Consumption of Shrews, Sorex spp., by Arctic Grayling, Thymallus arcticus

In an investigation of the dietary habits of Arctic Grayling (Thymallus arcticus) we found that two individuals out of 93 sampled in southwestern Alaska (approximately 59°N, 159°W) contained a total of five shrews (Sorex spp.). These shrews contained enriched levels of nitrogen stable isotopes, suggesting utilization of nutrients derived from salmon. We hypothesize that normally terrestrial shrews accidentally enter streams while foraging along the productive riparian zones of creeks with high densities of salmon. Shrews are apparently susceptible to opportunistic predation by resident stream fishes, including Arctic Grayling, when they enter the streams

Modeling hydrodynamic self-propulsion with Stokesian Dynamics. Or teaching Stokesian Dynamics to swim

We develop a general framework for modeling the hydrodynamic self-propulsion (i.e., swimming) of bodies (e.g., microorganisms) at low Reynolds number via Stokesian Dynamics simulations. The swimming body is composed of many spherical particles constrained to form an assembly that deforms via relative motion of its constituent particles. The resistance tensor describing the hydrodynamic interactions among the individual particles maps directly onto that for the assembly. Specifying a particular swimming gait and imposing the condition that the swimming body is force- and torque-free determine the propulsive speed. The body’s translational and rotational velocities computed via this methodology are identical in form to that from the classical theory for the swimming of arbitrary bodies at low Reynolds number. We illustrate the generality of the method through simulations of a wide array of swimming bodies: pushers and pullers, spinners, the Taylor=Purcell swimming toroid, Taylor’s helical swimmer, Purcell’s three-link swimmer, and an amoeba-like body undergoing large-scale deformation. An open source code is a part of the supplementary material and can be used to simulate the swimming of a body with arbitrary geometry and swimming gait

Long-term vegetation studies in the southwest

In this paper, we describe several long-term studies in the ponderosa pine (Pinus ponderosa) forests of the American Southwest, focusing on the unique insights and contributions of these studies. Many of the studies that we discuss were established by staff from the Fort Valley Experiment Station (FVES; http://www.rmrs.nau.edu/fortvalley/)

Juvenile Salmon Usage of the Skeena River Estuary

Migratory salmon transit estuary habitats on their way out to the ocean but this phase of their life cycle is more poorly understood than other phases. The estuaries of large river systems in particular may support many populations and several species of salmon that originate from throughout the upstream river. The Skeena River of British Columbia, Canada, is a large river system with high salmon population- and species-level diversity. The estuary of the Skeena River is under pressure from industrial development, with two gas liquefaction terminals and a potash loading facility in various stages of environmental review processes, providing motivation for understanding the usage of the estuary by juvenile salmon. We conducted a juvenile salmonid sampling program throughout the Skeena River estuary in 2007 and 2013 to investigate the spatial and temporal distribution of different species and populations of salmon. We captured six species of juvenile anadromous salmonids throughout the estuary in both years, and found that areas proposed for development support some of the highest abundances of some species of salmon. Specifically, the highest abundances of sockeye (both years), Chinook in 2007, and coho salmon in 2013 were captured in areas proposed for development. For example, juvenile sockeye salmon were 2–8 times more abundant in the proposed development areas. Genetic stock assignment demonstrated that the Chinook salmon and most of the sockeye salmon that were captured originated from throughout the Skeena watershed, while some sockeye salmon came from the Nass, Stikine, Southeast Alaska, and coastal systems on the northern and central coasts of British Columbia. These fish support extensive commercial, recreational, and First Nations fisheries throughout the Skeena River and beyond. Our results demonstrate that estuary habitats integrate species and population diversity of salmon, and that if proposed development negatively affects the salmon populations that use the estuary, then numerous fisheries would also be negatively affected

Resource Pulses Increase the Diversity of Successful Competitors in a Multi-Species Stream Fish Assemblage

