59 Works

Atomistic Simulations of the Elastic Compression of Platinum Nanoparticles

Ingrid M. Padilla Espinosa, Tevis D. B. Jacobs & Ashlie Martini
Abstract The elastic behavior of nanoparticles depends strongly on particle shape, size, and crystallographic orientation. Many prior investigations have characterized the elastic modulus of nanoscale particles using experiments or simulations; however their reported values vary widely depending on the methods for measurement and calculation. To understand these discrepancies, we used classical molecular dynamics simulation to model the compression of platinum nanoparticles with two different polyhedral shapes and a range of sizes from 4 to 20...

Additional file 1 of Needs and preferences of women with prior severe preeclampsia regarding app-based cardiovascular health promotion

Lili L. Kókai, Marte F. van der Bijl, Martin S. Hagger, Diarmaid T. Ó Ceallaigh, Kirsten I.M. Rohde, Hans van Kippersluis, Alex Burdorf, Johannes J. Duvekot, Jeanine E. Roeters van Lennep & Anne I. Wijtzes
Supplementary Material 1: Correlations between components of needs per health behavior

CCMI nursery coral disease 2019

Anya Brown, Dagny-Elyse Anastasiou, Monica Schul, Sophia MacVittie, Lindsay Spiers, Julie Meyer, Carrie Manfrino & Thomas Frazer
Marine infectious diseases are a leading cause of population declines globally due, in large part, to challenges in diagnosis and limited treatment options. Mitigating disease spread is particularly important for species targeted for conservation. In some systems, the strategic arrangement of organisms in space can constrain disease outbreaks, however, this approach has not been used in marine restoration. Reef-building corals have been particularly devastated by disease and continue to experience catastrophic population declines. Here, we...

Data for: Thermal vulnerability in a mountain stream network: Temporal, spatial, and biological data

Kyle Leathers, David Herbst, Mohammad Safeeq & Albert Ruhi
As climate change continues to increase air temperature in high-altitude ecosystems, it has become critical to understand the controls and scales of aquatic habitat vulnerability to warming. Here we used a nested array of high-frequency sensors, and advances in time-series models, to examine spatiotemporal variation in thermal vulnerability in a model Sierra Nevada watershed. Stream thermal sensitivity to atmospheric warming fluctuated strongly over the year and peaked in spring and summer—when hot days threaten invertebrate...

Additional file 1 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 1: Supplemental Figure S1. Automated fractionation system design, parts, and assembly. Supplemental Figure S2. Hyphosphere-SIP experimental design. Supplemental Figure S3. Myxococcota MAG CAZymes grouped with CAZymes from 25 genomes from Myxococcota GTDB type species (previously used in Murphy et al. [2]).

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Additional file 4 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 4: Supplemental Table S3. Assembly statistics, taxonomic lineage, and atom percent excess (APE) of the metagenome amplified genomes (MAGs) created in this study.

Additional file 5 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 5: Supplemental Table S4. Number of CAZyme family domains in the highly enriched MAGs (>10 atom% excess 13C). AOA = archaeal ammonia oxidizer, Fibro = Fibrobacterota, Myxo = Myxococcota (Myxococcaceae).

Files associated with: Species’ attributes predict the relative magnitude of ecological and genetic recovery following mass mortality

Lauren Schiebelhut, Gaylord Brian, Richard Grosberg, Laura Jurgens & Michael Dawson
Theoretically, species’ characteristics should allow estimation of dispersal potential and, in turn, explain levels of population genetic differentiation. However, a mismatch between traits and genetic patterns is often reported in marine species and interpreted as evidence that life-history traits do not influence dispersal. Here, we couple ecological and genomic methods to test the hypothesis that species with attributes favoring greater dispersal potential — e.g. longer pelagic duration, higher fecundity, and larger population size — have...

Additional file 1 of Atomistic Simulations of the Elastic Compression of Platinum Nanoparticles

Ingrid M. Padilla Espinosa, Tevis D. B. Jacobs & Ashlie Martini
Additional file 1. Effect of the simulation parameters of the virtual walls on elastic deformation, effect of the orientation in the deformation of fcc crystals, schematic of a representative element volume (RVE), and stresses in the direction-of and prependicular-to the load.

