Applications to Biological Networks of Adaptive Hagen-Poiseuille Flow on Graphs

Physarum polycephalum is a single-celled, multi-nucleated slime mold whose body constitutes a network of veins. As it explores its environment, it adapts and optimizes its network to external stimuli. It has been shown to exhibit complex behavior, like solving mazes, finding the shortest path, and creating cost-efficient and robust networks. Several models have been developed to attempt to mimic its network's adaptation in order to try to understand the mechanisms behind its behavior as well as to be able to create efficient networks. This thesis aims to study a recently developed, physically-consistent model based on adaptive Hagen-Poiseuille flows on graphs, determining the properties of the trees it creates and probing them to understand if they are realistic and consistent with experiment. It also intends to use said model to produce short and efficient networks, applying it to a real-life transport network example. We have found that the model is able to create networks that are consistent with biological networks: they follow Murray's law at steady state, exhibit structures similar to Physarum's networks, and even present peristalsis (oscillations of the vein radii) and shuttle streaming (the back-and-forth movement of cytoplasm inside Physarum's veins) in some parts of the networks. We have also used the model paired with different stochastic algorithms to produce efficient, short, and cost-efficient networks; when compared to a real transport network, mainland Portugal's railway system, all algorithms proved to be more efficient and some proved to be more cost-efficient.Comment: 106 pages, 59 figure

The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways

BACKGROUND Cancer constitutes a momentous health burden in our society. Critical information on cancer may be hidden in its signaling pathways. However, even though a large amount of money has been spent on cancer research, some critical information on cancer-related signaling pathways still remains elusive. Hence, new works towards a complete understanding of cancer-related signaling pathways will greatly benefit the prevention, diagnosis, and treatment of cancer. RESULTS We propose the node-weighted Steiner tree approach to identify important elements of cancer-related signaling pathways at the level of proteins. This new approach has advantages over previous approaches since it is fast in processing large protein-protein interaction networks. We apply this new approach to identify important elements of two well-known cancer-related signaling pathways: PI3K/Akt and MAPK. First, we generate a node-weighted protein-protein interaction network using protein and signaling pathway data. Second, we modify and use two preprocessing techniques and a state-of-the-art Steiner tree algorithm to identify a subnetwork in the generated network. Third, we propose two new metrics to select important elements from this subnetwork. On a commonly used personal computer, this new approach takes less than 2 s to identify the important elements of PI3K/Akt and MAPK signaling pathways in a large node-weighted protein-protein interaction network with 16,843 vertices and 1,736,922 edges. We further analyze and demonstrate the significance of these identified elements to cancer signal transduction by exploring previously reported experimental evidences. CONCLUSIONS Our node-weighted Steiner tree approach is shown to be both fast and effective to identify important elements of cancer-related signaling pathways. Furthermore, it may provide new perspectives into the identification of signaling pathways for other human diseases

Spacelab Science Results Study

Beginning with OSTA-1 in November 1981 and ending with Neurolab in March 1998, a total of 36 Shuttle missions carried various Spacelab components such as the Spacelab module, pallet, instrument pointing system, or mission peculiar experiment support structure. The experiments carried out during these flights included astrophysics, solar physics, plasma physics, atmospheric science, Earth observations, and a wide range of microgravity experiments in life sciences, biotechnology, materials science, and fluid physics which includes combustion and critical point phenomena. In all, some 764 experiments were conducted by investigators from the U.S., Europe, and Japan. The purpose of this Spacelab Science Results Study is to document the contributions made in each of the major research areas by giving a brief synopsis of the more significant experiments and an extensive list of the publications that were produced. We have also endeavored to show how these results impacted the existing body of knowledge, where they have spawned new fields, and if appropriate, where the knowledge they produced has been applied

Life Sciences Program Tasks and Bibliography for FY 1997

This document includes information on all peer reviewed projects funded by the Office of Life and Microgravity Sciences and Applications, Life Sciences Division during fiscal year 1997. This document will be published annually and made available to scientists in the space life sciences field both as a hard copy and as an interactive internet web page