cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1565640
title: Ecology BIOL2050 Lab 3 Dataset 4 Bird Species

description: This data set for the third BIOL2050 lab was conducted in the Stong pond grassland on Tuesday September 29, 2015 at about 4:00 PM. The temperature in the area during the time of data collection was roughly 15 degrees Celsius accompanied by rain and cloud cover with a light breeze. The objective of this dataset was to identify the different species of birds and the frequency of these species in the Stong pond grasslands. A pair of binoculars and transect tape were used to collect this data in the tall grass region of the grassland. First, a transect tape was laid out in the tall grass and 50 meters were measured. Then, my group members and I walked along the transect tape, looking all around us to spot any birds either flying around in the sky, swimming in the pond or walking on land. We used the binoculars to get closer looks at birds that were far away so we could better identify the species. Any birds that were spotted were recorded and these steps were carried out four more times for a total of five replicates. This dataset taught us how the line transect data collection method is very useful when you want to cover a large area quickly and/or are examining mobile organism which obviously were birds in this case. Since it was raining during the time of this data collection, not many birds were spotted and our data doesn’t reflect the true bird population of the Stong pond grassland.
DOI: 10.6084/m9.figshare.1565641
title: REL1206 Genome Annotation

description: To estimate the number and diversity of beneficial mutations, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population. We identified 1331 total mutations, affecting more than 600 different sites. Few mutations were shared among replicates, but a strong pattern of convergence emerged at the level of genes, operons, and functional complexes. Our experiment uncovered a set of primary functional targets of high temperature, but we estimate that many other beneficial mutations could contribute to similar adaptive outcomes. We inferred the pervasive presence of epistasis among beneficial mutations, which shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho.
DOI: 10.6084/m9.figshare.1565642
title: REL 1206 Reference Genome

description: To estimate the number and diversity of beneficial mutations, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population. We identified 1331 total mutations, affecting more than 600 different sites. Few mutations were shared among replicates, but a strong pattern of convergence emerged at the level of genes, operons, and functional complexes. Our experiment uncovered a set of primary functional targets of high temperature, but we estimate that many other beneficial mutations could contribute to similar adaptive outcomes. We inferred the pervasive presence of epistasis among beneficial mutations, which shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho.
DOI: 10.6084/m9.figshare.1565641.v1
title: REL1206 Genome Annotation

description: To estimate the number and diversity of beneficial mutations, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population. We identified 1331 total mutations, affecting more than 600 different sites. Few mutations were shared among replicates, but a strong pattern of convergence emerged at the level of genes, operons, and functional complexes. Our experiment uncovered a set of primary functional targets of high temperature, but we estimate that many other beneficial mutations could contribute to similar adaptive outcomes. We inferred the pervasive presence of epistasis among beneficial mutations, which shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho.
DOI: 10.6084/m9.figshare.1565642.v1
title: REL 1206 Reference Genome

description: To estimate the number and diversity of beneficial mutations, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population. We identified 1331 total mutations, affecting more than 600 different sites. Few mutations were shared among replicates, but a strong pattern of convergence emerged at the level of genes, operons, and functional complexes. Our experiment uncovered a set of primary functional targets of high temperature, but we estimate that many other beneficial mutations could contribute to similar adaptive outcomes. We inferred the pervasive presence of epistasis among beneficial mutations, which shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho.
DOI: 10.6084/m9.figshare.1565636
title: The Network Architecture of Embryo Developmental Regulation

description: Extended abstract submitted to the Network Frontiers Workshop, Northwestern University.
DOI: 10.6084/m9.figshare.1565639.v1
title: Ecology Lab 3 - Sweepnet Data Set - Insect Abundance

