Chaste: an open source C++ library for computational physiology and biology

Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials

Characteristics of Jupiter’s X‐ray auroral hot spot emissions using Chandra

To help understand and determine the driver of jovian auroral X-rays, we present the first statistical study to focus on the morphology and dynamics of the jovian northern hot spot (NHS) using Chandra data. The catalogue we explore dates from 18 December 2000 up to and including 8 September 2019. Using a numerical criterion, we characterize the typical and extreme behaviour of the concentrated NHS emissions across the catalogue. The mean power of the NHS is found to be 1.91 GW with a maximum brightness of 2.02 Rayleighs (R), representing by far the brightest parts of the jovian X-ray spectrum. We report a statistically significant region of emissions at the NHS center which is always present, the averaged hot spot nucleus (AHSNuc), with mean power of 0.57 GW and inferred average brightness of ∼ 1.2 R. We use a flux equivalence mapping model to link this distinct region of X-ray output to a likely source location and find that the majority of mappable NHS photons emanate from the pre-dusk to pre-midnight sector, coincident with the dusk flank boundary. A smaller cluster maps to the noon magnetopause boundary, dominated by the AHSNuc, suggesting that there may be multiple drivers of X-ray emissions. On application of timing analysis techniques (Rayleigh, Monte Carlo, Jackknife), we identify several instances of statistically significant quasi-periodic oscillations (QPOs) in the NHS photons ranging from ∼ 2.3-min to 36.4-min, suggesting possible links with ultra-low frequency activity on the magnetopause boundary (e.g. dayside reconnection, Kelvin-Helmholtz instabilities)

Self-esteem, stress and self-rated health in family planning clinic patients

BACKGROUND: The independent effects of stress on the health of primary care patients might be different for different types of clinic populations. This study examines these relationships in a low-income female population of patients attending a family planning clinic. METHODS: This study investigated the relevance of different sources of personal stress and social support to self-rated health, adjusting for mental health, health behavior and demographic characteristics of subjects. Five hundred women who attended family planning clinics were surveyed and 345 completed the form for a response rate of 72 percent. RESULTS: Multiple logistic regression analysis revealed that liking oneself was related to good self-rated health (Odds ratio = 7.11), but stress or support from children, parents, friends, churches or spouses were not significant. White non-Hispanic and non-white non-Hispanic respondents had lower odds of reporting good self-rated health than Hispanic respondents (odds ratios were 2.87 and 2.81, respectively). Exercising five or more days per week also was related to good self-rated health. Smoking 20 or more cigarettes per day, and obese III were negatively related to good self-rated health (odds ratios were .19 and .22, respectively with corresponding p-values equal to .0043 and .0332). CONCLUSIONS: Among younger low-income women, addressing low self-esteem might improve health status

Calibration of Traffic Simulation Models using SPSA

Εθνικό Μετσόβιο Πολυτεχνείο--Μεταπτυχιακή Εργασία. Διεπιστημονικό-Διατμηματικό Πρόγραμμα Μεταπτυχιακών Σπουδών (Δ.Π.Μ.Σ.) “Γεωπληροφορική

Identifying the Variety of Jovian X-Ray Auroral Structures: Tying the Morphology of X-Ray Emissions to Associated Magnetospheric Dynamics

We define the spatial clustering of X-rays within Jupiter's northern auroral regions by classifying their distributions into “X-ray auroral structures.” Using data from Chandra during Juno's main mission observations (24 May 2016 to 8 September 2019), we define five X-ray structures based on their ionospheric location and calculate the distribution of auroral photons. The morphology and ionospheric location of these structures allow us to explore the possibility of numerous X-ray auroral magnetospheric drivers. We compare these distributions to Hubble Space Telescope (HST) and Juno (Waves and MAG) data, and a 1D solar wind propagation model to infer the state of Jupiter's magnetosphere. Our results suggest that the five sub-classes of “X-ray structures” fall under two broad morphologies: fully polar and low latitude emissions. Visibility modeling of each structure suggests the non-uniformity of the photon distributions across the Chandra intervals are likely associated with the switching on/off of magnetospheric drivers as opposed to geometrical effects. The combination of ultraviolet (UV) and X-ray morphological structures is a powerful tool to elucidate the behavior of both electrons and ions and their link to solar wind/magnetospheric conditions in the absence of an upstream solar monitor. Although much work is still needed to progress the use of X-ray morphology as a diagnostic tool, we set the foundations for future studies to continue this vital research

