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"Towards a worldwide wood economics spectrum" - Paper with the published dataset

Abstract:

Wood performs several essential functions in plants, including mechanically supporting aboveground tissue, storing water and other resources, and transporting sap. Woody tissues are likely to face physiological, structural and defensive trade-offs. How a plant optimizes among these competing functions can have major ecological implications, which have been under-appreciated by ecologists compared to the focus they have given to leaf function. To draw together our current understanding of wood function, we identify and collate data on the major wood functional traits, including the largest wood density database to date (8412 taxa), mechanical strength measures and anatomical features, as well as clade-specific features such as secondary chemistry. We then show how wood traits are related to one another, highlighting functional trade-offs, and to ecological and demographic plant features (growth form, growth rate, latitude, ecological setting). We suggest that, similar to the manifold that tree species leaf traits cluster around the ‘leaf economics spectrum’, a similar ‘wood economics spectrum’ may be defined. We then discuss the biogeography, evolution and biogeochemistry of the spectrum, and conclude by pointing out the major gaps in our current knowledge of wood functional traits.

Citation:

Chave, J., Coomes, D., Jansen, S., Lewis, S. L., Swenson, N. G., & Zanne, A. E. (2009). Towards a worldwide wood economics spectrum. Ecology letters12(4), 351-366.

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Encyclopedia of Life entry for primates

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"Comparative Data Reveal Similar Mortality Patterns Across Primates" - Paper with the published dataset

Abstract 
Human senescence patterns – late onset of mortality increase, slow mortality acceleration, and exceptional longevity – are often described as unique in the animal world. Using an individual-based dataset from longitudinal studies of wild populations of seven primate species, we show that contrary to assumptions of human uniqueness, human senescence falls within the primate continuum of aging, the tendency for males to have shorter lifespans and higher age-specific mortality than females throughout much of adulthood is a common feature in many, but not all, primates, and the aging profiles of primate species do not reflect phylogenetic position. These findings suggest that mortality patterns in primates are shaped by local selective forces rather than phylogenetic history.

Citation:

Bronikowski AM, Altmann J, Brockman DK, Cords M, Fedigan LM, Pusey A, Stoinski T, Morris WF, Strier KB, Alberts SC (2011) Aging in the natural world: comparative data reveal similar mortality patterns across primates. Science 331(6022): 1325-1328.

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Natural history and additional images of artiodactyls

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"Hunting to extinction: biology and regional economy influence extinction risk and the impact of hunting in artiodactyls" - Paper with published dataset

Abstract 
Half of all artiodactyls (even-toed hoofed mammals) are threatened with extinction, around double the mammalian average. Here, using a complete species-level phylogeny, we construct a multivariate model to assess for the first time which intrinsic (biological) and extrinsic (anthropogenic and environmental) factors influence variation in extinction risk in artiodactyls. Globally artiodactyls at greatest risk live in economically less developed areas, have older weaning ages and smaller geographical ranges. Our findings suggest that identifying predictors of threat is complicated by interactions between both biological and anthropogenic factors, resulting in differential responses to threatening processes. Artiodactyl species that experience unregulated hunting live in significantly less economically developed areas than those that are not hunted; however, hunted species are more susceptible to extinction if they have slower reproductive rates (older weaning ages). In contrast, risk in non-hunted artiodactyls is unrelated to reproductive rate and more closely associated with the economic development of the region in which they live.

Citation:

Price SA, Gittleman JL (2007) Hunting to extinction: biology and regional economy influence extinction risk and the impact of hunting in artiodactyls. Proceedings of the Royal Society B 274: 1845-1851.

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The true cost of an egg

Local vs commercial eggs and the many costs.

From SISL:  In this lab activity, students compare nutrient data and the cost of locally produced eggs and commercially produced eggs. They will use Excel for data entry, rudimentary formula writing, and the creation of tables.

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Carrie Diaz Eaton onto Math and agricultural systems

Consumption of food in the US over time

In this activity, students research the historical food consumption data from the U.S. Department of Agriculture to observe trends, develop regressions, predict future behavior, and discuss broader impacts.

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Carrie Diaz Eaton onto Math and agricultural systems

Breakfast footprint

From SISL site:

"How does an individual calculate a carbon footprint? Can personal decisions alter the magnitude of a carbon footprint? How much does one person's carbon footprint really matter?

In this module students will explore the size, value and significance of personal carbon emissions. In particular, students will estimate the carbon footprint of a breakfast meal consisting of cereal, fresh berries, milk, and fruit juice. After comparing breakfast carbon emissions values with group members and the class, students will contextualize these results through analysis of the mathematical model, comparison with known carbon "sinks" and reflection on the meaning of the output."

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Carrie Diaz Eaton onto Math and agricultural systems

Dryad Lab modules

 

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Sam S Donovan onto sam test

Agent-Based Modeling of the Immune System: NetLogo, a Promising Framework

Author: F.  Chiacchio, M. Pennisi, G. Russo, S. Motta, F. Pappalardo

About: Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents. This behavior is unpredictable, as it does not follow linear rules. There are a lot of works that investigates the immune system with agent-based modeling and cellular automata. They have shown the ability to see clearly and intuitively into the nature of immunological processes. NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena. It is designed for both research and education and is used across a wide range of disciplines and education levels. In this paper, we summarize NetLogo applications to immunology and, particularly, how this framework can help in the development and formulation of hypotheses that might drive further experimental investigations of disease mechanisms.

