30 Works

Data from: Integrating abundance and diet data to improve inferences of food web dynamics

Jake M. Ferguson, , Brianna H. Witteveen, John B. Hopkins & Briana H. Witteveen
1. Both population abundances and chemical tracers are useful tools for studying consumer-resource interactions. Food web models parameterized with abundances are often used to understand how interactions structure communities and to inform management decisions of complex ecological systems. Unfortunately, collecting abundance data to parameterize these models is often expensive and time-consuming. Another approach is to use chemical tracers to estimate the proportional diets of consumers by relating the tracers in their tissues to those found...

Data from: Two pulses of morphological diversification in Pacific pelagic fishes following the Cretaceous–Palaeogene mass extinction

Elizabeth Sibert, Matthew Friedman, Pincelli Hull, Gene Hunt, Richard Norris & Matt Friedman
Molecular phylogenies suggest some major radiations of open-ocean fish clades occurred roughly coincident with the K/Pg boundary, however the timing and nature of this diversification is poorly constrained. Here we investigate evolutionary patterns in ray-finned fishes across the Cretaceous-Palaeogene (K/Pg) Mass Extinction 66 million years ago (Ma), using microfossils (isolated teeth) preserved in a South Pacific sediment core spanning 72-43 Ma. Our record does not show significant turnover of fish tooth morphotypes at the K/Pg...

Data from: Extinction risk in extant marine species integrating paleontological and biodistributional data

Katie S. Collins, Stewart M. Edie, Gene Hunt, Kaustuv Roy & David Jablonski
Extinction risk assessments of marine invertebrate species remain scarce, which hinders effective management of marine biodiversity in the face of anthropogenic impacts. In order to close this information gap, we developed a metric of relative extinction risk that combines paleontological data, in the form of extinction rates calculated from the fossil record, with two known correlates of risk in the modern day: geographic range size and realized thermal niche. We test the performance of this...

Data from: Human-like Cmah inactivation in mice increases running endurance and decreases muscle fatigability: implications for human evolution

Jonathan Okerblom, William Fletes, Hemal H. Patel, Simon Schenk, Ajit Varki & Ellen C. Breen
Compared to other primates, humans are exceptional long-distance runners, a feature that emerged in genus Homo ~2 million years ago (mya) and is classically attributed to anatomical and physiological adaptations such as an enlarged gluteus maximus and improved heat dissipation. However, no underlying genetic changes have currently been defined. Two-three mya, an exon deletion in the CMP-Neu5Ac Hydroxylase (CMAH) gene also became fixed in our ancestral lineage. Cmah loss in mice exacerbates disease severity in...

Training and Support for Student Library Employees in a Tiered Reference Service Model: Supporting Materials

Brian Quigley, Jeffery Loo, Lisa Ngo, Susan Powell, Samantha Teplitzky, Anna Sackmann & Kortney Rupp
To cultivate students’ reference skills, the Engineering and Physical Sciences Division of the UC Berkeley Library developed an active training program based upon a dynamic online reference manual continuously improved with student feedback. We evaluate the effectiveness of our training program and share procedures and tools for enhancing student training. Students were given a pre-test of reference skills and self-efficacy prior to attending an annual training session. One month afterwards, we distributed a post-test and...

Supporting Information: Toward learned chemical perception of force field typing rules

Camila Zanette, Caitlin C. Bannan, Christopher I. Bayly, Josh Fass, Michael K. Gilson, Michael R. Shirts, John D. Chodera & David L. Mobley
The Open Force Field Initiative seeks to to automate force field development in order to advance force fields and improve accuracy (openforcefield.org). An important part of this effort includes automating the determination of chemical perception --- that is, the way force field parameters are assigned to a molecule based on chemical environment. We developed a novel technology for this purpose, termed SMARTY. It generalizes atom typing by using direct chemical perception with SMARTS strings adopting...

Data from: Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

Benjamin E. R. Rubin, Jon G. Sanders, Kyle M. Turner, Naomi E. Pierce & Sarah D. Kocher
Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between...

Data from: Acid secretion by the boring organ of the burrowing giant clam, Tridacna crocea

Richard W. Hill, Eric J. Armstrong, Kazuo Inaba, Masaya Morita, Martin Tresguerres, Jonathon H. Stillman, Jinae N. Roa & Garfield T. Kwan
The giant clam Tridacna crocea, native to Indo-Pacific coral reefs, is noted for its unique ability to bore fully into coral rock and is a major agent of reef bioerosion. However, T. crocea’s mechanism of boring has remained a mystery despite decades of research. By exploiting a new, two-dimensional pH-sensing technology and manipulating clams to press their presumptive boring tissue (the pedal mantle) against pH-sensing foils, we show that this tissue lowers the pH of...

Data from: Rapid evolution of thermal plasticity in mountain lake Daphnia populations

Hamanda B. Cavalheri, Celia C. Symons, Marika Schulhof, Natalie T. Jones & Jonathan B. Shurin
Populations at risk of extinction due to climate change may be rescued by adaptive evolution or plasticity. Selective agents, such as introduced predators, may enhance or constrain plastic or adaptive responses to temperature. We tested responses of Daphnia to temperature by collecting populations from lakes across an elevational gradient in the presence and absence of fish predators (long-term selection). We subsequently grew these populations at two elevations in field mesocosms over two years (short-term selection),...

