cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1244900.v1
title: abundance of insects during day verse night

description: Method: The purpose of this experiment is to determine the abundance of different insect species during different time of the day in this case: number of insects during night (8:30 am) vs. number of insects during day time (8:30 pm). The experiment took place at York University Keele campus around east of Stong Pond (Grassland). The experiment was taken from October-14-2014 – October-21-2014. The data was collected after every 12 hours for 7 days. In this experiment pitfall trap technique was used to determine the abundance of insect. Three transects were used and placed at randomly in the middle of the grassland. After that for each transect 5 plastic cups were placed in a grassland area and each plastic cup was placed at 5m apart from each other. Each plastic cup was half filled with soap water, so that we can capture the insects inside the cup. After 12 hours the total numbers of insects inside the each cup were counted, total number of different species inside each cup was recorded, also temperature and plant density were noted After counting the insects, the water inside the cup was replace with new soap water for next experiment and this experiment was continued for 7 days. Data: Location: Grassland: East of Stond Pond at York University Keele campus. Time: The data will be collected for 7 days: the time period of 12 hr (8:00am -8:00pm) Transect Number: Three transects are being use at different location at grassland Pitfall: 15 pitfall trap cups are being used with 5m of distance from each other Temperature (°C): Temperature for each set of data is recorded in degree celcius. Number of Insects: All the insects captured inside the plastic cup is counted and recorded for each trail. Number of species: The different number of species visually observed inside the plastic cup for each trail and were recorded Plant Density: The plant density visually observed by using scale of 1=4 (1= no crowded, 2= very little, 3 =medium crowded, 4= heavily crowded)
DOI: 10.6084/m9.figshare.1244918
title: HIF1A regulates xenophagic degradation of adherent and invasive <i>Escherichia coli</i> (AIEC)

description: The hypoxia inducible transcription factor HIF1 activates autophagy, a general catabolic pathway involved in the maintenance of cellular homeostasis. Dysfunction in both autophagy and HIF1 has been implicated in an increasing number of human diseases, including inflammatory bowel disease (IBD), such as Crohn disease (CD). Adherent invasive <i>E. coli</i> (AIEC) colonize ileal mucosa of CD patients and strongly promote gastrointestinal inflammatory disorders by activation of HIF-dependent responses. Here, we aim to characterize the contribution of HIF1 in xenophagy, a specialized form of autophagy involved in the degradation of intracellular bacteria. Our results showed that endogenous HIF1A knockdown increased AIEC survival in intestinal epithelial cells. We demonstrate that the increase in survival rate correlates with a dramatic impairment of the autophagic flux at the autolysosomal maturation step. Furthermore, we show that AIEC remained within single-membrane LC3-II-positive vesicles and that they were unable to induce the phosphorylation of ULK1. These results suggested that, in the absence of HIF1A, AIEC were found within LC3-associated phagosomes. Using blocking antibodies against TLR5 and CEACAM6, the 2 well-known AIEC-bound receptors, we showed that downstream receptor signaling was necessary to mediate ULK1 phosphorylation. Finally, we provide evidence that HIF1 mediates CEACAM6 expression and that CEACAM6 is necessary to recruit ULK1 in a bacteria-containing signaling hub. Collectively, these results identify a new function for HIF1 in AIEC-dedicated xenophagy, and suggest that coactivation of autophagy and HIF1A expression may be a potential new therapy to resolve AIEC infection in CD patients.
DOI: 10.6084/m9.figshare.1244879
title: Tolerance of Winged and Wingless Insects to Variation in Temperature and Plant Density of a Grassland Habitat at York University: How Species Abundance Varies over Time and Space

