cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1232198
title: Human disturbance on insect diversity, abundance and plant diversity

description: The study that was conducted in this experiment is the human effect on insect diversity, insect abundance and plant diversity. Three sampling areas were selected based on the total vegetation coverage. The experimental areas were as follows: highly disturbed area intermediate disturbed area and last but not least, less disturbed area. The hypothesis of this study is that the area with moderate disturbance would contain the maximum species diversity. This prediction goes under the ecological theory of intermediate disturbance hypothesis. Furthermore at low level of disturbance, it is predicted to observe maximum abundance. Highly disturbed sampling area was selected near Vanier College. Two 20m transects were laid on the ground horizontally and vertically perpendicular to each other to measure 400 m2 sampling size. A numbered grid system was used to divide the 20m by 20m sampling area which was randomly selected into 25 grids using a random number table. Grids were numbered from 1 to 400, representing 1mx1m plots. Each experimenter then used the sweep nets of 35 centimeter (cm) diameter to catch the insects. The sweep nets were held about 10cm above the ground and moved back and forth from one edge to the opposite edge of quadrat. The sweeping motion was carried for about 1.5 seconds. The process was carried out similarly for the other randomly placed quadrats. Number of insect and different types of insects were observed and recorded in the data sheet. Based on visual observations of plant morphology or appearance, plant diversity was recorded. Plant diversity included grass and other different visible species of plant. The vegetation coverage was recorded based on visual observation by standing upright and making an estimate of the area covered by vegetation including grass. Vegetation coverage was recorded as a percentage value. The same process was done for Danby grassland which was sampled for intermediate disturbance level and for forest near the Pond road which was sampled for less disturbance level. The experiment was done on October 17, 2014 and October 24, 2014 from 2:30pm to 5:30pm in Keele campus of York University, Toronto Ontario. This experiment was done in groups of 3-4. Our group members included Sana Jamal, Ferinaz, Afraa Tarafdar and Maham Anees (me). The weather was cloudy. The temperature was approximately 16ᵒC.
DOI: 10.6084/m9.figshare.1232205.v1
title: Genome-wide DNA methylation analysis identifies a metabolic memory profile in patient-derived diabetic foot ulcer fibroblasts

description: Diabetic foot ulcers (DFUs) are a serious complication of diabetes. Previous exposure to hyperglycemic conditions accelerates a decline in cellular function through metabolic memory despite normalization of glycemic control. Persistent, hyperglycemia-induced epigenetic patterns are considered a central mechanism that activates metabolic memory; however, this has not been investigated in patient-derived fibroblasts from DFUs. We generated a cohort of patient-derived lines from DFU fibroblasts (DFUF), and site- and age-matched diabetic foot fibroblasts (DFF) and non-diabetic foot fibroblasts (NFF) to investigate global and genome-wide DNA methylation patterns using liquid chromatography/mass spectrometry and the Illumina Infinium HumanMethylation450K array. DFFs and DFUFs demonstrated significantly lower global DNA methylation compared to NFFs (p = 0.03). Hierarchical clustering of differentially methylated probes (DMPs, p = 0.05) showed that DFFs and DFUFs cluster together and separately from NFFs. Twenty-five percent of the same probes were identified as DMPs when individually comparing DFF and DFUF to NFF. Functional annotation identified enrichment of DMPs associated with genes critical to wound repair, including angiogenesis (p = 0.07) and extracellular matrix assembly (p = 0.035). Identification of sustained DNA methylation patterns in patient-derived fibroblasts after prolonged passage in normoglycemic conditions demonstrates persistent metabolic memory. These findings suggest that epigenetic-related metabolic memory may also underlie differences in wound healing phenotypes and can potentially identify therapeutic targets.
DOI: 10.6084/m9.figshare.1232198.v1
title: Human disturbance on insect diversity, abundance and plant diversity

