139 Works

Siderophore concentrations along the North Pacific Gradients 1.0 and 2.0 cruises transect

Jiwoon Park & Randelle Bundy
This dataset includes concentrations of siderophores (strong iron-binding ligands) measured from seawater samples taken during Gradients 1.0 (KOK1606) and 2.0 (MGL1704) cruises, which took place in April-May 2016 and May-June 2017 respectively. Concentrations were measured using a Thermo iCAP RQ ICP-MS coupled to a Dionex Ultimate 3000 HPLC.

Host Factor Experiment (IM006B-R)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG3/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^4 PFU.

Host Factor Experiment (IM006A-R)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG3/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^3 PFU.

Host Factor Experiment (ICL006-R)

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Purpose: To obtain samples from Calu-3 cells infected with A/CA/04/09 (H1N1) for both transcriptional and proteomics analyses. Details: Time Points = 0, 3, 7, 12, 18, 24, 30, 36 and 48 h post infection; Done in triplicate for both RNA and protein; Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates; Time matched mocks done in triplicate from same cell stock as rest of...

Host Factor Experiment (IM004-P)

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Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics.General Design: 20 week-old C57Bl6 mice; doses = 1E4 PFU; Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks

Host Factor Experiment (SCL008-R)

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Purpose: To obtain samples for transcriptional and proteomic analysis using wild type icSARS CoV and icSARS ExoNI and icSARS dNSP16 mutants in 2B-4 cells/sorted Calu-3 cells with high ACE2 expression. Details: Time Points = 0, 7, 12, 24, 36, 48, 60 and 72h post infection (Note: only 0, 24, 48 and 72hr samples analysed for proteomics); Done in triplicate for RNA and quadruplicate for protein; Replicates are defined as 3 or 4 different wells, plated...

Host Factor Experiment (CA04M001-R)

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Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics. General Design: 20 week-old C57Bl6 mice; Three Doses = 1E3, 1E4, 1E5, 1E6 (PFU); Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks

Host Factor Experiment (KL001-R)

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Polarized confluent monolayers of Calu-3 cells were infected apically with the avian-origin IAVs A/Anhui/01/2013 (H7N9) [Anhui01], A/Netherland/219/2003 (H7N7) [NL219], A/Vietnam/1203/2004 (H5N1) [VN1203], or a human seasonal virus A/Panama/2007/1999 (H3N2) [Pan99] at an MOI of 1. Time-matched mocks were also included using the same cell stock as the rest of the samples. Culture medium (same as what the virus stock is in) was used for the mock infections. Quadruplicate wells were infected for each virus/timepoint. Measured...

Host Factor Experiment (KL002-R)

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Groups of 6- to 8-week-old BALB/c mice were infected with either A/Anhui/01/2013 (H7N9), A/Netherlands/219/2003 (H7N7), A/Vietnam/1203/2004 (H5N1), or pandemic H1N1 human virus, A/Mexico/4482/2007 (H1N1). Infections were done at 10^5 PFU or time-matched mock infected. Time points were 1, 3 and 5 d.p.i. There were 4-5 infected and 3 mock infected animals/time point. Lung samples were collected for virus load and transcriptional analysis. Weight loss and animal survival were also monitored.

Host Factor Experiment (IM006A-P)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG3/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^3 PFU.

Host Factor Experiment (SM009-R)

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Purpose: To obtain lung samples from C57BL6 or PLAT knock-out mice infected with SARS MA15 virus for transcriptional analysis. Details: Time Points = 4 and 7 days post-infection; 2-3 replicates for infected and mock mice; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu.

Host Factor Experiment (SM003-R)

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Purpose: To obtain lung samples from C57BL6 mice infected with , icSARS, SARS MA15 or SARS BatSRBD mutant viruses for transcriptional analysis. Details: Time Points = 1, 2, 4 and 7 days post-infection; 3-5 replicates for infected and mock mice; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu for icSARS, 10^4 or 10^5pfu for MA15 and 10^4pfu BatSRBD.

