cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1597458
title: Co-occurrence and Limiting Similarity Null Model Type I and Type II Error Rate Dataset

description: THIS DATASET ACCOMPANIES: Lavender, T.M., Schamp, B.S., and Lamb, E.G., The influence of matrix size on statistical properties of co-occurrence and limiting similarity null models. PLoS ONE, In Review. <strong>ABSTRACT</strong> Null models exploring species co-occurrence and trait-based limiting similarity are increasingly used to explore the influence of competition on community assembly; however, assessments of common models have not thoroughly explored the influence of variation in matrix size on error rates, in spite of the fact that studies have explored community matrices that vary considerably in size. To determine how smaller matrices, which are of greatest concern, perform statistically, we generated biologically realistic presence-absence matrices ranging in size from 3-50 species and sites, as well as associated trait matrices. We examined co-occurrence tests using the C-Score statistic and independent swap algorithm. For trait-based limiting similarity null models, we used the mean nearest neighbour trait distance (NN) and the standard deviation of nearest neighbour distances (SDNN) as test statistics, and considered two common randomization algorithms: abundance independent trait shuffling (AITS), and abundance weighted trait shuffling (AWTS). Matrices as small as three × three resulted in acceptable type I error rates (p &lt; 0.05) for both the co-occurrence and trait-based limiting similarity null models when, exclusive p-values were used. The commonly used inclusive p-value (≤ or ≥, as opposed to exclusive p-values; &lt; or &gt;) was associated with increased type I error rates, particularly for matrices with fewer than eight species. Type I error rates increased for limiting similarity tests using the AWTS randomization scheme when community matrices contained more than 35 sites; a similar randomization used in null models of phylogenetic dispersion has previously been viewed as robust. Notwithstanding other potential deficiencies related to the use of small matrices to represent communities, the application of both classes of null model should be restricted to matrices with 10 or more species to avoid the possibility of type II errors. Additionally, researchers should restrict the use of the AWTS randomization to matrices with fewer than 35 sites to avoid type I errors when testing for trait-based limiting similarity. The AITS randomization scheme performed better in terms of type I error rates, and therefore may be more appropriate when considering systems for which traits are not clustered by abundance. Please see the README.txt file and associated manuscript for details on the data contained in this repository.
DOI: 10.6084/m9.figshare.1597450
title: Palynostratigraphy and palaeoenvironments of the Eagle Ford Group (Upper Cretaceous) at the Lozier Canyon outcrop reference section, west Texas, USA

description: This study describes the detailed palynology of the Eagle Ford Group at Lozier Canyon, its principal outcrop reference section in west Texas. Prominent marine phytoplankton assemblages are consistent with a proposed depositional setting for Lozier Canyon on a submarine platform within the Cretaceous Western Interior Seaway (KWIS) of the USA. The Lower Eagle Ford Formation (middle to upper Cenomanian) was deposited under restricted marine conditions with oxygen-deficient, probably anoxic bottom waters, as indicated by the black, organic-rich (ca. 1 to &gt; 6% total organic carbon) shale lithology. The formation comprises two fourth-order stratigraphical sequences, each showing sedimentary evidence of increasing water depth during deposition. Palynomorph assemblages from the sequences are dominated by green algal prasinophyte phycomata in the lower parts and peridinioid dinoflagellate cysts in the upper parts. The productivity of these marine phytoplankton groups may have been stimulated by availability of ammonium (prasinophytes) and nitrite (peridinioids) from upwelling, or vertical expansion of the oxygen-minimum zone. The transition from prasinophyte- to peridinioid-dominated assemblages may reflect elevation of the photic zone to a level less regularly encroached by deeper, ammonium-enriched waters of the denitrification zone. The overlying Upper Eagle Ford Formation (upper Cenomanian to upper Turonian or Coniacian) was deposited under deeper, relatively open marine conditions, as indicated by a decrease in organic carbon content and an increase in carbonate content. This is supported by the presence of diversified dinoflagellate cyst assemblages, including inter-regional (high- to mid-latitude) marker events; in the upper Cenomanian, base and acme <i>Cyclonephelium compactum-membraniphorum</i>, top consistent and frequent <i>Litosphaeridium siphoniphorum</i>, and top <i>Adnatosphaeridium tutulosum</i>; in the middle to upper Turonian, range bases of <i>Heterosphaeridium difficile</i> and <i>Senoniasphaera rotundata</i>. The stratigraphical resolution offered by palynology indicates potential application to wellsite ‘geosteering’ of commercial shale oil and shale gas wells drilled in the Eagle Ford Group.
DOI: 10.6084/m9.figshare.1597447
title: Enteric lactoferrin attenuates the development of high-fat and high-cholesterol diet-induced hypercholesterolemia and atherosclerosis in Microminipigs

