98 Works

Plant-based food choice selection when presented as a default

David Cleveland & Varun Iyer
The main objective of this study is to understand the effect of a default nudge on peoples’ meal choices. To decrease the climate and environmental impact of the food system, there needs to be a shift away from animal source food to plant foods. Our main hypothesis is that when the default meal choice is plant-based, a larger proportion of participants will accept this default, compared with the proportion opting out of the default when...

BEDMAP3 - Ice thickness, bed and surface elevation for Antarctica - standardised data points

Alice Fremand, Peter Fretwell, Julien Bodart, Hamish Pritchard, A. Aitken, Jonathan Bamber, R.E. Bell, C Bianchi, Robert Bingham, Donald Blankenship, G. Casassa, Ginny Catania, K Christianson, H Conway, Hugh Corr, X. Cui, D Damaske, V. Damn, R. Drews, G. Eagles, O. Eisen, H. Eisermann, Fausto Ferraccioli, Rene Forsberg, S Franke … & A. Zirizzotti
We present here the Bedmap3 ice thickness, bed and surface elevation standardised CSV data points that are used to create the Bedmap3 gridding products in addition to the previous data releases. The data consists of 50 million points acquired by 17 different data providers in Antarctica. The associated datasets consist of: - Bedmap1 standardised CSV data points: https://doi.org/10.5285/f64815ec-4077-4432-9f55-0ce230f46029 - Bedmap2 standardised CSV data points: https://doi.org/10.5285/2fd95199-365e-4da1-ae26-3b6d48b3e6ac - Bedmap3 statistically-summarised data points (shapefiles): https://doi.org/10.5285/a72a50c6-a829-4e12-9f9a-5a683a1acc4a This work is...

Data from: Genotype x environment interaction obscures genetic sources of variation in seed size in Dithyrea californica but provides the opportunity for selection on phenotypic plasticity

Eugenio Larios & Susan Mazer
Premise: Seed size is a functional trait that influences individual fitness but the genetic basis of variation in individual seed size in wild species remains still largely unknown. The evolutionary trajectory of seed size depends, in part, on whether seed size variation is determined by additive, maternal, or non-additive genetic variance. The expression of these sources of variance in seed size may be environment-dependent, reflecting genetic variation in phenotypic plasticity. In this study, we used...

Wins and Losses in Intergroup Conflicts Reflect Energy Balance in Red-Tailed Monkeys

Michelle Brown, Ronnie Steinitz & Melissa Emery Thompson
The energetic costs and benefits of intergroup conflicts over feeding sites are widely hypothesized to be significant, but rarely quantified. In this study, we use short-term measures of energy gain and expenditure to test whether winning an intergroup encounter is associated with greater benefits, and losing with greater costs. We also test an alternative perspective, where groups fight for access to large food sources that are neither depletable nor consistently monopolizable: in this case, a...

The Household Context of In Situ Conservation in a Center of Crop Diversity in Oaxaca, Mexico

Daniela Soleri, Flavio Aragón Cuevas, Humberto Castro García, David Cleveland & Steven Smith
Crop diversity conservation in situ is an ecosystem service with benefits at household, community, and global scales. These include risk reduction and adaptation to changing physical and sociocultural environments—both important given the accelerating changes in climate, human migration, and the industrialization of agriculture. In situ conservation typically occurs as part of small-scale, traditionally based agriculture and can support cultural identity and values. Although decisions regarding crop diversity occur at the household level, few data detail...

An Infrasound Array Study of Mount St. Helens

Robin S. Matoza & Alexandra Iezzi
The ongoing activity of Mount St. Helens provides an opportunity to study the infrasonic wavefield produced by an active, silica-rich volcano. In late October 2004, as a pilot experiment for the Acoustic Surveillance for Hazardous Eruptions (ASHE) project, we deployed two infrasound arrays, each co-located with a broadband seismometer and weather station, to continuously record seismo-acoustic signals from Mount St. Helens. The nearest array, Coldwater, was deployed on the northern flank of the volcano, ∼13...

Sexual signals persist over deep time: ancient co-option of bioluminescence for courtship displays in cypridinid ostracods

Emily Ellis, Jessica Goodheart, Nicholai Hensley, Vanessa González, Nicholas Reda, Trevor Rivers, James Morin, Elizabeth Torres, Gretchen Gerrish & Todd Oakley
Although the diversity, beauty, and intricacy of sexually selected courtship displays command the attention of evolutionists, the longevity of these traits in deep time is poorly understood. Population-based theory suggests sexual selection could either lower or raise extinction risk, resulting in high or low persistence of lineages with sexually selected traits. Furthermore, empirical studies that directly estimate longevity of sexually selected traits are uncommon. Sexually selected signals - including bioluminescent courtship - originated multiple times...

