New and Exciting in PLoS ONE

There are 22 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Measuring the Conservation Value of Tropical Primary Forests: The Effect of Occasional Species on Estimates of Biodiversity Uniqueness:

Developing effective conservation plans for multi-functional landscapes requires an accurate knowledge of the relative conservation value of different land-uses. A growing number of tropical ecologists have evaluated conservation value using the number (or proportion) of species that are unique to primary or old-growth forests. However, estimates of the conservation value of modified land-uses may be inflated by the presence of occasional species (e.g. singletons and doubletons) that may be unable to exist as viable populations in isolation. We use a unique 15-taxa dataset from a mixed-use forest landscape in the Brazilian Amazon to test the hypothesis that the removal of occasional species from sample data can increase estimates of the value of primary forest for biodiversity conservation. Estimates of conservation value that are based on the proportion of species that are unique to tropical primary or old-growth forests are highly sensitive to decisions researchers make regarding the inclusion or exclusion of occasional species. By removing singletons from modified forest samples, and considering only those species known to occur in primary forest, we almost double estimates of the conservation value of tropical primary forests.

Sedation at Sea of Entangled North Atlantic Right Whales (Eubalaena glacialis) to Enhance Disentanglement:

The objective of this study was to enhance removal of fishing gear from right whales (Eubalaena glacialis) at sea that evade disentanglement boat approaches. Titrated intra muscular injections to achieve sedation were undertaken on two free swimming right whales. Following initial trials with beached whales, a sedation protocol was developed for right whales. Mass was estimated from sighting and necropsy data from comparable right whales. Midazolam (0.01 to 0.025 mg/kg) was first given alone or with meperidine (0.17 to 0.25 mg/kg) either once or four times over two hours to whale #1102 by cantilevered pole syringe. In the last attempt on whale #1102 there appeared to be a mild effect in 20-30 minutes, with duration of less than 2 hours that included exhalation before the blowhole fully cleared the water. Boat avoidance, used as a measure of sedation depth, was not reduced. A second severely entangled animal in 2009, whale #3311, received midazolam (0.03 mg/kg) followed by butorphanol (0.03 mg/kg) an hour later, delivered ballistically. Two months later it was then given midazolam (0.07 mg/kg) and butorphanol (0.07 mg/kg) simultaneously. The next day both drugs at 0.1 mg/kg were given as a mixture in two darts 10 minutes apart. The first attempt on whale #3311 showed increased swimming speed and boat avoidance was observed after a further 20 minutes. The second attempt on whale #3311 showed respiration increasing mildly in frequency and decreasing in strength. The third attempt on whale #3311 gave a statistically significant increase in respiratory frequency an hour after injection, with increased swimming speed and marked reduction of boat evasion that enabled decisive cuts to entangling gear. We conclude that butorphanol and midazolam delivered ballistically in appropriate dosages and combinations may have merit in future refractory free swimming entangled right whale cases until other entanglement solutions are developed.

Modeling the Potential Distribution of Bacillus anthracis under Multiple Climate Change Scenarios for Kazakhstan:

Anthrax, caused by the bacterium Bacillus anthracis, is a zoonotic disease that persists throughout much of the world in livestock, wildlife, and secondarily infects humans. This is true across much of Central Asia, and particularly the Steppe region, including Kazakhstan. This study employed the Genetic Algorithm for Rule-set Prediction (GARP) to model the current and future geographic distribution of Bacillus anthracis in Kazakhstan based on the A2 and B2 IPCC SRES climate change scenarios using a 5-variable data set at 55 km2 and 8 km2 and a 6-variable BioClim data set at 8 km2. Future models suggest large areas predicted under current conditions may be reduced by 2050 with the A2 model predicting ~14-16% loss across the three spatial resolutions. There was greater variability in the B2 models across scenarios predicting ~15% loss at 55 km2, ~34% loss at 8 km2, and ~30% loss with the BioClim variables. Only very small areas of habitat expansion into new areas were predicted by either A2 or B2 in any models. Greater areas of habitat loss are predicted in the southern regions of Kazakhstan by A2 and B2 models, while moderate habitat loss is also predicted in the northern regions by either B2 model at 8 km2. Anthrax disease control relies mainly on livestock vaccination and proper carcass disposal, both of which require adequate surveillance. In many situations, including that of Kazakhstan, vaccine resources are limited, and understanding the geographic distribution of the organism, in tandem with current data on livestock population dynamics, can aid in properly allocating doses. While speculative, contemplating future changes in livestock distributions and B. anthracis spore promoting environments can be useful for establishing future surveillance priorities. This study may also have broader applications to global public health surveillance relating to other diseases in addition to B. anthracis.

