fuzzySim: applying fuzzy logic to binary similarity indices in ecology

Binary similarity indices are widely used in ecology, for example for detecting associations between species occurrence patterns, comparing regional and temporal species assemblages, and assessing beta diversity patterns, including spatial and temporal species loss and turnover. Such indices have widespread applications in biogeography, global change biology and biodiversity conservation. Similarity indices are commonly calculated upon binary presence/absence (or sometimes modelled suitable/unsuitable) data, which are generally incomplete and more categorical than their underlying natural patterns. Probable false absences are disregarded, amplifying the effects of data deficiencies and the scale dependence of the results. Fuzzy occurrence data, with a degree of uncertainty attributed to localities where presence or absence cannot be safely assigned, could better reflect species distributions, compensating for incomplete knowledge and methodological errors. Similarity indices would therefore also benefit from accommodating such fuzzy data directly. This study proposes fuzzy versions of the binary similarity indices most commonly used in ecology, so that they can be directly applied to continuous (fuzzy) rather than binary occurrence values, thus producing more realistic similarity assessments. Fuzzy occurrence can be obtained with several methods, some of which are also provided. The procedure is robust to data source disparities, gaps or other errors in species occurrence records, even for restricted species for which slight inaccuracies can affect substantial parts of their range. The method is implemented in a free and open-source software package, fuzzySim, which is available for the R statistical software and under implementation for the QGIS geographic information system. It is provided with sample data and an illustrated tutorial suitable for non-experienced users

Adjacency Effects in Developmental Correlations Among Tooth Organs in Human Fetuses

This study explores whether the "distance gradient" model shown for embryonic development and postnatal tooth growth is also characteristic of the fetal period. Histologic data and ratings from 26 human fetuses show that, unlike the embryonic and postnatal periods, changes occurring in two tooth germs are significantly alike, regardless of the number of intervening teeth.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67281/2/10.1177_00220345810600021401.pd

Genetic Assimilation and Canalisation in the Baldwin Effect

The Baldwin Effect indicates that individually learned behaviours acquired during an organism’s lifetime can influence the evolutionary path taken by a population, without any direct Lamarckian transfer of traits from phenotype to genotype. Several computational studies modelling this effect have included complications that restrict its applicability. Here we present a simplified model that is used to reveal the essential mechanisms and highlight several conceptual issues that have not been clearly defined in prior literature. In particular, we suggest that canalisation and genetic assimilation, often conflated in previous studies, are separate concepts and the former is actually not required for non-heritable phenotypic variation to guide genetic variation. Additionally, learning, often considered to be essential for the Baldwin Effect, can be replaced with a more general phenotypic plasticity model. These simplifications potentially permit the Baldwin Effect to operate in much more general circumstances

Hyperparathyroidism, platelet intracellular free calcium and hypertension in chronic renal failure

Hyperparathyroidism, platelet intracellular free calcium and hypertension in chronic renal failure. To investigate possible relationships between hyperparathyroidism, alterations in intracellular free calcium concentration ([Ca2+]i and hypertension in chronic renal failure, serum concentrations of intact parathyroid hormone (PTH) were measured by two-site immunometric assay, and platelet ([Ca2+]i) was assessed using the fluorescent indicator fura-2. Thirty-six patients with chronic renal failure were studied, 10 with normal serum PTH concentrations (mean 8.0 ± 0.6 pmol/liter), 17 with elevated serum PTH (35.0 ± 7.2 pmol/liter) and 9 patients with elevated PTH (36.2 ±5.9 pmol/liter) who were receiving nifedipine. Platelet [Ca2+]i was increased in patients with elevated PTH, compared with those in whom PTH was normal (138 ± 16 vs. 83 ± 7 nmol/liter, P < 0.01). A linear relation was observed between serum PTH and platelet [Ca2+]i in these patients (r = 0.818, P < 0.001). In contrast, platelet [Ca2+]i was not elevated (84 ± 9 nmol/liter) in the patients with elevated PTH who were receiving nifedipine. A linear relation was also present between both serum PTH (r = 0.616, P < 0.001) and platelet [Ca2+]i (r = 0.576, P < 0.005) and mean blood pressure. Nine patients with hyperparathyroidism were restudied after treatment with the vitamin D analogue alfacalcidol. This resulted in significant decreases in serum PTH (P < 0.01), platelet [Ca2+]i (P < 0.02), and mean blood pressure (P < 0.05). These studies indicate that [Ca2+]i may be increased early in renal failure, and that this increase occurs in association with both hyperparathyroidism and hypertension. Furthermore, treatment of hyperparathyroidism with alfacalcidol may result in reductions in both [Ca2+]i and blood pressure. The lack of elevation in [Ca2+]i in nifedipine-treated patients with hyperparathyroidism suggests that, in uremia, increases in cytosolic calcium induced by PTH or other factors may be mediated in part by dihydropyridine-sensitive mechanisms

