cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1228793.v1
title: Squirrel Abundance as a function of habitat and other factors

description: The data for “Squirrel Abundance as a function of habitat and other factors" was collected on Friday October 24 and 31, 2014 from 3:00 to 5:30pm at Woodlot and Urban areas in York University Keele Campus in Toronto Ontario. The weather was gloomy and the sky was covered with clouds not allowing much light to the ground in both days. The wind was not too strong and the temperature was around 13 degrees Celsius. The field experiments (the woodlot or urban areas at York) the time was split equally for both, 1 hour and 15 min. The squirrels we visualized by either binoculars or the naked eye and its characteristics were written down (color, size, activity) and the factors that would affect its abundance such as (human density, competition and food resources). We tried to search for different urban areas to see whether the abundance will change with the change of the other factors. So for the urban area experiment, it was done In front of Vari Hall, behind Lumbers building, and on the campus walk from Lumbers to Vari Hall. While for the woodlot experiment, it was done inside the woodlot and on the edges. The experiment was replicated to make sure that the data can be generalized as a rule for the squirrel abundance at York University and to be assured that the data was collected in the right way. The hypothesis for this experiment is the would the abundance of squirrels between urban and woodlot areas be affected by competition ( between same or different species), human density, and food resources. We predicted prior the experiment that we are going to find more squirrels in the urban areas than the woodlot wild area due to the high food resources which would attract the squirrels the most compared to the competition and human density. Group members who did this experiment are: Hasan, Angela, Brad and Enrique.
DOI: 10.6084/m9.figshare.1228794.v2
title: Examining the effects of sunlight and density on silver maple trees

description: Location: York University's woodlot Target adult silver maple trees that are twice our height were randomly chosen and their diameters were measured at breast height. A radius of 10m was measured using a transect from the target tree and each tree that was in that radius was counted. The sunlight percentage was estimated by seeing how much sky is shown throught the tree's canopy. A frame that was held up to the sky with our back facing the tree. The next target silver maple tree was chosen by walking 5m away from the previous radius. A total of 35 target trees were measured and radius counted.
DOI: 10.6084/m9.figshare.1228779
title: Effect of powerline on goldenrod

description: Gunjan Bhayani
DOI: 10.6084/m9.figshare.1228794.v1
title: Examining the effects of sunlight and density on silver maple trees

description: Location: York University's woodlot Target adult silver maple trees that are twice our height were randomly chosen and their diameters were measured at breast height. A radius of 10m was measured using a transect from the target tree and each tree that was in that radius was counted. The sunlight percentage was estimated by seeing how much sky is shown throught the tree's canopy. A frame that was held up to the sky with our back facing the tree. The next target silver maple tree was chosen by walking 5m away from the previous radius. A total of 35 target trees were measured and radius counted.
DOI: 10.6084/m9.figshare.1228779.v1
title: Effect of powerline on goldenrod

description: Gunjan Bhayani
DOI: 10.6084/m9.figshare.1228776
title: Effect of powerline and thicket on goldenrod growth and abundance of plant species

description: Gunjan Bhayani
DOI: 10.6084/m9.figshare.1228772
title: eology lab 5

description: This experiment was done to test the number of insects attracted by each coloured pan and to see whether the pan colour ,the location the pans are set at and temperature has an effect on attracting insects.<br>This experiment was done in two days for 2hours for a total of 4hours.<br>We set up the pans in three different locations woodlot, grassland and disturbed and assessed each area based on the number of insects each pan contained and the vegetation surrounding it. The vegetation crowding scale was within 50cm radius of the pans, and designed a scale for it where 0 is empty, 1 is fairly crowded and 2 is very crowded.. The equipments used in this experiment included Soapy water, transect tape, 15 blue pans, 15 white pans and 15 yellow pans for a total of 45 pans per day. to start with we pulled the transect tape 45m and set the pans 3m apart in alternating colours in this order blue, white , yellow. We filled the pans 3/4 full with soapy water and left for two hours then returned and collected the data to test our hypothesis.
DOI: 10.6084/m9.figshare.1228776.v1
title: Effect of powerline and thicket on goldenrod growth and abundance of plant species

