Recovering a lost baseline: missing kelp forests from a metropolitan coast

© 2008 AuthorThere is concern about historical and continuing loss of canopy-forming algae across the world’s temperate coastline. In South Australia, the sparse cover of canopy-forming algae on the Adelaide metropolitan coast has been of public concern with continuous years of anecdotal evidence culminating in 2 competing views. One view considers that current patterns existed before the onset of urbanisation, whereas the alternate view is that they developed after urbanisation. We tested hypotheses to distinguish between these 2 models, each centred on the reconstruction of historical covers of canopies on the metropolitan coast. Historically, the metropolitan sites were indistinguishable from contemporary populations of reference sites across 70 km (i.e. Gulf St. Vincent), and could also represent a random subset of exposed coastal sites across 2100 km of the greater biogeographic province. Thus there was nothing ‘special’ about the metropolitan sites historically, but today they stand out because they have sparser covers of canopies compared to equivalent locations and times in the gulf and the greater province. This is evidence of wholesale loss of canopy-forming algae (up to 70%) on parts of the Adelaide metropolitan coast since major urbanisation. These findings not only set a research agenda based on the magnitude of loss, but they also bring into question the logic that smaller metropolitan populations of humans create impacts that are trivial relative to that of larger metropolitan centres. Instead, we highlight a need to recognise the ecological context that makes some coastal systems more vulnerable or resistant to increasing human-domination of the world’s coastlines. We discuss challenges to this kind of research that receive little ecological discussion, particularly better leadership and administration, recognising that the systems we study out-live the life spans of individual research groups and operate on spatial scales that exceed the capacity of single research providers.Sean D. Connell, Bayden D. Russell, David J. Turner, Scoresby A. Shepherd, Timothy Kildea, David Miller, Laura Airoldi, Anthony Cheshir

Sashimi plots: Quantitative visualization of RNA sequencing read alignments

We introduce Sashimi plots, a quantitative multi-sample visualization of mRNA sequencing reads aligned to gene annotations. Sashimi plots are made using alignments (stored in the SAM/BAM format) and gene model annotations (in GFF format), which can be custom-made by the user or obtained from databases such as Ensembl or UCSC. We describe two implementations of Sashimi plots: (1) a stand-alone command line implementation aimed at making customizable publication quality figures, and (2) an implementation built into the Integrated Genome Viewer (IGV) browser, which enables rapid and dynamic creation of Sashimi plots for any genomic region of interest, suitable for exploratory analysis of alternatively spliced regions of the transcriptome. Isoform expression estimates outputted by the MISO program can be optionally plotted along with Sashimi plots. Sashimi plots can be used to quickly screen differentially spliced exons along genomic regions of interest and can be used in publication quality figures. The Sashimi plot software and documentation is available from: http://genes.mit.edu/burgelab/miso/docs/sashimi.htmlComment: 2 figure

On pricing of interest rate derivatives

At present, there is an explosion of practical interest in the pricing of interest rate (IR) derivatives. Textbook pricing methods do not take into account the leptokurticity of the underlying IR process. In this paper, such a leptokurtic behaviour is illustrated using LIBOR data, and a possible martingale pricing scheme is discussed.Comment: 9 pages, 13 figure

Stochastic blockmodels and community structure in networks

Stochastic blockmodels have been proposed as a tool for detecting community structure in networks as well as for generating synthetic networks for use as benchmarks. Most blockmodels, however, ignore variation in vertex degree, making them unsuitable for applications to real-world networks, which typically display broad degree distributions that can significantly distort the results. Here we demonstrate how the generalization of blockmodels to incorporate this missing element leads to an improved objective function for community detection in complex networks. We also propose a heuristic algorithm for community detection using this objective function or its non-degree-corrected counterpart and show that the degree-corrected version dramatically outperforms the uncorrected one in both real-world and synthetic networks.Comment: 11 pages, 3 figure

An efficient and principled method for detecting communities in networks

A fundamental problem in the analysis of network data is the detection of network communities, groups of densely interconnected nodes, which may be overlapping or disjoint. Here we describe a method for finding overlapping communities based on a principled statistical approach using generative network models. We show how the method can be implemented using a fast, closed-form expectation-maximization algorithm that allows us to analyze networks of millions of nodes in reasonable running times. We test the method both on real-world networks and on synthetic benchmarks and find that it gives results competitive with previous methods. We also show that the same approach can be used to extract nonoverlapping community divisions via a relaxation method, and demonstrate that the algorithm is competitively fast and accurate for the nonoverlapping problem.Comment: 14 pages, 5 figures, 1 tabl

Loss and Recovery Potential of Marine Habitats: An Experimental Study of Factors Maintaining Resilience in Subtidal Algal Forests at the Adriatic Sea