How variable is mixing efficiency in the abyss?

Takashi Ijichi, Louis St. Laurent, Kurt L. Polzin & John Toole
This directory contains BBTRE/DoMORE processed data (“all_BBTRE.mat” and “all_DoMORE.mat”) that was used to produce all figures in the above research letter. Each mat file has two structure arrays named “location” and “patch10”. The “location” array includes microstructure profile information used in this study (Table D1). The “patch10” array includes 10-m patch-wise parameter estimates used in this study (Table D2). Note that bulk averaged parameters can be constructed from parameters saved in “patch10” (see the above...

Host Factor Experiment (SM020-R)

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Purpose: To obtain lung samples from ppp1r14c knockout mutant mice infected with SARS MA15 virus for transcriptional analyses. Details: Time Points = days 4 and 7 post-infection; 2-3 replicate mice for each condition; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu.

What Code-Switching Strategies are Effective in Dialogue Systems?

Emily Ahn, Cecilia Jimenez, Yulia Tsvetkov & Alan Black

Automating autism: Disability, discourse, and Artificial Intelligence

Os Keyes
As Artificial Intelligence (AI) systems shift to interact with new domains and populations, so does AI ethics: a relatively nascent subdiscipline that frequently concerns itself with questions of “fairness” and “accountability.” This fairness-centred approach has been criticized for (amongst other things) lacking the ability to address discursive, rather than distributional, injustices. In this paper I simultaneously validate these concerns, and work to correct the relative silence of both conventional and critical AI ethicists around disability,...

Spatial-temporal growth, distribution, and diffusion of marine microplastic research and national plastic policies

Lyda Harris
Plastic accounts for 80% of material waste in the ocean. The field of marine microplastic research is relatively new and is growing rapidly, in terms of published papers as well as institutions and countries conducting research. To combat plastic pollution, there is sufficient evidence that policies can lead to reduced plastic production and consumption both locally and globally. We aim to understand how marine plastics research and policies have grown and spread. Specifically, we used...

Cryptic and extensive hybridization between ancient lineages of American crows

David L. Slager, Kevin L. Epperly, Renee R. Ha, Sievert Rohwer, Chris Wood, Caroline Van Hemert & John Klicka
Most species and therefore most hybrid zones have historically been defined using phenotypic characters. However, both speciation and hybridization can occur with negligible morphological differentiation. Recently developed genomic tools provide the means to better understand cryptic speciation and hybridization. The Northwestern Crow (Corvus caurinus) and American Crow (Corvus brachyrhynchos) are continuously distributed sister taxa that lack reliable traditional characters for identification. In this first population genomic study of Northwestern and American crows, we use genomic...

Dominant native and non-native graminoids differ in key leaf traits irrespective of nutrient availability

Arthur Broadbent, Jennifer Firn, James McGree, Elizabeth Borer, Yvonne Buckley, W. Stanley Harpole, Kimberly Komatsu, Andrew MacDougall, Kate Orwin, Nicholas Ostle, Eric Seabloom, Jonathan Bakker, Lori Biedermann, Maria Caldeira, Nico Eisenhauer, Nicole Hagenah, Yann Hautier, Joslin Moore, Carla Nogueira, Pablo Peri, Anita Risch, Christiane Roscher, Martin Schuetz & Carly Stevens
Aim Nutrient enrichment is associated with plant invasions and biodiversity loss. Functional trait advantages may predict the ascendancy of invasive plants following nutrient enrichment but this is rarely tested. Here, we investigate 1) whether dominant native and non-native plants differ in important morphological and physiological leaf traits, 2) how their traits respond to nutrient addition, and 3) whether responses are consistent across functional groups. Location Australia, Europe, North America and South Africa Time period 2007...

