cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1592706.v1
title: Fine-grained distribution of a non-native resource can alter the population dynamics of a native consumer

description: Map data used in simulations described in: Mifuyu Nakajima and Carol l. Boggs. 2015. Fine-grained distribution of a non-native resource can alter the population dynamics of a native consumer. PLOS ONE.
DOI: 10.6084/m9.figshare.1592365.v1
title: FracKin data at Old Woman Wash

description: This file consists of tab-delimited values in five columns, representing input to FracKin.m. The first row provides instructions to FracKin.m. The first value is strike (rhr) of layering and the second value is dip of layering. The following three values must be either 0 or 1: plot as measured (0) vs plot with layering restored to horizontal (1); plot discontinuity surfaces and movement directions (0) vs plot maximum and minimum principal strains (1); plot intermediate principal strains (0) vs onit intermediate principal strains (1). Each subsequent line represents a single displacement discontinuity in terms of four numerical values (in degrees) and a single letter for sense-of-movement. The first column indicates strike (rhr) of the discontinuity; second column indicates dip of discontinuity; third column indicates trend (downward) of movement direction; fourth column indicates plunge of movement direction. The fifth column indicates opening (O), closing (C), normal (N), thrust (T), right (R), or left (L). Content in this file represents 85 displacement discontinuities at Old Woman Wash, formated as input to FracKin.m.
DOI: 10.6084/m9.figshare.1592826.v1
title: Experimental Design Lab - Golden Rod Field Data

description: To examine the effect of proximity to water and pollution on plant health, we have selected the Golden Rod as our test plant species. After researching metrics of Golden Rod health, we've concluded that the best controls include individual stem yield, base stem width and plant height to measure population health. To control for variability within each species, we have chosen two plots on York University's Keele Campus. The first plot of data was gathered in the wetlands at Stong Pond and represents our wet ecosystem dataset while the second plot was gathered in the in the York Boulevard Woodlot / York University Busway and represents our dry ecosystem dataset. In each plot, we set up 3 pollution measurement devices which use petroleum as an adhesive to capture particulates of air pollution. These measurement devices were left in the field for exactly 5 days and were analyzed for content in the laboratory thereafter. Our field data collection includes a total of 5 transects per plot with 15-20 individual measurments per transect. We've collected measurments of plant height, base stem width, colour, perceived health and stem abundance, all recorded along a transect with the use of a measuring tape and a tally sheet. <br><br>Plant Height represents the measurment from base to leading stem in meters. Base stem width represents the distance in centimeters at the base of the plant stem. Colour and perceived health are arbitrary values which follow a score of 0-2 and will be attributed to either life cycle or health. Lastly, stem abundance includes all branching stems or flowering stems from the base of the plant to the top. The large sample size has allowed us to control for changes in water content throughout the two plots. Once all 5-6 transects were taken in each plot, we input the data into an excel spreadsheet for further analysis. Due to inconsistencies in the pollution measurement data, we will discuss whether a particulate density score of low and moderate will be included in our final results. If used, we will correlate this with the health data in each plot and examine if our experimental controls had a significant impact on the population health of the Golden Rod.
DOI: 10.6084/m9.figshare.1592773.v1
title: The Comparison of R.cathartica and Acerr at Danby's Woodlot

