A Progressive Folding Algorithm for RNA Secondary Structure Prediction

RNA secondary structure prediction is an area where computational techniques have shown great promise. Most RNA secondary structure prediction algorithms use dynamic programming to compute a secondary structure with minimum free energy. Energy minimization algorithms are less accurate on larger RNA molecules. One potential reason is that larger RNA molecules do not fold instantaneously. Instead, several studies show that RNA molecules fold progressively during transcription. This process could encourage the molecule to fold into a structure that is not at the global lowest energy level. Additionally, dynamic programming algorithms do not allow for a important type of structure called a pseudoknot. Secondary structure prediction allowing pseudoknots was recently shown to be NP-complete. We have created a simulation that captures these biological insights. Our simulation uses a probabilistic approach to fold the molecule progressively as it is synthesized. This thesis evaluates the performance of the simulation and presents several enhancements to improve efficiency and accuracy. Our results show that our progressive folding algorithm did not improve on current techniques. Additionally, we found that a simulated annealing algorithm using our probability models was more accurate than our progressive folding algorithm

Memorial of the quarter-centennial celebration of the establishment of normal schools in America, held at Framingham, July 1, 1864.

Addresses, &c., at the collation.--Address by Rev. Samuel J. May.--Historical sketch, by Rev. Eben S. Stearns.Mode of access: Internet

Simultaneous Magmatic and Hydrothermal Regimes in Alta–Little Cottonwood Stocks, Utah, USA, Recorded Using Multiphase U-Pb Petrochronology

Magmatic and hydrothermal systems are intimately linked, significantly overlapping through time but persisting in different parts of a system. New preliminary U-Pb and trace element petrochronology from zircon and titanite demonstrate the protracted and episodic record of magmatic and hydrothermal processes in the Alta stock–Little Cottonwood stock plutonic and volcanic system. This system spans the upper ~11.5 km of the crust and includes a large composite pluton (e.g., Little Cottonwood stock), dike-like conduit (e.g., Alta stock), and surficial volcanic edifices (East Traverse and Park City volcanic units). A temperature–time path for the system was constructed using U-Pb and tetravalent cation thermometry to establish a record of >10 Myr of pluton emplacement, magma transport, volcanic eruption, and coeval hydrothermal circulation. Zircons from the Alta and Little Cottonwood stocks recorded a single population of apparent temperatures of ~625 ± 35 °C, while titanite apparent temperatures formed two distinct populations interpreted as magmatic (~725 ± 50 °C) and hydrothermal (~575 ± 50 °C). The spatial and temporal variations required episodic magma input, which overlapped in time with hydrothermal fluid flow in the structurally higher portions of the system. The hydrothermal system was itself episodic and migrated within the margin of the Alta stock and its aureole through time, and eventually focused at the contact of the Alta stock. First-order estimates of magma flux in this system suggest that the volcanic flux was 2–5× higher than the intrusive magma accumulation rate throughout its lifespan, consistent with intrusive volcanic systems around the world

Practical Hydration Solutions for Sport

Personalized hydration strategies play a key role in optimizing the performance and safety of athletes during sporting activities. Clinicians should be aware of the many physiological, behavioral, logistical and psychological issues that determine both the athlete’s fluid needs during sport and his/her opportunity to address them; these are often specific to the environment, the event and the individual athlete. In this paper we address the major considerations for assessing hydration status in athletes and practical solutions to overcome obstacles of a given sport. Based on these solutions, practitioners can better advise athletes to develop practices that optimize hydration for their sports