Data from: Assessing cetacean populations using integrated population models: an example with Cook Inlet beluga whales

Eiren Jacobson, Charlotte Boyd, Tamara McGuire, Kim Shelden, Gina Himes Boor & André Punt
Effective conservation and management of animal populations requires knowledge of abundance and trends. For many species, these quantities are estimated using systematic visual surveys. Additional individual-level data are available for some species. Integrated population modelling (IPM) offers a mechanism for leveraging these datasets into a single estimation framework. IPMs that incorporate both population- and individual-level data have previously been developed for birds, but have rarely been applied to cetaceans. Here, we explore how IPMs can...

It's a wormy world: Meta-analysis reveals several decades of change in the global abundance of the parasitic nematodes Anisakis spp. and Pseudoterranova spp. in marine fishes and invertebrates

Evan Fiorenza, Catrin Wendt, Katie Dobkowski, Teri King, Marguerite Pappaionou, Peter Rabinowitz, Jameal Samhouri & Chelsea Wood
The Anthropocene has brought substantial change to ocean ecosystems, but whether this age will bring more or less marine disease is unknown. In recent years, the accelerating tempo of epizootic and zoonotic disease events has made it seem as if disease is on the rise. Is this apparent increase in disease due to increased observation and sampling effort, or to an actual rise in the abundance of parasites and pathogens? We examined the literature to...

Data from: The future of food from the sea

Tracey Mangin, Christopher Costello, Ling Cao, Stefan Gelcich, Miguel A. Cisneros-Mata, Christopher M. Free, Halley E. Froehlich, Christopher D. Golden, Gakushi Ishimura, Jason Maier, Ilan Macadam-Somer, Michael C. Melnychuk, Masanori Miyahara, Carryn L. De Moor, Rosamond Naylor, Linda Nøstbakken, Elena Ojea, Erin O’Reilly, Ana M. Parma, Andrew J. Plantinga, Shakuntala H. Thilsted & Jane Lubchenco
Global food demand is on the rise and serious questions remain about whether supply can increase sustainably. Land-based expansion is possible, but may exacerbate climate change and biodiversity loss and compromise the delivery of other ecosystem services. As food from the sea represents only 17% of current edible meat production, we ask: How much food can we expect the ocean to sustainably produce by 2050? We examine the main food-producing sectors in the ocean—wild fisheries,...

Changes in taxonomic and phylogenetic diversity in the Anthropocene

Daijiang Li, Julian Olden, Julie Lockwood, Sydne Record, Michael McKinney & Benjamin Baiser
To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness and evolutionary history across spatial scales is needed. Here we compiled 162 datasets for fish, bird, and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at different spatial scales (within site α diversity and between sites spatial β diversity). Biodiversity change is measured from these datasets in three ways: across land use gradients,...

Data from: Fluid preservation causes minimal reduction of parasite detectability in fish specimens: a new approach for reconstructing parasite communities of the past?

Evan Fiorenza, Katie Leslie, Mark Torchin, Katherine Maslenikov, Luke Tornabene & Chelsea Wood
Long-term datasets are needed to evaluate temporal patterns in wildlife disease burdens, but historical data on parasite abundance are extremely rare. For more than a century, natural history collections have been accumulating fluid-preserved specimens, which should contain the parasites infecting the host at the time of its preservation. However, before this unique data source can be exploited, we must identify the artefacts that are introduced by the preservation process. Here, we experimentally address whether the...

Cold-induced hyperphagia requires AgRP-neuron activation in mice

Jennifer Deem
To maintain energy homeostasis during cold exposure, the increased energy demands of thermogenesis must be counterbalanced by increased energy intake. To investigate the neurobiological mechanisms underlying this cold-induced hyperphagia, we asked whether agouti-related peptide (AgRP) neurons are activated when animals are placed in a cold environment and, if so, whether this response is required for the associated hyperphagia. We report that AgRP-neuron activation occurs rapidly upon acute cold exposure, as do increases of both energy...

Registration Year

  • 2020
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Affiliations

  • University of Washington
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