description: The data was collected on October 14th, and October 21st, 2015 at Danby’s Woodlot located at York University Keele Campus. At the beginning of the data collection, a member from the group noted down the time, weather conditions, and other information about the woodlot then proceeded towards data collection. To begin with, a 100m transect using the tape measures was set up from a randomly chosen edge to the middle of the woodlot. The samples were taken at every 5m starting from 0m that were labelled as station in a consecutive order. At each station sample 1, 2, 3 were taken on the right side of transect by Reena and Olivia. On the other side, sample 4 to 6 were taken by Fara, Huda, and Ratiba. To obtain the samples, a 2mX2m quadrat was set up using the tape measures; in which , the following was collected. First, the abundance of native seedlings in the quadrat was determined by counting the number of native seedlings present in the quadrat. The native plant that was incorporated for the native tree seedling sample was Acer. Since, it was observed as the dominant native species in the woodlot. Moreover, the seedlings of 50-120cm, and with orange, green, red and yellow maple leaves were visually determined and counted. Secondly, the abundance of R.cathartica shrub was determined. In the quadrat to do this large trees with black berried along with smaller plants about the same size as the Acer seedlings were incorporated. These R.cathartica was visually identified based on the leaf shape, and the presence of black berries on the large trees. In addition, the unchanged colour green made the invader more distinguishable. Third, percentage of light in each quadrat was measured by standing at a random point in the quadrat. The extent of canopy coverage was determined to see how much light is reaching the ground. A square is made using the fingers of the observer and held up. The percentage of the square not covered by the trees is the percentage of light reaching the ground. This information was collected for each variable.
DOI: 10.6084/m9.figshare.1592826.v3
title: Experimental Design Lab - Golden Rod Field Data

description: To examine the effect of proximity to water and pollution on plant health, we have selected the Golden Rod as our test plant species. After researching metrics of Golden Rod health, we've concluded that the best controls include individual stem yield, base stem width and plant height to measure population health. To control for variability within each species, we have chosen two plots on York University's Keele Campus. The first plot of data was gathered in the wetlands at Stong Pond and represents our wet ecosystem dataset while the second plot was gathered in the in the York Boulevard Woodlot / York University Busway and represents our dry ecosystem dataset. In each plot, we set up 3 pollution measurement devices which use petroleum as an adhesive to capture particulates of air pollution. These measurement devices were left in the field for exactly 5 days and were analyzed for content in the laboratory thereafter. Our field data collection includes a total of 5 transects per plot with 15-20 individual measurments per transect. We've collected measurments of plant height, base stem width, colour, perceived health and stem abundance, all recorded along a transect with the use of a measuring tape and a tally sheet. <br><br>Plant Height represents the measurment from base to leading stem in meters. Base stem width represents the distance in centimeters at the base of the plant stem. Colour and perceived health are arbitrary values which follow a score of 0-2 and will be attributed to either life cycle or health. Lastly, stem abundance includes all branching stems or flowering stems from the base of the plant to the top. The large sample size has allowed us to control for changes in water content throughout the two plots. Once all 5-6 transects were taken in each plot, we input the data into an excel spreadsheet for further analysis. Due to inconsistencies in the pollution measurement data, we will discuss whether a particulate density score of low and moderate will be included in our final results. If used, we will correlate this with the health data in each plot and examine if our experimental controls had a significant impact on the population health of the Golden Rod.
DOI: 10.6084/m9.figshare.1591919
title: Supplementary Table 3. List of all the exposure variables assessed in this study, which includes the demographics and characteristics of the participants

description: Supplementary Table 3. List of all the exposure variables assessed in this study, which includes the demographics and characteristics of the participants
DOI: 10.6084/m9.figshare.1591920
title: Abundance and Diversity of insects- Lab4--Experimental Design

description: This experiment was conducted in 6 different locations, over the course of 2 days. The field experiment was conducted at York University; consisted of 5 group members, D. Hosseini J. Chera, M. Francetic and N. Maximin. Two data set was collected in total, the first data set was collected on October 14th, and the second was collected on October 21st. The purpose of this experiment was to compare and contrast the abundance and distribution of insects between high and low human traffic areas (High traffic area means areas with the most population in the York University in contrast low traffic area means woodlot, or grassland). The 3 high human traffic areas are: in front of Vari Hall, between Lumbers and Lassonde, and campus walk (which is in front of Stong) and the 3 low traffic areas are: Danby woodlot, Osgoode woodlot and Stong woodlot. 10 pan traps, each spaced equally from each other were placed at each location. The pan traps were set for an hour from the time it was placed, after which the group members observed, counted and documented the insects captured. The same process was repeated for a second time a week later. A total of 60 pan traps were placed each day, adding to a total of 120 pan traps for both days. Note: The color of the pan traps was not under consideration, meaning the colors did not matter to the experiment.
DOI: 10.6084/m9.figshare.1592826.v2
title: Experimental Design Lab - Golden Rod Field Data

