Busy Beaver Scores and Alphabet Size

We investigate the Busy Beaver Game introduced by Rado (1962) generalized to non-binary alphabets. Harland (2016) conjectured that activity (number of steps) and productivity (number of non-blank symbols) of candidate machines grow as the alphabet size increases. We prove this conjecture for any alphabet size under the condition that the number of states is sufficiently large. For the measure activity we show that increasing the alphabet size from two to three allows an increase. By a classical construction it is even possible to obtain a two-state machine increasing activity and productivity of any machine if we allow an alphabet size depending on the number of states of the original machine. We also show that an increase of the alphabet by a factor of three admits an increase of activity

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

BACKGROUND: We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. RESULTS: We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. CONCLUSION: Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses

Annual and seasonal movements of migrating short-tailed shearwaters reflect environmental variation in sub-Arctic and Arctic waters

The marine ecosystems of the Bering Sea and adjacent southern Chukchi Sea are experiencing rapid changes due to recent reductions in sea ice. Short-tailed shearwaters Puffinus tenuirostris visit this region in huge numbers between the boreal summer and autumn during non-breeding season, and represent one of the dominant top predators. To understand the implications for this species of ongoing environmental change in the Pacific sub-Arctic and Arctic seas, we tracked the migratory movements of 19 and 24 birds in 2010 and 2011, respectively, using light-level geolocators. In both years, tracked birds occupied the western (Okhotsk Sea and Kuril Islands) and eastern (southeast Bering Sea) North Pacific from May to July. In August–September of 2010, but not 2011, a substantial proportion (68 % of the tracked individuals in 2010 compared to 38 % in 2011) moved through the Bering Strait to feed in the Chukchi Sea. Based on the correlation with oceanographic variables, the probability of shearwater occurrence was highest in waters with sea surface temperatures (SSTs) of 8–10 °C over shallow depths. Furthermore, shearwaters spent more time flying when SST was warmer than 9 °C, suggesting increased search effort for prey. We hypothesized that the northward shift in the distribution of shearwaters may have been related to temperature-driven changes in the abundance of their dominant prey, krill (Euphausiacea), as the timing of krill spawning coincides with the seasonal increase in water temperature. Our results indicate a flexible response of foraging birds to ongoing changes in the sub-Arctic and Arctic ecosystems

Zooplankton growth rates: the larvaceans Appendicularia, Fritillaria and Oikopleura in tropical waters

The growth rates of Appendicularia sicula, Fritillaria borealis sargassi, Fritillaria haplostoma, Oikopleura dioica and Oikopleura longicauda were determined from microcosms incubated in situ at 28°C in Jamaican waters. Experiments were conducted from oligotrophic offshore waters, through mesotrophic Lime Cay and eutrophic Kingston Harbour in both natural and nutrient-enhanced phytoplankton communities. Length-weight relationships were calculated for two of these species: O.longicauda log W = 2.47 log TL - 6.10 and F.haplostoma log W = 2.44 log TL - 7.37, where weight (W) is in micrograms and trunk length (TL) is in micrometres. Instantaneous growth rates averaged 1.7-2.5 day-1 for the five species and were observed as high as 3.3 day-1. These instantaneous rates are equivalent to daily specific growth rates averaging 4.6-11.4 and ranging up to 28. In larger genera, growth rates were related positively to picoplankton and nanoplankton concentration, and negatively to the biomass of larvaceans, but in the smallest species growth was unrelated to these factors. However, because the variability in these two factors within microcosms exceeded their natural range of variability, growth rates of larvaceans may normally be unlimited by resources or population density effects

Evaluation of trade-offs in traditional methodologies for measuring metazooplankton growth rates: Assumptions, advantages and disadvantages for field applications.

Zooplankton growth rates ultimately shape the functional response of marine ecosystems to regional and global climate changes, because they determine the quantity and distribution of matter and energy within the zooplankton community available to higher trophic levels. Despite the variety of techniques available for measuring zooplankton growth, no or few approaches have been universally applied to the natural zooplankton populations or community and there are only a limited number of comparisons among the methods. Here we review and compile data for the traditional methods for estimating metazooplankton weight-specific growth rates, describe the principles and underlying assumptions of each method, and finally their advantages and disadvantages. This review encompasses the analysis of time-series (i.e., Natural Cohort method), three experimental approaches (i.e., Artificial Cohort, Molting Rate and Egg Production) and several empirical models that have been applied to specific stages, populations or community guilds of metazooplankton in the field. Whereas, some methodological problems and their resolution have been proposed in the past, no single method adequately addresses the high biodiversity of metazooplankton communities and resolves our limited capacity determining rates. We recommend a more formal comparison of methodologies be undertaken that would allow for their direct crosscalibration to facilitate future cross-site synthesis