Mentoring is an intellectual pillar of ethnobiology

Ethnobiology relies on community partnerships and relationships between elders or other knowledge keepers and students. Our Society of Ethnobiology, like all academic organizations, has its own issues with discrimination and abuses of power. But more than other academic disciplines, contemporary ethnobiology is practiced with and strengthened by close, respectful working relationships. As such, we offer our thoughts on the lessons ethnobiology brings to mentorship and accountability while outlining some of the specific steps we are taking as an academic and practicing community.Published versio

Design and Construction of a Programmable Electroporation system for Biological Applications

Studies into electroporation have grown rapidly in biotechnology and medicine in recent years. This paper presents the design and construction of a low cost programmable electroporation system for biological applications. The system consists of a control module, a pulse generation circuit and a high voltage switch using a power MOSFET. The programmable electroporation has been designed, developed and tested. Using a standard commercial electroporation cuvette, it is possible to generate electric fields of 100 to 1000V/cm with programmed pulse lengths of 10?sec to 20msec. The system was evaluated with Hela cells and propidium dye to evaluate transfection rates under a variety of electroporation conditions. Initial results showed that the electroporation system achieved a peak cell transfection efficiency of 48.74% at 600V/cm with pulse lengths of 10 ms

Behavioural simulation of biological neuron systems using VHDL and VHDL-AMS

The investigation of neuron structures is an incredibly difficult and complex task that yields relatively low rewards in terms of information from biological forms (either animals or tissue). The structures and connectivity of even the simplest invertebrates are almost impossible to establish with standard laboratory techniques, and even when this is possible it is generally time consuming, complex and expensive. Recent work has shown how a simplified behavioural approach to modelling neurons can allow “virtual” experiments to be carried out that map the behaviour of a simulated structure onto a hypothetical biological one, with correlation of behaviour rather than underlying connectivity. The problems with such approaches are numerous. The first is the difficulty of simulating realistic aggregates efficiently, the second is making sense of the results and finally, it would be helpful to have an implementation that could be synthesised to hardware for acceleration. In this paper we present a VHDL implementation of Neuron models that allow large aggregates to be simulated. The models are demonstrated using a system level VHDL and VHDL-AMS model of the C. Elegans locomotory system

Thirty Minutes or Less: The Inelasticity of Commuting

This Comment urges the legislature to manipulate travel time in order to reduce GHGE (greenhouse gas emissions). Specifically, the legislature must incentivize mass transit by creating easier, quicker transit systems while simultaneously disincentivizing personal automobiles by increasing automobile travel time. By manipulating the travel time for various modes of travel, the legislature can effectively reduce GHGE while increasing individuals’ quality of life by creating an infrastructure that costs less and provides transportation systems not dependent on the automobile. This Comment explains why the Sustainable Communities Act will fail to significantly reduce vehicle emissions, and this Comment proposes legislative action to reach the goals established in the Global Warming Solutions Act. Part I of this Comment discusses the relationship between the automobile and urban decentralization in America. Part II discusses legislation in California targeting automobile emissions, including regional smart-growth measures and state legislative actions targeted at reducing GHGE. Part III explains the impacts on travel mode choice from urban design, temporal components, and individual components such as attitude, preferences, costs, and the duration of the trip. To demonstrate the power of time, Part III also explains the inelasticity of travel time, the relationship between primary and substitute goods, and how different transportation modes have different values of quality. Part IV proposes changes to make public transit a “close substitute” for the personal automobile and describes savings these policies can bring. Part V demonstrates the viability of these policies by discussing several cities with similar policies. The Conclusion calls the California legislature to act by making funding changes. In order to make significant reductions in GHGE from the transportation industry, as set out in the Global Warming Solutions Act and in the Sustainable Communities Act, the legislature must make meaningful funding changes that significantly reduce automobile infrastructure while making other modes of travel more viable options

Thirty Minutes or Less: The Inelasticity of Commuting

This Comment urges the legislature to manipulate travel time in order to reduce GHGE (greenhouse gas emissions). Specifically, the legislature must incentivize mass transit by creating easier, quicker transit systems while simultaneously disincentivizing personal automobiles by increasing automobile travel time. By manipulating the travel time for various modes of travel, the legislature can effectively reduce GHGE while increasing individuals’ quality of life by creating an infrastructure that costs less and provides transportation systems not dependent on the automobile. This Comment explains why the Sustainable Communities Act will fail to significantly reduce vehicle emissions, and this Comment proposes legislative action to reach the goals established in the Global Warming Solutions Act. Part I of this Comment discusses the relationship between the automobile and urban decentralization in America. Part II discusses legislation in California targeting automobile emissions, including regional smart-growth measures and state legislative actions targeted at reducing GHGE. Part III explains the impacts on travel mode choice from urban design, temporal components, and individual components such as attitude, preferences, costs, and the duration of the trip. To demonstrate the power of time, Part III also explains the inelasticity of travel time, the relationship between primary and substitute goods, and how different transportation modes have different values of quality. Part IV proposes changes to make public transit a “close substitute” for the personal automobile and describes savings these policies can bring. Part V demonstrates the viability of these policies by discussing several cities with similar policies. The Conclusion calls the California legislature to act by making funding changes. In order to make significant reductions in GHGE from the transportation industry, as set out in the Global Warming Solutions Act and in the Sustainable Communities Act, the legislature must make meaningful funding changes that significantly reduce automobile infrastructure while making other modes of travel more viable options

The Most Distant Stars in the Milky Way

We report on the discovery of the most distant Milky Way (MW) stars known to date: ULAS J001535.72$+$015549.6 and ULAS J074417.48$+$253233.0. These stars were selected as M giant candidates based on their infrared and optical colors and lack of proper motions. We spectroscopically confirmed them as outer halo giants using the MMT/Red Channel spectrograph. Both stars have large estimated distances, with ULAS J001535.72$+$015549.6 at $274 \pm 74$ kpc and ULAS J074417.48$+$253233.0 at 238 $\pm$ 64 kpc, making them the first MW stars discovered beyond 200 kpc. ULAS J001535.72$+$015549.6 and ULAS J074417.48$+$253233.0 are both moving away from the Galactic center at $52 \pm 10$ km s$^{-1}$ and $24 \pm 10$ km s$^{-1}$, respectively. Using their distances and kinematics, we considered possible origins such as: tidal stripping from a dwarf galaxy, ejection from the MW's disk, or membership in an undetected dwarf galaxy. These M giants, along with two inner halo giants that were also confirmed during this campaign, are the first to map largely unexplored regions of our Galaxy's outer halo.Comment: Accepted and in print by ApJL. Seven pages, 2 figure

Magnetized black holes and black rings in the higher dimensional dilaton gravity

In this paper we consider magnetized black holes and black rings in the higher dimensional dilaton gravity. Our study is based on exact solutions generated by applying a Harrison transformation to known asymptotically flat black hole and black ring solutions in higher dimensional spacetimes. The explicit solutions include the magnetized version of the higher dimensional Schwarzschild-Tangherlini black holes, Myers-Perry black holes and five dimensional (dipole) black rings. The basic physical quantities of the magnetized objects are calculated. We also discuss some properties of the solutions and their thermodynamics. The ultrarelativistic limits of the magnetized solutions are briefly discussed and an explicit example is given for the $D$-dimensional magnetized Schwarzschild-Tangherlini black holes.Comment: LaTeX, 23 pages; v2 references and comments added, some typos corrected;v3 minor change

A cancer cell-line titration series for evaluating somatic classification.

BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)