Published In: BioMed research international, 2014

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Is the Whole the Sumof Its Parts? Agent-Based Modelling of Wastewater Treatment Systems

Authors: A. J. Schuler, N. Majed, V. Bucci, F. L. Hellweger, Y. Tu and A. Z. Gu

About: Agent-based models (ABMs) simulate individual units within a system, such as the bacteria in a biological wastewater treatment system. This paper outlines past, current and potential future applications of ABMs to wastewater treatment. ABMs track heterogeneities within microbial populations, and this has been demonstrated to yield different predictions of bulk behaviors than the conventional, “lumped” approaches for enhanced biological phosphorus removal (EBPR) completely mixed reactors systems. Current work included the application of the ABM approach to bacterial adaptation/evolution, using the model system of individual EBPR bacteria that are allowed to evolve a kinetic parameter (maximum glycogen storage) in a competitive environment. 

Published In: Water Science and Technology Volume 63 Issue 8 (pages 1590-1598)

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Agent-Based Modeling of an Activated Sludge Process in a Batch Reactor

Authors: Pereda, M., & Zamarreno, J. M. 

About: The aim of this work is to study the feasibility of using agent-based modeling to study the activated sludge process.  A model in MetLogo has been proposed, and experiments have been developed comparing the model behavior with a classical modeling approximation for this process, the Monod model.

Published In: 2011 19th Mediterranean Conference on Control & Automation (MED) (pages 1128-1133)

Date of Conference: 20-23 June 2011

 

 

 

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R for Biologists

Author: Marco Martinez

This material is intended as an introductory guide to data analysis with the R system, to assist in statistical computing training for life science researchers.  It was produced as companion material for a seminar (R Tutorial for Life Sciences) given at The University of Tennessee in the spring of 2009, sponsored by the National Institute for Mathematical and Biological Synthesis (NIMBioS).

The principal aim is to provide a step-by-step guide on the use of R to carry out statistical analysis and techniques widely used in the life sciences.  In each section, there is a detailed explanation of a command in R, followed by a biological example with all the instructions (in red) needed to run the test and with the corresponding output in R (in blue).  There is assumed previous knowledge in statistics and experimental design, essentially corresponding to a basic undergraduate introductory statistic course.

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Wendy Jo Levenson onto Books About Using R

The to do function being made available straight from the group's side bar would be awesome, rather than having to hunt for it inside the project. It would really help with trying to get…

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Alissa Nedossekina onto Mine

How People Learn: Brain, Mind, Experience & School

How People Learn is a classic - I don’t think you can go wrong with it. 

Survey of ed psych and cognitive science research.

Full text available online. 

http://www.nap.edu/openbook.php?isbn=0309070368

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Sam S Donovan onto BQCC Recommended Readings

Describing and Measuring STEM Teaching Practices

I think you can order print copies of this from AAAS. 

Description here: http://www.aaas.org/news/new-aaas-resources-support-undergraduate-stem-education-reform

Download here: http://ccliconference.org/measuring-teaching-practices/

Much more focused on assessment.

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Sam S Donovan onto BQCC Recommended Readings

Screening snails for larval trematode infection

This is a laboratory activity focused on identifying first and second intermediate host infections by trematodes of pond snails. 

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Jeremy M Wojdak onto Laboratory activities

Cercaria of Metagonomoides oregonensis

Darkfield image of M. oregonensis stained with Lugol's solution. Specimen from a snail sampled from a VA stream.

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Jeremy M Wojdak onto Parasite images

An evolutionary constraint: Small size

This is an article that discusses how evolutionary constraints limit the size of arthropods.

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Ellen Wisner onto Tree of Life: Mechanisms

YAY PROTISTS!

This is a tool that is currently being developed by the working group. In this activity students will be given several interesting protists to research.  Then based on morphological characteristics students will create a hypothesis tree.  Then, students will be given a tree of their organisms based on genetic data.  They will then use Mesquite to map characters onto the tree they are given.

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Ellen Wisner onto Tree of Life: Biodiversity

Mesquite

From the developers, "Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms." Students can use Mesquite to build trees, plot characters onto trees, and explore ancestral state reconstructions.

Mesquite can be run directly on the Hub here, or downloaded from mesquiteproject.org.

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Arietta Fleming-Davies onto Tree of Life: Speciation

Natural Selection Concept Inventory

Anderson DL, Fisher KM, Norman JG. 2002. Development and validation of the conceptual inventory of natural selection. Journal of Research in Science Teaching 39: 952-978.

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Ellen Wisner onto Tree of Life: Mechanisms

Quick bites and quirky adaptations

Interesting news article about convergent evolution of trap jaws in ants. Includes slow motion videos of the ants using these jaws to propel themselves through the air as a defense mechanism.

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Ellen Wisner onto Tree of Life: Mechanisms

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