description: The study that was conducted in this experiment is the human effect on insect diversity, insect abundance and plant diversity. Three sampling areas were selected based on the total vegetation coverage. The experimental areas were as follows: highly disturbed area intermediate disturbed area and last but not least, less disturbed area. The hypothesis of this study is that the area with moderate disturbance would contain the maximum species diversity. This prediction goes under the ecological theory of intermediate disturbance hypothesis. Furthermore at low level of disturbance, it is predicted to observe maximum abundance. Highly disturbed sampling area was selected near Vanier College. Two 20m transects were laid on the ground horizontally and vertically perpendicular to each other to measure 400 m2 sampling size. A numbered grid system was used to divide the 20m by 20m sampling area which was randomly selected into 25 grids using a random number table. Grids were numbered from 1 to 400, representing 1mx1m plots. Each experimenter then used the sweep nets of 35 centimeter (cm) diameter to catch the insects. The sweep nets were held about 10cm above the ground and moved back and forth from one edge to the opposite edge of quadrat. The sweeping motion was carried for about 1.5 seconds. The process was carried out similarly for the other randomly placed quadrats. Number of insect and different types of insects were observed and recorded in the data sheet. Based on visual observations of plant morphology or appearance, plant diversity was recorded. Plant diversity included grass and other different visible species of plant. The vegetation coverage was recorded based on visual observation by standing upright and making an estimate of the area covered by vegetation including grass. Vegetation coverage was recorded as a percentage value. The same process was done for Danby grassland which was sampled for intermediate disturbance level and for forest near the Pond road which was sampled for less disturbance level. The experiment was done on October 17, 2014 and October 24, 2014 from 2:30pm to 5:30pm in Keele campus of York University, Toronto Ontario. This experiment was done in groups of 3-4. Our group members included Sana Jamal, Ferinaz, Afraa Tarafdar and Maham Anees (me). The weather was cloudy. The temperature was approximately 16ᵒC.
DOI: 10.6084/m9.figshare.1232201.v1
title: MI Wolf Survey 2013

description: Abstract: Whereas past wolf management in the United States was restricted to recovery, managers must now contend with publicly contentious post-recovery issues including regulated hunting seasons. Understanding stakeholder concerns associated with hunting can inform stakeholder engagement, communication, and policy development and evaluation. Social identity theory (SIT) has been used to understand how groups interact, why they conflict, and how collaboration may be achieved. Applying SIT to stakeholder conflicts about wolf hunting may help delineate groups according to their concern about, support for or opposition to the policy choice of hunting wolves. Our objective was to assess concerns about hunting as a tool to resolve conflict in Michigan, using SIT as a framework. We used a mixed-modal sampling approach (e.g., paper, Internet) with wolf hunting-related public meeting participants in March 2013. Survey questions focused on 12 concerns previously identified as associated with hunting as a management tool to resolve conflict. Respondents (n = 666) cared greatly about wolves but were divided over hunting wolves. Wolf conflicts, use of science in policy decisions, and maintaining a wolf population were the highest ranked concerns. Principle components analysis reduced concerns into three factors that explained 50.7% of total variance; concerns crystallized over justifications for hunting. General linear models revealed a lack of geographic influence on care, fear and support for hunting related to wolves. These findings challenge assumptions about regional differences and suggest a strong role for social identity in driving dichotomized public perceptions in wildlife management.
DOI: 10.6084/m9.figshare.1232179
title: Squirrel Abundance in Urban and Woodlot Environments