Female Field Crickets Incur Increased Parasitism Risk When Near Preferred Song:

Female animals often prefer males with conspicuous traits because these males provide direct or indirect benefits. Conspicuous male traits, however, can attract predators. This not only increases the risk of predation for conspicuous males but also for the females that prefer them. In the variable field cricket, Gryllus lineaticeps, males that produce preferred song types provide females with greater material benefits, but they are also more likely to attract lethal parasitoid flies. First, we conducted a field experiment that tested the hypothesis that females have a greater risk of fly parasitism when in association with preferred high chirp rate males. Females were nearly twice as likely to be parasitized when caged with high chirp rate song than when caged with low chirp rate song. Females may thus be forced to trade off the quality of the benefits they receive from mating with preferred males and the risk of being killed by a predator when near these males. Second, we assessed female parasitism rates in a natural population. Up to 6% of the females were parasitized in field samples. Because the females we collected could have become parasitized had they not been collected, this provides a minimum estimate of the female parasitism rate in the field. In a laboratory study, we found no difference in the proportion of time parasitized and unparasitized females spent hiding under shelters; thus, differences in activity patterns do not appear to have biased our estimate of female parasitism rates. Overall, our results suggest that female association costs have the potential to shape the evolution of female mating preferences.

A Demonstration of the Transition from Ready-to-Hand to Unready-to-Hand:

The ideas of continental philosopher Martin Heidegger have been influential in cognitive science and artificial intelligence, despite the fact that there has been no effort to analyze these ideas empirically. The experiments reported here are designed to lend empirical support to Heidegger’s phenomenology and more specifically his description of the transition between ready-to-hand and unready-to-hand modes in interactions with tools. In experiment 1, we found that a smoothly coping cognitive system exhibits type positively correlated noise and that its correlated character is reduced when the system is perturbed. This indicates that the participant and tool constitute a self-assembled, extended device during smooth coping and this device is disrupted by the perturbation. In experiment 2, we examine the re-organization of awareness that occurs when a smoothly coping, self-assembled, extended cognitive system is perturbed. We found that the disruption is accompanied by a change in attention which interferes with participants’ performance on a simultaneous cognitive task. Together these experiments show that a smoothly coping participant-tool system can be temporarily disrupted and that this disruption causes a change in the participant’s awareness. Since these two events follow as predictions from Heidegger’s work, our study offers evidence for the hypothesized transition from readiness-to-hand to unreadiness-to-hand.

Random Texts Do Not Exhibit the Real Zipf’s Law-Like Rank Distribution:

Zipf’s law states that the relationship between the frequency of a word in a text and its rank (the most frequent word has rank , the 2nd most frequent word has rank ,…) is approximately linear when plotted on a double logarithmic scale. It has been argued that the law is not a relevant or useful property of language because simple random texts – constructed by concatenating random characters including blanks behaving as word delimiters – exhibit a Zipf’s law-like word rank distribution. In this article, we examine the flaws of such putative good fits of random texts. We demonstrate – by means of three different statistical tests – that ranks derived from random texts and ranks derived from real texts are statistically inconsistent with the parameters employed to argue for such a good fit, even when the parameters are inferred from the target real text. Our findings are valid for both the simplest random texts composed of equally likely characters as well as more elaborate and realistic versions where character probabilities are borrowed from a real text. The good fit of random texts to real Zipf’s law-like rank distributions has not yet been established. Therefore, we suggest that Zipf’s law might in fact be a fundamental law in natural languages.

Computational Study of Evolutionary Selection Pressure on Rainbow Trout Estrogen Receptors:

Molecular dynamics simulations were used to determine the binding affinities between the hormone 17-estradiol (E2) and different estrogen receptor (ER) isoforms in the rainbow trout, Oncorhynchus mykiss. Previous phylogenetic analysis indicates that a whole genome duplication prior to the divergence of ray-finned fish led to two distinct ER isoforms, ER and ER, and the recent whole genome duplication in the ancestral salmonid created two ER isoforms, ER and ER. The objective of our computational studies is to provide insight into the underlying evolutionary pressures on these isoforms. For the ER subtype our results show that E2 binds preferentially to ER over ER. Tests of lineage specific N/S ratios indicate that the ligand binding domain of the ER gene is evolving under relaxed selection relative to all other ER genes. Comparison with the highly conserved DNA binding domain suggests that ER may be undergoing neofunctionalization possibly by binding to another ligand. By contrast, both ER and ER bind similarly to E2 and the best fitting model of selection indicates that the ligand binding domain of all ER genes are evolving under the same level of purifying selection, comparable to ER.

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