reduce canopy size had two effects on the source-sink ratio; it reduced the source (canopy) but increased fruit yield, an important sink. Therefore, the time of trimming is an important management consideration because it can delay and slow ripening due to reduced source leaves but could potentially accentuate the delay via increasing yield (sink). This technique may represent a way to offset the acceleration of phenology and grape ripening that has been observed to occur as a result of warmer seasons

Resolved-sideband Raman cooling to the ground state of an optical lattice

We trap neutral Cs atoms in a two-dimensional optical lattice and cool them close to the zero-point of motion by resolved-sideband Raman cooling. Sideband cooling occurs via transitions between the vibrational manifolds associated with a pair of magnetic sublevels and the required Raman coupling is provided by the lattice potential itself. We obtain mean vibrational excitations \bar{n}_x \approx \bar{n}_y \approx 0.01, corresponding to a population \sim 98% in the vibrational ground state. Atoms in the ground state of an optical lattice provide a new system in which to explore quantum state control and subrecoil laser coolingComment: PDF file, 13 pages including 3 figure

Oxygen mapping of melanoma spheroids using small molecule platinum probe and phosphorescence lifetime imaging microscopy

Solid tumours display varied oxygen levels and this characteristic can be exploited to develop new diagnostic tools to determine and exploit these variations. Oxygen is an efficient quencher of emission of many phosphorescent compounds, thus oxygen concentration could in many cases be derived directly from relative emission intensity and lifetime. In this study, we extend our previous work on phosphorescent, low molecular weight platinum(II) complex as an oxygen sensing probe to study the variation in oxygen concentration in a viable multicellular 3D human tumour model. The data shows one of the first examples of non-invasive, real-time oxygen mapping across a melanoma tumour spheroid using one-photon phosphorescence lifetime imaging microscopy (PLIM) and a small molecule oxygen sensitive probe. These measurements were quantitative and enabled real time oxygen mapping with high spatial resolution. This combination presents as a valuable tool for optical detection of both physiological and pathological oxygen levels in a live tissue mass and we suggest has the potential for broader clinical application