Additional file 1 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 1: Figure S1. Venn diagram of gene lists linked to type 2 diabetes by different types of evidence. Figure S2. Heterozygosity inferred by comparing the paternal and maternal scaffolded contigs, shown on the paternal scaffolds. Figure S3. Length distributions of structural variants. Figure S4. Functional classification of duplicated genes. Figure S5. Sequence alignment of Nile rat Gckr proteins to 113 mammalian orthologs. Figure S6. Missing Nile rat Hadh gene present in alternate haplotype...

Healthy beverage initiatives: A case study of scenarios for optimizing their environmental benefits on a university campus

David Arthur Cleveland, Kyle Meisterling, Jacklyn Vo, Kelly Ann Garvey, Hallie E. Brown & Marie T. Tumbleson
The association between consumption of sugar sweetened beverages (SSBs) and diseases including diabetes, liver disease and dental disease is well known, yet SSBs continue to be aggressively promoted, including on university campuses. Healthy beverage initiatives (HBIs) are focused on improving health by decreasing consumption of SSBs. Some HBIs also aim to improve environmental sustainability, e.g. by substituting tap water for SSBs, including the HBI on the 10 campuses of the University of California. However, there...

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Abstract Background The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic. Results We report a 2.5 Gb, chromosome-level reference genome assembly with...

Additional file 1 of Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing

Shuting Lin, Soojin Yi & Peng Qiu
Additional file 1. Multi-cancer CpG-exon correlations. This file contains 36,470 CpG-exon correlations across all the cancer types, for CpG-exon pairs that show significant correlations in more than one cancer type.

Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing

Shuting Lin, Soojin Yi & Peng Qiu
Abstract The effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with...

2003 Piru Fire Historical Imagery

Shane Dewees, Carla D'Antonio & Nicole Molinari
The increased occurrences of drought and fire may be contributing to the loss of biodiverse ecosystems in Mediterranean regions. Specifically, the conversion of diverse native shrublands, such as chaparral, to non-native annual grassland by fire is of great conservation concern in California. To avoid or slow the loss of chaparral, it is important to understand the underlying causes of landscape conversion. Studies investigating the interaction of multiple potential drivers are particularly crucial to identification of...

Coincidencias y no coincidencias. Octavio Paz, Efraín Huerta y José Revueltas en Mérida

Sarah Poot Herrera
pp. 38-46.

Established and potentially invasive fish of the Laurentian Great Lakes

Christopher Jerde, Andrew Mahon & Erin Grey
Environmental DNA (eDNA) metabarcoding has shown promise as a tool for estimating biodiversity and early detection of invasive species. In aquatic systems, advantages of this method include the ability to concurrently monitor biodiversity and detect incipient invasions simply through the collection and analysis of water samples. However, depending on the molecular markers chosen for a given study, reference libraries containing target sequences from present species may limit the usefulness of eDNA metabarcoding. To explore the...

Climatology of Sundowner Winds in Coastal Santa Barbara, California, Based on 30 yr High Resolution WRF Downscaling

Charles Jones, Leila M.V. Carvalho, Gert-Jan Duine & Katelyn Zigner
Weather Research and Forecasting (WRF) model version 4.0.1 was used to produce a 32 yr high-resolution (1km horizontal grid spacing and hourly resolution) downscaling climatology over Santa Barbara County. Data in this repository contain surface meteorological variables from WRF downscaling simulations during a series of Sundowner wind events. The list of events is: -- Painted Cave Fire 1990: 26-June, 27-June, 28-June-- Tea Fire 2008: 13-November, 14-November-- 2004: 24-April, 27-April, 28-April, 2-May, 3-May-- Jesusita Fire 2009:...

Dynamics of active liquid interfaces

Raymond Adkins, Itamar Kolvin, Zhihong You, Sven Witthaus, M. Cristina Marchetti & Zvonimir Dogic
Controlling interfaces of phase separating fluid mixtures is key to creating diverse functional soft materials. Traditionally, this is accomplished with surface-modifying agents. Using a combination of experiment and theory, we study how mechanical activity shapes soft interfaces of a phase separating mixture of an active and a passive fluid. Chaotic flows in the active fluid give rise to giant interfacial fluctuations and non-inertial propagating active waves. At high activities, stresses disrupt interface continuity and drive...

Optimal Green Infrastructure: Reducing Stormwater Pollution in Maunalua Bay, O'ahu, Hawai'i

Kristin Gill, Elmera Azadpour, Genevieve Chiong, Lauren Skube & Catherine Takata
High runoff from urban areas has negative impacts on receiving water bodies. In Hawai'i, this problem is exacerbated by the natural landscape, which rapidly changes from steep ridges to low-lying valleys nearshore. Maunalua Bay, a region located on the southeastern coast of O‘ahu, has been declared an impaired water body by the Hawai‘i Department of Health due to high levels of nutrients and pollutants. Nine highly urbanized watersheds feed into Maunalua Bay, and runoff during...