description: Gunjan Bhayani
DOI: 10.6084/m9.figshare.1228761
title: Molecular placement of rutin in MNV-1 RdRp

description: Rutin conformation in MNV-1 RdRp (3UPF) after 50ns molecular dynamic simulation starting from the XP pose.
DOI: 10.6084/m9.figshare.1228772.v1
title: eology lab 5

description: This experiment was done to test the number of insects attracted by each coloured pan and to see whether the pan colour ,the location the pans are set at and temperature has an effect on attracting insects.<br>This experiment was done in two days for 2hours for a total of 4hours.<br>We set up the pans in three different locations woodlot, grassland and disturbed and assessed each area based on the number of insects each pan contained and the vegetation surrounding it. The vegetation crowding scale was within 50cm radius of the pans, and designed a scale for it where 0 is empty, 1 is fairly crowded and 2 is very crowded.. The equipments used in this experiment included Soapy water, transect tape, 15 blue pans, 15 white pans and 15 yellow pans for a total of 45 pans per day. to start with we pulled the transect tape 45m and set the pans 3m apart in alternating colours in this order blue, white , yellow. We filled the pans 3/4 full with soapy water and left for two hours then returned and collected the data to test our hypothesis.
DOI: 10.6084/m9.figshare.1228757
title: Suplementary-material

description: Suplementary material from the article "Floristic survey of Restinga Forests in southern Bahia reveals the effect of geography on community composition" by Fernandes & Queiroz
DOI: 10.6084/m9.figshare.1228761.v1
title: Molecular placement of rutin in MNV-1 RdRp

description: Rutin conformation in MNV-1 RdRp (3UPF) after 50ns molecular dynamic simulation starting from the XP pose.
DOI: 10.6084/m9.figshare.1228727
title: Invasive vs. Native Species

description: Method<br>Materials required (4 transects 25mX25m) were obtained and every member of the group was given specific responsibility.<br>Fourth group member was asked to take all the observations on the data table.<br>Two group members were asked to setup 4 transects making a square quadrant.<br>Third group member was given the responsibility of counting all the trees within that quadrant.<br>Once the transects were set 2 group members marked all the buck thorns and maple trees in that quadrant with rubber bands.<br>Fourth group member was asked to write down all the observations on the data table.<br>DBH of every buckthorn tree and the maple tree was measured and was written down in the observation table.<br>First quadrant was set up almost at the edge of the Danby Woodlot and consecutive quadrant was set up diagonally to the first one.<br>Due to lack of time only 3 quadrants were completed on Day 1 and a tree was marked with a yellow tape and a picture was taken to determine where set up 4th quadrant next week.<br>Next week, Wednesday, the experiment was continued; tree marked with yellow tape was found and a 4th quadrant was set up.<br>A total of 5 quadrants were observed and the number of buckthorns and maple trees were recorded in each quadrant
DOI: 10.6084/m9.figshare.1228757.v1
title: Suplementary-material

description: Suplementary material from the article "Floristic survey of Restinga Forests in southern Bahia reveals the effect of geography on community composition" by Fernandes & Queiroz
DOI: 10.6084/m9.figshare.1228760.v1
title: galvani test data

description: Data for the unit tests of galvani
DOI: 10.6084/m9.figshare.1228727.v1
title: Invasive vs. Native Species

description: Method<br>Materials required (4 transects 25mX25m) were obtained and every member of the group was given specific responsibility.<br>Fourth group member was asked to take all the observations on the data table.<br>Two group members were asked to setup 4 transects making a square quadrant.<br>Third group member was given the responsibility of counting all the trees within that quadrant.<br>Once the transects were set 2 group members marked all the buck thorns and maple trees in that quadrant with rubber bands.<br>Fourth group member was asked to write down all the observations on the data table.<br>DBH of every buckthorn tree and the maple tree was measured and was written down in the observation table.<br>First quadrant was set up almost at the edge of the Danby Woodlot and consecutive quadrant was set up diagonally to the first one.<br>Due to lack of time only 3 quadrants were completed on Day 1 and a tree was marked with a yellow tape and a picture was taken to determine where set up 4th quadrant next week.<br>Next week, Wednesday, the experiment was continued; tree marked with yellow tape was found and a 4th quadrant was set up.<br>A total of 5 quadrants were observed and the number of buckthorns and maple trees were recorded in each quadrant
DOI: 10.6084/m9.figshare.1228726
title: Docking analysis insights quercetin can be a non-antibiotic adjuvant by inhibiting Mmr drug efflux pump in <i>Mycobacterium</i> sp. and its homologue EmrE in <i>Escherichia coli</i>