description: This experiment took place in the Grassland east of Stong Pond at York University between October 14 and October 22, 2014. Between 2:30PM and 5:30PM on October 14, 15, 21 and 22, three 100 foot transects were laid down in different areas. Two transects were laid westward from the east edge of the Grassland, where one of the two transects was 20 meters North of the other. The third transect was laid southward on the field directly east of the Grassland. For one of the two westward transects, experimenters used scissors to cut a random number of plants (excluding grass) from the bottom of their stems if the bottom of their stem was within 0.5 meters of the outer edge of the transect. To estimate the abundance of winged and wingless insects in a certain area, a quadrat would be centred along each transect every 5 meters. This meant that the distance between the centres of two consecutive quadrats would measure 5 meters. For each quadrat that was placed, experimenters estimated plant density within the inner edges of each quadrat. Following this, a pan trap would be placed directly adjacent to a pitfall trap in the centre of each quadrat that was placed. A pan trap consisted of a white plastic bowl that was half full with soapy water and rested on the surface of the ground. A pitfall trap consisted of a white Styrofoam cup buried and anchored into the ground with a white Styrofoam bowl suspended on top. A total of six quadrats were placed for each transect on a single day. At the end of placing all 18 pairs of traps in a day, the outdoor temperature was recorded. 24 hours after placing the traps, experimenters returned to measure the abundance of winged insects and the abundance of wingless insects in each pair of a pan trap and pitfall trap. These abundances were later taken to calculate the total insect abundance, proportion of winged insects, and the proportion of wingless insects for each replicate.
DOI: 10.6084/m9.figshare.1244918.v4
title: HIF1A regulates xenophagic degradation of adherent and invasive <i>Escherichia coli</i> (AIEC)

description: The hypoxia inducible transcription factor HIF1 activates autophagy, a general catabolic pathway involved in the maintenance of cellular homeostasis. Dysfunction in both autophagy and HIF1 has been implicated in an increasing number of human diseases, including inflammatory bowel disease (IBD), such as Crohn disease (CD). Adherent invasive <i>E. coli</i> (AIEC) colonize ileal mucosa of CD patients and strongly promote gastrointestinal inflammatory disorders by activation of HIF-dependent responses. Here, we aim to characterize the contribution of HIF1 in xenophagy, a specialized form of autophagy involved in the degradation of intracellular bacteria. Our results showed that endogenous HIF1A knockdown increased AIEC survival in intestinal epithelial cells. We demonstrate that the increase in survival rate correlates with a dramatic impairment of the autophagic flux at the autolysosomal maturation step. Furthermore, we show that AIEC remained within single-membrane LC3-II-positive vesicles and that they were unable to induce the phosphorylation of ULK1. These results suggested that, in the absence of HIF1A, AIEC were found within LC3-associated phagosomes. Using blocking antibodies against TLR5 and CEACAM6, the 2 well-known AIEC-bound receptors, we showed that downstream receptor signaling was necessary to mediate ULK1 phosphorylation. Finally, we provide evidence that HIF1 mediates CEACAM6 expression and that CEACAM6 is necessary to recruit ULK1 in a bacteria-containing signaling hub. Collectively, these results identify a new function for HIF1 in AIEC-dedicated xenophagy, and suggest that coactivation of autophagy and HIF1A expression may be a potential new therapy to resolve AIEC infection in CD patients.
DOI: 10.6084/m9.figshare.1244918.v3
title: HIF1A regulates xenophagic degradation of adherent and invasive <i>Escherichia coli</i> (AIEC)