description: To examine the effect of proximity to water and pollution on plant health, we have selected the Golden Rod as our test plant species. After researching metrics of Golden Rod health, we've concluded that the best controls include individual stem yield, base stem width and plant height to measure population health. To control for variability within each species, we have chosen two plots on York University's Keele Campus. The first plot of data was gathered in the wetlands at Stong Pond and represents our wet ecosystem dataset while the second plot was gathered in the in the York Boulevard Woodlot / York University Busway and represents our dry ecosystem dataset. In each plot, we set up 3 pollution measurement devices which use petroleum as an adhesive to capture particulates of air pollution. These measurement devices were left in the field for exactly 5 days and were analyzed for content in the laboratory thereafter. Our field data collection includes a total of 5 transects per plot with 15-20 individual measurments per transect. We've collected measurments of plant height, base stem width, colour, perceived health and stem abundance, all recorded along a transect with the use of a measuring tape and a tally sheet. <br><br>Plant Height represents the measurment from base to leading stem in meters. Base stem width represents the distance in centimeters at the base of the plant stem. Colour and perceived health are arbitrary values which follow a score of 0-2 and will be attributed to either life cycle or health. Lastly, stem abundance includes all branching stems or flowering stems from the base of the plant to the top. The large sample size has allowed us to control for changes in water content throughout the two plots. Once all 5-6 transects were taken in each plot, we input the data into an excel spreadsheet for further analysis. Due to inconsistencies in the pollution measurement data, we will discuss whether a particulate density score of low and moderate will be included in our final results. If used, we will correlate this with the health data in each plot and examine if our experimental controls had a significant impact on the population health of the Golden Rod.
DOI: 10.6084/m9.figshare.1592773.v3
title: The Comparison of R.cathartica and Acer at Danby

description: The data was collected on October 14th, and October 21st, 2015 at Danby’s Woodlot located at York University Keele Campus. At the beginning of the data collection, a member from the group noted down the time, weather conditions, and other information about the woodlot then proceeded towards data collection. To begin with, a 100m transect using the tape measures was set up from a randomly chosen edge to the middle of the woodlot. The samples were taken at every 5m starting from 0m that were labelled as station in a consecutive order. At each station sample 1, 2, 3 were taken on the right side of transect by Reena and Olivia. On the other side, sample 4 to 6 were taken by Fara, Huda, and Ratiba. To obtain the samples, a 2mX2m quadrat was set up using the tape measures; in which , the following was collected. First, the abundance of native seedlings in the quadrat was determined by counting the number of native seedlings present in the quadrat. The native plant that was incorporated for the native tree seedling sample was Acer. Since, it was observed as the dominant native species in the woodlot. Moreover, the seedlings of 50-120cm, and with orange, green, red and yellow maple leaves were visually determined and counted. Secondly, the abundance of R.cathartica shrub was determined. In the quadrat to do this large trees with black berried along with smaller plants about the same size as the Acer seedlings were incorporated. These R.cathartica was visually identified based on the leaf shape, and the presence of black berries on the large trees. In addition, the unchanged colour green made the invader more distinguishable. Third, percentage of light in each quadrat was measured by standing at a random point in the quadrat. The extent of canopy coverage was determined to see how much light is reaching the ground. A square is made using the fingers of the observer and held up. The percentage of the square not covered by the trees is the percentage of light reaching the ground. This information was collected for each variable.
DOI: 10.6084/m9.figshare.1591918
title: Supplementary Data 2: Information of the 2114 Staphylococcus aureus fastq files obtained from the NCBI SRA database to estimate the specificity and sensitivity of binstrain software.

