On Similarity Indices and Correction for Chance Agreement

Similarity indices can be used to compare partitions (clusterings) of a data set. Many such indices were introduced in the literature over the years. We are showing that out of 28 indices we were able to track, there are 22 different ones. Even though their values differ for the same clusterings compared, after correcting for agreement attributed to chance only, their values become similar and some of them even become equivalent. Consequently, the problem of choice of the index to be used for comparing different clusterings becomes less important.     

Spatial vegetation patterns and imminent desertification in Mediterranean arid ecosystems

Humans and climate affect ecosystems and their services, which may involve continuous and discontinuous transitions from one stable state to another. Discontinuous transitions are abrupt, irreversible and among the most catastrophic changes of ecosystems identified. For terrestrial ecosystems, it has been hypothesized that vegetation patchiness could be used as a signature of imminent transitions. Here, we analyse how vegetation patchiness changes in arid ecosystems with different grazing pressures, using both field data and a modelling approach. In the modelling approach, we extrapolated our analysis to even higher grazing pressures to investigate the vegetation patchiness when desertification is imminent. In three arid Mediterranean ecosystems in Spain, Greece and Morocco, we found that the patch-size distribution of the vegetation follows a power law. Using a stochastic cellular automaton model, we show that local positive interactions among plants can explain such power-law distributions. Furthermore, with increasing grazing pressure, the field data revealed consistent deviations from power laws. Increased grazing pressure leads to similar deviations in the model. When grazing was further increased in the model, we found that these deviations always and only occurred close to transition to desert, independent of the type of transition, and regardless of the vegetation cover. Therefore, we propose that patch-size distributions may be a warning signal for the onset of desertification.     

Genome-wide association study identifies novel breast cancer susceptibility loci

Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r2 > 0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P < 10(-7)). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P < 0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach.     

A complex of Shc and Ran-GTPase localises to the cell nucleus

The three isoforms of the adaptor protein Shc play diverse roles in cell signalling. For example, the observation of p46 Shc in the nuclei of hepatocellular carcinoma cells suggests a function quite distinct from the better characterised cytoplasmic role. Ligands responsible for the transport of various Shc isoforms into organelles such as the nucleus have yet to be reported. To identify such ligands a far western approach was used to determine the p52 Shc interactome. The Ran-GTPase nuclear transport protein was identified and found to bind to p52 Shc in vitro with low micromolar affinity. Co-immunoprecipitation, pull down and fluorescence lifetime imaging microscopy experiments in stable cells confirmed cellular interaction and nuclear localisation. The nuclear transport factor protein NTF2, which functions in cohort with Ran, was shown to form a complex with both RAN and Shc, suggesting a mechanism for Shc entry into the nucleus as part of a tertiary complex. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Received 20 October 2008; received after revision 04 December 2008; accepted 15 December 2008     

Linking morphology and molecules: integrative taxonomy of spathidiids (Protista: Ciliophora: Litostomatea) from Korea

We isolated seven spathidiids from various terrestrial habitats in Korea: Enchelys megaspinata sp. nov.; Spathidium ascendens Wenzel, 1955; S. papilliferum Kahl, 1930; S. polynucleatum (Foissner et al., 2002) comb. nov.; S. rectitoratum Kahl, 1930; S. securiforme Kahl, 1930 stat. nov.; and Apobryophyllum schmidingeri Foissner and Al-Rasheid, 2007. Their vegetative and resting cyst morphology were studied in vivo and after protargol impregnation. Their phylogenetic relationships were inferred from the analysis of 18S rRNA gene and ITS1-5.8S-ITS2 region sequences. Enchelys megaspinata is nested within the Semispathidium breviarmatum cluster. It differs from all multi-macronucleate congeners either by the number of macronuclear nodules and ciliary rows or by the presence of prominent spines on resting cysts. Both morphological and molecular data support species-level status for S. rectitoratum and S. securiforme. Although S. papilliferum is one of the morphologically most distinct spathidiids due to the presence of oral bulge papillae, it is non-monophyletic. Based on molecular analyses, we suggest reassigning the morphologically transitional S. ascendens and S. polynucleatum, both formerly combined with Epispathidium, to the genus Spathidium. Korean and German populations of Apobryophyllum schmidingeri are highly similar, both morphologically and genetically. The present study highlights the complexity of spathidiid taxonomy, which requires a combination of morphological and molecular approaches to resolve.

