cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/z9noms
title: UBC Farm Monthly Bird Surveys

description: Nature Vancouver, a not-for-profit charitable society based in Vancouver, BC, has conducted monthly bird surveys at UBC Farm since March 2007, in part to record the seasonal bird species over the year in nine different habitat areas of the Farm. Surveys occur on the third Sunday of the month starting at 8am (March to September) or 9am (October to February) and typically last two to three hours. Bird occurrences are recorded by genus and species, or when identification is not clear, then simply to genus. The nine stations of the farm include the market garden fields, the herb and flower gardens, the biodiversity hedgerows, and the forested portion of the farm. This data is also available on eBird under the ‘hotspot’ named Vancouver—UBC south campus Farm. Site-specific and georeferenced data is available for the nine habitat areas of UBC Farm. Please contact Dr. Matthew Mitchell to request this data.
DOI: 10.5683/sp2/qop670
title: UBC Farm Soil Amendment Records

description: This dataset contains records of soil amendment applications at UBC Farm since 2018. The “Soil Actions” dataset includes field location and area; crop and/or rotation group targeted; nutrient required and associated soil test result (detailed data available in UBC Farm Soil Lab Results); amendment name, nutrient percentage, and application rate; amendment amount needed and applied in field (if applied); and whether an amendment was applied. “Compost” dataset includes field and bed location; rotation group targeted; compost type; field area and volume of application; total weight and volume of nutrients; and whether the compost was applied. Please note that the UBC Farm’s data management practices have grown and evolved over time, and some forms of data have been consistently collected for more years than others. UBC Farm staff are also busy and imperfect humans and sometimes forget to log activities. On rare occasion, erroneous data may accidentally be entered, and these errors may not get corrected during quality control checks. While we do our best to ensure the data we release is complete and accurate, we provide this data to you “as is”, through the disclaimer in the CC BY-NC-SA 4.0 license.
DOI: 10.5683/sp2/smnmgf
title: UBC Farm Integrated Pest Management Records

description: This dataset contains UBC Farm integrated pest management records since 2018. Two types of data are present: pest observations (which are informal and incomplete) and actions (applications of pest control products and releases of beneficial insects). Other agronomic practices that contribute to pest control (such as pruning plants, cultivating soil, and physically removing pests) are not recorded here. Please note that the UBC Farm’s data management practices have grown and evolved over time, and some forms of data have been consistently collected for more years than others. UBC Farm staff are also busy and imperfect humans and sometimes forget to log activities. On rare occasion, erroneous data may accidentally be entered, and these errors may not get corrected during quality control checks. While we do our best to ensure the data we release is complete and accurate, we provide this data to you “as is”, through the disclaimer in the CC BY-NC-SA 4.0 license.
DOI: 10.5683/sp2/y1g0px
title: UBC Farm Cover Crop Planting Records

description: This dataset contains records of cover crop planting at UBC Farm since 2018. Information includes crop types, field and bed locations and areas, and planting dates, rates, and weights. Please note that the UBC Farm’s data management practices have grown and evolved over time, and some forms of data have been consistently collected for more years than others. UBC Farm staff are also busy and imperfect humans and sometimes forget to log activities. On rare occasion, erroneous data may accidentally be entered, and these errors may not get corrected during quality control checks. While we do our best to ensure the data we release is complete and accurate, we provide this data to you “as is”, through the disclaimer in the CC BY-NC-SA 4.0 license.
DOI: 10.5683/sp2/qsxh6h
title: UBC Farm Seed and Transplant Records

description: This dataset contains records of seed planting and transplanting at UBC Farm since 2015. Information includes crop types, varieties, and amounts sown; planting and transplanting dates; transplanting field locations; and sowing methods. Please note that the UBC Farm’s data management practices have grown and evolved over time, and some forms of data have been consistently collected for more years than others. UBC Farm staff are also busy and imperfect humans and sometimes forget to log activities. On rare occasion, erroneous data may accidentally be entered, and these errors may not get corrected during quality control checks. While we do our best to ensure the data we release is complete and accurate, we provide this data to you “as is”, through the disclaimer in the CC BY-NC-SA 4.0 license.
DOI: 10.5683/sp2/n3rgmw
title: UBC Farm Harvest Records

description: This dataset contains records of harvest activities at UBC Farm since 2019, including product, crop, and rotation group information, forecast information, and quantities harvested. Please note that the UBC Farm’s data management practices have grown and evolved over time, and some forms of data have been consistently collected for more years than others. UBC Farm staff are also busy and imperfect humans and sometimes forget to log activities. On rare occasion, erroneous data may accidentally be entered, and these errors may not get corrected during quality control checks. While we do our best to ensure the data we release is complete and accurate, we provide this data to you “as is”, through the disclaimer in the CC BY-NC-SA 4.0 license.
DOI: 10.5683/sp2/ivr7ta
title: UBC Farm Sales Records