description: In grassland unmode area, a transect of 30 seconds was swept using a sweep net. After 30 seconds of sweeping in a straight line, total insects captured were recorded, and individual number of recognizable taxonomic units were recorded. Sweep-net was emptied after every transect. A repetition of 10 transect sweeps were carried out.
DOI: 10.6084/m9.figshare.1565640.v1
title: Ecology BIOL2050 Lab 3 Dataset 4 Bird Species

description: This data set for the third BIOL2050 lab was conducted in the Stong pond grassland on Tuesday September 29, 2015 at about 4:00 PM. The temperature in the area during the time of data collection was roughly 15 degrees Celsius accompanied by rain and cloud cover with a light breeze. The objective of this dataset was to identify the different species of birds and the frequency of these species in the Stong pond grasslands. A pair of binoculars and transect tape were used to collect this data in the tall grass region of the grassland. First, a transect tape was laid out in the tall grass and 50 meters were measured. Then, my group members and I walked along the transect tape, looking all around us to spot any birds either flying around in the sky, swimming in the pond or walking on land. We used the binoculars to get closer looks at birds that were far away so we could better identify the species. Any birds that were spotted were recorded and these steps were carried out four more times for a total of five replicates. This dataset taught us how the line transect data collection method is very useful when you want to cover a large area quickly and/or are examining mobile organism which obviously were birds in this case. Since it was raining during the time of this data collection, not many birds were spotted and our data doesn’t reflect the true bird population of the Stong pond grassland.
DOI: 10.6084/m9.figshare.1565632
title: Bacillus subtilis bactofilins are essential for flagellar hook- and filament assembly and dynamically localize into structures of less than 100 nm diameter underneath the cell membrane

description: Figures and Movies included in PLOS ONE
DOI: 10.6084/m9.figshare.1565632.v1
title: Bacillus subtilis bactofilins are essential for flagellar hook- and filament assembly and dynamically localize into structures of less than 100 nm diameter underneath the cell membrane

description: Figures and Movies included in PLOS ONE
DOI: 10.6084/m9.figshare.1565636.v2
title: The Network Architecture of Embryo Developmental Regulation

description: Extended abstract submitted to the Network Frontiers Workshop, Northwestern University.
DOI: 10.17632/n78m9f3cpr.2
title: Supplemental Table E-4

description: Supplemental Table E-4
DOI: 10.6084/m9.figshare.1565623
title: Video Game Ontology Competency Questions

description: A listing of Competency Questions used to create the Video Game Ontology.
DOI: 10.6084/m9.figshare.1565600
title: RNAseq_count_tables

description: RNAseq count data tables of S.acidocaldarius
DOI: 10.6084/m9.figshare.1565626.v1
title: MoCA Poster

description: Poster presented at the USC MCB Retreat 2015.
DOI: 10.6084/m9.figshare.1565600.v1
title: RNAseq_count_tables

description: RNAseq count data tables of S.acidocaldarius
DOI: 10.6084/m9.figshare.1565580
title: Bio 2050 Wk 4 Techniques and data: field sample training with animals

description: The dataset 4 was collected on September 27, 2015 at 2:55 pm by a group of 5 Ecology (Bio 2050) students. It is important to note that the data was collected at the time of a rainstorm and a temperature below 20 degrees Celsius, which may be a poor representation of possible numerical results for this experiment. The group arrived to Osgoode woodlot and chose a location with a maximal amount of light and minimal blockage or possible interference with other vegetation during the given experiment. Students evenly spread out 9 solo bowls on top of ground in the following order, 3 blue bowls, 3 yellow bowls and 3 white bowls. Each bowl was filled with soapy water to ensure that any possible trapped insects would securely remain inside the bowl throughout the entire duration of the experiment. Afterward, the group relocated to the Stong Pond grassland and repeated the previously mentioned steps at a new location. The bowls were safely left for the duration of the laboratory at both locations. Once the entire laboratory was finished, the students returned to the woodlot and grassland to collect data based on the count of trapped insects. Once the data was collected, the insects were safely released and the equipment (bowls) was brought back to laboratory room.
DOI: 10.6084/m9.figshare.1565581
title: Nec Malaysia