www.zoobank.org/urn:lsid:zoobank.org:pub:781F932B-97D1-4B15-9E35-602DC6D3AE67     

Identity of Mertensia oblongifolia (Nutt.) G. Don (Boraginaceae) and its allies in western North America

The current status of Mertensia oblongifolia (Nutt.) G. Don and its allied taxa is surveyed. On the bases of continuously coherent morphological characters and/or regionally correlated variations, more than 30 taxa, including species, subspecies, varieties, and 1 forma, previously considered different from M. oblongifolia , are now placed under synonymy of this species. Those taxa currently known as M. fusiformis Greene, M. bakeri Greene, and M. bakeri var. osterhoutii Williams are among the new synonyms. Typification, taxonomy, and morphological problems of M. oblongifolia are discussed.     

Effect of silica fume on the fresh and hardened properties of fly ash-based self-compacting geopolymer concrete

The effect of silica fume on the fresh and hardened properties of fly ash-based self-compacting geopolymer concrete (SCGC) was investigated in this paper. The work focused on the concrete mixes with a fixed water-to-geopolymer solid (W/Gs) ratio of 0.33 by mass and a constant total binder content of 400 kg/m3. The mass fractions of silica fume that replaced fly ash in this research were 0wt%, 5wt%, 10wt%, and 15wt%. The workability-related fresh properties of SCGC were assessed through slump flow, V-funnel, and L-box test methods. Hardened concrete tests were limited to compressive, splitting tensile and flexural strengths, all of which were measured at the age of 1, 7, and 28 d after 48-h oven curing. The results indicate that the addition of silica fume as a partial replacement of fly ash results in the loss of workability; nevertheless, the mechanical properties of hardened SCGC are significantly improved by incorporating silica fume, especially up to 10wt%. Applying this percentage of silica fume results in 4.3% reduction in the slump flow; however, it increases the compressive strength by 6.9%, tensile strength by 12.8% and flexural strength by 11.5%.     

Effect of controlled rolling on the martensitic hardenability of dual phase steel

The C-Mn and C-Mn-Nb steels were thermo-mechanically processed to develop dual phase steel and to study the effect of controlled rolling on the martensitic hardenability of austenite. The steel specimens were intercritically annealed at 790℃, rolled at that temperature to the reductions of 10%, 23%, and 47% and immediately cooled at different rates. Quantitative metallography was used to construct the microstructure map, which illustrated that increasing deformation progressively reduced the proportion of new ferrite formed at all cooling rates and increased the amount of martensite at fast and intermediate rates. The martensitic hardenability of austenite remaining after all the rolling reductions was plotted as a function of cooling rates. It was observed that for the austenite-martensite conversion efficiencies greater than about 25%, controlled rolling increased the martensitic hardenability of austenite.     

Correlated binocular activity guides recovery from monocular deprivation

Monocular deprivation (MD) has much more rapid and severe effects on the ocular dominance of neurons in the primary visual cortex (V1) than does binocular deprivation. This finding underlies the widely held hypothesis that the developmental plasticity of ocular dominance reflects competitive interactions for synaptic space between inputs from the two eyes. According to this view, the relative levels of evoked activity in afferents representing the two eyes determine functional changes in response to altered visual experience. However, if the deprived eye of a monocularly deprived kitten is simply reopened, there is substantial physiological and behavioural recovery, leading to the suggestion that absolute activity levels, or some other non-competitive mechanisms, determine the degree of recovery from MD. Here we provide evidence that correlated binocular input is essential for such recovery. Recovery is far less complete if the two eyes are misaligned after a period of MD. This is a powerful demonstration of the importance of cooperative, associative mechanisms in the developing visual cortex.