description: Previously, we found that enteric lactoferrin (eLF) could reduce the visceral fat accumulation known to associate strongly with metabolic syndrome symptoms and consequently with an increased risk of atherosclerosis. In this study, the atherosclerosis-preventive potential of LF was assessed in a high-fat and high-cholesterol diet (HFCD)-induced hypercholesterolemia and atherosclerosis model using Microminipig™. Eight-week orally administered eLF remarkably reduced the HFCD-induced serum total and low-density lipoprotein cholesterol levels but not high-density lipoprotein cholesterol levels. A histological analysis of 15 arteries revealed that eLF systemically inhibited the development of atherosclerotic lesions. Pathway analysis using identified genes that characterized eLF administration in liver revealed significant changes in the steroid biosynthesis pathway (ssc00100) and all affected genes in this pathway were upregulated, suggesting that cholesterol synthesis inhibited by HFCD was recovered by eLF. In summary, eLF could potentially prevent the hypercholesterolemia and atherosclerosis through protecting homeostasis from HFCD-induced dysfunction of cholesterol metabolism.
DOI: 10.6084/m9.figshare.1597450.v2
title: Palynostratigraphy and palaeoenvironments of the Eagle Ford Group (Upper Cretaceous) at the Lozier Canyon outcrop reference section, west Texas, USA

description: This study describes the detailed palynology of the Eagle Ford Group at Lozier Canyon, its principal outcrop reference section in west Texas. Prominent marine phytoplankton assemblages are consistent with a proposed depositional setting for Lozier Canyon on a submarine platform within the Cretaceous Western Interior Seaway (KWIS) of the USA. The Lower Eagle Ford Formation (middle to upper Cenomanian) was deposited under restricted marine conditions with oxygen-deficient, probably anoxic bottom waters, as indicated by the black, organic-rich (ca. 1 to &gt; 6% total organic carbon) shale lithology. The formation comprises two fourth-order stratigraphical sequences, each showing sedimentary evidence of increasing water depth during deposition. Palynomorph assemblages from the sequences are dominated by green algal prasinophyte phycomata in the lower parts and peridinioid dinoflagellate cysts in the upper parts. The productivity of these marine phytoplankton groups may have been stimulated by availability of ammonium (prasinophytes) and nitrite (peridinioids) from upwelling, or vertical expansion of the oxygen-minimum zone. The transition from prasinophyte- to peridinioid-dominated assemblages may reflect elevation of the photic zone to a level less regularly encroached by deeper, ammonium-enriched waters of the denitrification zone. The overlying Upper Eagle Ford Formation (upper Cenomanian to upper Turonian or Coniacian) was deposited under deeper, relatively open marine conditions, as indicated by a decrease in organic carbon content and an increase in carbonate content. This is supported by the presence of diversified dinoflagellate cyst assemblages, including inter-regional (high- to mid-latitude) marker events; in the upper Cenomanian, base and acme <i>Cyclonephelium compactum-membraniphorum</i>, top consistent and frequent <i>Litosphaeridium siphoniphorum</i>, and top <i>Adnatosphaeridium tutulosum</i>; in the middle to upper Turonian, range bases of <i>Heterosphaeridium difficile</i> and <i>Senoniasphaera rotundata</i>. The stratigraphical resolution offered by palynology indicates potential application to wellsite ‘geosteering’ of commercial shale oil and shale gas wells drilled in the Eagle Ford Group.
DOI: 10.6084/m9.figshare.1597447.v1
title: Enteric lactoferrin attenuates the development of high-fat and high-cholesterol diet-induced hypercholesterolemia and atherosclerosis in Microminipigs