description: Our Cloud PBX service puts everything in the cloud, so your IT team needs to manage & because it's future proof you don't have to worry about upgrades.
DOI: 10.6084/m9.figshare.1565581.v1
title: Nec Malaysia

description: Our Cloud PBX service puts everything in the cloud, so your IT team needs to manage & because it's future proof you don't have to worry about upgrades.
DOI: 10.6084/m9.figshare.1565626.v2
title: MoCA Poster

description: Poster presented at the USC MCB Retreat 2015.
DOI: 10.17632/x4mxnjmc76.2
title: Supplementary Tables and Methods

description: Supplemental Methods
DOI: 10.6084/m9.figshare.1565580.v2
title: Bio 2050 Wk 4 Techniques and data: field sample training with animals

description: The dataset 4 was collected on September 27, 2015 at 2:55 pm by a group of 5 Ecology (Bio 2050) students. It is important to note that the data was collected at the time of a rainstorm and a temperature below 20 degrees Celsius, which may be a poor representation of possible numerical results for this experiment. The group arrived to Osgoode woodlot and chose a location with a maximal amount of light and minimal blockage or possible interference with other vegetation during the given experiment. Students evenly spread out 9 solo bowls on top of ground in the following order, 3 blue bowls, 3 yellow bowls and 3 white bowls. Each bowl was filled with soapy water to ensure that any possible trapped insects would securely remain inside the bowl throughout the entire duration of the experiment. Afterward, the group relocated to the Stong Pond grassland and repeated the previously mentioned steps at a new location. The bowls were safely left for the duration of the laboratory at both locations. Once the entire laboratory was finished, the students returned to the woodlot and grassland to collect data based on the count of trapped insects. Once the data was collected, the insects were safely released and the equipment (bowls) was brought back to laboratory room.
DOI: 10.6084/m9.figshare.1565578
title: Lab3: Birds species observed in York University

description: This experiment was performed on Monday September 28, 2015 in York university at Danby woodlot and Stong pond region. Temperature was around 21°C with cloudy weather and a cold breeze. Experiment was performed between 2:45 - 4:45 pm. Group members who participated in this experiment were: Sarah, Sharon, Anosha and Sayed. Grassland was the first location to start bird observation, abundance was determined by placing a 40 m long transect tape randomly in a straight line and the experimenter would walk along the tape and observe every bird in sight for 5 minutes each meter. This process was replicated 5 times in Grassland and then another 5 times at the Danby woodlots except for changing the transect length to 30 meters. What is worth mentioning is that one virtual line was made across the pond to observe geese at the Stong pond area. Characteristics of each species were written and then identified using the guiding book and the guides provided on the course blog.
DOI: 10.6084/m9.figshare.1565578.v1
title: Lab3: Birds species observed in York University

description: This experiment was performed on Monday September 28, 2015 in York university at Danby woodlot and Stong pond region. Temperature was around 21°C with cloudy weather and a cold breeze. Experiment was performed between 2:45 - 4:45 pm. Group members who participated in this experiment were: Sarah, Sharon, Anosha and Sayed. Grassland was the first location to start bird observation, abundance was determined by placing a 40 m long transect tape randomly in a straight line and the experimenter would walk along the tape and observe every bird in sight for 5 minutes each meter. This process was replicated 5 times in Grassland and then another 5 times at the Danby woodlots except for changing the transect length to 30 meters. What is worth mentioning is that one virtual line was made across the pond to observe geese at the Stong pond area. Characteristics of each species were written and then identified using the guiding book and the guides provided on the course blog.
DOI: 10.6084/m9.figshare.1565523
title: Determining insect diversity, density and abundance using quadrat method

