Digital Three-Dimensional Atlas of Quail Development Using High-Resolution MRI

We present an archetypal set of three-dimensional digital atlases of the quail embryo based on microscopic magnetic resonance imaging (µMRI). The atlases are composed of three modules: (1) images of fixed ex ovo quail, ranging in age from embryonic day 5 to 10 (e05 to e10); (2) a coarsely delineated anatomical atlas of the µMRI data; and (3) an organ system–based hierarchical graph linked to the anatomical delineations. The atlas is designed to be accessed using SHIVA, a free Java application. The atlas is extensible and can contain other types of information including anatomical, physiological, and functional descriptors. It can also be linked to online resources and references. This digital atlas provides a framework to place various data types, such as gene expression and cell migration data, within the normal three-dimensional anatomy of the developing quail embryo. This provides a method for the analysis and examination of the spatial relationships among the different types of information within the context of the entire embryo

Coordinates and maps of the Apollo 17 landing site

We carried out an extensive cartographic analysis of the Apollo 17 landing site and determined and mapped positions of the astronauts, their equipment, and lunar landmarks with accuracies of better than ±1 m in most cases. To determine coordinates in a lunar body‐fixed coordinate frame, we applied least squares (2‐D) network adjustments to angular measurements made in astronaut imagery (Hasselblad frames). The measured angular networks were accurately tied to lunar landmarks provided by a 0.5 m/pixel, controlled Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) orthomosaic of the entire Taurus‐Littrow Valley. Furthermore, by applying triangulation on measurements made in Hasselblad frames providing stereo views, we were able to relate individual instruments of the Apollo Lunar Surface Experiment Package (ALSEP) to specific features captured in LROC imagery and, also, to determine coordinates of astronaut equipment or other surface features not captured in the orbital images, for example, the deployed geophones and Explosive Packages (EPs) of the Lunar Seismic Profiling Experiment (LSPE) or the Lunar Roving Vehicle (LRV) at major sampling stops. Our results were integrated into a new LROC NAC‐based Apollo 17 Traverse Map and also used to generate a series of large‐scale maps of all nine traverse stations and of the ALSEP area. In addition, we provide crater measurements, profiles of the navigated traverse paths, and improved ranges of the sources and receivers of the active seismic experiment LSPE

Interpretable statistics for complex modelling: quantile and topological learning

As the complexity of our data increased exponentially in the last decades, so has our need for interpretable features. This thesis revolves around two paradigms to approach this quest for insights. In the first part we focus on parametric models, where the problem of interpretability can be seen as a “parametrization selection”. We introduce a quantile-centric parametrization and we show the advantages of our proposal in the context of regression, where it allows to bridge the gap between classical generalized linear (mixed) models and increasingly popular quantile methods. The second part of the thesis, concerned with topological learning, tackles the problem from a non-parametric perspective. As topology can be thought of as a way of characterizing data in terms of their connectivity structure, it allows to represent complex and possibly high dimensional through few features, such as the number of connected components, loops and voids. We illustrate how the emerging branch of statistics devoted to recovering topological structures in the data, Topological Data Analysis, can be exploited both for exploratory and inferential purposes with a special emphasis on kernels that preserve the topological information in the data. Finally, we show with an application how these two approaches can borrow strength from one another in the identification and description of brain activity through fMRI data from the ABIDE project

An Algorithm for Cellular Reprogramming

The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology, providing data-guided frameworks that allow us to develop better predictions about and methods for control over specific biological processes and system-wide cell behavior. In this paper we describe an approach to optimizing the use of transcription factors in the context of cellular reprogramming. We construct an approximate model for the natural evolution of a synchronized population of fibroblasts, based on data obtained by sampling the expression of some 22,083 genes at several times along the cell cycle. (These data are based on a colony of cells that have been cell cycle synchronized) In order to arrive at a model of moderate complexity, we cluster gene expression based on the division of the genome into topologically associating domains (TADs) and then model the dynamics of the expression levels of the TADs. Based on this dynamical model and known bioinformatics, we develop a methodology for identifying the transcription factors that are the most likely to be effective toward a specific cellular reprogramming task. The approach used is based on a device commonly used in optimal control. From this data-guided methodology, we identify a number of validated transcription factors used in reprogramming and/or natural differentiation. Our findings highlight the immense potential of dynamical models models, mathematics, and data guided methodologies for improving methods for control over biological processes