description: Previously, we found that enteric lactoferrin (eLF) could reduce the visceral fat accumulation known to associate strongly with metabolic syndrome symptoms and consequently with an increased risk of atherosclerosis. In this study, the atherosclerosis-preventive potential of LF was assessed in a high-fat and high-cholesterol diet (HFCD)-induced hypercholesterolemia and atherosclerosis model using Microminipig™. Eight-week orally administered eLF remarkably reduced the HFCD-induced serum total and low-density lipoprotein cholesterol levels but not high-density lipoprotein cholesterol levels. A histological analysis of 15 arteries revealed that eLF systemically inhibited the development of atherosclerotic lesions. Pathway analysis using identified genes that characterized eLF administration in liver revealed significant changes in the steroid biosynthesis pathway (ssc00100) and all affected genes in this pathway were upregulated, suggesting that cholesterol synthesis inhibited by HFCD was recovered by eLF. In summary, eLF could potentially prevent the hypercholesterolemia and atherosclerosis through protecting homeostasis from HFCD-induced dysfunction of cholesterol metabolism.
DOI: 10.6084/m9.figshare.1597450.v1
title: Palynostratigraphy and palaeoenvironments of the Eagle Ford Group (Upper Cretaceous) at the Lozier Canyon outcrop reference section, west Texas, USA

description: This study describes the detailed palynology of the Eagle Ford Group at Lozier Canyon, its principal outcrop reference section in west Texas. Prominent marine phytoplankton assemblages are consistent with a proposed depositional setting for Lozier Canyon on a submarine platform within the Cretaceous Western Interior Seaway (KWIS) of the USA. The Lower Eagle Ford Formation (middle to upper Cenomanian) was deposited under restricted marine conditions with oxygen-deficient, probably anoxic bottom waters, as indicated by the black, organic-rich (ca. 1 to &gt; 6% total organic carbon) shale lithology. The formation comprises two fourth-order stratigraphical sequences, each showing sedimentary evidence of increasing water depth during deposition. Palynomorph assemblages from the sequences are dominated by green algal prasinophyte phycomata in the lower parts and peridinioid dinoflagellate cysts in the upper parts. The productivity of these marine phytoplankton groups may have been stimulated by availability of ammonium (prasinophytes) and nitrite (peridinioids) from upwelling, or vertical expansion of the oxygen-minimum zone. The transition from prasinophyte- to peridinioid-dominated assemblages may reflect elevation of the photic zone to a level less regularly encroached by deeper, ammonium-enriched waters of the denitrification zone. The overlying Upper Eagle Ford Formation (upper Cenomanian to upper Turonian or Coniacian) was deposited under deeper, relatively open marine conditions, as indicated by a decrease in organic carbon content and an increase in carbonate content. This is supported by the presence of diversified dinoflagellate cyst assemblages, including inter-regional (high- to mid-latitude) marker events; in the upper Cenomanian, base and acme <i>Cyclonephelium compactum-membraniphorum</i>, top consistent and frequent <i>Litosphaeridium siphoniphorum</i>, and top <i>Adnatosphaeridium tutulosum</i>; in the middle to upper Turonian, range bases of <i>Heterosphaeridium difficile</i> and <i>Senoniasphaera rotundata</i>. The stratigraphical resolution offered by palynology indicates potential application to wellsite ‘geosteering’ of commercial shale oil and shale gas wells drilled in the Eagle Ford Group.
DOI: 10.6084/m9.figshare.1597044
title: Plant Height Symphyotrichum ericoides and Solidago Canadensis in relation to distance to water source