description: This dataset contains sales records for UBC Farm since 2019, including total revenue per product through its main sales channels: markets, community-supported agriculture (CSA) programs, and wholesale. Please note that a product does not represent a specific crop (e.g. kale), but a specific quantity and packaging of that crop. For example, 'kale, tote (10 lb)' and 'kale, bunch (0.67 lb)' are different products, but the same crop. Please note that the UBC Farm’s data management practices have grown and evolved over time, and some forms of data have been consistently collected for more years than others. UBC Farm staff are also busy and imperfect humans and sometimes forget to log activities. On rare occasion, erroneous data may accidentally be entered, and these errors may not get corrected during quality control checks. While we do our best to ensure the data we release is complete and accurate, we provide this data to you “as is”, through the disclaimer in the CC BY-NC-SA 4.0 license.
DOI: 10.5683/sp2/hzvxdu
title: Data for: A Living Laboratory for Water Sustainability at UBC Farm

description: This dataset contains data collected through the UBC Farm Long-Term Water Monitoring Program, which started in July 2019. The project will develop a water innovations node for UBC’s Campus as a Living Laboratory initiative to conduct water monitoring and evaluate water use reduction strategies to minimize the water footprint of agriculture at UBC Farm and support UBC’s Water Action Plan. The project will increase the capacity of UBC Farm as a leading living laboratory for research, teaching and learning on water sustainability with academic, public sector and industrial partners. The project will implement new, smart, integrated water and climate monitoring technology at UBC Farm. This will enable living-lab based research to develop water conserving strategies and conduct innovative research across the food-energy-water nexus. The project will also inform best practices on water management and irrigation for urban agriculture and climate change, which can be scaled across campus to reduce UBC’s water footprint, and serve as a focal node for research related to water use in the regional agrifood system.
DOI: 10.5683/sp2/xcfr9t
title: Data for: UBC Farm Long-Term Biodiversity Monitoring Program

description: This dataset contains data collected through the UBC Farm Long-Term Biodiversity Monitoring Program, which started in May 2019. Project Description: The UBC Farm Long-term Biodiversity Monitoring Program assesses biodiversity across multiple scales and levels at the UBC Farm. Biodiversity is the foundation of agricultural productivity and contributes essential ecosystem functions and services to food systems. The UBC Farm provides a unique opportunity to monitor the biodiversity important for agroecosystem food production and other ecosystem services on a working, diversified, and organic farm and pilot new technologies and survey techniques to assess agrobiodiversity. The Long-Term Biodiversity Monitoring program focuses on assessing bumble bees, earthworms, forest and crop plants, birds, mammals, bats, and soil fauna each year. The program aims to improve understanding of the biodiversity at the UBC Farm, how it is changing over time, and how this affects important ecosystem services (the benefits people receive from the natural environment) that benefit people, help crops grow, and contribute to overall agroecosystem sustainability.
DOI: 10.5683/sp2/zvu1at
title: UBC Farm Base Field Maps

description: This dataset contains PDFs of UBC Farm annual field maps since 2015, including relative field locations and sizes, field codes, crop rotation groups, and infrastructure types. Please note that these maps are used for field planning purposes only, and the actual crops grown in fields may differ from the rotation groups provided here. The best uses of these maps are: 1) to determine locations of field codes in other UBC Farm datasets; 2) to look up field codes for UBC Farm research projects, and 3) to understand the general layout of the Farm.
DOI: 10.5683/sp2/l9vhb0
title: Into the Hedge: The Prevalence and Existence of Fungal Pathogens at UBC Farm

description: During this project, we discovered, identified, and cultured fungal pathogens found within the UBC Farm hedgerows and crops. We started with information from the UBC Farm on the known diseases infecting their crops each year. After collecting live plant material from the hedgerows and crops, we compared and contrasted the pathogens we found in each with the diseases they are associated with that may be present at the UBC Farm. The future of fungal pathogen management at the UBC Farm requires more investigation into the severity of the pathogens present and the conformation of the source of inoculum for the crops. The findings of this biodiversity study will contribute to the ongoing biodiversity assessment at the UBC Farm. Undergraduate thesis advisor: Dr. Brett Couch (UBC Botany)
DOI: 10.5683/sp2/ziomgm
title: UBC Farm Land Use Map - GIS Files

description: This dataset contains shape files and supporting files for the most up-to-date (as of the published date) land use map at the UBC Farm. The best uses of these maps are: 1) to visualize locations of field codes in other UBC Farm datasets; 2) to visualize field codes for UBC Farm research projects, and 3) to understand the general layout of the Farm.
DOI: 10.5683/sp2/cz2kfi
title: Wheat, barley, and oat rust differentials screening to natural rust pressure