description: <strong> Introduction</strong> This field study was conducted in collaboration with Angela Joseph, Enrique Sapena Ventura, and Hasan Hamam. The topic of squirrel abundance was prompted by a shared curiosity about the friendly nature of squirrels that were observed on campus. After some discussion of the environmental factors that may lead to such behaviour, it was decided to investigate the abundance of squirrels found in heavy traffic areas of the York University campus, in comparison to a more natural habitat in a woodlot environment. The remains of food left by humans on the campus, both in garbage cans and on the ground, is believed to play a role in the abundance of squirrels in the urban environment. With more food readily available in the more urban areas of the campus, the squirrels are hypothesized to be more abundant in these areas, as commensalism between the humans and the squirrels should be present. There is no cost to humans, as the garbage being thrown out is waste to us regardless, but the squirrels have a chance of gaining a meal by scavenging the scraps. <strong>Predictions</strong> If there is commensalism between humans and squirrels, it should be expected that there will be a higher abundance of squirrels located in close proximity to the busiest areas of the campus. This should result in most of the squirrels being near to the central area of the campus, and a much lower number of squirrels in the woodlot. As there is some risk to the squirrels of being in such close contact with humans (we are fairly large omnivores in comparison), the amount of food present should be enough to outweigh the risks, but also be less than the competition of other squirrels feeding elsewhere. This implies that there may be a threshold where the squirrels will have a large enough amount of food to outweigh the risk of coming into too close of a contact with humans, but far enough away to not get trampled or captured. <strong>Methods</strong> Data was collected from pre-determined areas of the York University, Keele campus. Efforts were made to maintain a consistent size in the areas sampled by comparing size on Google Maps. The Urban environment data was collected along a path beginning at the front of Vari Hall and following Campus Walk around the west end of Steacie Building, ending at the north-east side of Farquharson building just before the greenhouses. The woodlot environment datasets were collected from the woodlot directly south of Chimneystack road on the east end of the campus. A staggered path was followed beginning at the center of the south side and leading through the woodlot to the north end, then looping around the west side to observe the separate copse of trees at the very south west corner. Both the woodlot and urban paths were followed for both datasets and were walked for a total of 45 minutes each time. Data was collected on two consecutive Fridays between 2:30 and 5:30. Weather conditions on the first field day were overcast with light rain, and weather was was warm and sunny on the second field day.
DOI: 10.6084/m9.figshare.1232205.v2
title: Genome-wide DNA methylation analysis identifies a metabolic memory profile in patient-derived diabetic foot ulcer fibroblasts

description: Diabetic foot ulcers (DFUs) are a serious complication of diabetes. Previous exposure to hyperglycemic conditions accelerates a decline in cellular function through metabolic memory despite normalization of glycemic control. Persistent, hyperglycemia-induced epigenetic patterns are considered a central mechanism that activates metabolic memory; however, this has not been investigated in patient-derived fibroblasts from DFUs. We generated a cohort of patient-derived lines from DFU fibroblasts (DFUF), and site- and age-matched diabetic foot fibroblasts (DFF) and non-diabetic foot fibroblasts (NFF) to investigate global and genome-wide DNA methylation patterns using liquid chromatography/mass spectrometry and the Illumina Infinium HumanMethylation450K array. DFFs and DFUFs demonstrated significantly lower global DNA methylation compared to NFFs (p = 0.03). Hierarchical clustering of differentially methylated probes (DMPs, p = 0.05) showed that DFFs and DFUFs cluster together and separately from NFFs. Twenty-five percent of the same probes were identified as DMPs when individually comparing DFF and DFUF to NFF. Functional annotation identified enrichment of DMPs associated with genes critical to wound repair, including angiogenesis (p = 0.07) and extracellular matrix assembly (p = 0.035). Identification of sustained DNA methylation patterns in patient-derived fibroblasts after prolonged passage in normoglycemic conditions demonstrates persistent metabolic memory. These findings suggest that epigenetic-related metabolic memory may also underlie differences in wound healing phenotypes and can potentially identify therapeutic targets.
DOI: 10.6084/m9.figshare.1232174
title: Analysis of the trade-off theory: Comparing growth and reproduction of American buckthorn (Rhamnus frangula) at York University

