Methods For Creating XSEDE Compatible Clusters

The Extreme Science and Engineering Discovery Environment has created a suite of software that is collectively known as the basic XSEDE-compatible cluster build. It has been distributed as a Rocks roll for some time. It is now available as individual RPM packages, so that it can be downloaded and installed in portions as appropriate on existing and working clusters. In this paper, we explain the concept of the XSEDE-compatible cluster and explain how to install individual components as RPMs through use of Puppet and the XSEDE compatible cluster YUM repository.This document was developed with support from National Science Foundation (NSF) grant OCI-1053575. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF

Refractory hyperparathyroidism with a T3 bony lesion—differential diagnoses

We report a case of severe hyperparathyroidism complicated by osteitis fibrosa cystica in an 83-year-old man post-myocardial infarction. The lesions were evident on magnetic resonance imaging only. A diagnosis of parathyroid carcinoma was considered due to clinical appearance of the parathyroid intraoperatively and the presence of an invasive T3 lesion mimicking metastatic disease. Differentiating parathyroid carcinoma from the benign causes at presentation can be difficult due to overlapping clinical, biochemical, radiological and histological features. The presence of bony lesions increases the diagnostic complexity of the case and demonstrates the challenges involved in the management of this disorder

Advances in restoration ecology: rising to the challenges of the coming decades

Simultaneous environmental changes challenge biodiversity persistence and human wellbeing. The science and practice of restoration ecology, in collaboration with other disciplines, can contribute to overcoming these challenges. This endeavor requires a solid conceptual foundation based in empirical research which confronts, tests and influences theoretical developments. We review conceptual developments in restoration ecology over the last 30 years. We frame our review in the context of changing restoration goals which reflect increased societal awareness of the scale of environmental degradation and the recognition that inter-disciplinary approaches are needed to tackle environmental problems. Restoration ecology now encompasses facilitative interactions and network dynamics, trophic cascades, and above- and below ground linkages. It operates in a non-equilibrium, alternative states framework, at the landscape scale, and in response to changing environmental, economic and social conditions. Progress has been marked by conceptual advances in the fields of trait-environment relationships, community assembly, and understanding the links between biodiversity and ecosystem functioning. Conceptual and practical advances have been enhanced by applying evolving technologies, including treatments to increase seed germination and overcome recruitment bottlenecks, high throughput DNA sequencing to elucidate soil community structure and function, and advances in satellite technology and GPS tracking to monitor habitat use. The synthesis of these technologies with systematic reviews of context dependencies in restoration success, model based analyses and consideration of complex socio-ecological systems will allow generalizations to inform evidence based interventions. Ongoing challenges include setting realistic, socially acceptable goals for restoration under changing environmental conditions, and prioritizing actions in an increasingly space-competitive world. Ethical questions also surround the use of genetically modified material, translocations, taxon substitutions, and de-extinction, in restoration ecology. Addressing these issues, as the Ecological Society of America looks to its next century, will require current and future generations of researchers and practitioners, including economists, engineers, philosophers, landscape architects, social scientists and restoration ecologists, to work together with communities and governments to rise to the environmental challenges of the coming decades

Nutrient enrichment diminishes plant diversity and density, and alters long-term ecological trajectories, in a biodiverse forest restoration

Nutrient enrichment can negatively affect natural plant communities and result in the loss of species diversity and productivity. Despite this, fertiliser (especially phosphorus) is typically applied to restore highly biodiverse communities. Long-term effects of nutrient addition to restored plant communities, particularly those adapted to inherently low nutrient soils, have received little attention. We report results of a large-scale 20-year field experiment established in West Australian jarrah forest restored after bauxite mining Three P-application rates were applied (0, 80 and 120 kg ha−1) once at the beginning of the experiment, and plant communities monitored after 1, 6, 13 and 20 years. One year after the onset of restoration, native plant species richness and plant density was highest at 80 and 120 kg P ha−1. Subsequently, native species richness, plant density, and the richness and density of seeder and slow-growing resprouter species were highest without fertilisation, establishing the negative impact of P enrichment on plant community and ecosystem development in P impoverished soils. Total plant cover was similar for all P treatments across the chronosequence which, when combined with higher stem densities at zero P, suggests zero P favoured smaller, slower growing species. Applied-P initially favoured weeds and ephemerals and, while these species declined over time, other species were lost from these plots. The similarity of the restored communities to unmined reference jarrah forest increased over time and was consistently highest at in the absence of P fertiliser. Jarrah forest restoration is assumed to follow the initial floristic model of plant succession. However, we question this assumption and instead suggest that successional outcomes are contingent on P fertilisation rather than initial floristics per se. Applied P retarded recruitment of resprouter species that were present at zero P, debunking the assumption under IFM that these species do not disperse to restored areas. Consequently, based on the most comprehensive long-term study of P-fertilisation in the context of restoration of P-impoverished ecosystems yet reported, we propose that P limitation is important for the recreation of species diversity in inherently P impoverished forests. These results highlight the necessity of long-term experiments for understanding forest successional dynamics and implications for restoration practices