description: The hypoxia inducible transcription factor HIF1 activates autophagy, a general catabolic pathway involved in the maintenance of cellular homeostasis. Dysfunction in both autophagy and HIF1 has been implicated in an increasing number of human diseases, including inflammatory bowel disease (IBD), such as Crohn disease (CD). Adherent invasive <i>E. coli</i> (AIEC) colonize ileal mucosa of CD patients and strongly promote gastrointestinal inflammatory disorders by activation of HIF-dependent responses. Here, we aim to characterize the contribution of HIF1 in xenophagy, a specialized form of autophagy involved in the degradation of intracellular bacteria. Our results showed that endogenous HIF1A knockdown increased AIEC survival in intestinal epithelial cells. We demonstrate that the increase in survival rate correlates with a dramatic impairment of the autophagic flux at the autolysosomal maturation step. Furthermore, we show that AIEC remained within single-membrane LC3-II-positive vesicles and that they were unable to induce the phosphorylation of ULK1. These results suggested that, in the absence of HIF1A, AIEC were found within LC3-associated phagosomes. Using blocking antibodies against TLR5 and CEACAM6, the 2 well-known AIEC-bound receptors, we showed that downstream receptor signaling was necessary to mediate ULK1 phosphorylation. Finally, we provide evidence that HIF1 mediates CEACAM6 expression and that CEACAM6 is necessary to recruit ULK1 in a bacteria-containing signaling hub. Collectively, these results identify a new function for HIF1 in AIEC-dedicated xenophagy, and suggest that coactivation of autophagy and HIF1A expression may be a potential new therapy to resolve AIEC infection in CD patients.
DOI: 10.6084/m9.figshare.1243768
title: Impact of Plant Richness and Closeness to water on Insect Abundance

description: In order to study the relationship between plant species diversity, distance from a water source and insect abundance, a study was done at the Grassland, East of Osgoode Hall, beside the Pond (York University) on October 14 and October 21, 2014. October 14, 2014 was sunny and 18°C and October 21st was 5°C with rain. Distance from the pond was measured using three discrete areas; the first area from the start of the pond to 20m away, the second from 20m to 40m and the final area from 40m to 60m away from the pond. 1m x 1m quadrats were used to measure plant species richness, and sweepnets were used to sweep for insects in order to determine insect abundance. Transects were used to mark out regions across the perimeter of the pond. Each transect was placed 5m away from the first transect, along the perimeter of Strong Pond.
DOI: 10.6084/m9.figshare.1244879.v1
title: Tolerance of Winged and Wingless Insects to Variation in Temperature and Plant Density of a Grassland Habitat at York University: How Species Abundance Varies over Time and Space

description: This experiment took place in the Grassland east of Stong Pond at York University between October 14 and October 22, 2014. Between 2:30PM and 5:30PM on October 14, 15, 21 and 22, three 100 foot transects were laid down in different areas. Two transects were laid westward from the east edge of the Grassland, where one of the two transects was 20 meters North of the other. The third transect was laid southward on the field directly east of the Grassland. For one of the two westward transects, experimenters used scissors to cut a random number of plants (excluding grass) from the bottom of their stems if the bottom of their stem was within 0.5 meters of the outer edge of the transect. To estimate the abundance of winged and wingless insects in a certain area, a quadrat would be centred along each transect every 5 meters. This meant that the distance between the centres of two consecutive quadrats would measure 5 meters. For each quadrat that was placed, experimenters estimated plant density within the inner edges of each quadrat. Following this, a pan trap would be placed directly adjacent to a pitfall trap in the centre of each quadrat that was placed. A pan trap consisted of a white plastic bowl that was half full with soapy water and rested on the surface of the ground. A pitfall trap consisted of a white Styrofoam cup buried and anchored into the ground with a white Styrofoam bowl suspended on top. A total of six quadrats were placed for each transect on a single day. At the end of placing all 18 pairs of traps in a day, the outdoor temperature was recorded. 24 hours after placing the traps, experimenters returned to measure the abundance of winged insects and the abundance of wingless insects in each pair of a pan trap and pitfall trap. These abundances were later taken to calculate the total insect abundance, proportion of winged insects, and the proportion of wingless insects for each replicate.
DOI: 10.6084/m9.figshare.1243768.v1
title: Impact of Plant Richness and Closeness to water on Insect Abundance