A Multicellular Model of Intestinal Crypt Buckling and Fission

Crypt fission is an in vivo tissue deformation process that is involved in both intestinal homeostasis and colorectal tumourigenesis. Despite its importance, the mechanics underlying crypt fission are currently poorly understood. Recent experimental development of organoids, organ-like buds cultured from crypt stem cells in vitro, has shown promise in shedding light on crypt fission. Drawing inspiration from observations of organoid growth and fission in vivo, we develop a computational model of a deformable epithelial tissue layer. Results from in silico experiments show the stiffness of cells and the proportions of cell subpopulations affect the nature of deformation in the epithelial layer. In particular, we find that increasing the proportion of stiffer cells in the layer increases the likelihood of crypt fission occurring. This is in agreement with and helps explain recent experimental work

Combined changes in Wnt signalling response and contact inhibition induce altered proliferation in radiation treated intestinal crypts

Curative intervention is possible if colorectal cancer is identified early, underscoring the need to detect the earliest stages of malignant transformation. A candidate biomarker is the expanded proliferative zone observed in crypts before adenoma formation, also found in irradiated crypts. However, the underlying driving mechanism for this is not known. Wnt signaling is a key regulator of proliferation, and elevated Wnt signaling is implicated in cancer. Nonetheless, how cells differentiate Wnt signals of varying strengths is not understood. We use computational modeling to compare alternative hypotheses about how Wnt signaling and contact inhibition affect proliferation. Direct comparison of simulations with published experimental data revealed that the model that best reproduces proliferation patterns in normal crypts stipulates that proliferative fate and cell cycle duration are set by the Wnt stimulus experienced at birth. The model also showed that the broadened proliferation zone induced by tumorigenic radiation can be attributed to cells responding to lower Wnt concentrations and dividing at smaller volumes. Application of the model to data from irradiated crypts after an extended recovery period permitted deductions about the extent of the initial insult. Application of computational modeling to experimental data revealed how mechanisms that control cell dynamics are altered at the earliest stages of carcinogenesis

Jupiter's X‐Ray and UV Dark Polar Region

We present 14 simultaneous Chandra X-ray Observatory (CXO)-Hubble Space Telescope (HST) observations of Jupiter's Northern X-ray and ultraviolet (UV) aurorae from 2016 to 2019. Despite the variety of dynamic UV and X-ray auroral structures, one region is conspicuous by its persistent absence of emission: the dark polar region (DPR). Previous HST observations have shown that very little UV emission is produced by the DPR. We find that the DPR also produces very few X-ray photons. For all 14 observations, the low level of X-ray emission from the DPR is consistent (within 2-standard deviations) with scattered solar emission and/or photons spread by Chandra's Point Spread Function from known X-ray-bright regions. We therefore conclude that for these 14 observations the DPR produced no statistically significant detectable X-ray signature

Post-consent assessment of dental subjects' understanding of informed consent in oral health research in Nigeria

Abstract Background Research participants may not adequately understand the research in which they agree to enroll. This could be due to a myriad of factors. Such a missing link in the informed consent process contravenes the requirement for an "informed" consent prior to the commencement of research. This study assessed the post consent understanding of Nigerian study participants of the oral health research they were invited to join. Methods A descriptive cross sectional study with research participants who had just consented to one of three ongoing research studies on oral health. Study sites included two centers, one in the northern and one in the southern part of Nigeria. Data were collected using a combination of quantitative and qualitative methods. Results A total of 113 research participants were interviewed. The southern part of the country had 58 respondents with the north having 55. The age range was 21 – 80 years. Mean age was 46.1 (SD16.3). The sample was predominantly male (69.9%) and married (64.6%). There was poor understanding of some key elements of the informed consent process such as involvement in research, benefits, contacts, confidentiality and voluntariness. Some identified factors potentially compromising understanding were poverty, illiteracy, therapeutic misconception and confusion about the dual roles of the Dentist and the researcher. Conclusion The participants recruited into the oral health research in Nigeria did not adequately understand the studies they were invited to join nor do they understand their rights as research participants. Measures should be taken to include research bioethics into the curricula of Dental schools and to train oral health researchers in the country on research ethics.</p