description: Drug efflux pumps (EP) like Mmr in <i>Mycobacterium</i> transported drugs out of cell, a main reason for drug resistance developing in <i>Mycobacterium tuberculosis</i>. In this <i>in silico</i> study, mainly analysed EP inhibitory potential of a plant-derived flavonoid, quercetin, through docking analysis. Mmr present in <i>Mycobacterium smegmatis</i> and <i>M. tuberculosis,</i> and its homologue EmrE of <i>Escherichia coli</i> was used<i>.</i> Initially, homology modelling of EP monomers and dimers constructed from <i>M. smegmatis</i>, <i>M. tuberculosis</i> and <i>E. coli</i>; the stabilities of models were analysed from Ramachandran plots prepared in PROCHECK. Docking analysis of quercetin with EP protein showed that in all three organisms, the residues for function and stability are important and quercetin had best interactions comparing to compounds such as, verapamil, reserpine, chlorpromazine, Carbonyl Cyanide m- Chloro Phenylhydrazone. Molecular dynamics and simulation studies showed that during the entire course of simulation quercetin-Mmr complex were stable. It insights quercetin can act as a non-antibiotic adjuvant for treatment of tuberculosis by bring down the efflux of drug from bacteria.
DOI: 10.6084/m9.figshare.1228724
title: The Relationship Between Tree Sapling Density and Competing Adult Density Between North American Deciduous Trees

description: York University’s Danby Woodlot is a small deciduous forest on the outskirts of Toronto. The woodlot is home to many common North American trees such as maple, elm, and oak. This study was designed to find out if there is a correlation between the density of saplings surrounding its parent tree, and the density of competing adult trees that surround it. The two main factors of this experiment include the density of daughter saplings in a six-metre radius surrounding its parent, and the density of competing adults in the same six-metre radius. A third factor was measured, and that is the amount of light penetrating the forest canopy. It is expected that as the density of competing adult trees increases, the density of saplings surrounding its parent should decrease. This competition could arise from many factors, including, but not limited to, the availability of light and soil nutrients. The data was obtained by measuring 6m from a target tree in three directions, using three transects, and doing a physical count of specimens inside the circumference generated by the transects. All of the daughter saplings in the area were counted, as were all competing adults (of any species). Saplings were defined as any tree less than six feet tall. Daughter saplings were defined as any sapling of the same species as the parent (target) tree, regardless of proximity to other trees of the same species. Light availability under the canopy was estimated using thumb-and-forefinger rectangles aimed skyward at four points under the target tree. The four estimates were then averaged to generate the approximate amount of light reaching the forest floor under that tree. Thirty target trees were selected randomly.
DOI: 10.6084/m9.figshare.1228726.v1
title: Docking analysis insights quercetin can be a non-antibiotic adjuvant by inhibiting Mmr drug efflux pump in <i>Mycobacterium</i> sp. and its homologue EmrE in <i>Escherichia coli</i>