description: In order to study the relationship between plant species diversity, distance from a water source and insect abundance, a study was done at the Grassland, East of Osgoode Hall, beside the Pond (York University) on October 14 and October 21, 2014. October 14, 2014 was sunny and 18°C and October 21st was 5°C with rain. Distance from the pond was measured using three discrete areas; the first area from the start of the pond to 20m away, the second from 20m to 40m and the final area from 40m to 60m away from the pond. 1m x 1m quadrats were used to measure plant species richness, and sweepnets were used to sweep for insects in order to determine insect abundance. Transects were used to mark out regions across the perimeter of the pond. Each transect was placed 5m away from the first transect, along the perimeter of Strong Pond.
DOI: 10.6084/m9.figshare.1244589
title: Ecology experimental design

description: We conducted the experimental study at York university Stong pond grassland at two different timings one at 8:00 pm (morning) and the second at 8:00 am (night). The study was conducted for 7 days, but not on the days that had rain because there were be fewer insects on those days. During the study we used 15 pitfall traps for each time of day (total of 210 treatments), which can be assemble by digging a small hole in the ground and placing Styrofoam cup inside it with soapy water, then cover the cup with foam bowl making sure there is some space for the insects to get inside and placing nail on either side of the bowl to secure it in place. The 15 pitfall traps were placed in three random location (5 pitfall for each location) in the grassland every 5 meters from each other for a total of 25 meters by using a transect. When placing the pitfall traps, we observed the plant density at those area by using a scale from 1 to 4, (1= no plant density, 2=low plant density, 3=some plant density and 4=high plant density). After assembling the pitfall trap and recording the plant density for each of them, we took our first recording of abundance and diversity of insects after 12 hours at 8:00 am for the morning result. Each person from the group went out to the site of the pitfall at time they are schedule for and recorded the number of insects in each cup at that time. They also recorded the highest temperature of the day for both morning and night treatments by using the website weathernetwork.com, and the different recognizable taxonomic units of insects they could identify in the cup by observation.
DOI: 10.6084/m9.figshare.1244882.v1
title: Supporting information for Rebich-Hespanha, et al. (2014) "Image themes and frames in US print news stories about climate change", Environmental Communication

description: These files contain supporting information forRebich-Hespanha, S., Rice, R.E., Montello, D.R., Retzloff, S., Tien, S., and Hespanha, J.P. (2015) Image Themes and Frames in U.S. Print News Stories about Climate Change, Environmental Communication, 9(4), 491-519. doi:10.1080/17524032.2014.983534. Please see individual item descriptions for more details about contents. Please cite included items individually.
DOI: 10.6084/m9.figshare.1243757
title: The effects of plant densities and temperature on crawling and dying insect abundances(Data set)

description: The abundance of insects in different levels of plant abunance will be measured on October 14th,15th, 21st and 22nd over 24 hour periods in the grasslands near stong pond.<br>In three different levels of plant density( Low, medium and high), a transect will be layed out. Along every 5 meters of the transect up to 50 meters in each<br>different plant density, 1 pitfall trap and 1 pan trap will be placed. After a 24 hour period has passed, the amount of insects captured in the two traps was recorded.
DOI: 10.6084/m9.figshare.1244589.v1
title: Ecology experimental design

description: We conducted the experimental study at York university Stong pond grassland at two different timings one at 8:00 pm (morning) and the second at 8:00 am (night). The study was conducted for 7 days, but not on the days that had rain because there were be fewer insects on those days. During the study we used 15 pitfall traps for each time of day (total of 210 treatments), which can be assemble by digging a small hole in the ground and placing Styrofoam cup inside it with soapy water, then cover the cup with foam bowl making sure there is some space for the insects to get inside and placing nail on either side of the bowl to secure it in place. The 15 pitfall traps were placed in three random location (5 pitfall for each location) in the grassland every 5 meters from each other for a total of 25 meters by using a transect. When placing the pitfall traps, we observed the plant density at those area by using a scale from 1 to 4, (1= no plant density, 2=low plant density, 3=some plant density and 4=high plant density). After assembling the pitfall trap and recording the plant density for each of them, we took our first recording of abundance and diversity of insects after 12 hours at 8:00 am for the morning result. Each person from the group went out to the site of the pitfall at time they are schedule for and recorded the number of insects in each cup at that time. They also recorded the highest temperature of the day for both morning and night treatments by using the website weathernetwork.com, and the different recognizable taxonomic units of insects they could identify in the cup by observation.
DOI: 10.6084/m9.figshare.1243747
title: SPSS Data File of the Study