Food resources are often patchily distributed through space and time and are classified as resource pulses when hyperabundant. Resource pulses can benefit growth, reproduction, and abundance of various consumers. Yet, it is relatively unknown how such resources are partitioned among competing consumers and how this is influenced by the magnitude of the pulse. Here, we examined how the magnitude of a pulsed resource influences resource partitioning among diverse sizes and species of consumers in a natural setting over small spatial and temporal scales. We focused on salmon egg subsidies to stream fish consumers. We experimentally added different quantities of pink salmon eggs to five meter long experimental stream sections. Egg additions spanned three orders of magnitude from 6 to 3575 eggs. Stream fish (egg consumers) were captured and gastric lavaged at each experimental section to determine how many eggs each individual fish consumed. We modeled taxon‐specific individual egg consumption as a function of egg availability, individual mass, community composition, number of competitors, and stream velocity using hurdle models in a Bayesian framework. We found that there were diminishing returns for increasing egg abundance increasing egg consumption (i.e., type II functional response) for individual size classes of fish, but that higher egg numbers were needed to benefit diverse consumers. Top models indicated that egg availability and individual fish characteristics (size and taxon) drove egg consumption, while community characteristics (species composition and number of competitors) were not supported. Our results suggest that resource pulses can provide rare opportunities for less dominant sizes and species of fish to consume abundant resources. The current paradigm in the stream fish literature suggests that stream fish communities are structured by dominance hierarchies; however, dominance hierarchies may be less influential where pulsed resources comprise a large portion of the resource base

The discovery of two spotted leopards (Panthera pardus) in Peninsular Malaysia

We discovered the presence of two individual spotted leopards Panthera pardus in Ulu Muda Forest Reserve, a previously under-researched selectively logged rainforest of Peninsular Malaysia. These findings are unexpected, because only two other studies have detected the spotted morph amongst many other melanistic leopards caught on camera traps in Peninsular Malaysia. We discuss the implications of our findings with respect to the prevalence of melanism among leopards in the region

TCR hypervariable regions expressed by T cells that respond to effective tumor vaccines

A major goal of immunotherapy for cancer is the activation of T cell responses against tumor-associated antigens (TAAs). One important strategy for improving antitumor immunity is vaccination with peptide variants of TAAs. Understanding the mechanisms underlying the expansion of T cells that respond to the native tumor antigen is an important step in developing effective peptide-variant vaccines. Using an immunogenic mouse colon cancer model, we compare the binding properties and the TCR genes expressed by T cells elicited by peptide variants that elicit variable antitumor immunity directly ex vivo. The steady-state affinity of the natural tumor antigen for the T cells responding to effective peptide vaccines was higher relative to ineffective peptides, consistent with their improved function. Ex vivo analysis showed that T cells responding to the effective peptides expressed a CDR3β motif, which was also shared by T cells responding to the natural antigen and not those responding to the less effective peptide vaccines. Importantly, these data demonstrate that peptide vaccines can expand T cells that naturally respond to tumor antigens, resulting in more effective antitumor immunity. Future immunotherapies may require similar stringent analysis of the responding T cells to select optimal peptides as vaccine candidates. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00262-012-1217-5) contains supplementary material, which is available to authorized users

Live manipulation of documentary audio in a narrative electroacoustic concert piece

Documentary musical and theatrical works span a wide variety of genres, styles, and media. Such musical works typically involve fixed electronic media, either alone or--as in Steve Reich's Different Trains--with an accompanying acoustic ensemble. Most documentary theatrical works, by contrast, are live performances in which interviewees' original words are re-created by an actor. With this thesis, I have attempted a new blend of documentary styles involving the live performance of both acoustic and electronic elements. I have composed a piece, There Was No Question, using narrative audio clips taken from interviews with my father. His recorded speech is triggered and manipulated live during performance by two laptop players using Wii remotes, and is accompanied by an acoustic ensemble. This thesis investigates the precedents, both musical and theatrical, informing this new work. It also introduces two frameworks for understanding the compositional techniques used, both in treating the documentary audio and in constructing a compelling dramatic narrative. I provide the text of the narration (Appendix A), a score of the work (Appendix B), a concert recording (Appendix C) and the Max/MSP patches used to perform the two electronics parts (Appendix D)