The Foundational Model of Anatomy Ontology

Anatomy is the structure of biological organisms. The term also denotes the scientific discipline devoted to the study of anatomical entities and the structural and developmental relations that obtain among these entities during the lifespan of an organism. Anatomical entities are the independent continuants of biomedical reality on which physiological and disease processes depend, and which, in response to etiological agents, can transform themselves into pathological entities. For these reasons, hard copy and in silico information resources in virtually all fields of biology and medicine, as a rule, make extensive reference to anatomical entities. Because of the lack of a generalizable, computable representation of anatomy, developers of computable terminologies and ontologies in clinical medicine and biomedical research represented anatomy from their own more or less divergent viewpoints. The resulting heterogeneity presents a formidable impediment to correlating human anatomy not only across computational resources but also with the anatomy of model organisms used in biomedical experimentation. The Foundational Model of Anatomy (FMA) is being developed to fill the need for a generalizable anatomy ontology, which can be used and adapted by any computer-based application that requires anatomical information. Moreover it is evolving into a standard reference for divergent views of anatomy and a template for representing the anatomy of animals. A distinction is made between the FMA ontology as a theory of anatomy and the implementation of this theory as the FMA artifact. In either sense of the term, the FMA is a spatial-structural ontology of the entities and relations which together form the phenotypic structure of the human organism at all biologically salient levels of granularity. Making use of explicit ontological principles and sound methods, it is designed to be understandable by human beings and navigable by computers. The FMA’s ontological structure provides for machine-based inference, enabling powerful computational tools of the future to reason with biomedical data

Monte Carlo Analysis of Optical Interactions in Reflectance and Transmittance Finger Photoplethysmography

Photoplethysmography (PPG) is a non-invasive photometric technique that measures the volume changes in arterial blood. Recent studies have reported limitations in developing and optimising PPG-based sensing technologies due to unavailability of the fundamental information such as PPG-pathlength and penetration depth in a certain region of interest (ROI) in the human body. In this paper, a robust computational model of a dual wavelength PPG system was developed using Monte Carlo technique. A three-dimensional heterogeneous volume of a specific ROI (i.e., human finger) was exposed at the red (660 nm) and infrared (940 nm) wavelengths in the reflectance and transmittance modalities of PPG. The optical interactions with the individual pulsatile and non-pulsatile tissue-components were demonstrated and the optical parameters (e.g., pathlength, penetration depth, absorbance, reflectance and transmittance) were investigated. Results optimised the source-detector separation for a reflectance finger-PPG sensor. The analysis with the recorded absorbance, reflectance and transmittance confirmed the maximum and minimum impact of the dermis and bone tissue-layers, respectively, in the formation of a PPG signal. The results presented in the paper provide the necessary information to develop PPG-based transcutaneous sensors and to understand the origin of the ac and dc components of the PPG signal

Monster Anatomy

We investigate the two-dimensional conformal field theories (CFTs) of $c=\frac{47}{2}$, $c=\frac{116}{5}$ and $c=23$ `dual' to the critical Ising model, the three state Potts model and the tensor product of two Ising models, respectively. We argue that these CFTs exhibit moonshines for the double covering of the baby Monster group, $2\cdot \mathbb{B}$, the triple covering of the largest Fischer group, $3\cdot \text{Fi}_{24}'$ and multiple-covering of the second largest Conway group, $2\cdot 2^{1+22} \cdot \text{Co}_2$. Various twined characters are shown to satisfy generalized bilinear relations involving Mckay-Thompson series. We also rediscover that the `self-dual' two-dimensional bosonic conformal field theory of $c=12$ has the Conway group $\text{Co}_{0}\simeq2\cdot\text{Co}_1$ as an automorphism group.Comment: 23 pages, revised according to suggestions from JHEP refere

Emil Zuckerkandl, M.D. (1849-1910): Bridging Anatomic Study and the Operating Room Table.

In the mid-19th century, the Vienna School of Anatomy was at the epicenter of the rapidly growing field of anatomy. One of the school’s most distinguished professors, Hungarian-born anatomist Emil Zuckerkandl was instrumental in transforming anatomy from a descriptive science to one of practical and clinical value. A prolific researcher interested in nearly all areas of morphology and most famously, the chromaffin system, Zuckerkandl’s discoveries from more than a century ago still provide a foundation for surgeons to this day

From "silent teachers" to models

For decades, embalmed cadavers have played an important role in teaching anatomy to the scientists and doctors of the future. Most anatomy departments use a traditional formaldehyde-based embalming method, but formalin embalming makes the bodies very rigid, which limits their usefulness for procedures other than dissection. A more recent embalming method developed by W. Thiel has allowed these "silent teachers" to take on a further role in applied anatomy research and teaching: to act as models for surgical training and medical research

Integrating Genomic Knowledge Sources through an Anatomy Ontology

Modern genomic research has access to a plethora of knowledge sources. Often, it is imperative that researchers combine and integrate knowledge from multiple perspectives. Although some technology exists for connecting data and knowledge bases, these methods are only just begin-ning to be successfully applied to research in modern cell biology. In this paper, we argue that one way to integrate multiple knowledge sources is through anatomy—both generic cellular anatomy, as well as anatomic knowledge about the tissues and organs that may be studied via microarray gene expression experiments. We present two examples where we have combined a large ontology of human anatomy (the FMA) with other genomic knowledge sources: the gene ontology (GO) and the mouse genomic databases (MGD) of the Jackson Labs. These two initial examples of knowledge integration provide a proof of concept that anatomy can act as a hub through which we can usefully combine a variety of genomic knowledge and data

Uberon: towards a comprehensive multi-species anatomy ontology

The lack of a single unified species-neutral ontology covering the anatomy of a variety of metazoans is a hindrance to translating model organism research to human health. We have developed an Uber-anatomy ontology to fill this need, filling the gap between the CARO upper-level ontology and species-specific anatomical ontologies

The anatomy of sovereign risk contagion

The channels for the cross-border propagation of sovereign risk in the international sovereign debt market are analysed. Identifying sovereign credit events as extraordinary jumps in CDS spreads, we distinguish between the immediate effects of such events and their longer term spillover effects. To analyse “fast and furious” contagion, we use daily CDS data to conduct event studies around a total of 89 identified credit events in a global country sample. To analyse “slow-burn” spillover effects, we apply a multifactor risk model, distinguishing between global and regional risk factors. We find that “fast and furious” contagion has been primarily a regional phenomenon, whilst “slow-burn” spillover effects can often be global in scope, especially those of the recent European debt crisis. The global risk factors are found to be driven by investor risk appetites and debt levels, whilst the regional factors depend on economic fundamentals of countries within a region

Andreas Vesalius: Celebrating 500 years of dissecting nature

December 31st, 2014 marked the 500-year anniversary of the birth of Andreas Vesalius. Vesalius, considered as the founder of modern anatomy, had profoundly changed not only human anatomy, but also the intellectual structure of medicine. The impact of his scientific revolution can be recognized even today. In this article we review the life, anatomical work, and achievements of Andreas Vesalius