891 Works

Data for the article \"The lack of avoidance of total dissolved gas supersaturation in juvenile rainbow trout\"

Naomi K. Pleizier, Beatrice Rost-Komiya, Steven J. Cooke & Colin J. Brauner
We investigated whether individual rainbow trout (Oncorhynchus mykiss; 9-53g) avoid a potentially lethal level of total dissolve gas (TDG) supersaturation using lateral movements during an acute exposure. As there is no mechanism by which fish can detect and avoid TDG supersaturation in shallow water, we hypothesize that rainbow trout do not directly detect TDG supersaturation. Most previous studies have tested TDG avoidance in groups of fish, which may confound responses because many fishes, such as...

BC Seed Trials and CANOVI Replicated Corno di Toro Pepper Variety Trials 2018-2019

Alexandra Lyon & Chris Thoreau
This dataset comprises data from 2 years of replicated corno di toro pepper variety trials carried out at the UBC Farm. Production and quality data were collected as part of a farmer-participatory variety trialing project that sought to identify vegetable varieties with strong performance for both fresh market sales and seed production in British Columbia. Trials used the “mother-baby” design; the UBC Farm served as a "mother" site that conducted replicated trials, and several on-farm...

Data from: Examining the dynamics of Epstein-Barr virus shedding in the tonsils and the impact of HIV-1 coinfection on daily saliva viral loads

Catherine Byrne, Christine Johnston, Jackson Orem, Fred Okuku, Meei-Li Huang, Habibur Rahman, Anna Wald, Lawrence Corey, Joshua Schiffer, Corey Casper, Daniel Coombs & Soren Gantt
<b>Abstract</b><br/><p>Epstein-Barr virus (EBV) is transmitted by saliva and is a major cause of cancer, particularly in people living with HIV/AIDS. Here, we describe the frequency and quantity of EBV detection in the saliva of Ugandan adults with and without HIV-1 infection and use these data to develop a novel mathematical model of EBV infection in the tonsils. Eligible cohort participants were not taking antiviral medications, and those with HIV-1 infection had a CD4 count &gt;200...

CapnoBase Simulation Dataset

Walter Karlen
The simulation dataset was produced with a computer model that simulates the behavior of the human cardio-respiratory system. Producing artificial capnography signals is useful when signals that are otherwise hard to obtain are required, or when the condition or change in state of the patient must to be precisely known.

CapnoBase IEEE TBME Respiratory Rate Benchmark

Walter Karlen
The CapnoBase TBME RR benchmark dataset contains 42 cases of 8-min recordings. In addition to the CO2 waveforms (capnograms), these cases have also the Photoplethysmogram (PPG) from pulse oximetry available. Labels from an expert are available for pulse peaks from PPG and breaths from CO2. Also, the benchmark contains the results from the Karlen et al. IEEE TBME paper on multi-parameter RR calculation. This can be used to directly compare algorithm performances. The benchmark dataset...

Forest management impacts on greenhouse gas fluxes from riparian soils along headwater streams

Teresa Silverthorn & John Richardson
This data supports the 2021 publication "Forest management impacts on greenhouse gas fluxes from riparian soils along headwater streams" in Ecosystems. Abstract: Increasing concentrations of atmospheric greenhouse gases (GHGs; CO2, CH4, N2O) causes climate change. Depending on the conditions, soils have the potential to store carbon or to be a source of GHGs to the atmosphere. Riparian soils in particular have high potential to store carbon, but also to be sources of CH4 and N2O....

“@alex, this fixes #9” : analysis of referencing patterns in Pull Request discussions : [supplementary material]

Ashish Chopra
The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.

MESSENGER orbit activity indices

Lydia Philpott, Catherine Johnson, Brian Anderson & Reka Winslow
MESSENGER orbit activity indices

Application and evaluation of automated semantic annotation of gene expression experiments

French Leon, Lane Suzanne, Law Tamryn, Xu Lydia & Pavlidis Paul
MOTIVATION: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets. RESULTS: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts...