description: This experiment explored primarily if there was a correlation between plant height and distance from the closest water source. The experiment was conducted at York Univeristy, three bodies of water were chosen in the relative vicinity. Stong Pond, Village Pond and Black creek were the three locations to ensure that if any variation was found it was due to the factors observed.After the three locations were chosen, through observation and finding out which plants grew at all the locations, Symphyotrichum ericoides and Solidago canadensis were chosen, Symphyotrichum ericoides more commonly known as white aster and Solidago canadensis known as goldenrod or Canadian golden rod. The experiment was performed on the 1st, 8th and 15th of October 2015 at 2:30 each time. All three locations were visited each data collection day. The group of 4 visited each location together to lower inter-observer variability. The materials used were two transects and a quadrate. One transect would be placed from the water’s edge to 15m. The three distances observers were the distance where the bank ended and plants began to grow, for this experiment it was approximately 3m for each water source, 12m and 15m. The bank that was most accessible was chosen so we could safely conclude the experiment, a distance of 10m was measured along the water edge (vertically) and through an Excel random number generator worksheet, the number chosen would be where the transect would be placed horizontally away from the water. At each distance, the random number generator would be used to designate the location of where the quadrate would be placed. Within each quadrate, the abundance and height of Symphyotrichum ericoides and Solidago canadensis were recorded.To average the height, 5 samples were taken per plant species per quadrate. The second transect was used to measure the heights.
DOI: 10.6084/m9.figshare.1597210
title: Exploring the Relationship amongst Interacting Plant Communities of Solidago canadensis and Symphyotrichum ericoides as Distance from a Water Source Increases

description: In order to better understand the relationship between plant height and distance from a water source, a study was conducted on successive weeks during the afternoons (from 2:30PM to 5:00PM EST) of October 1st, 8th and 15th 2015 at York University’s Keele campus (43° 46' 9.228"N, 79° 30' 29.556’’W). We selected three sources of water (Stong Pond, Black Creek Pond and Dan Iannuzzi Park Pond) with similar characteristics in terms of surrounding herbaceous vegetation (all three locations were dominated by herbaceous perennial plants), canopy coverage (little to no canopy coverage), and elevation gradients and soil types. The two plants in question were the Symphyotrichum ericoides (white aster) and the Solidago canadensis (Canadian goldenrod), both of which are native to North America. A stratified random sampling procedure was adopted where the area surrounding each water source was stratified into three concentric categories based on soil type: dry, weathered and wet (Figure 2). Soil types at approximately 3 m were considered “wet,” at 12 m “weathered” and at 15 m “dry.” These three strata were visually identified based on a consensus of all four observers in the study, in order to minimize estimate errors due to observer bias. At all three locations, one line transect was transversed at the most shallow edge of the pond. A one by one meter quadrat was then placed from the point where the transect ends. The direction of quadrat placement for each stratum was determined through a randomization procedure, using a random number table on Microsoft Excel. In each sample plot, the following variables were measured: plant height and distance from water source. Plant height was measured using a second transect, where we measured from the base of the stem to the apical bud. Plants measured along quadrat margins were included if more than half of the rooted system was visibly inside the quadrat. Three replicate plots were sampled for each stratum, at each location, resulting in a total of 81 replicates. Mean temperature and precipitation during the month of October in southern Ontario ranged from 14-18 °C and 64 mm, respectively. We conducted statistical tests using SPSS where the independent variable was distance from water source and the dependent variable was plant height. We performed a one-way ANOVA to compare differences in plant height as distance from the water source increased, based on soil type. Means were separated by application of the Tukey post-hoc test. We considered there to be no significance when the value of the probability of significance (p-value) was greater than 0.05. To further test whether there were differences in growth between the two species, regardless if one was inherently smaller than the other, we used a two-tailed, independent sample t-test assuming equal variance.
DOI: 10.6084/m9.figshare.1597044.v1
title: Plant Height Symphyotrichum ericoides and Solidago Canadensis in relation to distance to water source