Estimating Mountain Lion Habitat Connectivity to Guide Wildlife Conservation at The Nature Conservancy’s Jack and Laura Dangermond Preserve; University of California Santa Barbara; 2021-2022.

Nikole Vannest & Grace Kumaishi
This submission is from a master's group thesis project at The Bren School of Environmental Science & Management at the University of California, Santa Barbara, and contains the final written report and associated datasets. The graduate student researchers who completed this project include: Meghan Fletcher, Alyssa Kibbe, Grace Kumaishi, Anna Talken, and Nikole Vannest. The California landscape has been fragmented by urban development, infrastructure, and agriculture. Maintaining connectivity between areas of wildlife habitat is important...

Long-term Transverse Imaging of the Hippocampus with Glass Microperiscopes

William Redman, Nora Wolcott, Luca Montelisciani, Gabriel Luna, Tyler Marks, Kevin Sit, Che-Hang Yu, Spencer Smith & Michael Goard
The hippocampus consists of a stereotyped neuronal circuit repeated along the septal-temporal axis. This transverse circuit contains distinct subfields with stereotyped connectivity that support crucial cognitive processes, including episodic and spatial memory. However, comprehensive measurements across the transverse hippocampal circuit in vivo are intractable with existing techniques. Here, we developed an approach for two-photon imaging of the transverse hippocampal plane in awake mice via implanted glass microperiscopes, allowing optical access to the major hippocampal subfields...

Experimental evidence that host species composition alters host-pathogen dynamics in a ranavirus-amphibian assemblage

Paul Snyder, Chloe Ramsay, Carmen Harjoe, Emily Khazan, Cheryl Briggs, Jason Hoverman, Pieter Johnson, Daniel Preston, Jason Rohr & Andrew Blaustein
Losses in biodiversity can alter disease risk through changes in host species composition. Host species vary in pathogen susceptibility and competence. Yet how changes in diversity alter host-pathogen dynamics remains unclear in many systems, particularly with respect to generalist pathogens. Amphibians are experiencing worldwide population declines linked to generalist pathogens, such as ranavirus, and thus represent an ideal group to investigate how host species composition affects disease risk. We conducted experiments where individuals in the...

Additional file 2 of A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

Huishi Toh, Chentao Yang, Giulio Formenti, Kalpana Raja, Lily Yan, Alan Tracey, William Chow, Kerstin Howe, Lucie A. Bergeron, Guojie Zhang, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, John Fogg, Bogdan Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain, Daisuke Kihara, Arang Rhie, Adam M. Phillippy, Scott A. Swanson, Peng Jiang, Dennis O. Clegg, Erich D. Jarvis … & Yury V. Bukhman
Additional file 2: Supplementary Table 1. TOGA status of 18430 ancestral placental mammal genes in muroid rodent genome assemblies. Supplementary Table 2. Positively selected genes and their mutation tolerance in humans according to gnomAD.

Forecasting live fuel moisture of Adenostema fasciculatum and its relationship to regional wildfire dynamics across southern California shrublands

Isaac Park, Kristina Fauss & Max Moritz
In seasonally dry environments, the amount of water held in living plant tissue—live fuel moisture (LFM)—is central to vegetation flammability. LFM-driven changes in wildfire size and frequency are particularly important throughout southern California shrublands, which typically produce intense, rapidly spreading wildfires. However, the relationship between spatiotemporal variation in LFM and resulting long-term regional patterns in wildfire size and frequency within these shrublands is less understood. In this study, we demonstrated a novel method for forecasting...

Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing

Shuting Lin, Soojin Yi & Peng Qiu
Abstract The effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with...

BEDMAP3 - Ice thickness, bed and surface elevation for Antarctica - standardised shapefiles and geopackages

Peter Fretwell, Hamish Pritchard, Alice Fremand, Julien Bodart, A. Aitken, Jonathan Bamber, R.E. Bell, C Bianchi, Robert Bingham, Donald Blankenship, G. Casassa, Ginny Catania, K Christianson, H Conway, Hugh Corr, X. Cui, D Damaske, V. Damn, R. Drews, G. Eagles, O. Eisen, H. Eisermann, F Ferraccioli, Rene Forsberg, S Franke … & A. Zirizzotti
We present here the Bedmap3 ice thickness, bed and surface elevation aggregated points and survey lines. The aggregated points consist of statistically-summarised shapefile points (centred on a continent-wide 500 m x 500 m grid) that reports the average values of Antarctic ice thickness, bed and surface elevation from the full-resolution survey data and information on their distribution. The points presented here correspond to the added points since the last release of Bedmap2. The data comes...

Registration Year

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    98

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