description: The following data was collected on September 29, 2015 between 2:30-5:30. The weather was rainy, with a temperature of 17°C. My group members consisted of Tonia, Amanda, Michael, and I. Amanda and I paired up to collect data to study distribution and abundance of insects at Danby woodlot and grassland at York University. The first half of the experiment was done in the grassland, where a 1x1m quadrat was randomly placed in a grassy patch. The total number of insects recognizable with naked eye, different recognizable taxonomic units (RTUs) such as bees, flies, etc, and their numbers were recorded as well. This method was replicated 10 times. Using a cell phone, a random number was generated between 1 and 10; the distance from one quadrat to the next one, in feet. This random distance between each quadrat helps limit the effect of unmeasured variables. After collecting data from 10 replicates, we headed to the woodlot and performed the experiment again, using the same approach. The collected data will help us determine the abundance and density of these insect species at York. Due to heavy rain, it is important to note that, many insects were most likely hid under leaves or grass. This reduced the number of insects we would have seen in comparison to a day where it had not been raining. However, we did manage to see earthworms and snails, which would likely not have been possible without the rain.
DOI: 10.6084/m9.figshare.1565576
title: Danby Grasslands Insect diversity and abundance transect experiment

description: The data in the excel sheet was from an experiment conducted on Tuesday September 29th 2015, in the Danby Grasslands at York University between the times of 2:45pm and 4:45pm. Group members that assisted in data collection: Naduni, Sharan, and Stanley. The temperature was 15 degrees celsius, light winds and moderate precipitation was constant through the collection. a transect was measured for 15 meters, and insects were swept in a scooping motion along the entire distance, perpendicular to the transect itself. After sweeping, number of insects, and total amount of species were recorded. The process was repeated 10 times in somewhat randomly selected areas. By means of that the conductor of the experiment closed their eyes and spun around 3 times took 10 steps and laid down the transect. The experiment was conducted by Bryson Chandrarajan.
DOI: 10.6084/m9.figshare.1565576.v1
title: Danby Grasslands Insect diversity and abundance transect experiment

description: The data in the excel sheet was from an experiment conducted on Tuesday September 29th 2015, in the Danby Grasslands at York University between the times of 2:45pm and 4:45pm. Group members that assisted in data collection: Naduni, Sharan, and Stanley. The temperature was 15 degrees celsius, light winds and moderate precipitation was constant through the collection. a transect was measured for 15 meters, and insects were swept in a scooping motion along the entire distance, perpendicular to the transect itself. After sweeping, number of insects, and total amount of species were recorded. The process was repeated 10 times in somewhat randomly selected areas. By means of that the conductor of the experiment closed their eyes and spun around 3 times took 10 steps and laid down the transect. The experiment was conducted by Bryson Chandrarajan.
DOI: 10.6084/m9.figshare.1565580.v1
title: Bio 2050 Wk 4 Techniques and data: field sample training with animals

description: The dataset 4 was collected on September 27, 2015 at 2:55 pm by a group of 5 Ecology (Bio 2050) students. It is important to note that the data was collected at the time of a rainstorm and a temperature below 20 degrees Celsius, which may be a poor representation of possible numerical results for this experiment. The group arrived to Osgoode woodlot and chose a location with a maximal amount of light and minimal blockage or possible interference with other vegetation during the given experiment. Students evenly spread out 9 solo bowls on top of ground in the following order, 3 blue bowls, 3 yellow bowls and 3 white bowls. Each bowl was filled with soapy water to ensure that any possible trapped insects would securely remain inside the bowl throughout the entire duration of the experiment. Afterward, the group relocated to the Stong Pond grassland and repeated the previously mentioned steps at a new location. The bowls were safely left for the duration of the laboratory at both locations. Once the entire laboratory was finished, the students returned to the woodlot and grassland to collect data based on the count of trapped insects. Once the data was collected, the insects were safely released and the equipment (bowls) was brought back to laboratory room.
DOI: 10.6084/m9.figshare.1565626.v3
title: MoCA: A Tool for Motif Conservation Analysis