description: Supplementary Data 2: Information of the 2114 <em>Staphylococcus aureus</em> fastq files obtained from the NCBI SRA database to estimate the specificity and sensitivity of binstrain software.
DOI: 10.6084/m9.figshare.1591912
title: Supplementary Data 1: Estimated ancestral sequence of Staphylococcus aureus used for reference mapping in this study

description: Supplementary Data 1: Estimated ancestral sequence of <em>Staphylococcus aureus</em> used for reference mapping in this study
DOI: 10.6084/m9.figshare.1591918.v1
title: Supplementary Data 2: Information of the 2114 Staphylococcus aureus fastq files obtained from the NCBI SRA database to estimate the specificity and sensitivity of binstrain software.

description: Supplementary Data 2: Information of the 2114 <em>Staphylococcus aureus</em> fastq files obtained from the NCBI SRA database to estimate the specificity and sensitivity of binstrain software.
DOI: 10.6084/m9.figshare.1591909
title: Supplementary Figure 1: Figure showing the binstrain estimates for the analysis on 10 simulated sequence read sets of between 0.00625X and 5 X genome coverage for each of the 40 subtype-defining genomes and repeated the analysis 9 times (a total of 3600 fastq files and binstrain runs)

description: Supplementary Figure 1: Figure showing the binstrain estimates for the analysis on 10 simulated sequence read sets of between 0.00625X and 5 X genome coverage for each of the 40 <em>Staphylococcus aureus</em> subtype-defining genomes and repeated the analysis 9 times (a total of 3600 fastq files and binstrain runs).
DOI: 10.6084/m9.figshare.1591910
title: Supplementary Table 2: List of Staphylococcus aureus genomes used for the version 1(19 genomes) and version 2 (an additional 21 genomes) for constructing the SNP pattern file used in this study.

description: Supplementary Table 2: List of <em>Staphylococcus aureus</em> genomes used for the version 1(19 genomes) and version 2 (an additional 21 genomes) for constructing the SNP pattern file used in this study.
DOI: 10.6084/m9.figshare.1591912.v1
title: Supplementary Data 1: Estimated ancestral sequence of Staphylococcus aureus used for reference mapping in this study

description: Supplementary Data 1: Estimated ancestral sequence of <em>Staphylococcus aureus</em> used for reference mapping in this study
DOI: 10.6084/m9.figshare.1592773.v2
title: The Comparison of R.cathartica and Acer at Danby's Woodlot

description: The data was collected on October 14th, and October 21st, 2015 at Danby’s Woodlot located at York University Keele Campus. At the beginning of the data collection, a member from the group noted down the time, weather conditions, and other information about the woodlot then proceeded towards data collection. To begin with, a 100m transect using the tape measures was set up from a randomly chosen edge to the middle of the woodlot. The samples were taken at every 5m starting from 0m that were labelled as station in a consecutive order. At each station sample 1, 2, 3 were taken on the right side of transect by Reena and Olivia. On the other side, sample 4 to 6 were taken by Fara, Huda, and Ratiba. To obtain the samples, a 2mX2m quadrat was set up using the tape measures; in which , the following was collected. First, the abundance of native seedlings in the quadrat was determined by counting the number of native seedlings present in the quadrat. The native plant that was incorporated for the native tree seedling sample was Acer. Since, it was observed as the dominant native species in the woodlot. Moreover, the seedlings of 50-120cm, and with orange, green, red and yellow maple leaves were visually determined and counted. Secondly, the abundance of R.cathartica shrub was determined. In the quadrat to do this large trees with black berried along with smaller plants about the same size as the Acer seedlings were incorporated. These R.cathartica was visually identified based on the leaf shape, and the presence of black berries on the large trees. In addition, the unchanged colour green made the invader more distinguishable. Third, percentage of light in each quadrat was measured by standing at a random point in the quadrat. The extent of canopy coverage was determined to see how much light is reaching the ground. A square is made using the fingers of the observer and held up. The percentage of the square not covered by the trees is the percentage of light reaching the ground. This information was collected for each variable.
DOI: 10.6084/m9.figshare.1591908
title: Supplementary Table 1: The list of the 43 complete genomes of Staphylococcus aureus used for the fineStructure analysis.