Impact of forest fires, biogenic emissions and high temperatures on the elevated Eastern Mediterranean ozone levels during the hot summer of 2007

International audienceThe hot summer of 2007 in southeast Europe has been studied using two regional atmospheric chemistry models; WRF-Chem and EMEP MSC-W. The region was struck by three heat waves and a number of forest fire episodes, greatly affecting air pollution levels. We have focused on ozone and its precursors using state-of-the-art inventories for anthropogenic, biogenic and forest fire emissions. The models have been evaluated against measurement data, and processes leading to ozone formation have been quantified. Heat wave episodes are projected to occur more frequently in a future climate, and therefore this study also makes a contribution to climate change impact research. The plume from the Greek forest fires in August 2007 is clearly seen in satellite observations of CO and NO2 columns, showing extreme levels of CO in and downwindof the fires. Model simulations reflect the location and influence of the fires relatively well, but the modelled magnitude of CO in the plume core is too low. Most likely, this is caused by underestimation of CO in the emission inventories, suggesting that the CO/NOx ratios of fire emissions should be re-assessed. Moreover, higher maximum values are seen in WRF-Chem than in EMEP MSC-W, presumably due to differences in plume rise altitudes as the first model emits a larger fraction of the fire emissions in the lowermost model layer. The model results are also in fairly good agreement with surface ozone measurements. Biogenic VOC emissions reacting with anthropogenic NOx emissions are calculated to contribute significantly to the levels of ozone in the region, but the magnitude and geographical distribution depend strongly on the model and biogenic emission module used. During the July and August heat waves, ozone levels increased substantially due to a combination of forest fire emissions and the effect of high temperatures. We found that the largest temperature impact on ozone was through the temperature dependence of the biogenic emissions, closely followed by the effect of reduced dry deposiion caused by closing of the plants' stomata at very high temperatures. The impact of high temperatures on the ozone chemistry was much lower. The results suggest that forest fire emissions, and the temperature effect on biogenic emissions and dry deposition, will potentially lead to substantial ozone increases in a warmer climate

A radium assay technique using hydrous titanium oxide adsorbent for the Sudbury Neutrino Observatory

As photodisintegration of deuterons mimics the disintegration of deuterons by neutrinos, the accurate measurement of the radioactivity from thorium and uranium decay chains in the heavy water in the Sudbury Neutrino Observatory (SNO) is essential for the determination of the total solar neutrino flux. A radium assay technique of the required sensitivity is described that uses hydrous titanium oxide adsorbent on a filtration membrane together with a beta-alpha delayed coincidence counting system. For a 200 tonne assay the detection limit for 232Th is a concentration of 3 x 10^(-16) g Th/g water and for 238U of 3 x 10^(-16) g U/g water. Results of assays of both the heavy and light water carried out during the first two years of data collection of SNO are presented.Comment: 12 pages, 4 figure

Mitochondria Exert a Negative Feedback on the Propagation of Intracellular Ca2+ Waves in Rat Cortical Astrocytes

We have used digital fluorescence imaging techniques to explore the interplay between mitochondrial Ca2+ uptake and physiological Ca2+ signaling in rat cortical astrocytes. A rise in cytosolic Ca2+ ([Ca2+]cyt), resulting from mobilization of ER Ca2+ stores was followed by a rise in mitochondrial Ca2+ ([Ca2+]m, monitored using rhod-2). Whereas [Ca2+]cyt recovered within ∼1 min, the time to recovery for [Ca2+]m was ∼30 min. Dissipating the mitochondrial membrane potential (Δψm, using the mitochondrial uncoupler carbonyl cyanide p-trifluoromethoxy-phenyl-hydrazone [FCCP] with oligomycin) prevented mitochondrial Ca2+ uptake and slowed the rate of decay of [Ca2+]cyt transients, suggesting that mitochondrial Ca2+ uptake plays a significant role in the clearance of physiological [Ca2+]cyt loads in astrocytes. Ca2+ signals in these cells initiated either by receptor-mediated ER Ca2+ release or mechanical stimulation often consisted of propagating waves (measured using fluo-3). In response to either stimulus, the wave traveled at a mean speed of 22.9 ± 11.2 μm/s (n = 262). This was followed by a wave of mitochondrial depolarization (measured using tetramethylrhodamine ethyl ester [TMRE]), consistent with Ca2+ uptake into mitochondria as the Ca2+ wave traveled across the cell. Collapse of Δψm to prevent mitochondrial Ca2+ uptake significantly increased the rate of propagation of the Ca2+ waves by 50%. Taken together, these data suggest that cytosolic Ca2+ buffering by mitochondria provides a potent mechanism to regulate the localized spread of astrocytic Ca2+ signals