description: Stripe rust, a fungal disease caused by the fungus Puccinia striiformis, is one of the most devastating diseases of wheat and barley worldwide, including western Canada. Stripe rust is a disease which is prevalent across the planet and can easily be spread via airborne transmission. In recent years, stripe rust has become an increasingly greater threat to western Canada due to newer virulent strains. The Pacific Northwest (PNW) of the USA is hotspot of stripe rust disease in North America, and the province of British Columbia being closer to the PNW is expected to have natural pathogen inoculum coming northward with wind trajectories. Purpose of the research was to collect wheat and barley stripe rust and oat crown rust severity data from natural disease pressure of these rust pathogens. For that, we planted wheat, barley, and oat genotypes carrying known rust resistance genes. We rated our plants for severity of the disease on flag and penultimate leaves in Early August.
DOI: 10.5683/sp2/ttqtsh
title: Tree inventory of UBC Farm to accelerate agroforestry research

description: Juxtaposed with the agricultural production systems at the UBC Farm is a large area of second growth forest that is currently classified as an area for agroforestry. While this forest is not currently actively managed for agroforestry or forestry production, it provides an unparalleled resource on campus for research and learning. The objective is to undertake a 100% inventory of all trees &gt;10cm diameter at breast height (DBH), identify and record them in an UBC campus-wide database format, and share the data on an open-source platform for students and researchers at UBC to access. This will provide the necessary baseline for further research on urban forestry, ecosystem services, biodiversity, climate change, potential sustainable timber production, and agroforestry, among others, to take place at UBC Farm. It represents an essential tool for the future sustainable management of the remaining forest on the UBC Farm.
DOI: 10.5683/sp2/9xrrsj
title: Replication Data for: Effects of lameness definition and assessment frequency on lameness incidence estimates in dairy cattle

description: The objectives of the manuscript for which this data was used were to evaluate how (1) lameness definition, and (2) assessment frequency, affect identification and classification (mild or severe lameness) of new lameness cases in dairy cattle. Dairy cows (n = 262) were followed from the cessation of lactation until the next calving, and locomotion was assessed weekly. Two data set are available - one including all locomotion assessments for each cow, and one with the data summarised by animal.
DOI: 10.5683/sp2/9cpole
title: Public Attitudes to Housing Systems for Pregnant Pigs

description: Understanding concerns about the welfare of farm animals is important for the development of socially sustainable practices. This study reports findings from an online survey used to test how views on group versus stall housing for pregnant sows varied when Canadian and US participants were provided information about these systems including access to scientific papers, YouTube videos, Google images, and a frequently-asked-questions page. Results are reported in a paper under review by PLOS One. Initial responses and changes in responses after accessing the information were analyzed from Likert scores of 242 participants and from their written comments. Participants were less willing to accept the use of gestation stalls after viewing information on sow housing. Qualitative analysis of comments showed that supporters of gestation stalls expressed concern about the spread of disease and aggression between animals in less confined systems, whereas supporters of group housing placed more emphasis on the sow's ability to interact socially and perform natural behaviors. Support for both systems was also influenced by misperceptions, for example that group housing commonly contains straw bedding. The data provided give qualitative and quantitative responses to two questions regarding level of support for either housing system (before (referred to in data set as 257) and after (439) the provision of additional information), demographic data, qualitative data on unique comments authored by specific participants, as well as data on which comments participants voted on to support their position. Data is also shared regarding self-reports of which types of information participants accessed and how this affected their attitudes.
DOI: 10.5683/sp2/q4nl1c
title: Appendices for: Dairy Cattle Transition Period: Disease Prevalence and Risk Factors in Grazing and Freestall Systems (thesis) by Ruan Daros

description: On this file I combine all appendices and supplementary material related to my PhD thesis (available at http://hdl.handle.net/2429/71099). Please use READ.ME for more details.
DOI: 10.5683/sp2/ytzmkx
title: Replication Data for: Lameness during the dry period: epidemiology and associated factors

description: Original data, R script (code) and code output for the paper published on Journal of Dairy Science. For best use, replicate analysis using R. Importing data using the .csv file may cause some variables (columns of the spreadsheet) to be imported with the wrong format. Any issues, do not hesitate in contact. Happy coding!
DOI: 10.5683/sp2/uhwpx9
title: Replication Data for: The relationship between transition period diseases and lameness, feeding time, and body condition during the dry period

description: This file contains the original data used to run the statistical analysis for the paper "The relationship between transition period diseases and lameness, feeding time, and body condition during the dry period" by Daros et al., 2020 published in the Journal of Dairy Science. Here you will also find the supplementary material for the original publication and the code used to generate the supplementary material. Any issues, do not hesitate in contact. Happy coding!
DOI: 10.5683/sp2/ommcyw
title: Modeling sources of inter-laboratory variability in electrophysiological properties of mammalian neurons