description: This is the raw data file with which the analysis of the paper entitled ' Gratefully received, gratefully repaid: the role of perceived fairness in cooperative interactions' was carried out. Please refer to the dataset explanatory document (http://figshare.com/articles/Explanatory_Document_for_the_SPSS_Data_File_of_the_Study/1243735) for details.
DOI: 10.6084/m9.figshare.1243735
title: Explanatory Document for the SPSS Data File of the Study

description: This file is an explanatory document as regards the different variables included in the SPSS data file (DOI:http://figshare.com/articles/SPSS_Data_File_of_the_Study/1243747) of the present study.
DOI: 10.6084/m9.figshare.1243716
title: Capillary Consolidation Method

description: These files contain all the original data reported in a paper by the authors: "A method for characterizing desiccation-induced consolidation and permeability loss of organic soils" in Water Resources Research, 10.1002/2014WR015745.
DOI: 10.6084/m9.figshare.1243716.v1
title: Capillary Consolidation Method

description: These files contain all the original data reported in a paper by the authors: "A method for characterizing desiccation-induced consolidation and permeability loss of organic soils" in Water Resources Research, 10.1002/2014WR015745.
DOI: 10.6084/m9.figshare.1243712
title: Joint Modeling of Multiple Network Views

description: Latent space models (LSM) for network data rely on the basic assumption that each node of the network has an unknown position in a <i>D</i>-dimensional Euclidean latent space: generally the smaller the distance between two nodes in the latent space, the greater their probability of being connected. In this article, we propose a variational inference approach to estimate the intractable posterior of the LSM. In many cases, different network views on the same set of nodes are available. It can therefore be useful to build a model able to jointly summarize the information given by all the network views. For this purpose, we introduce the latent space joint model (LSJM) that merges the information given by multiple network views assuming that the probability of a node being connected with other nodes in each network view is explained by a unique latent variable. This model is demonstrated on the analysis of two datasets: an excerpt of 50 girls from “Teenage Friends and Lifestyle Study” data at three time points and the <i>Saccharomyces cerevisiae</i> genetic and physical protein–protein interactions. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1243712.v2
title: Joint Modeling of Multiple Network Views

description: Latent space models (LSM) for network data rely on the basic assumption that each node of the network has an unknown position in a <i>D</i>-dimensional Euclidean latent space: generally the smaller the distance between two nodes in the latent space, the greater their probability of being connected. In this article, we propose a variational inference approach to estimate the intractable posterior of the LSM. In many cases, different network views on the same set of nodes are available. It can therefore be useful to build a model able to jointly summarize the information given by all the network views. For this purpose, we introduce the latent space joint model (LSJM) that merges the information given by multiple network views assuming that the probability of a node being connected with other nodes in each network view is explained by a unique latent variable. This model is demonstrated on the analysis of two datasets: an excerpt of 50 girls from “Teenage Friends and Lifestyle Study” data at three time points and the <i>Saccharomyces cerevisiae</i> genetic and physical protein–protein interactions. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1243709
title: Data for Haff et al. Journal of Avian Biology 2014

description: Four data files, plus a read me file that describes in detail the data files and all the fields in each file. "Scrubwren feeds" provides data on adult and nestling behaviour around the nest in the 2 minutes before and after a nest provisioning visit; "Scrubwren transcripts" provides data on the behaviour of other scrubwrens on the territory, and tablulates nestling calling in each minute for each nest watch; "Visit synchrony" provides data on how many nest provisioning visits were synchronous for each nest watched; and "Chip Zz" provides measurements for a sample of both chip and zz calls used near nests. The "Read Me" file describes in detail every field in each data file.