description: On October 17 and October 24, 2014, 3 students (Cait Carew, Lilach Halevi, and Nitharsija Srikanthan) located a woodlot on the East end of York University, Keele campus. The first day was marked by periods of overcast skies with temperatures of 11degrees Celsius and the second day with clear skies and temperatures near 15degrees Celsius during sampling hours (between 3:00-5:00pm). Observations of leaf morphology, bark, and berries identified the tree of interest as American buckthorn, Rhamnus frangula. Using a block sampling method, a transect tape was placed along the forest edge with the 0 mark aligned with the base of the first tree sample. Trees that fell along the transect tape were only observed if their diameter at breast height (dbh in cm) was greater than, or equal to 13cm. Height intervals were used to roughly estimate tree height, 1=less than 3m; 2=between 3.4-6m; and 3 greater than 6m. Height estimates were made by using known height of a student and assuming how many times bigger the tree was in comparison. Three random branches were sampled from each tree (branches defined as terminal outgrowths of approximately 40cm in length from the point of divergence from the point of attachment to the tip). The berries on each of the branches were counted, and three berries were removed, at random, from each of the three branches in order to measure the diameter using a small, millimetre measuring tape (total of nine berries per tree). The total number of berries was averaged to get the number of berries per branch and the diameter of the nine berries was used to find the average berry diameter of each individual tree. Three random leaves were also removed from each branch and the length and width were recorded. These values were used to calculate the approximate surface area of the leaf using the equation for area of a rhombus (A=[(l*w)/2]), since the leaves were elliptical and this was the easiest method of approximation. The approximate leaf area was averaged for each individual tree. The entire process was repeated for each tree which fell along the transect tape, as long as the dbh was greater than or equal to 13cm until 50 samples were obtained. Statistical analyses of berry diameter in relation to leaf area; of berry diameter in relation to tree height; and of leaf area in relation to tree height were used to identify result significance and possible correlations between tree traits.
DOI: 10.6084/m9.figshare.1232179.v1
title: Squirrel Abundance in Urban and Woodlot Environments

description: <strong> Introduction</strong> This field study was conducted in collaboration with Angela Joseph, Enrique Sapena Ventura, and Hasan Hamam. The topic of squirrel abundance was prompted by a shared curiosity about the friendly nature of squirrels that were observed on campus. After some discussion of the environmental factors that may lead to such behaviour, it was decided to investigate the abundance of squirrels found in heavy traffic areas of the York University campus, in comparison to a more natural habitat in a woodlot environment. The remains of food left by humans on the campus, both in garbage cans and on the ground, is believed to play a role in the abundance of squirrels in the urban environment. With more food readily available in the more urban areas of the campus, the squirrels are hypothesized to be more abundant in these areas, as commensalism between the humans and the squirrels should be present. There is no cost to humans, as the garbage being thrown out is waste to us regardless, but the squirrels have a chance of gaining a meal by scavenging the scraps. <strong>Predictions</strong> If there is commensalism between humans and squirrels, it should be expected that there will be a higher abundance of squirrels located in close proximity to the busiest areas of the campus. This should result in most of the squirrels being near to the central area of the campus, and a much lower number of squirrels in the woodlot. As there is some risk to the squirrels of being in such close contact with humans (we are fairly large omnivores in comparison), the amount of food present should be enough to outweigh the risks, but also be less than the competition of other squirrels feeding elsewhere. This implies that there may be a threshold where the squirrels will have a large enough amount of food to outweigh the risk of coming into too close of a contact with humans, but far enough away to not get trampled or captured. <strong>Methods</strong> Data was collected from pre-determined areas of the York University, Keele campus. Efforts were made to maintain a consistent size in the areas sampled by comparing size on Google Maps. The Urban environment data was collected along a path beginning at the front of Vari Hall and following Campus Walk around the west end of Steacie Building, ending at the north-east side of Farquharson building just before the greenhouses. The woodlot environment datasets were collected from the woodlot directly south of Chimneystack road on the east end of the campus. A staggered path was followed beginning at the center of the south side and leading through the woodlot to the north end, then looping around the west side to observe the separate copse of trees at the very south west corner. Both the woodlot and urban paths were followed for both datasets and were walked for a total of 45 minutes each time. Data was collected on two consecutive Fridays between 2:30 and 5:30. Weather conditions on the first field day were overcast with light rain, and weather was was warm and sunny on the second field day.
DOI: 10.6084/m9.figshare.1232173
title: Squirrel Abundance

