12 Works

Stochastic Persistence in Nucleated Polymerization Model

Suzanne Sindi & Jason Dark
The code in this repository was created by Dr. Jason K. Dark in completing his PhD at the University of California, Merced. The stochastic model of prion persistence is detailed in Chapter 3 of his Dissertation which is available at the following link: https://escholarship.org/uc/item/8tq2w26b Questions should be emailed to: Prof Suzanne Sindi (ssindi@ucmerced.edu)

Data from: High-severity wildfire leads to multi-decadal impacts on soil biogeochemistry in mixed-conifer forests

Nicholas Dove & Stephen Hart
During the past century, systematic wildfire suppression has decreased fire frequency and increased fire severity in the western United States of America. While this has resulted in large ecological changes aboveground such as altered tree species composition and increased forest density, little is known about the long-term, belowground implications of altered, ecologically novel fire regimes, especially on soil biological processes. To better understand the long-term implications of ecologically novel, high-severity fire, we used a 44-y...

Supplemental material for Climate forcing by battered-and-breaded fillets and crab-flavored sticks from Alaska pollock

Brandi McKuin, Jordan Watson, Alan Haynie & J. Elliott Campbell
Detailed supplemental datasets: inputs and output information and emission factors for ingredients, non-ingredient materials, and embodied energy of pollock products.

Data from: Using a multi-isotope approach to inform waterfowl movement in southern Africa

Gregory Mutumi, Graeme Cumming, Alexandre Caron, Mažeika Sullivan & Carlos Caceres
Many far-ranging species depend heavily on relatively small or temporary resources within a heterogeneous landscape. For waterfowl, most species rely on deep, permanent waterbodies as refugia from predators during annual flightless molt periods when synchronous loss and regrowth of the flight feathers occurs. The movements of ducks to and from molt sites are, however, poorly documented for most Afrotropical species and the dependencies of Afrotropical ducks on key sites are unclear, yet this information is...

Large dataset of disambiguated publication profiles for studying researcher mobility

Alexander Petersen
Researcher mobility facilitates the exchange of scientific, institutional, and cultural knowledge. Yet whether globalization and advances in virtual communication technologies have altered the impact of researcher mobility is a relevant and open question. To this end, we developed and leveraged a large and internationally broad disambiguated dataset of researchers in physics over the period 1985-2009; we used the article-level metadata contained in the American Physical Society "Article and Citations dataset" as the starting point. After...

Assessing the impact of product inhibition in a chromogenic assay

Michael Stobb, Karin Leiderman, Suzanne Sindi & Dougald Monroe
Chromogenic substrates (CS) are synthetic substrates used to monitor the activity of a target enzyme. It has been reported that some CSs display competitive product inhibition with their target enzyme. Thus, in assays where enzyme activity is continuously monitored over long periods of time, the product inhibition may significantly interfere with the reactions being monitored. Despite this knowledge, it is rare for CSs to be directly incorporated into mathematical models that simulate these assays. This...

Growth rate assays reveal fitness consequences of β-lactamases

Fabian Santiago, Evin Doscher, Jay Kim, Manel Camps, Juan Meza, Suzanne Sindi & Miriam Barlow
Clinical resistance determination is critical for monitoring the spread of antibiotic resistance. However, clinical methods of detecting resistance lack the sensitivity necessary to make strong conclusions about fitness. Growth rates are a far more sensitive method of measuring resistance, but they differ from clinical methods in that a single concentration of antibiotic is used for the assay. Here we show that in spite of this key difference, the results of growth rates correlate well with...

Remineralizing Enamel : A Literature Review

Carolina Karuppiah
Background: Tooth enamel is a non-living tissue, once matured it can no longer remineralization itself. Unfortunately, there are only a few studies that analyze the risks and benefits in applications towards remineralization. The objective was to examine the effectiveness and risks of synthetic applications towards remineralizing tooth enamel. Methods: Experimental trials focusing on the effect of synthetic applications on tooth enamel such as, surface hardness, surface thickness and overall effectiveness were included in this review....

Juxtaposition of climate change contrarians and scientists in the media using Media Cloud data

Alexander Petersen
We document the media visibility and climate change research achievements of two groups of individuals representing some of the most prominent figures in their respective domains: 386 climate change contrarians (CCC) juxtaposed with 386 expert climate change scientists (CCS). These data were collected from the Media Cloud project (MC), an open data project hosted by the MIT Center for Civic Media and the Berkman Klein Center for Internet & Society at Harvard University. Enclosed are...

A mathematical model of flow-mediated coagulation identifies factor V as a modifier of thrombin generation in hemophilia A

Michael Stobb, Kathryn Link, Matthew Sorrells, Maria Bortot, Katherine Ruegg, Marilyn Manco-Johnson, Jorge DiPaola, Suzanne Sindi, Aaron Fogelson, Karin Leiderman & Keith Neeves
Hemophilia A is a bleeding disorder categorized as severe, mild, and moderate deficiencies in factor VIII (FVIII). Within these categories the variance in bleeding severity is significant and the origins unknown. The number of parameters that could modify bleeding are so numerous that experimental approaches are not feasible for considering all possible combinations. Consequently, we turn to a mathematical model of coagulation under flow to act as a screening tool to identify parameters that are...

Data from: Evidence for adaptive responses to historic drought across a native plant species range

Erin E. Dickman, Lillie K. Pennington, Steven J. Franks & Jason P. Sexton
As climatic conditions change, species will be forced to move or adapt to avoid extinction. Exacerbated by ongoing climate change, California recently experienced a severe and exceptional drought from 2011-2017. To investigate whether an adaptive response occurred during this event, we conducted a “resurrection” study of the cutleaf monkeyflower (Mimulus laciniatus), an annual plant, by comparing trait means and variances of ancestral seed collections ("pre-drought") with contemporary descendant collections ("drought"). Plants were grown under common...

Saturated Hydraulic Conductivity Pedotransfer Models

Samuel N. Araya & Teamrat A. Ghezzehei
This repository contains machine learning-based pedotransfer models that predict saturated hydraulic conductivity (Ks). An app with a graphical user interface to run these models and other relevant materials including R codes used to build and test the models are available at the author's GitHub repository: https://github.com/saraya209/soil_ksat. Detailed description of this work is available in our paper published in the Journal of Water Resources Research: Araya and Ghezzehei (2019).

Registration Year

  • 2019

Resource Types

  • Dataset


  • University of California, Merced
  • University of California, Santa Cruz
  • Colorado School of Mines
  • The Ohio State University
  • University of North Carolina
  • Alaska Fisheries Science Center
  • ARC Centre of Excellence For Coral Reef Studies
  • University of Colorado Denver
  • University of Colorado Boulder
  • National Marine Fisheries Service