description: Patch-clamp electrophysiology is widely used to characterize neuronal electrical phenotypes. However, there are no standard experimental conditions for in vitro whole-cell patch-clamp electrophysiology, complicating direct comparisons between datasets. Here, we sought to understand how basic experimental conditions differ among labs and how these differences might impact measurements of electrophysiological parameters. We curated the compositions of external bath solutions (ACSF), internal pipette solutions, and other methodological details such as animal strain and age from 509 published neurophysiology articles studying rodent neurons. We found that very few articles used the exact same experimental solutions as any other and some solution differences stem from recipe inheritance from adviser to advisee as well as changing trends over the years. Next, we used statistical models to understand how the use of different experimental conditions impacts downstream electrophysiological measurements such as resting potential and action potential width. While these experimental condition features could explain up to 43% of the study-to-study variance in electrophysiological parameters, the majority of the variability was left unexplained. Our results suggest that there are likely additional experimental factors that contribute to cross-laboratory electrophysiological variability, and identifying and addressing these will be important to future efforts to assemble consensus descriptions of neurophysiological phenotypes for mammalian cell types.
DOI: 10.5683/sp2/qjwyah
title: Transcriptomic correlates of neuron electrophysiological diversity

description: How neuronal diversity emerges from complex patterns of gene expression remains poorly understood. Here we present an approach to understand electrophysiological diversity through gene expression by integrating pooled- and single-cell transcriptomics with intracellular electrophysiology. Using neuroinformatics methods, we compiled a brain-wide dataset of 34 neuron types with paired gene expression and intrinsic electrophysiological features from publically accessible sources, the largest such collection to date. We identified 420 genes whose expression levels significantly correlated with variability in one or more of 11 physiological parameters. We next trained statistical models to infer cellular features from multivariate gene expression. Such models were predictive of gene-electrophysiological relationships in an independent collection of 12 visual cortex cell types from the Allen Institute, suggesting that these correlations might reflect general principles relating expression patterns to phenotypic diversity across very different cell types. Many associations reported here have the potential to provide new insights into how neurons generate functional diversity, and correlations of ion channel genes like Gabrd and Scn1a (Nav1.1) with resting potential and spiking frequency are consistent with known causal mechanisms. Our work highlights the promise and inherent challenges in using cell type-specific transcriptomics to understand the mechanistic origins of neuronal diversity.
DOI: 10.5683/sp2/hvuiyz
title: Protease-inhibitor interaction predictions: Lessons on the complexity of protein-protein interactions

description: Protein interactions shape proteome function and thus biology. Identification of protein interactions is a major goal in molecular biology, but biochemical methods, although improving, remain limited in coverage and accuracy. Whereas computational predictions can guide biochemical experiments, low validation rates of predictions remain a major limitation. Here, we investigated computational methods in the prediction of a specific type of interaction, the inhibitory interactions between proteases and their inhibitors. Proteases generate thousands of proteoforms that dynamically shape the functional state of proteomes. Despite the important regulatory role of proteases, knowledge of their inhibitors remains largely incomplete with the vast majority of proteases lacking an annotated inhibitor. To link inhibitors to their target proteases on a large scale, we applied computational methods to predict inhibitory interactions between proteases and their inhibitors based on complementary data including coexpression, phylogenetic similarity, structural information, co-annotation, and colocalization, and also surveyed general protein interaction networks for potential inhibitory interactions. In testing nine predicted interactions biochemically, we validated the inhibition of kallikrein 5 by serpin B12. Despite the use of a wide array of complementary data, we found a high false positive rate of computational predictions in biochemical follow-up. Based on a protease-specific definition of true negatives derived from the biochemical classification of proteases and inhibitors, we analyzed prediction accuracy of individual features. Thereby we identified feature-specific limitations, which also affected general protein interaction prediction methods. Interestingly, proteases were often not coexpressed with most of their functional inhibitors, contrary to what is commonly assumed and extrapolated predominantly from cell culture experiments. Predictions of inhibitory interactions were indeed more challenging than predictions of non-proteolytic and non-inhibitory interactions. In summary, we describe a novel and well-defined but difficult protein interaction prediction task, and thereby highlight limitations of computational interaction prediction methods.
DOI: 10.5683/sp2/qzvioi
title: Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data

description: Establishing the molecular diversity of cell types is crucial for the study of the nervous system. We compiled a cross-laboratory database of mouse brain cell type-specific transcriptomes from 36 major cell types from across the mammalian brain using rigorously curated published data from pooled cell type microarray and single cell RNA-sequencing studies. We used these data to identify cell type-specific marker genes, discovering a substantial number of novel markers, many of which we validated using computational and experimental approaches. We further demonstrate that summarized expression of marker gene sets in bulk tissue data can be used to estimate the relative cell type abundance across samples. To facilitate use of this expanding resource, we provide a user-friendly web interface at Neuroexpresso.org.