Atomistic Simulations of the Elastic Compression of Platinum Nanoparticles

Ingrid M. Padilla Espinosa, Tevis D. B. Jacobs & Ashlie Martini
Abstract The elastic behavior of nanoparticles depends strongly on particle shape, size, and crystallographic orientation. Many prior investigations have characterized the elastic modulus of nanoscale particles using experiments or simulations; however their reported values vary widely depending on the methods for measurement and calculation. To understand these discrepancies, we used classical molecular dynamics simulation to model the compression of platinum nanoparticles with two different polyhedral shapes and a range of sizes from 4 to 20...

Additional file 2 of mRNAs encoding neurodevelopmental regulators have equal N6-methyladenosine stoichiometry in Drosophila neuroblasts and neurons

Josephine D. Sami, Robert C. Spitale & Michael D. Cleary
Additional file 2: Supplemental Table 2. Neuroblast and neuron mRNA half-lives.

Data associated with: Minor genetic consequences of a major mass mortality: Short-term effects in Pisaster ochraceus

Lauren Schiebelhut, Melina Giakoumis, Rita Castilho, Paige Duffin, Jonathan Puritz, John Wares, Gary Wessel & Michael Dawson
Mass mortality events (MMEs) are increasing globally in frequency and magnitude, largely due to human-induced change. The effects of these MMEs, both in the long- and short-term, are of imminent concern because of their ecosystem impacts. Genomic data can be used to reveal some of the population-level changes associated with MMEs. Here, we use reduced-representation sequencing to identify potential short-term genetic impacts of an MME associated with a sea star wasting (SSW) outbreak. We tested...

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Abstract Background Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing—SIP—remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput...

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Lived experiences and unique psychosocial impacts following bariatric surgery in a publicly funded Australian tertiary hospital: a qualitative study

Charlene Wright, Jaimon T. Kelly, Rebecca Healy, Jane Musial, Katrina L. Campbell & Kyra Hamilton
Gain an understanding of the lived experiences and unique psychosocial impacts following bariatric surgery. Qualitative study design, consisting of semi-structured interviews. Based on thematic analysis principles, transcripts were inductively coded. Fifteen participants were included; predominantly female (n = 9, 60%) and underwent Roux-en-Y gastric bypass (n =12, 80%), with a mean age of 57 years. Five themes were generated including ‘Key Motivators to Undergo Bariatric Surgery’, “Positive Changes”, “Facing the Challenges”, “Tackling Social Relationships”, and...

Lived experiences and unique psychosocial impacts following bariatric surgery in a publicly funded Australian tertiary hospital: a qualitative study

Charlene Wright, Jaimon T. Kelly, Rebecca Healy, Jane Musial, Katrina L. Campbell & Kyra Hamilton
Gain an understanding of the lived experiences and unique psychosocial impacts following bariatric surgery. Qualitative study design, consisting of semi-structured interviews. Based on thematic analysis principles, transcripts were inductively coded. Fifteen participants were included; predominantly female (n = 9, 60%) and underwent Roux-en-Y gastric bypass (n =12, 80%), with a mean age of 57 years. Five themes were generated including ‘Key Motivators to Undergo Bariatric Surgery’, “Positive Changes”, “Facing the Challenges”, “Tackling Social Relationships”, and...

Data from: Decoding the dynamics of dental distributions: insights from shark demography and dispersal

Sora Kim, Justin Yeakel, Juergen Kriwet, Meghan Balk, Jaelyn Eberle, Sarah Zeichner & Dina Fieman
Shark teeth are the most abundant vertebrate fossil, and because tooth size generally correlates with body size, their accumulations document the size structure of populations. Understanding how ecological and environmental processes influence size structure, and how this extends to influence these dental distributions, may offer a window into the ecological and environmental dynamics of past and present shark populations. Here we examine the dental distributions of sand tigers, including extant Carcharias taurus and extinct Striatolamia...