Defining biodiverse reforestation: Why it matters for climate change mitigation and biodiversity

Mixed species plantings present an attractive alternative to monoculture reforestation through their added benefits to biodiversity. Yet there is ambiguity in the use of the term ‘biodiversity’ in carbon and biodiversity markets, which may create perverse outcomes when designing schemes and projects. Here, we review how the concept of biodiversity is defined and applied in reforestation projects, and restoration more broadly. Improved transparency around the use of the term biodiversity is urgently needed to provide rigour in emerging market mechanisms, which seek to benefit the environment and people. Summary: Reforestation to capture and store atmospheric carbon is increasingly championed as a climate change mitigation policy response. Reforestation plantings have the potential to provide conservation co-benefits when diverse mixtures of native species are planted, and there are growing attempts to monetise biodiversity benefits from carbon reforestation projects, particularly within emerging carbon markets. But what is meant by ‘biodiverse’ across different stakeholders and groups implementing and overseeing these projects and how do these perceptions compare with long-standing scientific definitions? Here, we discuss approaches to, and definitions of, biodiversity in the context of reforestation for carbon sequestration. Our aim is to review how the concept of biodiversity is defined and applied among stakeholders (e.g., governments, carbon certifiers and farmers) and rights holders (i.e., First Nations people) engaging in reforestation, and to identify best-practice methods for restoring biodiversity in these projects. We find that some stakeholders have a vague understanding of diversity across varying levels of biological organisation (genes to ecosystems). While most understand that biodiversity underpins ecosystem functions and services, many stakeholders may not appreciate the difficulties of restoring biodiversity akin to reference ecosystems. Consequently, biodiversity goals are rarely explicit, and project goals may never be achieved because the levels of restored biodiversity are inadequate to support functional ecosystems and desired ecosystem services. We suggest there is significant value in integrating biodiversity objectives into reforestation projects and setting specific restoration goals with transparent reporting outcomes will pave the way for ensuring reforestation projects have meaningful outcomes for biodiversity, and legitimate incentive payments for biodiversity and natural capital accounting

Phosphorus supply affects seedling growth of mycorrhizal but not cluster-root forming jarrah-forest species

Aims Fertiliser is often used to kick-start ecological restoration despite growing evidence of the potentially negative impacts on plant diversity. Jarrah (Eucalyptus marginata) forest species growing on nutrient (especially phosphorus) impoverished soils in southwestern Australia have a suite of adaptations for phosphorus (P) acquisition, including the formation of cluster roots, and associations with mycorrhizal fungi. Here we investigated how escalating P supply, along with a stoichiometric adjustment of nitrogen (N) supply, impacted the growth and nutrition of a wide range of jarrah forest seedlings. Methods In a pot experiment, we measured seedling biomass and nutritional responses of 12 jarrah forest species to a gradient of P supply in relation to N supply, and for the mycorrhizal species, inoculation with arbuscular mycorrhizal fungi. Results Three cluster-root forming species did not respond to increasing P, probably because they were reliant on seed P. Generally, mycorrhizal species showed a positive biomass response to increasing P when N was available. Mycorrhizas benefited seedling growth at low P (9 mg P added per kg of jarrah forest soil) when N was also available, and were parasitic to seedling growth at high P (243 mg P/ kg soil) without additional N. Conclusions These results highlight importance of P and N supply in determining the nature of the symbiosis between plants and mycorrhizal fungi. Since P supply has the potential to reduce plant growth, for a range of species, our results suggest careful consideration of fertiliser amounts for ecological restoration of ecosystems adapted to nutrient poor soils