Ten Simple (Empirical) Rules for Writing Science

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Thermal Stabilization of Digesters of Biogas Plants by Means of Optimization of the Surface Radiative Properties of the Gasometer Domes

A new incentive scheme for power generation from biogas is favoring in Italy the construction of small plants. These ones, however, have poorer financial viability and biological stability than larger plants. In order to ensure adequate performance and a reasonable payback period it is therefore essential that every aspect of their operations is carefully designed. In this respect, summer overheating of anaerobic digesters due to solar gains must be prevented. A solution relies upon the implementation of a ‘cool’ gasometer dome with properly chosen solar reflectance, whose effectiveness was assessed through the use of a calculation code specifically built and validated by comparison with experimental data

Emergence of structural and dynamical properties of ecological mutualistic networks

Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the organization of ecological communities. Such networks in ecology have generically evolved a nested architecture independent of species composition and latitude - specialists interact with proper subsets of the nodes with whom generalists interact. Despite sustained efforts to explain observed network structure on the basis of community-level stability or persistence, such correlative studies have reached minimal consensus. Here we demonstrate that nested interaction networks could emerge as a consequence of an optimization principle aimed at maximizing the species abundance in mutualistic communities. Using analytical and numerical approaches, we show that because of the mutualistic interactions, an increase in abundance of a given species results in a corresponding increase in the total number of individuals in the community, as also the nestedness of the interaction matrix. Indeed, the species abundances and the nestedness of the interaction matrix are correlated by an amount that depends on the strength of the mutualistic interactions. Nestedness and the observed spontaneous emergence of generalist and specialist species occur for several dynamical implementations of the variational principle under stationary conditions. Optimized networks, while remaining stable, tend to be less resilient than their counterparts with randomly assigned interactions. In particular, we analytically show that the abundance of the rarest species is directly linked to the resilience of the community. Our work provides a unifying framework for studying the emergent structural and dynamical properties of ecological mutualistic networks.Comment: 10 pages, 4 figure

Linking the Green and Brown Worlds: the Prevalence and Effect of Multichannel Feeding in Food Webs

Recent advances in food‐web ecology highlight that most real food webs (1) represent an interplay between producer‐ and detritus‐based webs and (2) are governed by consumers which are rampant omnivores; feeding on varied prey across trophic levels and resource channels. A possible avenue to unify these advances comes from models demonstrating that predators feeding on distinctly different channels may stabilize food webs. Empirical studies suggest many consumers engage in such behavior by feeding on prey items from both living‐autotroph (green) and detritus‐based (brown) webs, what we term “multichannel feeding,” yet we know little about how common such feeding is across systems and trophic levels, or its effect on system stability. Considering 23 empirical webs, we find that multichannel feeding is equally common across terrestrial, freshwater, and marine systems, with \u3e50% of consumers classified as multichannel consumers. Multichannel feeding occurred most often at the first consumer level, indicating that most taxa at the herbivore/detritivore level are more aptly described as multichannel consumers, and that such feeding is not restricted to predators. We next developed a simple four‐compartment nutrient cycling model for consumers eating both autotrophs and detritus with separate parameter sets to represent aquatic vs. terrestrial ecosystems. Modeling results showed that, across terrestrial and aquatic ecosystems, multichannel feeding is stabilizing at low attack rates on autotrophs or when attack rates are asymmetric (moderate on autotrophs while low on detritus), but destabilizing at high attack rates on autotrophs, compared to herbivory‐ or detritivory‐only models. The set of conditions with stable webs with multichannel consumers is narrower, however, for aquatic systems, suggesting that multichannel feeding may generally be more stabilizing in terrestrial systems. Together, our results demonstrate that multichannel feeding is common across ecosystems and may be a stabilizing force in real webs that have consumers with low or asymmetric attack rates

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model

Food webs, networks of feeding relationships among organisms, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. Despite long-standing interest in the compartmental structure of food webs, past network analyses of food webs have been constrained by a standard definition of compartments, or modules, that requires many links within compartments and few links between them. Empirical analyses have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure in food webs using a flexible definition of a group that can describe both functional roles and standard compartments. The Serengeti ecosystem provides an opportunity to examine structure in a newly compiled food web that includes species-level resolution among plants, allowing us to address whether groups in the food web correspond to tightly-connected compartments or functional groups, and whether network structure reflects spatial or trophic organization, or a combination of the two. We have compiled the major mammalian and plant components of the Serengeti food web from published literature, and we infer its group structure using our method. We find that network structure corresponds to spatially distinct plant groups coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial patterns, in contrast to the standard compartments typically identified in ecological networks. From data consisting only of nodes and links, the group structure that emerges supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence.Comment: 28 pages, 6 figures (+ 3 supporting), 2 tables (+ 4 supporting

Random Walks on Stochastic Temporal Networks

In the study of dynamical processes on networks, there has been intense focus on network structure -- i.e., the arrangement of edges and their associated weights -- but the effects of the temporal patterns of edges remains poorly understood. In this chapter, we develop a mathematical framework for random walks on temporal networks using an approach that provides a compromise between abstract but unrealistic models and data-driven but non-mathematical approaches. To do this, we introduce a stochastic model for temporal networks in which we summarize the temporal and structural organization of a system using a matrix of waiting-time distributions. We show that random walks on stochastic temporal networks can be described exactly by an integro-differential master equation and derive an analytical expression for its asymptotic steady state. We also discuss how our work might be useful to help build centrality measures for temporal networks.Comment: Chapter in Temporal Networks (Petter Holme and Jari Saramaki editors). Springer. Berlin, Heidelberg 2013. The book chapter contains minor corrections and modifications. This chapter is based on arXiv:1112.3324, which contains additional calculations and numerical simulation

BioMaPS: A Roadmap for Success

The manuscript outlines the impact that our National Science Foundation Interdisciplinary Training for Undergraduates in Biological and Mathematical Sciences program, BioMaPS, has had on the students and faculty at Murray State University. This interdisciplinary program teams mathematics and biology undergraduate students with mathematics and biology faculty and has produced research insights and curriculum developments at the intersection of these two disciplines. The goals, structure, achievements, and curriculum initiatives are described in relation to the effects they have had to enhance the study of biomathematics

Measuring Nepotism through Shared Last Names: The Case of Italian Academia

Nepotistic practices are detrimental for academia. Here I show how disciplines with a high likelihood of nepotism can be detected using standard statistical techniques based on shared last names among professors. As an example, I analyze the set of all 61,340 Italian academics. I find that nepotism is prominent in Italy, with particular disciplinary sectors being detected as especially problematic. Out of 28 disciplines, 9 – accounting for more than half of Italian professors – display a significant paucity of last names. Moreover, in most disciplines a clear north-south trend emerges, with likelihood of nepotism increasing with latitude. Even accounting for the geographic clustering of last names, I find that for many disciplines the probability of name-sharing is boosted when professors work in the same institution or sub-discipline. Using these techniques policy makers can target cuts and funding in order to promote fair practices