description: The lab was conducted by myself and 3 peers: Hassan, Enrique and Brad. The experiment investigated the differences in squirrel abundance in urban and woodland areas of York University. The objective of the experiment was to answer the biological question regarding the differences in abundance of the squirrels in the two areas and the reasons why they differed. It was hypothesized that there would be a greater abundance of squirrels in woodland areas as opposed to urban areas because of greater food, decreased stress (due to people) and increased space for shelter. The hypothesis was based on the predictions that food supply would be vital for squirrel survival with winter approaching. Therefore there would be a greater presence of squirrels in the woodland areas with many acorn baring trees and bushes present. The experiment took place over the duration of 2 labs, with approximately 45 minutes designated to the woodland and urban area per lab. We started in Vari Hall (urban) area and followed Campus Walk towards the west end of Steacies Building where we ended at the east side of the Lumbers- Farquharson tunnel. Using Google maps to mark these designated areas, observations were made for the urban area. For the woodlot area, data was collected from the woodlot located south of the Chimneystack road at the end of campus. We started walking from the centre and in towards the woodlot and then looped around the west side. Squirrels were observed for and recorded. The variables that were investigated were: density of people present, the number of squirrels, color, activity, competition, resources and size. The density of people was a visual approximation using a scale from 0-2, where 0 was no human density, 1 was a medium amount of people, and 2 was a high amount of human density. This variable was investigated to test whether stress caused by abundance of people affected the abundance of squirrels. The number of squirrels were then counted during time of observation in the designated area. Any squirrels present in the area were counted and noted for. The colour of the squirrels counted were also noted for based on the most abundant colour seen on the squirrel. The activity of the squirrel was observed to see whether it was standing, eating or running. Competition measured other mammals such as birds, groundhogs and chipmunks that were present during the time of observation. If the animal used the same resources as the squirrels, it was considered competition and noted as active. If there were animals that present but did not compete for the same resources as the squirrels, it was denoted as present or absent if no animals were seen. Resources was noted as present or absent based on if there were acorn baring trees and bushes with berries. It also took into account various bushes and trees where squirrels would climb and shelter themselves. The size of the squirrels were visually observed based on how big they were and were scaled from 1-5, where 1 was a small squirrel and 5 was a large squirrel.
DOI: 10.6084/m9.figshare.1232205.v3
title: Genome-wide DNA methylation analysis identifies a metabolic memory profile in patient-derived diabetic foot ulcer fibroblasts

description: Diabetic foot ulcers (DFUs) are a serious complication of diabetes. Previous exposure to hyperglycemic conditions accelerates a decline in cellular function through metabolic memory despite normalization of glycemic control. Persistent, hyperglycemia-induced epigenetic patterns are considered a central mechanism that activates metabolic memory; however, this has not been investigated in patient-derived fibroblasts from DFUs. We generated a cohort of patient-derived lines from DFU fibroblasts (DFUF), and site- and age-matched diabetic foot fibroblasts (DFF) and non-diabetic foot fibroblasts (NFF) to investigate global and genome-wide DNA methylation patterns using liquid chromatography/mass spectrometry and the Illumina Infinium HumanMethylation450K array. DFFs and DFUFs demonstrated significantly lower global DNA methylation compared to NFFs (p = 0.03). Hierarchical clustering of differentially methylated probes (DMPs, p = 0.05) showed that DFFs and DFUFs cluster together and separately from NFFs. Twenty-five percent of the same probes were identified as DMPs when individually comparing DFF and DFUF to NFF. Functional annotation identified enrichment of DMPs associated with genes critical to wound repair, including angiogenesis (p = 0.07) and extracellular matrix assembly (p = 0.035). Identification of sustained DNA methylation patterns in patient-derived fibroblasts after prolonged passage in normoglycemic conditions demonstrates persistent metabolic memory. These findings suggest that epigenetic-related metabolic memory may also underlie differences in wound healing phenotypes and can potentially identify therapeutic targets.