The Impact of Multifunctional Genes on \"Guilt by Association\" Analysis

Gillis Jesse & Pavlidis Paul
Many previous studies have shown that by using variants of "guilt-by-association", gene function predictions can be made with very high statistical confidence. In these studies, it is assumed that the "associations" in the data (e.g., protein interaction partners) of a gene are necessary in establishing "guilt". In this paper we show that multifunctionality, rather than association, is a primary driver of gene function prediction. We first show that knowledge of the degree of multifunctionality alone...

Altered Hippocampal Transcript Profile Accompanies an Age-Related Spatial Memory Deficit in Mice

Verbitsky Miguel, Yonan Amanda L., Malleret Gael, Eric R. Kandel, Gilliam T. Conrad & Pavlidis Paul
We have carried out a global survey of age-related changes in mRNA levels in the C57BL/6NIA mouse hippocampus and found a difference in the hippocampal gene expression profile between 2-month-old young mice and 15-month-old middle-aged mice correlated with an age-related cognitive deficit in hippocampal-based explicit memory formation. Middle-aged mice displayed a mild but specific deficit in spatial memory in the Morris water maze. By using Affymetrix GeneChip microarrays, we found a distinct pattern of age-related...

Using ANOVA for gene selection from microarray studies of the nervous system

Pavlidis Paul
Methods are presented for detecting differential expression using statistical hypothesis testing methods including analysis of variance (ANOVA). Practicalities of experimental design, power, and sample size are discussed. Methods for multiple testing correction and their application are described. Instructions for running typical analyses are given in the R programming environment. R code and the sample data set used to generate the examples are available at http://microarray.cpmc.columbia.edu/pavlidis/pub/aovmethods/.

FTO, obesity and the adolescent brain

Melka Melkaye G., Gillis Jesse, Bernard Manon, Abrahamowicz Michal, Chakravarty M. Maller, Leonard Gabriel T., Perron Michel, Richer Louis, Veillette Suzanne, Banaschewski Tobias, Barker Gareth J., Buchel Christian, Conrod Patricia, Flor Herta, Heinz Andreas, Garavan Hugh, Bruhl Rudiger, Mann Karl, Artiges Eric, Lourdusamy Anbarasu, Lathrop Mark, Loth Eva, Schwartz Yannick, Frouin Vincent, Rietschel Marcella … & Pausova Zdenka
Genetic variations in fat mass- and obesity (FTO)-associated gene, a well-replicated gene locus of obesity, appear to be associated also with reduced regional brain volumes in elderly. Here, we examined whether FTO is associated with total brain volume in adolescence, thus exploring possible developmental effects of FTO. We studied a population-based sample of 598 adolescents recruited from the French Canadian founder population in whom we measured brain volume by magnetic resonance imaging. Total fat mass...

The role of indirect connections in gene networks in predicting function

Gillis Jesse & Pavlidis Paul
MOTIVATION: Gene networks have been used widely in gene function prediction algorithms, many based on complex extensions of the 'guilt by association' principle. We sought to provide a unified explanation for the performance of gene function prediction algorithms in exploiting network structure and thereby simplify future analysis. RESULTS: We use co-expression networks to show that most exploited network structure simply reconstructs the original correlation matrices from which the co-expression network was obtained. We show the...

A methodology for the analysis of differential coexpression across the human lifespan

Gillis Jesse & Pavlidis Paul
BACKGROUND: Differential coexpression is a change in coexpression between genes that may reflect 'rewiring' of transcriptional networks. It has previously been hypothesized that such changes might be occurring over time in the lifespan of an organism. While both coexpression and differential expression of genes have been previously studied in life stage change or aging, differential coexpression has not. Generalizing differential coexpression analysis to many time points presents a methodological challenge. Here we introduce a method...

Data from: Composition and functional diversity of macrofaunal assemblages on vertical walls of a deep northeast Pacific fjord

Ryan Gasbarro, Di Wan & V Tunnicliffe
This dataset contains three types of data associated with Gasbarro et al. (2018) Marine Ecology Progress Series, collected from remotely operated vehicle imagery surveys in Douglas Channel, British Columbia, Canada. Biological data (i.e. animal abundance and size measurements) from photoquadrats, ROV/water column data (e.g. temperature, depth, dissolved oxygen, etc.) from four dives, and seasonal along-channel current data from a year-long deployment of two moored Acoustic Doppler Current Profilers comprise the three data types. Data was...

