Probabilistic sensitivity analysis of biochemical reaction systems

Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. We develop here a probabilistic approach to sensitivity analysis of biochemical reaction systems. The proposed technique employs a biophysically derived model for parameter fluctuations and, by using a recently suggested variance-based approach to sensitivity analysis [Saltelli et al., Chem. Rev. (Washington, D.C.) 105, 2811 (2005)], it leads to a powerful sensitivity analysis methodology for biochemical reaction systems. The approach presented in this paper addresses many problems associated with derivative-based sensitivity analysis techniques. Most importantly, it produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of high-order interaction effects. By employing a computational model of the mitogen-activated protein kinase signaling cascade, we demonstrate that our approach is well suited for sensitivity analysis of biochemical reaction systems and can produce a wealth of information about the sensitivity properties of such systems. The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical

Bankruptcy Reform: An Orderly Development of Public Policy

In legislating the pending bankruptcy reform, Congress has made many of the key decisions behind closed doors. In fact, the process has been characterized as a congressional effort to pass a stealth bankruptcy bill. This secrecy brings into question the democratic nature of congressional deliberation. When the Framers designed the legislative branch, open debate was envisioned as the rule, not the exception. Unfortunately, Congress has adopted a secretive, approach to pushing through recent bankruptcy legislation. In a sharp departure from the decades-long congressional approach to bankruptcy legislation, Congress stopped seeking expert advice and instead turned to special interest lobbyists…” Thus, Congress utilized the cover of secrecy to boldly tailor the bankruptcy laws to serve special interests. Consequently, theuse of the term \u27bankruptcy reform\u27 is considered an oxymoron to most organizations of bankruptcy professionals .... Virtually every group of bankruptcy professionals, regardless of the constituency represented, opposed both the substance of the legislation and the process ... taken by Congress. Recent efforts to alter the bankruptcy system under the cover of secrecy have received harsh criticism. Proponents of bankruptcy reform are so intent upon enacting legislation favoring special interests that they have taken the unprecedented step of attempting to enact the legislation under the guise of a completely unrelated, already-enacted bill. These tactics of congressional secrecy are contrary to the process of open, reasoned, and deliberate decision making that is a cornerstone of American democracy. This secrecy is wholly inconsistent with the process of public deliberation which the Founders envisioned

Bankruptcy Reform: An Orderly Development of Public Policy

In legislating the pending bankruptcy reform, Congress has made many of the key decisions behind closed doors. In fact, the process has been characterized as a congressional effort to pass a stealth bankruptcy bill. This secrecy brings into question the democratic nature of congressional deliberation. When the Framers designed the legislative branch, open debate was envisioned as the rule, not the exception. Unfortunately, Congress has adopted a secretive, approach to pushing through recent bankruptcy legislation. In a sharp departure from the decades-long congressional approach to bankruptcy legislation, Congress stopped seeking expert advice and instead turned to special interest lobbyists…” Thus, Congress utilized the cover of secrecy to boldly tailor the bankruptcy laws to serve special interests. Consequently, theuse of the term \u27bankruptcy reform\u27 is considered an oxymoron to most organizations of bankruptcy professionals .... Virtually every group of bankruptcy professionals, regardless of the constituency represented, opposed both the substance of the legislation and the process ... taken by Congress. Recent efforts to alter the bankruptcy system under the cover of secrecy have received harsh criticism. Proponents of bankruptcy reform are so intent upon enacting legislation favoring special interests that they have taken the unprecedented step of attempting to enact the legislation under the guise of a completely unrelated, already-enacted bill. These tactics of congressional secrecy are contrary to the process of open, reasoned, and deliberate decision making that is a cornerstone of American democracy. This secrecy is wholly inconsistent with the process of public deliberation which the Founders envisioned

PhOTO Zebrafish: A Transgenic Resource for In Vivo Lineage Tracing during Development and Regeneration

