From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data

Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically derive knowledge of a cellular signaling system at a conceptual level from systematic perturbation-response data. In this study, we explored a framework that unifies knowledge mining and data mining approaches towards the goal. The framework consists of the following automated processes: 1) applying an ontology-driven knowledge mining approach to identify functional modules among the genes responding to a perturbation in order to reveal potential signals affected by the perturbation; 2) applying a graph-based data mining approach to search for perturbations that affect a common signal with respect to a functional module, and 3) revealing the architecture of a signaling system organize signaling units into a hierarchy based on their relationships. Applying this framework to a compendium of yeast perturbation-response data, we have successfully recovered many well-known signal transduction pathways; in addition, our analysis have led to many hypotheses regarding the yeast signal transduction system; finally, our analysis automatically organized perturbed genes as a graph reflecting the architect of the yeast signaling system. Importantly, this framework transformed molecular findings from a gene level to a conceptual level, which readily can be translated into computable knowledge in the form of rules regarding the yeast signaling system, such as "if genes involved in MAPK signaling are perturbed, genes involved in pheromone responses will be differentially expressed"

Exposure of Escherichia coli to low-frequency vibrations

Low frequency mechanical vibration effects on biochemical mutant formation in E. col

Affordable heat: A whole-buildings efficiency service for Vermont families and businesses

Policy Leadership Initiative Year III Addressing Energy Challenges for Low-income Families in Northern New Englan

Growth of Staphylococcus aureus in a null magnetic field environment

Growth of Staphylococcus in magnetic field environmen

Simpler ISS Flight Control Communications and Log Keeping via Social Tools and Techniques

The heart of flight operations control involves a) communicating effectively in real time with other controllers in the room and/or in remote locations and b) tracking significant events, decisions, and rationale to support the next set of decisions, provide a thorough shift handover, and troubleshoot/improve operations. International Space Station (ISS) flight controllers speak with each other via multiple voice circuits or loops, each with a particular purpose and constituency. Controllers monitor and/or respond to several loops concurrently. The primary tracking tools are console logs, typically kept by a single operator and not visible to others in real-time. Information from telemetry, commanding, and planning systems also plays into decision-making. Email is very secondary/tertiary due to timing and archival considerations. Voice communications and log entries supporting ISS operations have increased by orders of magnitude because the number of control centers, flight crew, and payload operations have grown. This paper explores three developmental ground system concepts under development at Johnson Space Center s (JSC) Mission Control Center Houston (MCC-H) and Marshall Space Flight Center s (MSFC) Payload Operations Integration Center (POIC). These concepts could reduce ISS control center voice traffic and console logging yet increase the efficiency and effectiveness of both. The goal of this paper is to kindle further discussion, exploration, and tool development

Effective Use of Slaughter Checks for Identification and Control of Swine Disease

Swine producers, individually and as an industry are faced with numerous and complicated challenges. It is a\u3e dynamic industi^^,. .One area of interaction within tiie infrast^cture-is that of.animal health.^lere are m^ny. diseases known to affect swihe and their production efficiencies,, These diseases Impact producers and the industry in numerous, interrelated ways ., Severe animal disease can cause producers•to dramatically limit or even halt,production [1]. Disease can be clinical or subclinical.. Clinical disease is easily observable and actions can be taken to reduce its level; However, many swine diseases are subclinical and are riot visually observableFor subclinical disease, detection and accurate diagnoses in the live animal can be difficult.;-,.Yet these diseases can result in significant reductions in\u27animal efficiency and.^roduqef, losse

Isotopic studies in the natural sources of radium in groundwater in Illinois

Stable and radioactive isotopes in groundwater were studied in an investigation of the natural geologic sources of high concentrations of ²²⁶Ra and ²²⁸Ra in confined aquifers in the Cambrian and Ordovician bedrock of northern Illinois. The covariation of ¹⁸0 and D determined that the groundwater has a meteoric isotopic composition. Groundwater in unconfined aquifers has ¹⁸0 values (-6.6 to -7.9⁰/₀₀) that are similar to contemporary meteoric water. However, a source of recharge related to glaciation is required for groundwater in confined aquifers of the Cambrian and Ordovician that is significantly depleted in ¹⁸0 (¹⁸0 values range to -12.7⁰/₀₀ and are less than -9⁰/₀₀ over large regions) . The covariation of ³⁴S and ¹⁸0 in dissolved sulfates determined a mixing line between two sources; oxidation of sulfide minerals and dissolution of marine evaporites. Dissolved sulfates from evaporite sources are present in large concentrations in confined aquifers but are of a different isotopic composition than evaporites of Cambrian or Ordovician age. Glaciation may be important with regard to recharge of the sulfates. The ²³⁴U/²³⁸U activity ratio in groundwater from the Cambrian and Ordovician are unexpectedly high; values range from 2.1 to 40.7. The lowest ratios occur in primary recharge zones. In confined aquifers values are greater than 20 over large regions. Alpha recoil damage is a mechanism that contributes to the disequilibrium. However, the regional variation in activity ratios and in ²³⁴U concentrations supports the concept that glacial recharge has contributed to the high ratios. Radiological and geochemical mechanisms that partition ²³⁸U, ²³⁴U and ²³⁰Th on the sandstone matrix are important to the dissolved ²²⁶Ra concentration.U.S. Department of the InteriorU.S. Geological Surve