22 Works

Source Data for Crowdsourcing Bridge Dynamic Monitoring with Smartphone Vehicle Trips

Thomas Matarazzo, Daniel Kondor, Sebastiano Milardo, Soheil Eshkevari, Paolo Santi, Shamim Pakzad, Markus Buehler & Carlo Ratti
This data accompanies the study "Crowdsourcing Bridge Dynamic Monitoring with Smartphone Vehicle Trips" published in (Nature) Communications Engineering. This paper focuses on using large and inexpsensive datasets for obtaining information on the dynamics of bridges. In this study, data is collected by smartphones in moving vehicles as the cross over a bridge, in three distinct applications. Smartphone data was collected in controlled field experiments and uncontrolled Uber rides on a long-span suspension bridge in the...

Additional file 1 of Chimeric forecasting: combining probabilistic predictions from computational models and human judgment

Thomas McAndrew, Allison Codi, Juan Cambeiro, Tamay Besiroglu, David Braun, Eva Chen, Luis Enrique Urtubey De Cèsaris & Damon Luk
Additional file 1. A. Questions and Resolution Criteria. B. Forecasting platforms. C. List of included computational models form the COVID-19 Forecast Hub. D. Paired difference in WIS between a performance based and equally weighted ensemble across surveys. E. Counts of computational and human judgement models that submitted before the COVID-19 Forecast Hub deadlines.

Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

Annette Govindarajan, Luke McCartin, Allan Adams, Elizabeth Allan, Abhimanyu Belani, Rene Francolini, Justin Fujii, Daniel Gomez-Ibanez, Amy Kukulya, Frederick Marin, Kaitlyn Tradd, Dana Yoerger, Jill McDermott & Santiago Herrera
Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large – volume eDNA sampler with in situ filtration, capable of taking up...

Additional file 3 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 3

Additional file 4 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 4

Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Abstract Background Aggression is observed across the animal kingdom, and benefits animals in a number of ways to increase fitness and promote survival. While aggressive behaviors vary widely across populations and can evolve as an adaptation to a particular environment, the complexity of aggressive behaviors presents a challenge to studying the evolution of aggression. The Mexican tetra, Astyanax mexicanus exists as an aggressive river-dwelling surface form and multiple populations of a blind cave form, some...

Additional file 5 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 5

All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed Synaptotagmin-SNARE-complexin complex

Josep Rizo, Levent Sari, Yifei Qi, Wonpil Im & Milo Lin
Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca2+-binding to Syt1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to Syt1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally. To shed light into these questions, we performed all-atom molecular dynamics...

Novel husbandry practices result in rapid rates of growth and sexual maturation without impacting adult behavior in the blind Mexican cavefish

Robert Kozol, Anders Yuiska, John Han, Bernadeth Tolentino, Arthur Lapatto, Peter Lewis, Alexandra Paz, Alex Keene, Johanna Kowalko & Erik Duboue
The development of animal model systems is dependent on the standardization of husbandry protocols that increase fecundity and reduce generation time. The blind Mexican tetra, Astyanax mexicanus, is an emerging genetic vertebrate model for evolution and biomedical research. Surface and cave populations of A. mexicanus have independently evolved, providing a model system for studying the genetic basis of divergent biological traits. While a rapid increase in the use of A. mexicanus has led to the...

Additional file 1 of Chimeric forecasting: combining probabilistic predictions from computational models and human judgment

Thomas McAndrew, Allison Codi, Juan Cambeiro, Tamay Besiroglu, David Braun, Eva Chen, Luis Enrique Urtubey De Cèsaris & Damon Luk
Additional file 1. A. Questions and Resolution Criteria. B. Forecasting platforms. C. List of included computational models form the COVID-19 Forecast Hub. D. Paired difference in WIS between a performance based and equally weighted ensemble across surveys. E. Counts of computational and human judgement models that submitted before the COVID-19 Forecast Hub deadlines.

Additional file 6 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 6

Additional file 1 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 1

Additional file 1 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 1

Additional file 2 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 2

Additional file 3 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 3

Chimeric forecasting: combining probabilistic predictions from computational models and human judgment

Thomas McAndrew, Allison Codi, Juan Cambeiro, Tamay Besiroglu, David Braun, Eva Chen, Luis Enrique Urtubey De Cèsaris & Damon Luk
Abstract Forecasts of the trajectory of an infectious agent can help guide public health decision making. A traditional approach to forecasting fits a computational model to structured data and generates a predictive distribution. However, human judgment has access to the same data as computational models plus experience, intuition, and subjective data. We propose a chimeric ensemble—a combination of computational and human judgment forecasts—as a novel approach to predicting the trajectory of an infectious agent. Each...

Additional file 6 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 6

Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Abstract Background Aggression is observed across the animal kingdom, and benefits animals in a number of ways to increase fitness and promote survival. While aggressive behaviors vary widely across populations and can evolve as an adaptation to a particular environment, the complexity of aggressive behaviors presents a challenge to studying the evolution of aggression. The Mexican tetra, Astyanax mexicanus exists as an aggressive river-dwelling surface form and multiple populations of a blind cave form, some...

Additional file 2 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 2

Additional file 4 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 4

Additional file 5 of Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Roberto Rodriguez-Morales, Paola Gonzalez-Lerma, Anders Yuiska, Ji Heon Han, Yolanda Guerra, Lina Crisostomo, Alex C. Keene, Erik R. Duboue & Johanna E. Kowalko
Supplementary Material 5

Chimeric forecasting: combining probabilistic predictions from computational models and human judgment

Thomas McAndrew, Allison Codi, Juan Cambeiro, Tamay Besiroglu, David Braun, Eva Chen, Luis Enrique Urtubey De Cèsaris & Damon Luk
Abstract Forecasts of the trajectory of an infectious agent can help guide public health decision making. A traditional approach to forecasting fits a computational model to structured data and generates a predictive distribution. However, human judgment has access to the same data as computational models plus experience, intuition, and subjective data. We propose a chimeric ensemble—a combination of computational and human judgment forecasts—as a novel approach to predicting the trajectory of an infectious agent. Each...

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