Restoring function: positive responses of carbon and nitrogen to 20 years of hydrologic restoration in montane meadows

Cody Reed, Cody Reed, Asmeret Berhe, Kimber Moreland, Jim Wilcox & Benjamin Sullivan
Montane meadows are highly productive ecosystems that contain high densities of soil carbon (C) and nitrogen (N). However, anthropogenic disturbances that lead to channel incision and disconnected floodplain hydrology have altered the C balance of many meadows, converting them from net C sinks to net sources of C to the atmosphere. Restoration efforts designed to reconnect floodplain hydrology may slow rates of soil C loss from degraded meadows and restore conditions for C sequestration and...

Data for: Water system simulation modeling with hydropower optimization and environmental flows: An example with Pywr

David Rheinheimer, Gustavo Facincani Dourado, Anna Rallings, Aditya Sood & Joshua Viers
This dataset was used in the CenSierraPywr model created for the project "Optimizing Hydropower Operations While Sustaining Ecosystem Functions in a Changing Climate", for the California Energy Commission. Specifically, this data is to support reproducibility of the article describing the basic methods (Rheinheimer et al., in review). The model was built in Pywr, an open-source, linear programming-based Python package for modeling basin-scale water systems in the Central Sierra Nevada, California. Here, we focus on the...

Data from: Boosts in leaf-level photosynthetic capacity aid Pinus ponderosa recovery from wildfire

Kelsey Bryant, Hyojung Kwon, Crystal Kolden, Jeffrey Stenzel, Justin Mathias, Laurel Lynch & Tara Hudiburg
Forests mitigate climate change by sequestering massive amounts of carbon, but recent increases in wildfire activity are threatening carbon storage. Currently, our understanding of wildfire impacts on forest resilience and the mechanisms controlling post-fire recovery remains unresolved due to a lack of empirical data on mature trees in natural settings. Here, we quantify the physiological mechanisms controlling carbon uptake immediately following wildfire in mature individuals of ponderosa pine (Pinus ponderosa), a wide-spread and canopy-dominant tree...

Transcriptome assemblies associated with: A cnidarian phylogenomic tree fitted with hundreds of 18S leaves

Melissa DeBiasse
Cnidarians have been an experimental system for a diversity of research areas ranging from development to biomechanics to global change biology. Yet we still lack a well-resolved, taxonomically balanced, cnidarian tree of life to place this research in appropriate phylogenetic context. To move towards this goal, we combined data from 26 new anthozoan transcriptomes with 86 previously published cnidarian and outgroup datasets to generate two 748-locus alignments containing 123,051 (trimmed) and 449,935 (untrimmed) amino acids....

Dataset for: Water, environment, and socioeconomic justice in California: A multi-benefit cropland repurposing framework

Angel Santiago Fernandez-Bou, José Manuel Rodríguez-Flores, Alexander Guzman, J. Pablo Ortiz-Partida, Leticia Margarita Classen-Rodriguez, Humberto Florez-Landeros, Jorge Valero-Fandiño, Chantelise Pells, Thomas Harmon & Josué Medellín-Azuara
Low-income, rural frontline communities of California’s Central Valley experience environmental and socioeconomic injustice, water insecurity, extremely poor air quality, and lack of fundamental infrastructure (sewage, green areas, health services), which makes them less resilient. Many communities depend financially on agriculture, while water scarcity and associated policy may trigger farmland retirement, further hindering socioeconomic opportunities. Here we propose a multi-benefit framework to repurpose cropland in buffers inside and around (400-m and 1600-m buffers) 154 rural disadvantaged...

Additional file 4 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 4: Supplemental Table S3. Assembly statistics, taxonomic lineage, and atom percent excess (APE) of the metagenome amplified genomes (MAGs) created in this study.

Additional file 6 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 6: Supplemental Table S5. Genomic abundance of MEROPS proteae gene per MAG. Columns indicate MEROPS protease families. APE = atom percent excess.

Registration Year

  • 2022
    59

Resource Types

  • Dataset
    43
  • Collection
    8
  • Text
    8

Affiliations

  • University of California, Merced
    59
  • University of California, Berkeley
    19
  • Lawrence Livermore National Laboratory
    19
  • University of Massachusetts Amherst
    18
  • Lawrence Berkeley National Laboratory
    18
  • Joint Genome Institute
    18
  • University of California, Irvine
    6
  • Erasmus MC
    4
  • University of Pittsburgh
    4
  • University of Idaho
    4