Data from: A phylogenomic resolution of the sea urchin tree of life

Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E.G. Briggs, Rich Mooi & Greg W. Rouse
Background: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a...

Data from: Underlying mechanisms and ecological context of variation in exploratory behavior of the Argentine ant, Linepithema humile

Hannah Page, Andrew Sweeney, Anna Pilko & Noa Pinter-Wollman
Uncovering how and why animals explore their environment is fundamental for understanding population dynamics, the spread of invasive species, species interactions, etc. In social animals, individuals within a group can vary in their exploratory behavior, and the behavioral composition of the group can determine its collective success. Workers of the invasive Argentine ant (Linepithema humile) exhibit individual variation in exploratory behavior, which affects the colony’s collective nest selection behavior. Here, we examine the mechanisms underlying...

Data from: Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host

Aaron Hartmann, Kristen Marhaver, Anke Klueter, Michael Lovci, Collin Closek, Erika Diaz Almeyda, Valerie Chamberland, Frederick Archer, Dimitri Deheyn, Mark Vermeij & Monica Medina
Theory suggests that the direct transmission of endosymbionts from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile’s ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae)...

Data from: Evolution of the exclusively human-pathogen Neisseria gonorrhoeae: human-specific engagement of immunoregulatory Siglecs

Corinna S. Landig, Ashley Hazel, Benjamin P. Kellman, Jerry J. Fong, Flavio Schwarz, Sarika Agarwal, Nissi Varki, Paola Massari, Nathan E. Lewis, Sanjay Ram & Ajit Varki
Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhea exclusively in humans and uses multiple strategies to infect, including acquisition of host sialic acids that cap and mask lipooligosaccharide termini, while restricting complement activation. We hypothesized that gonococci selectively target human anti-inflammatory sialic acid-recognizing Siglec receptors on innate immune cells to blunt host responses, and that pro-inflammatory Siglecs and SIGLEC pseudogene polymorphisms represent host evolutionary adaptions to counteract this interaction. N. gonorrhoeae can indeed engage multiple...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

Data from: Simultaneous radiation of bird and mammal lice following the K-Pg boundary

Kevin P. Johnson, Nam-Phuong Nguyen, Andrew D. Sweet, Bret M. Boyd, Tandy Warnow & Julie M. Allen
The diversification of parasite groups often occurs at the same time as the diversification of their hosts. However, most studies demonstrating this concordance only examine single host-parasite groups. Multiple diverse lineages of ectoparasitic lice occur across both birds and mammals. Here we describe the evolutionary history of lice based on analyses of 1,107 single copy orthologous genes from sequenced genomes of 46 species of lice. We identify three major diverse groups of lice: one exclusively...

Contract design thinking: a service oriented architecture SOA for contract models, maintenance and testing

Christopher Felker & Sue Ahl
Contract variances complicate academic medical center accounts receivables because they are one driver of ambiguity when calculating future free cash flows FFCF [1]. UC Health provides leadership and strategic direction for UC’s five academic medical centers and 18 health professional schools. Contract variations within 1 (one) medical center has a multiplier effect in the consolidated annual financial reporting. In December 2017 we created an internal project charter [2] to consolidate contracts financial accounts receivables activity...

Revenue design thinking: constructing an accelerated cash /phased write down story

Christopher Felker
A well-designed data story is a launch point for revenue cycle professionals using analytics to manage accounts receivable according to portfolio principles. In the last 100 (one hundred) days before the close of a fiscal year, holding accounts receivables too long poses an inordinate risk on the perceived value of UCSD Health's trial balance inventory. In April 2018, we started to design a Tableau dashboard that would more accurately forecast two things First Future free...

Data from: Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa

Lin Li, Xiaodong Jiao, Ilaria D’Atri, Fumihito Ono, Ralph Nelson, Chi-Chao Chan, Naoki Nakaya, Zhiwei Ma, Yan Ma, Xiaoying Cai, Longhua Zhang, Siying Lin, Abdul Hameed, Barry A. Chioza, Holly Hardy, Gavin Arno, Sarah Hull, Muhammad Imran Khan, James Fasham, V. Gaurav Harlalka, Michel Michaelides, Anthony T. Moore, Zeynep Hande Coban Akdemir, Shalini Jhangiani, James R. Lupski … & Frans P. M. Cremers
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post...

Revenue design thinking: implementing enterprise tableau reporting at UC San Diego Health

Christopher Felker, Sue Ahl & Tiffany Kavanaugh
In February 2018, the authors agreed to participate in an Enterprise Tableau implementation. There were 17 (seventeen) pilot projects identified at UCSD Health. This data pertains to 2 (two) agile data analytics projects Atlas of sustainable operations indicators Contracts maintenance co operative strategy with other UC medical centers The authors committed to becoming certified users of Tableau software ('superusers') capable of assisting in a broader use of data analytics in ongoing business and clinical operations....