description: Poster presented at the USC MCB Retreat 2015.
DOI: 10.6084/m9.figshare.1565404
title: Week 4 Transect Sweep Net data in YorkU Grasslands

description: The following data was collected by Kyle, Drew and I while our other group members collected the quadrat data. This was all done at York University's grasslands on September 30, 2015 from 2:30-430. The Weather was sunny with a temperature of around 18 degrees. We measured 30M with the transect and used the sweep nets to catch insects that were within 30cm of the transect (belt method). This was done by walking along the transect and sweeping left to right with the net. We had 5 replicates done in the mowed area but only 3 replicates done in the unmowed because we ran out of time. The insects caught were recorded by the total number caught in the net and also by number of reconganizable taxonomical units (RTU). The RTUs were spider, beetle, caterpillar, ant, leaf hopper and fly. The spider is not an insect but for our purposes we included the spider in our data. The transect was moved randomly via a random number generator ranging from 1-15 steps.
DOI: 10.6084/m9.figshare.1565411
title: Distance Based Dataset- Bird Sightings

description: The experiment was conducted on Tuesday September 28th 2015 from approximately 4:00-4:30 PM at the Stong Pond area at York University. The temperature of the area was around 14°C with pouring rain. The experiment happened in the mowed grass located around the Stong Pond area. We laid down a transect and walked along observing if there were any bird species after every 30 metres. We waited around 1 minute at each stop on the transect tape. At each stop we observed the wind speed using the Beaufort scale. For every bird observed at a stop we recorded its species and the frequency of the bird species. We tried to only observe each bird once in the experiment. We also recorded the approximate distance of the bird from the stop in metres. We did a total of 5 stops along the transect tape. In this experiment it allows the students to learn how to make large scale observations using a belt transect and how to use the Beaufort scale to calculate wind speed.
DOI: 10.6084/m9.figshare.1565461
title: Insect Population of Danby Grassland and Woodlot via Pant Trap

description: This experiment was conducted on Tuesday September 29 2015 in the Danby Woodlot and the Danby Grassland at York University Keele Campus from 3:00pm-5:15pm, with group members Houra, Alexandera and Kathy. The weather was approximately 21°C with cloudy skies, and light to moderate rain fall. Houra and I, were assigned the <strong>pan trap dataset</strong> by the instruction of the TA. The purpose of the pan trap experiment was to collect field data in order to estimate the abundance and diversity of, but not limited to, flying insects. This experiment required us to fill 9 solo bowls (instead of 10) with soapy water and place them in the woodlot, and the same repeated for the grassland. The bowls were arranged in groups of three, giving a total of 3 groups in each location. Each group of bowls consisted of three different colors; yellow, blue and white. When all the lab groups had set up and filled their bowls, the time was noted (3:20pm) and the bowls were left alone for an hour in order for bugs to get trapped the bowl. In the meantime we helped our group members collect their field data. After one hour (4:20pm) the bowls were collected and observed. The total insect count, number of RTU's, Type of RTU, and bowl color was noted for each bowl by looking at the mixture in the bowl from above, giving a total of 18 bowls. After the observation was complete, the soapy water containing the insects was poured onto the ground and the bowls were collected and taken back to the lab. Within the woodlot and grasslands, the group of bowls were placed in various locations, which may have affected the number, and type of insects collected. In the woodlot, group 1 was placed under a tree, group 2-beside a log, and group 3-in the open, on top of some leaves. In the grasslands, group 4 was set next to a common plantain, group 5 -in the grass where no plants near it an group 6- under a tree. It was concluded that not many insects were collected through the pan trap because of the rainy weather conditions, since they were probably sheltering from the rain. The small time frame could have also caused not many bugs to get traped.
DOI: 10.6084/m9.figshare.1565626.v4
title: MoCA: A Tool for Motif Conservation Analysis

description: Poster presented at the USC MCB Retreat 2015.