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

Former Students\u27 Perceptions of How Theatre Impacted Life Skills and Psychological Needs

The purpose of this qualitative case study was to investigate former high school theatre students\u27 perceptions of how theatre education addressed their psychological needs and impacted life skills. Participants were graduates of a large metropolitan high school, located near Atlanta, GA. A focus group, individual semi-structured interviews and collection of artifacts were the data collection procedures utilized to discover students\u27 perceptions. Pseudonyms were used to protect the identities of the participants. The data analysis process included initial coding, axial coding and memo writing. Based on the information from the interviews, this case study showed the benefits of offering youth opportunities to engage in theatre education and supported research that indicates the positive outcomes of arts education. The findings of the study indicate that theatre education impacts students\u27 life skills and psychological needs. Participants report gaining life skills, such as, hard-work, social skills, perseverance and career training. The data also revealed that participants experienced psychological benefits, such as, confidence, sense of belongingness, accomplishment and cognitive abilities

Robin Hood as Sheriff in Medieval Estates Model Literature

In his book, Robin Hood: An Historical Enquiry, John Bellamy asserts that the lack of a study of the relationship between Robin Hood and the sheriff stems from very little evidence in the ballads and external sources. However, the Robin Hood ballads originate in the fourteenth century when tales of justice and chivalry experienced widespread appeal alongside complaint literature addressing social upheaval bubbling to the surface of English life; why would an audience celebrate an outlaw during this time and long after Gawain and Arthur fade in popularity in the ensuing centuries? There must be more to the relationship between Robin Hood and the sheriff of Nottingham. In order to find a deeper relationship between the outlaw and lawman, the estates model should be used as a framework from which to begin the study of Robin Hood and his shrieval desires and not as a specific exercise of explication and application. By doing so, one can see that Robin Hood does assume the role of the sheriff in the early ballads by assuming his duties of managing the forests, collecting money from individuals within the community, albeit mostly from dishonest clergy, maintaining an army for defense, and settling disputes between various parties within the shire. By examining the shrieval position Robin attempts to fill as imagined through the estates model and the period’s accepted role of sheriff, Robin Hood appears as the idealized form of the sheriff in a real-world environment that could not support the ideal

From the Vault: May Days

What you may not have known, remembered, or thought possible at Furma