Background: Elucidating the complex cell dynamics (divisions, movement, morphological changes, etc.) underlying embryonic development and adult tissue regeneration requires an efficient means to track cells with high fidelity in space and time. To satisfy this criterion, we developed a transgenic zebrafish line, called PhOTO, that allows photoconvertible optical tracking of nuclear and membrane dynamics in vivo. Methodology: PhOTO zebrafish ubiquitously express targeted blue fluorescent protein (FP) Cerulean and photoconvertible FP Dendra2 fusions, allowing for instantaneous, precise targeting and tracking of any number of cells using Dendra2 photoconversion while simultaneously monitoring global cell behavior and morphology. Expression persists through adulthood, making the PhOTO zebrafish an excellent tool for studying tissue regeneration: after tail fin amputation and photoconversion of a ~100µm stripe along the cut area, marked differences seen in how cells contribute to the new tissue give detailed insight into the dynamic process of regeneration. Photoconverted cells that contributed to the regenerate were separated into three distinct populations corresponding to the extent of cell division 7 days after amputation, and a subset of cells that divided the least were organized into an evenly spaced, linear orientation along the length of the newly regenerating fin. Conclusions/Significance: PhOTO zebrafish have wide applicability for lineage tracing at the systems-level in the early embryo as well as in the adult, making them ideal candidate tools for future research in development, traumatic injury and regeneration, cancer progression, and stem cell behavior

Lunar Surface Systems Supportability Technology Development Roadmap

The Lunar Surface Systems Supportability Technology Development Roadmap is a guide for developing the technologies needed to enable the supportable, sustainable, and affordable exploration of the Moon and other destinations beyond Earth. Supportability is defined in terms of space maintenance, repair, and related logistics. This report considers the supportability lessons learned from NASA and the Department of Defense. Lunar Outpost supportability needs are summarized, and a supportability technology strategy is established to make the transition from high logistics dependence to logistics independence. This strategy will enable flight crews to act effectively to respond to problems and exploit opportunities in an environment of extreme resource scarcity and isolation. The supportability roadmap defines the general technology selection criteria. Technologies are organized into three categories: diagnostics, test, and verification; maintenance and repair; and scavenge and recycle. Furthermore, "embedded technologies" and "process technologies" are used to designate distinct technology types with different development cycles. The roadmap examines the current technology readiness level and lays out a four-phase incremental development schedule with selection decision gates. The supportability technology roadmap is intended to develop technologies with the widest possible capability and utility while minimizing the impact on crew time and training and remaining within the time and cost constraints of the program

A ring-like accretion structure in M87 connecting its black hole and jet

The nearby radio galaxy M87 is a prime target for studying black hole accretion and jet formation^{1,2}. Event Horizon Telescope observations of M87 in 2017, at a wavelength of 1.3 mm, revealed a ring-like structure, which was interpreted as gravitationally lensed emission around a central black hole^3. Here we report images of M87 obtained in 2018, at a wavelength of 3.5 mm, showing that the compact radio core is spatially resolved. High-resolution imaging shows a ring-like structure of 8.4_{-1.1}^{+0.5} Schwarzschild radii in diameter, approximately 50% larger than that seen at 1.3 mm. The outer edge at 3.5 mm is also larger than that at 1.3 mm. This larger and thicker ring indicates a substantial contribution from the accretion flow with absorption effects in addition to the gravitationally lensed ring-like emission. The images show that the edge-brightened jet connects to the accretion flow of the black hole. Close to the black hole, the emission profile of the jet-launching region is wider than the expected profile of a black-hole-driven jet, suggesting the possible presence of a wind associated with the accretion flow.Comment: 50 pages, 18 figures, 3 tables, author's version of the paper published in Natur

First M87 Event Horizon Telescope Results. IV. Imaging the Central Supermassive Black Hole

We present the first Event Horizon Telescope (EHT) images of M87, using observations from April 2017 at 1.3 mm wavelength. These images show a prominent ring with a diameter of similar to 40 mu as, consistent with the size and shape of the lensed photon orbit encircling the "shadow" of a supermassive black hole. The ring is persistent across four observing nights and shows enhanced brightness in the south. To assess the reliability of these results, we implemented a two-stage imaging procedure. In the first stage, four teams, each blind to the others' work, produced images of M87 using both an established method (CLEAN) and a newer technique (regularized maximum likelihood). This stage allowed us to avoid shared human bias and to assess common features among independent reconstructions. In the second stage, we reconstructed synthetic data from a large survey of imaging parameters and then compared the results with the corresponding ground truth images. This stage allowed us to select parameters objectively to use when reconstructing images of M87. Across all tests in both stages, the ring diameter and asymmetry remained stable, insensitive to the choice of imaging technique. We describe the EHT imaging procedures, the primary image features in M87, and the dependence of these features on imaging assumptions