Data design thinking: data cleaning improvements using tableau prep

Christopher Felker
Tableau Prep automatically shows errors and outliers in data and employs fuzzy clustering to help you with the common, repetitive tasks like fixing spellings errors or reconciling entities across data sources. Project Maestro shares the same calc language and governance structure as the rest of Tableau, so you can get started easily. And with a streamlined sharing experience to Tableau Desktop, Tableau Server and Tableau Online, a user can experience data prep and analysis in...

Data from: Gain-of-function experiments in bacteriophage lambda uncover residues under diversifying selection in nature

Rohan Maddamsetti, Daniel T. Johnson, Stephanie J. Spielman, Katherine L. Petrie, Debora S. Marks & Justin R. Meyer
Viral gain-of-function mutations frequently evolve during laboratory experiments. Whether the specific mutations that evolve in the lab also evolve in nature and whether they have the same impact on evolution in the real world is unknown. We studied a model virus, bacteriophage λ, that repeatedly evolves to exploit a new host receptor under typical laboratory conditions. Here we demonstrate that two residues of λ’s J protein are required for the new function. In natural λ...

Data from: To grunt or not to grunt: factors governing call production in female olive baboons, Papio anubis

Joan B. Silk, Eila R. Roberts, Veronika Staedele, Shirley C. Strum & Veronika Städele
Vocal signals often play an important role in synchronizing the activities of group members, coordinating decisions about when and where to travel, and facilitating social interactions in which there are potential conflicts of interest. In chacma baboons, Papio ursinus, low amplitude grunts facilitate nonaggressive social interactions and reconcile conflicts. Grunts seem to function as signals of benign intent and reduce uncertainty about the signaler's subsequent behavior. Here, we replicate and extend these findings in another...

Data from: Before platelets: the production of platelet activating factor during growth and stress in a basal marine organism

Ines Galtier D’Auriac, Robert A. Quinn, Heather Maughan, Louis-Felix Nothias, Mark Little, Clifford A. Kapono, Ana Cobian Guemes, Brandon T. Reyes, Kevin Green, Steven D. Quistad, Matthieu Leray, Jennifer E. Smith, Pieter C. Dorrestein, Forest Rohwer, Dimitri D. Deheyn, Aaron C. Hartmann, Ana Cobian & Ines Galtier D'Auriac
Corals and humans represent two extremely disparate metazoan lineages and are therefore useful for comparative evolutionary studies. Two lipid-based molecules that are central to human immunity, platelet activating factor (PAF) and Lyso-PAF were recently identified in scleractinian corals. To identify processes in corals that involve these molecules, PAF and Lyso-PAF biosynthesis was quantified in conditions known to stimulate PAF production in mammals (tissue growth and exposure to elevated levels of ultraviolet light) and in conditions...

Data from: Social interactions shape individual and collective personality in social spiders

Edmund R. Hunt, Brian Mi, Camila Fernandez, Brandyn M. Wong, Jonathan N. Pruitt & Noa Pinter-Wollman
The behavioural composition of a group and the dynamics of social interactions can both influence how social animals work collectively. For example, individuals exhibiting certain behavioural tendencies may have a disproportionately large impact on the group, and so are referred to as keystone individuals, while interactions between individuals can facilitate information transmission about resources. Despite the potential impact of both behavioural composition and interactions on collective behaviour, the relationship between consistent behaviours, also known as...

Data from: Revisiting protein aggregation as pathogenic in sporadic Parkinson’s and Alzheimer’s diseases

Alberto J. Espay, Joaquin A. Vizcarra, Luca Marsili, Anthony E. Lang, David K. Simon, Aristide Merola, Keith A. Josephs, Alfonso Fasano, Francesca Morgante, Rodolfo Savica, J. Timothy Greenamyre, Franca Cambi, Tritia R. Yamasaki, Caroline M. Tanner, Ziv Gan-Or, Irene Litvan, Ignacio F. Mata, Cyrus P. Zabetian, Patrik Brundin, Hubert H. Fernandez, David G. Standaert, Marcelo A. Kauffman, Michael A. Schwarzschild, S. Pablo Sardi, Todd Sherer … & James B. Leverenz
The gold standard for a definitive diagnosis of Parkinson’s disease (PD) is the pathologic finding of aggregated alpha-synuclein into Lewy bodies and for Alzheimer’s disease (AD) aggregated amyloid into plaques and hyperphosphorylated tau into tangles. Implicit in this clinico-pathologic-based nosology is the assumption that pathological protein aggregation at autopsy reflect pathogenesis at disease onset. While these aggregates may in exceptional cases be on a causal pathway in humans (e.g., aggregated alpha-synuclein in SNCA gene multiplication...

Registration Year

  • 2018

Resource Types

  • Dataset


  • University of California, San Diego
  • Smithsonian Institution
  • Yale University
  • University of Minnesota
  • University of Pittsburgh
  • University of California, Berkeley
  • University of Kentucky
  • University of Toronto
  • University of British Columbia
  • Harvard University