Using the clustering coefficient to guide a genetic-based communities finding algorithm

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-23878-9_20Proceedings of 12th International Conference IDEAL, Norwich, UK, September 7-9, 2011.We describe an approach taken for automatically associating entries from an on-line encyclopedia with concepts in an ontology or a lexical semantic network. It has been tested with the Simple English Wikipedia and WordNet, although it can be used with other resources. The accuracy in disambiguating the sense of the encyclopedia entries reaches 91.11% (83.89% for polysemous words). It will be applied to enriching ontologies with encyclopedic knowledge

Targeting translation initiation by synthetic rocaglates for treating MYC-driven lymphomas.

MYC-driven lymphomas, especially those with concurrent MYC and BCL2 dysregulation, are currently a challenge in clinical practice due to rapid disease progression, resistance to standard chemotherapy, and high risk of refractory disease. MYC plays a central role by coordinating hyperactive protein synthesis with upregulated transcription in order to support rapid proliferation of tumor cells. Translation initiation inhibitor rocaglates have been identified as the most potent drugs in MYC-driven lymphomas as they efficiently inhibit MYC expression and tumor cell viability. We found that this class of compounds can overcome eIF4A abundance by stabilizing target mRNA-eIF4A interaction that directly prevents translation. Proteome-wide quantification demonstrated selective repression of multiple critical oncoproteins in addition to MYC in B-cell lymphoma including NEK2, MCL1, AURKA, PLK1, and several transcription factors that are generally considered undruggable. Finally, (-)-SDS-1-021, the most promising synthetic rocaglate, was confirmed to be highly potent as a single agent, and displayed significant synergy with the BCL2 inhibitor ABT199 in inhibiting tumor growth and survival in primary lymphoma cells in vitro and in patient-derived xenograft mouse models. Overall, our findings support the strategy of using rocaglates to target oncoprotein synthesis in MYC-driven lymphomas.P30 CA036727 - NCI NIH HHS; R24 GM111625 - NIGMS NIH HHS; R35 GM118173 - NIGMS NIH HHS; LB506 - Nebraska Department of Health and Human Services (Nebraska DHHS)Accepted manuscriptSupporting documentatio

Genetic algorithm dynamics on a rugged landscape

The genetic algorithm is an optimization procedure motivated by biological evolution and is successfully applied to optimization problems in different areas. A statistical mechanics model for its dynamics is proposed based on the parent-child fitness correlation of the genetic operators, making it applicable to general fitness landscapes. It is compared to a recent model based on a maximum entropy ansatz. Finally it is applied to modeling the dynamics of a genetic algorithm on the rugged fitness landscape of the NK model.Comment: 10 pages RevTeX, 4 figures PostScrip

Anytime Algorithms for Solving Possibilistic MDPs and Hybrid MDPs

The ability of an agent to make quick, rational decisions in an uncertain environment is paramount for its applicability in realistic settings. Markov Decision Processes (MDP) provide such a framework, but can only model uncertainty that can be expressed as probabilities. Possibilistic counterparts of MDPs allow to model imprecise beliefs, yet they cannot accurately represent probabilistic sources of uncertainty and they lack the efficient online solvers found in the probabilistic MDP community. In this paper we advance the state of the art in three important ways. Firstly, we propose the first online planner for possibilistic MDP by adapting the Monte-Carlo Tree Search (MCTS) algorithm. A key component is the development of efficient search structures to sample possibility distributions based on the DPY transformation as introduced by Dubois, Prade, and Yager. Secondly, we introduce a hybrid MDP model that allows us to express both possibilistic and probabilistic uncertainty, where the hybrid model is a proper extension of both probabilistic and possibilistic MDPs. Thirdly, we demonstrate that MCTS algorithms can readily be applied to solve such hybrid models. © Springer International Publishing Switzerland 2016.This work is partially funded by EPSRC PACES project (Ref: EP/J012149/1).Peer Reviewe

Hydrologic Processes of Forested Headwater Watersheds Across a Physiographic Gradient in the Southeastern United States

2008 S.C. Water Resources Conference - Addressing Water Challenges Facing the State and Regio

Future Dominance by Quaking Aspen Expected Following Short-Interval, Compounded Disturbance Interaction

The spatial overlap of multiple ecological disturbances in close succession has the capacity to alter trajectories of ecosystem recovery. Widespread bark beetle outbreaks and wildfire have affected many forests in western North America in the past two decades in areas of important habitat for native ungulates. Bark beetle outbreaks prior to fire may deplete seed supply of the host species, and differences in fire‐related regeneration strategies among species may shift the species composition and structure of the initial forest trajectory. Subsequent browsing of postfire tree regeneration by large ungulates, such as elk (Cervus canadensis), may limit the capacity for regeneration to grow above the browse zone to form the next forest canopy. Five stand‐replacing wildfires burned ~60,000 ha of subalpine forest that had previously been affected by severe ( \u3e90% mortality) outbreaks of spruce beetle (SB, Dendroctonus rufipennis) in Engelmann spruce (Picea engelmannii) in 2012–2013 in southwestern Colorado. Here we examine the drivers of variability in abundance of newly established conifer tree seedlings [spruce and subalpine fir (Abies lasiocarpa)] and resprouts of quaking aspen (Populus tremuloides) following the short‐interval sequence of SB outbreaks and wildfire (2–8 yr between SB outbreak and fire) at sites where we previously reconstructed severities of SB and fire. We then examine the implications of ungulate browsing for forest recovery. We found that abundances of postfire spruce seedling establishment decreased substantially in areas of severe SB outbreak. Prolific aspen resprouting in stands with live aspen prior to fire will favor an initial postfire forest trajectory dominated by aspen. However, preferential browsing of postfire aspen resprouts by ungulates will likely slow the rate of canopy recovery but browsing is unlikely to alter the species composition of the future forest canopy. Collectively, our results show that SB outbreak prior to fire increases the vulnerability of spruce–fir forests to shifts in forest type (conifer to aspen) and physiognomic community type (conifer forest to non‐forest). By identifying where compounded disturbance interactions are likely to limit recovery of forests or tree species, our findings are useful for developing adaptive management strategies in the context of warming climate and shifting disturbance regimes