BACKGROUND: Predicting and abating the loss of natural habitats present a huge challenge in science, conservation and management. Algal forests are globally threatened by loss and severe recruitment failure, but our understanding of resilience in these systems and its potential disruption by anthropogenic factors lags well behind other habitats. We tested hypotheses regarding triggers for decline and recovery potential in subtidal forests of canopy-forming algae of the genus Cystoseira. METHODOLOGY/PRINCIPAL FINDINGS: By using a combination of historical data, and quantitative in situ observations of natural recruitment patterns we suggest that recent declines of forests along the coasts of the north Adriatic Sea were triggered by increasing cumulative impacts of natural- and human-induced habitat instability along with several extreme storm events. Clearing and transplantation experiments subsequently demonstrated that at such advanced stages of ecosystem degradation, increased substratum stability would be essential but not sufficient to reverse the loss, and that for recovery to occur removal of the new dominant space occupiers (i.e., opportunistic species including turf algae and mussels) would be required. Lack of surrounding adult canopies did not seem to impair the potential for assisted recovery, suggesting that in these systems recovery could be actively enhanced even following severe depletions. CONCLUSIONS/SIGNIFICANCE: We demonstrate that sudden habitat loss can be facilitated by long term changes in the biotic and abiotic conditions in the system, that erode the ability of natural ecosystems to absorb and recover from multiple stressors of natural and human origin. Moreover, we demonstrate that the mere restoration of environmental conditions preceding a loss, if possible, may be insufficient for ecosystem restoration, and is scarcely cost-effective. We conclude that the loss of complex marine habitats in human-dominated landscapes could be mitigated with appropriate consideration and management of incremental habitat changes and of attributes facilitating system recovery

Effects of Natural Resources Wealth on Political Participation and Political Outcome

The emergence of natural resources wealth in the United States has sparked intensive debates between the two political parties, Democratic and Republican, on their stance in support of the industry. As actions, taken by party or candidate in power, have impact on the regulations revolving the management of natural resources in the region, it is hypothesized that the significance of the industry within a county plays a role in influencing the county’s voting behavior in national and local elections. Recent studies have also found respectively that (1) the energy boom and increased drilling activities drive economic growth in local counties and (2) economic conditions influence election outcomes by holding the incumbent responsible for economic performance. The two findings suggest that the wealth and management of natural resources could contribute toward incumbency advantage. In examination of the industry’s influence in shaping voting behavior, the present study showed that oil and gas production in the industry are significant factors in increasing the Republican Party vote share, which aligns with the party’s supportive rhetoric of the industry. In the second part of the study, relationship between the two past findings are tested and it is found that oil and gas production remain as important factors in deciding the incumbent’s vote share in elections. It is also found that natural resources employment strongly contributes towards incumbency advantage

Structural changes induced by dehydration in the crystalline layered silicate Na-RUB-18: a computational/experimental combined study

Na-RUB-18 layered silicate (Na(8)Si(32)O(64)(OH)(8) center dot 32H(2)O) is prepared following the procedure reported in the literature (ref. 1: K. Kosuge and A. Tsunashima, J. Chem. Soc., Chem. Commun., 1995, 2427) and its significant structural modifications induced by progressive removal of hydration water molecules are studied for the first time by a combined experimental (TGA and variable temperature XRD and FTIR) and theoretical approach. A novel structure of a partially de-hydrated Na-RUB-18 obtained upon heating at 75 degrees C under inert gas flow, which leads to a reversible phase transformation in agreement with XRD and FTIR results, is found. TGA indicates that at this stage, two of the four hydration water molecules per Na ion are lost. Theoretical results based on DFT calculations suggest that the apical water molecules of the solvated octahedrally coordinated sodium ion, forming weak H-bonds with the silicate oxygen atoms, are removed at this stage. As a consequence of the dehydration, the silicate layers get closer, and, similarly to that observed for zeolites, the sodium ions move towards lattice oxygen atoms, to restore their coordination shell. A combination of IR spectroscopy and computational models is used to describe the vibrational properties of silanol/silanolate (SiOH/SiO)(-1) bridges, which are responsible for the proton conduction of Na-RUB-18. The method described can be of general utility to refine structures which are not fully accessible to standard X-ray structure analysis.191726102617European CommunityRegione Piemont

Homophily and Contagion Are Generically Confounded in Observational Social Network Studies

We consider processes on social networks that can potentially involve three factors: homophily, or the formation of social ties due to matching individual traits; social contagion, also known as social influence; and the causal effect of an individual's covariates on their behavior or other measurable responses. We show that, generically, all of these are confounded with each other. Distinguishing them from one another requires strong assumptions on the parametrization of the social process or on the adequacy of the covariates used (or both). In particular we demonstrate, with simple examples, that asymmetries in regression coefficients cannot identify causal effects, and that very simple models of imitation (a form of social contagion) can produce substantial correlations between an individual's enduring traits and their choices, even when there is no intrinsic affinity between them. We also suggest some possible constructive responses to these results.Comment: 27 pages, 9 figures. V2: Revised in response to referees. V3: Ditt