description: This experiment explored primarily if there was a correlation between plant height and distance from the closest water source. The experiment was conducted at York Univeristy, three bodies of water were chosen in the relative vicinity. Stong Pond, Village Pond and Black creek were the three locations to ensure that if any variation was found it was due to the factors observed.After the three locations were chosen, through observation and finding out which plants grew at all the locations, Symphyotrichum ericoides and Solidago canadensis were chosen, Symphyotrichum ericoides more commonly known as white aster and Solidago canadensis known as goldenrod or Canadian golden rod. The experiment was performed on the 1st, 8th and 15th of October 2015 at 2:30 each time. All three locations were visited each data collection day. The group of 4 visited each location together to lower inter-observer variability. The materials used were two transects and a quadrate. One transect would be placed from the water’s edge to 15m. The three distances observers were the distance where the bank ended and plants began to grow, for this experiment it was approximately 3m for each water source, 12m and 15m. The bank that was most accessible was chosen so we could safely conclude the experiment, a distance of 10m was measured along the water edge (vertically) and through an Excel random number generator worksheet, the number chosen would be where the transect would be placed horizontally away from the water. At each distance, the random number generator would be used to designate the location of where the quadrate would be placed. Within each quadrate, the abundance and height of Symphyotrichum ericoides and Solidago canadensis were recorded.To average the height, 5 samples were taken per plant species per quadrate. The second transect was used to measure the heights.
DOI: 10.6084/m9.figshare.1596953
title: Data & Metadata

description: This is my data and my metadata for the 3 weeks of data collection.
DOI: 10.6084/m9.figshare.1597026
title: Methods

description: Methods and Comments
DOI: 10.6084/m9.figshare.1596759
title: Bird feeding preference DATA

description: Data and Metadata of bird feeding preferences tested at York University in Toronto ON. Feeding preferences observed through the use of red,yellow,and green colored bird seed and five distances from bird occupied trees from 1, 5, 10, 15 and 20m away. Weight of seed is measured after 2 hours of observation and recorded from a 30g reference. Distance is held constant at 1, 5, 10, 15 and 20m of a bird occupied tree.
DOI: 10.6084/m9.figshare.1597026.v1
title: Methods

description: Methods and Comments
DOI: 10.6084/m9.figshare.1596004
title: Bird Study Data Set Biol 3250

description: Using four decimals scale, 900 grams of bird seed was measured three times and placed in three identical plastic containers. Each container was then treated with water and one dye colour: red, green or yellow. Water allowed the dye to be absorbed by seed in order for seed to express the desired colour. 30 grams of coloured seed was then placed in 25 empty white bowls, and this was repeated for each colour. In total there was 125 bowls of seed each with 30 grams of either yellow, red or green in each bow. Bowls were brought to five chosen forest on York University campus in Toronto Ontario on October 1st, 2015. The edges of each forest were designated with a number from 1-4; North-1, South-2, West-3, and East-4. Using a random number generator, one of the four edges of the forest was chosen. The chosen edge was further divided horizontally along the edge into four equal sections, each section was then designated with a number from 1-4. Using a random number generator one of the section along the chosen edge was selected. The trees along the edge of the chosen section was then numbered, and using a random number generator a tree was selected. Starting from the chosen tree, orientated perpendicularly to the edge of the forest, 20 meter of the transect tape was placed on the ground. Walking along the transect tape three bowls each containing 30.00 grams of bird seed was placed in triangular orientation on the ground at the 1-meter mark of the transect tape. Each bowl within the triangular orientation contained a different colour bird seed; 1 bowl contained green bird seed, 1 bowl contained red bird seed and 1 bowl contained yellow bird seeds. This was repeated at 5, 10, 15, and 20 meters’ mark of the transect tape. Next the recorder stood in close proximity of the bowls until exactly 3:00 p.m. Eastern Pacific time, ensuring that no birds began eating the birds seed. At exactly 3:00 p.m.- 5:00 p.m. Eastern Pacific time, the recorder moved 30 feet away from bowls allowing the birds to begin to eat the bird seeds. At 5:00 p.m. the bird seeds remaining in each bowl was then weighed and recorded. This was repeated again on Thursday October 8th , 2015 and Thursday October 15th, 2015.
DOI: 10.6084/m9.figshare.1596953.v1
title: Data & Metadata

description: This is my data and my metadata for the 3 weeks of data collection.