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

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

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

2016 AAPP Monograph Series: African American Professors Program

The African American Professors Program (AAPP) at the University of South Carolina is honored to publish this fifteenth edition of its annual monograph series. AAPP recognizes the significance of offering scholars a venue through which to engage actively in research and to publish their refereed papers. Parallel with the publication of their manuscripts is the opportunity to gain visibility among colleagues throughout postsecondary institutions at national and international levels. Scholars who have contributed papers for this monograph are acknowledged for embracing the value of including this responsibility within their academic milieu. Writing across disciplines adds to the intellectual diversity of these manuscripts. From neophytes to quite experienced individuals, the chapters have been researched and written in depth. Founded in 1997 through the Department of Educational Leadership and Policies in the College of Education, AAPP was designed originally to address the under-representation of African American professors on college and university campuses. Its mission is to expand the pool of these professors in critical academic and research areas. Sponsored historically by the University of South Carolina, the W.K. Kellogg Foundation, and the South Carolina General Assembly, the program recruits doctoral students for disciplines in which African Americans currently are underrepresented among faculty in higher education. The continuation of this monograph series is seen as responding to a window of opportunity to be sensitive to academic expectation of graduates as they pursue career placement and, at the same time, to allow for the dissemination of products of scholarship to a broader community. The importance of this series has been voiced by one of our 2002 AAPP graduates, Dr. Shundelle LaTjuan Dogan, formerly an Administrative Fellow at Harvard University, a Program Officer for the Southern Education Foundation, and a Program Officer for the Arthur M. Blank Foundation in Atlanta, Georgia. She is currently a Corporate Citizenship and Corporate Affairs Manager for IBM-International Business Machines in Atlanta, Georgia and has written the Foreword for the 2014 monograph. Dr. Dogan wrote: One thing in particular that I want to thank you for is having the African American Professors Program scholars publish articles for the monograph. I have to admit that writing the articles seemed like extra work at the time. However, in my recent interview process, organizations have asked me for samples of my writing. Including an article from a published monograph helped to make my portfolio much more impressive. You were \u27right on target\u27 in having us do the monograph series. (AAPP 2003 Monograph, p. xi) The African American Professors Program continues the tradition as a promoter of international scholarship in higher education evidenced through the inspiration from this group of interdisciplinary manuscripts. I hope that you will envision these published papers to serve as an invaluable contribution to your own professional development and career enhancement. John McFadden, PhD The Benjamin Elijah Mays Distinguished Professor Emeritus Director, African American Professors Program University of South Carolinahttps://scholarcommons.sc.edu/mcfadden_monographs/1003/thumbnail.jp

Biodiversity on Broadway - Enigmatic Diversity of the Societies of Ants (Formicidae) on the Streets of New York City

Each year, a larger proportion of the Earth's surface is urbanized, and a larger proportion of the people on Earth lives in those urban areas. The everyday nature, however, that humans encounter in cities remains poorly understood. Here, we consider perhaps the most urban green habitat, street medians. We sampled ants from forty-four medians along three boulevards in New York City and examined how median properties affect the abundance and species richness of native and introduced ants found on them. Ant species richness varied among streets and increased with area but was independent of the other median attributes measured. Ant assemblages were highly nested, with three numerically dominant species present at all medians and additional species present at a subset of medians. The most common ant species were the introduced Pavement ant (Tetramorium caespitum) and the native Thief ant (Solenopsis molesta) and Cornfield ant (Lasius neoniger). The common introduced species on the medians responded differently to natural and disturbed elements of medians. Tetramorium caespitum was most abundant in small medians, with the greatest edge/area ratio, particularly if those medians had few trees, whereas Nylanderia flavipes was most abundant in the largest medians, particularly if they had more trees. Many of the species encountered in Manhattan were similar to those found in other large North American cities, such that a relatively small subset of ant species probably represent most of the encounters humans have with ants in North America

Anti-Transforming Growth Factor ß Antibody Treatment Rescues Bone Loss and Prevents Breast Cancer Metastasis to Bone

Breast cancer often metastasizes to bone causing osteolytic bone resorption which releases active TGFβ. Because TGFβ favors progression of breast cancer metastasis to bone, we hypothesized that treatment using anti-TGFβ antibody may reduce tumor burden and rescue tumor-associated bone loss in metastatic breast cancer. In this study we have tested the efficacy of an anti-TGFβ antibody 1D11 preventing breast cancer bone metastasis. We have used two preclinical breast cancer bone metastasis models, in which either human breast cancer cells or murine mammary tumor cells were injected in host mice via left cardiac ventricle. Using several in vivo, in vitro and ex vivo assays, we have demonstrated that anti-TGFβ antibody treatment have significantly reduced tumor burden in the bone along with a statistically significant threefold reduction in osteolytic lesion number and tenfold reduction in osteolytic lesion area. A decrease in osteoclast numbers (p = 0.027) in vivo and osteoclastogenesis ex vivo were also observed. Most importantly, in tumor-bearing mice, anti-TGFβ treatment resulted in a twofold increase in bone volume (p<0.01). In addition, treatment with anti-TGFβ antibody increased the mineral-to-collagen ratio in vivo, a reflection of improved tissue level properties. Moreover, anti-TGFβ antibody directly increased mineralized matrix formation in calverial osteoblast (p = 0.005), suggesting a direct beneficial role of anti-TGFβ antibody treatment on osteoblasts. Data presented here demonstrate that anti-TGFβ treatment may offer a novel therapeutic option for tumor-induced bone disease and has the dual potential for simultaneously decreasing tumor burden and rescue bone loss in breast cancer to bone metastases. This approach of intervention has the potential to reduce skeletal related events (SREs) in breast cancer survivors

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes