13 Works

Dataset used in the article: Evaluation of goal recognition systems on unreliable data and uninspectable agents

Pavan Kantharaju, Irina Rabkina, Jason Wilson, Mark Roberts & Laura Hiatt
Goal or intent recognition, where one agent recognizes the goals or intentions of another, can be a powerful tool for effective teamwork and improving interaction between agents. Such reasoning can be challenging to perform, however, because observations of an agent can be unreliable and, often, an agent does not have access to the reasoning processes and mental models of the other agent. Despite this difficulty, recent work has made great strides in addressing these challenges....

Additional file 2 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 2: Table S1. Equipment sourcing and alternatives. Table S2. Sample information. Table S3. Culturing information. Table S4. Cost estimates.

Additional file 3 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 3. Isolate taxonomic information, genome assembly statistics, and other metadata.

Additional file 4 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 4. Review History.

Additional file 1 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 1: Figure S1. Alluvial plot of protocol efficiency. Figure S2. Relationship between assembly quality and library concentration. Figure S3. Intraspecific nucleotide diversity. Figure S4. Genomic dissimilarity within 16S haplotypes.

Additional file 2 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 2: Table S1. Equipment sourcing and alternatives. Table S2. Sample information. Table S3. Culturing information. Table S4. Cost estimates.

Litter decomposition rates across tropical montane and lowland forests are controlled foremost by climate

Rebecca Ostertag, Carla Restrepo, Iveren Abeim, Roxana Aragón, Michelle Ataroff, Hazel Chapman, Belen Fadrique, Grizelle González, Achim Häger, Jürgen Homeier, Luis Daniel Llambí, Rikke Reese Næsborg, Laura Nohemy Poma López, Jorge Andrés Ramirez Correa, Klara Scharnagl, Conrado Tobón, James W. Dalling, Patrick H. Martin, Iveren Abiem, Shin‐Ichiro Aiba, Esteban Alvarez‐Dávila, Augusta Y. Cueva‐Agila, Romina D. Fernández, Sybil G. Gotsch, Carlos Iñiguez‐Armijos … & Cameron B. Williams
The “hierarchy of factors” hypothesis states that decomposition rates are controlled primarily by climatic, followed by biological and soil variables. Tropical montane forests (TMF) are globally important ecosystems, yet there have been limited efforts to provide a biome-scale characterization of litter decomposition. We designed a common litter decomposition experiment replicated in 23 tropical montane sites across the Americas, Asia, and Africa and combined these results with a previous study of 23 sites in tropical lowland...

A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Abstract Earth’s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify...

Additional file 4 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 4. Review History.

A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Abstract Earth’s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify...

Heat shock protein gene expression varies among tissues and populations in free living birds

Mary J. Woodruff, Cedric Zimmer, Daniel R. Ardia, Maren N. Vitousek & Kimberly A. Rosvall
Climate change is dramatically altering our planet, yet our understanding of mechanisms of thermal tolerance is limited in wild birds. We characterized natural variation in heat shock protein (HSP) gene expression among tissues and populations of free-living Tree Swallows (Tachycineta bicolor). We focused on HSPs because they prevent cellular damage and promote recovery from heat stress. We used quantitative PCR to measure gene expression of three HSPs, including those in the HSP70 and HSP90 families...

Additional file 1 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 1: Figure S1. Alluvial plot of protocol efficiency. Figure S2. Relationship between assembly quality and library concentration. Figure S3. Intraspecific nucleotide diversity. Figure S4. Genomic dissimilarity within 16S haplotypes.

Additional file 3 of A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn & Andrew H. Moeller
Additional file 3. Isolate taxonomic information, genome assembly statistics, and other metadata.

Registration Year

  • 2022
    13

Resource Types

  • Text
    6
  • Dataset
    5
  • Collection
    2

Affiliations

  • Franklin & Marshall College
    13
  • Cornell University
    11
  • University of Pennsylvania
    10
  • Washington University in St. Louis
    10
  • Lukuru Foundation
    10
  • Emory University
    10
  • University of Montpellier
    10
  • Sorbonne Paris Cité
    1
  • University of Jos
    1
  • University of California, Berkeley
    1