description: Drug efflux pumps (EP) like Mmr in <i>Mycobacterium</i> transported drugs out of cell, a main reason for drug resistance developing in <i>Mycobacterium tuberculosis</i>. In this <i>in silico</i> study, mainly analysed EP inhibitory potential of a plant-derived flavonoid, quercetin, through docking analysis. Mmr present in <i>Mycobacterium smegmatis</i> and <i>M. tuberculosis,</i> and its homologue EmrE of <i>Escherichia coli</i> was used<i>.</i> Initially, homology modelling of EP monomers and dimers constructed from <i>M. smegmatis</i>, <i>M. tuberculosis</i> and <i>E. coli</i>; the stabilities of models were analysed from Ramachandran plots prepared in PROCHECK. Docking analysis of quercetin with EP protein showed that in all three organisms, the residues for function and stability are important and quercetin had best interactions comparing to compounds such as, verapamil, reserpine, chlorpromazine, Carbonyl Cyanide m- Chloro Phenylhydrazone. Molecular dynamics and simulation studies showed that during the entire course of simulation quercetin-Mmr complex were stable. It insights quercetin can act as a non-antibiotic adjuvant for treatment of tuberculosis by bring down the efflux of drug from bacteria.
DOI: 10.6084/m9.figshare.1228724.v1
title: The Relationship Between Tree Sapling Density and Competing Adult Density Between North American Deciduous Trees

description: York University’s Danby Woodlot is a small deciduous forest on the outskirts of Toronto. The woodlot is home to many common North American trees such as maple, elm, and oak. This study was designed to find out if there is a correlation between the density of saplings surrounding its parent tree, and the density of competing adult trees that surround it. The two main factors of this experiment include the density of daughter saplings in a six-metre radius surrounding its parent, and the density of competing adults in the same six-metre radius. A third factor was measured, and that is the amount of light penetrating the forest canopy. It is expected that as the density of competing adult trees increases, the density of saplings surrounding its parent should decrease. This competition could arise from many factors, including, but not limited to, the availability of light and soil nutrients. The data was obtained by measuring 6m from a target tree in three directions, using three transects, and doing a physical count of specimens inside the circumference generated by the transects. All of the daughter saplings in the area were counted, as were all competing adults (of any species). Saplings were defined as any tree less than six feet tall. Daughter saplings were defined as any sapling of the same species as the parent (target) tree, regardless of proximity to other trees of the same species. Light availability under the canopy was estimated using thumb-and-forefinger rectangles aimed skyward at four points under the target tree. The four estimates were then averaged to generate the approximate amount of light reaching the forest floor under that tree. Thirty target trees were selected randomly.
DOI: 10.6084/m9.figshare.1228760.v2
title: galvani test data

description: Data for the unit tests of galvani
DOI: 10.6084/m9.figshare.1228636
title: Traditional and geometric morphometric analyses reveal homogeneity in European <i>Scutacarus acarorum</i> Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)

description: The mite <i>Scutacarus acarorum</i> (Scutacaridae, Heterostigmatina) is one of the dominant bumblebee inquilines in the Holarctic. The wide distribution and the host generalist behaviour of <i>S. acarorum</i> suggest that it could be a group of multiple cryptic species. European <i>S. acarorum</i> populations and a small population from New York were studied using traditional and geometric morphometric methods to detect possible geographical or host-dependent variation. The analyses revealed homogeneity of all populations, suggesting that the species experienced a bottleneck during the last ice age and that gene flow between the populations is maintained. High variability within populations indicates a high genetic diversity. No host-related morphological differences were detected, suggesting that <i>S. acarorum</i> is a true generalist. Fresh mite samples from locations all over the Holarctic are needed to draw further conclusions on the species’ phylogeography and also on its population genetic structure.
DOI: 10.6084/m9.figshare.1228508
title: pytnt test data

description: Data files for the pytnt unit tests
DOI: 10.6084/m9.figshare.1228636.v2
title: Traditional and geometric morphometric analyses reveal homogeneity in European <i>Scutacarus acarorum</i> Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)

description: The mite <i>Scutacarus acarorum</i> (Scutacaridae, Heterostigmatina) is one of the dominant bumblebee inquilines in the Holarctic. The wide distribution and the host generalist behaviour of <i>S. acarorum</i> suggest that it could be a group of multiple cryptic species. European <i>S. acarorum</i> populations and a small population from New York were studied using traditional and geometric morphometric methods to detect possible geographical or host-dependent variation. The analyses revealed homogeneity of all populations, suggesting that the species experienced a bottleneck during the last ice age and that gene flow between the populations is maintained. High variability within populations indicates a high genetic diversity. No host-related morphological differences were detected, suggesting that <i>S. acarorum</i> is a true generalist. Fresh mite samples from locations all over the Holarctic are needed to draw further conclusions on the species’ phylogeography and also on its population genetic structure.
DOI: 10.6084/m9.figshare.1228507
title: Log Sbwriel Eryri :: Snowdon Litter Log