description: Supplementary Table 1: The list of the 43 complete genomes of<em> Staphylococcus aureus</em> used for the fineStructure analysis.
DOI: 10.6084/m9.figshare.1591910.v1
title: Supplementary Table 2: List of Staphylococcus aureus genomes used for the version 1(19 genomes) and version 2 (an additional 21 genomes) for constructing the SNP pattern file used in this study.

description: Supplementary Table 2: List of <em>Staphylococcus aureus</em> genomes used for the version 1(19 genomes) and version 2 (an additional 21 genomes) for constructing the SNP pattern file used in this study.
DOI: 10.6084/m9.figshare.1591907
title: The Effect of Light and Abundance of Buckthorn on Native Samplings

description: This experiment was executed at York University's woodlot on Ocober 14, 2015 from 3:00 - 5:00 P.M and October 21, 2015 from 3:00 - 4:20. A group of 5 students, Ratiba, Farka,Reena, Olivia and Huda were gathering the Data. The temperature for both days were around 12 degrees and 10 degrees celcius respectively. In general, on both days the wind was cold and it was breezy. The data was collected by the following means: the group began at the edge of the woodlot and walked inward (north of the woodlot) along a 100 meter transect towards the centre. The students set up a station at every 5 meters of the transect. 0m on the transect marking station 0, 5m on the transect marking station 1, 10m on the transect marking station 2 and so on.A 2x2 meter measuring tape was used to make the quadrats.At every station, 6 quadrats were set up. Three quadrats were made to the right of the transect tape and another 3 quadrats were made on the left side of the transect for a total of 6 quadrats at each station. There was a total of 20 stations(one station every 5m of the 100m transect), and a total of 120 quadrats.The abundance of the native sapling, Acer, and the adundance of Buckthorn plant in each quadrat were recorded by visually counting. Also, the percentage of light reaching the ground at each quadrat was recorded. To measure the amount of light the students used their fingures to form a quadrat-like square and estimate the amount of light they see through that square. All the data points collected were contiuous. On the fist day, the students walked through 0 - 50 meters of the transect and on the second day, they walked through 55 - 100 meters.The purpose of this experiment is to examine the effects of light and abundance of Buckthorn on the abundanc of native saplings.
DOI: 10.6084/m9.figshare.1591905
title: Week 7 Field Data: Population and Abundance of Birds at York University

description: Data for this field experiment was collected over 2 days; October 13th, 2015 and October 20th, 2015. On October 13th, the environmental conditions were windy, heavily clouded, and humid, with a temperature of 15 degrees Celsius. On October 20th, the environmental conditions were windy, cloudy, and light precipitation, with a temperature of 17 degrees Celsius. Data was recorded on the Keele Campus of York University in grasslands, woodlots, and urban areas. The field experiment involved laying 8-10 transects in urban areas and 8-10 transects in natural areas. An urban area was defined as having at least 75% manmade materials (pavement, buildings, etc,) and a natural area was defined as having at least 75% vegetation on the earth. Once these 120 metre transects were placed, birds within the length of the transect were recorded. The vicinity of the birds in relation to the transect was 20-30 metres on each side and 15 metres vertically. Birds who entered the vicinity more than once were only recorded once. This method was repeated for each transect.
DOI: 10.6084/m9.figshare.1591909.v1
title: Supplementary Figure 1: Figure showing the binstrain estimates for the analysis on 10 simulated sequence read sets of between 0.00625X and 5 X genome coverage for each of the 40 subtype-defining genomes and repeated the analysis 9 times (a total of 3600 fastq files and binstrain runs)

description: Supplementary Figure 1: Figure showing the binstrain estimates for the analysis on 10 simulated sequence read sets of between 0.00625X and 5 X genome coverage for each of the 40 <em>Staphylococcus aureus</em> subtype-defining genomes and repeated the analysis 9 times (a total of 3600 fastq files and binstrain runs).