Disassembly of an epibenthic assemblage under sustained stress: lessons from hypoxic events in a northeast Pacific basin

Ryan Gasbarro, Jackson Chu & Verena Tunnicliffe
These data include biological (i.e. animal counts) and environmental data from three remotely imagery surveys in Saanich Inlet, a fjord incising Vancouver Island, British Columbia, Canada. All three dives occurred in 2016. Data are organized by row, with each row representing a second of ROV video with metadata related to the ROV dive, water column data (e.g. temperature, salinity, dissolved oxygen, etc.) and species data (animal counts or binary presence/absence tallies). Data was collected as...

Narratives in Ibadan Yoruba

Samuel Akinbo, Clement Oyeleke & Emeka Onwuegbuzia
This folder contains narratives from speakers of Ibadan Yoruba. The data were elicited at the University of Ibadan by students in LIY121 class, which was taught by Clement Oyeleke with the assistance of Samuel Akinbo and Emeka Onwuegbuzia. The narratives were recorded with a ZOOMH5 recorder at 48.1kHZ sampling rate in .wav. The data were transcribed by the students using ELAN (https://tla.mpi.nl/tools/tla-tools/elan/).

Rocky intertidal monitoring of Wizard Islet in 2003

In 1997 the Bamfield Marine Sciences Centre established a long-term monitoring project to collect baseline data on the distribution and abundance of macroorganisms at two intertidal sites on Wizard Islet in Barkley Sound. Both sites were resampled in 2001, and the exposed site was resampled in 2002. In 2003 fifteen transects at the exposed site only were sampled again. Tag numbers were 7, 9, 10, 11, 12, 13, 18, 20, 25, 26, 27, 34, 44,...

Field visit metadata for cluster 2.5: Aichi, Nagoya (Japan)

Meiqiao Zhang & Xue Wang
Field visit metadata for Cluster 2.5 in Aichi, Nagoya (Japan), 2017.

Data for: Forest and pasture catchment dissolved organic matter in Southern Amazonia

Higo D'Almagro, Michael J. Lathuillière, Fernando Da S. Sallo, Maurel F. Guerreiro, Osvaldo B. Pinto, Paulo H.Z. De Arruda, Eduardo G. Couto & Mark S. Johnson
This data collection includes the Supporting Information for the paper: Forest and pasture catchment dissolved organic matter in Southern Amazonia. It contains measurements of precipitation, temperature, oxidation-reduction potential, discharge, baseflow, dissolved organic carbon (DOC), DOC components, slope ratio, and fluorescence indices (FI, HIX, BIX)

Peel-1 negative selection promotes screening-free CRISPR-Cas9 genome editing in Caenorhabditis elegans.

Troy McDiarmid
Raw and processed data for "Peel-1 negative selection promotes screening-free CRISPR-Cas9 genome editing in Caenorhabditis elegans." This includes data demonstrating the effectiveness of peel-1 negative selection on improving CRISPR-Cas9 genome editing, and functional data investigating the roles of two genes using Multi-Worm Tracker software. Further details about this project, including a README.md, paper abstract, and the R code necessary to regenerate all of the figures and formal analyses in the manuscript using the data in...

Assessing the efficacy of tablet-based simulations for learning pseudo-surgical instrumentation : [supplementary material]

J. H. Kryklywy, V. A. Roach & R. M. Todd
A publication based on this data is under review at PLOS-ONE.

Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text

Leon French, Suzanne Lane, Lydia Xu, Celia Siu, Cathy Kwok, Yigi Chen, Claudia Krebs & Paul Pavlidis
Motivation: Automated annotation of neuroanatomical connectivity statements from the neuroscience literature would enable accessible and large-scale connectivity resources. Unfortunately, the connectivity findings are not formally encoded and occur as natural language text. This hinders aggregation, indexing, searching and integration of the reports. We annotated a set of 1377 abstracts for connectivity relations to facilitate automated extraction of connectivity relationships from neuroscience literature. We tested several baseline measures based on co-occurrence and lexical rules. We compare...


Leonard Foster
PCP-SILAC, scripts, instructions and sample data for informatics treatment of PCP-SILAC data.

Registration Year

  • 2021
  • 2020
  • 2019
  • 2018
  • 2017

Resource Types

  • Dataset