description: Results of ongoing surveys to gauge the amount of litter located on Snowdon in North Wales, close to paths popular with walkers and other casual visitors. It is intended to show the types of litter as an indicator of behaviour and littering-motivation.
DOI: 10.6084/m9.figshare.1228636.v1
title: Traditional and geometric morphometric analyses reveal homogeneity in European <i>Scutacarus acarorum</i> Goeze, 1780 populations (Acari: Scutacaridae: Heterostigmatina)

description: The mite <i>Scutacarus acarorum</i> (Scutacaridae, Heterostigmatina) is one of the dominant bumblebee inquilines in the Holarctic. The wide distribution and the host generalist behaviour of <i>S. acarorum</i> suggest that it could be a group of multiple cryptic species. European <i>S. acarorum</i> populations and a small population from New York were studied using traditional and geometric morphometric methods to detect possible geographical or host-dependent variation. The analyses revealed homogeneity of all populations, suggesting that the species experienced a bottleneck during the last ice age and that gene flow between the populations is maintained. High variability within populations indicates a high genetic diversity. No host-related morphological differences were detected, suggesting that <i>S. acarorum</i> is a true generalist. Fresh mite samples from locations all over the Holarctic are needed to draw further conclusions on the species’ phylogeography and also on its population genetic structure.
DOI: 10.6084/m9.figshare.1228508.v12
title: pytnt test data

description: Data files for the pytnt unit tests
DOI: 10.6084/m9.figshare.1228456
title: Gaussian Job Archive for C50H66N6O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1228456.v1
title: Gaussian Job Archive for C50H66N6O2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1228508.v13
title: pytnt test data

description: Data files for the pytnt unit tests
DOI: 10.6084/m9.figshare.1228366
title: ecology exparimental design data set

description: Methods: First two sites were found in the Yorku grassland, one with only flattened grass or bare soil and one with at least waist high vegetation. They were both 25 meters in length measured by transects. Some plants were removed to make the flattened grass section uniform. Then 9 Pan Traps of alternating colours (yellow, blue, white 3 of each) were placed along the transects with 2 meters in between each pan trap. Then weather and conditions of the area were recorded. Then pan traps were left for 3 hours. The contents of traps were collected and sorted by species counted and identified to see the difference in variation of species in the two areas, recorded then disposed of. This was repeated on the same day one week later.
DOI: 10.6084/m9.figshare.1228507.v1
title: Log Sbwriel

description: Results of surveys to gauge the amount of litter located on Snowdon in North Wales, close to paths popular with walkers and other casual visitors. It was intended to show the types of litter as an indicator of behaviour and littering-motivation.
DOI: 10.6084/m9.figshare.1228366.v1
title: ecology exparimental design data set

description: Methods: First two sites were found in the Yorku grassland, one with only flattened grass or bare soil and one with at least waist high vegetation. They were both 25 meters in length measured by transects. Some plants were removed to make the flattened grass section uniform. Then 9 Pan Traps of alternating colours (yellow, blue, white 3 of each) were placed along the transects with 2 meters in between each pan trap. Then weather and conditions of the area were recorded. Then pan traps were left for 3 hours. The contents of traps were collected and sorted by species counted and identified to see the difference in variation of species in the two areas, recorded then disposed of. This was repeated on the same day one week later.
DOI: 10.6084/m9.figshare.1228364
title: Experiment 5 (Pantrap experiment)

description: This field data was collected at the grasslands situated in York University on 3rd November 2014 at around 3pm in 10*C weather. This research was done by a group of undergraduate students under the supervison of a T.A. Three colours of pantraps were used and were placed in 3 rows of 12 in alternating colours ranging from yellow-white-blue. The pantraps were half filled with soapy water. After the duration of 2 hours the pantraps were observed again and the total number and type of macro-invertebrates trapped in each bowl were counted and recorded.