cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1243712.v1
title: Joint Modelling of Multiple Network Views

description: Latent space models (LSM) for network data were introduced by Holf et al. (2002) under 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 paper 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 summarise 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 Saccharomyces cerevisiae genetic and physical protein-protein interactions.
DOI: 10.6084/m9.figshare.1243709.v1
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.
DOI: 10.6084/m9.figshare.1243691
title: Effective two-phase <i>p</i>-median approach for the balanced cell formation in the design of cellular manufacturing system

description: In this paper, we present an effective two-phase <i>p</i>-median approach for the balanced cell formation (CF) in the design of cellular manufacturing system. In phase 1, the <i>p</i>-median mathematical model of machine CF, which adopts a linear integer programming formulation, is developed. Our formulation uses a new similarity coefficient based on the generalised nonbinary part-machine incidence matrix (PMIM) which incorporates realistic manufacturing aspects such as setup time, processing time, operation sequences and lot size of parts and duplicate machine types. In phase 2, a systematic part assignment procedure based on the new classification scheme of part types is established in pursuit of balancing the workload among machine cells. New efficiency measures for evaluating the quality of the binary and nonbinary PMIM-based block diagonal solutions are proposed to judge the degree of cell load imbalance. Computational experiments with moderately intermediate-sized data-sets selected from the literature show effectiveness of our two-phase <i>p</i>-median approach for the balanced CF.
DOI: 10.6084/m9.figshare.1243678
title: Exploring the effects of plant species richness and distance to a water source on insect abundance in a representative pond ecosystem - Metadata and Methods

description: To measure insect abundance under different ecological conditions, n=20 transects were randomly placed along Stong Pond (43°46'13.2"N 79°30'25.9"W) on October 14th 2014 and October 21st 2014 from 2:30-4:30pm. The weather conditions varied between the two days of sampling with October 14th being clearer and warmer in comparison to October 21st , which had occasional showers and was colder. In order to separate our sampling areas, transects were equally divided into 3 portions. These areas along the transect were denoted as “Areas” 0,1, and 2 (Approximate length of 60m transect separated into three 20m sections). These represent the locations close to the pond, moderately close and far from the pond, respectively. In these locations, sweep nets were used along the transect in a straight line from the Area starting point to the starting point of the adjacent Area (approximately 20m). After the sweep nets were used, the insect abundance was measured by counting the approximate amount of individuals present within the sweep net. Following the recording of insect abundance, two 1x1m quadrats were placed randomly within the boundaries of the Area and the number of unique plant species was measured. The number of species counted in both quadrats was averaged for each Area. This process was repeated for 20 transects (10 on each sampling day). An area to place the next transect was selected by moving 5m to the left of the previous transect. The subsequent transect was placed and the process was repeated. To ensure the same area wasn’t sampled twice in the same day, a new sample area was selected by moving 20-30m away from the previous two sample areas and the procedure was repeated. After the experiment concluded, the results were aggregated for each Area to produce average insect abundances. An ANOVA test was performed in comparing the average insect abundances for the 3 Areas.
DOI: 10.6084/m9.figshare.1243678.v1
title: Exploring the effects of plant species richness and distance to a water source on insect abundance in a representative pond ecosystem - Metadata and Methods

description: To measure insect abundance under different ecological conditions, n=20 transects were randomly placed along Stong Pond (43°46'13.2"N 79°30'25.9"W) on October 14th 2014 and October 21st 2014 from 2:30-4:30pm. The weather conditions varied between the two days of sampling with October 14th being clearer and warmer in comparison to October 21st , which had occasional showers and was colder. In order to separate our sampling areas, transects were equally divided into 3 portions. These areas along the transect were denoted as “Areas” 0,1, and 2 (Approximate length of 60m transect separated into three 20m sections). These represent the locations close to the pond, moderately close and far from the pond, respectively. In these locations, sweep nets were used along the transect in a straight line from the Area starting point to the starting point of the adjacent Area (approximately 20m). After the sweep nets were used, the insect abundance was measured by counting the approximate amount of individuals present within the sweep net. Following the recording of insect abundance, two 1x1m quadrats were placed randomly within the boundaries of the Area and the number of unique plant species was measured. The number of species counted in both quadrats was averaged for each Area. This process was repeated for 20 transects (10 on each sampling day). An area to place the next transect was selected by moving 5m to the left of the previous transect. The subsequent transect was placed and the process was repeated. To ensure the same area wasn’t sampled twice in the same day, a new sample area was selected by moving 20-30m away from the previous two sample areas and the procedure was repeated. After the experiment concluded, the results were aggregated for each Area to produce average insect abundances. An ANOVA test was performed in comparing the average insect abundances for the 3 Areas.
DOI: 10.6084/m9.figshare.1243676
title: Characterization and expression analyses of two plastidic enolase genes in rice

description: To verify the presence of enolase related to the chloroplastic glycolysis in rice, database search was carried out and identified seven putative enolase genes in the rice genome. Among them, <i>OsEno1</i> and <i>OsEno3</i> encode long proteins with N-terminal extensions. GFP protein fusions of these N-terminal extensions were both targeted to plastids of onion epidermal cell. Promoter::<i>GUS</i> analysis showed that <i>OsEno3</i> was highly expressed in young developing leaves, but its expression was drastically decreased during leaf development and greening. On the other hand, the expression of <i>OsEno1</i> was low and detected in limited portions such as leaf sheath at the tiller base. Recombinant OsEno1 protein showed enolase activity with a pH optimum at pH 8.0, whereas OsEno3 did not exhibit detectable activity. Although it remains obscure if OsEno3 encodes a functional enolase <i>in vivo</i>, our results demonstrate that the entire glycolytic pathway does not operate in rice chloroplasts.
DOI: 10.6084/m9.figshare.1243677
title: Metals in commonly eaten groceries in Western Australia: a market basket survey and dietary assessment

description: Children’s dietary exposure to metals has received limited attention in Australia. This study undertook a market basket survey and analysed 253 food and beverages for metals. These data were used in conjunction with recent average diet data for children in Western Australia to model dietary metals exposure, with mean metals intakes calculated for boys and girls aged 8, 12, 13 and 16 years. Results show that for some metals, including cadmium, nickel and manganese, dietary intake guidelines have been exceeded in younger children. The mean modelled cadmium intake in children aged 8 years was almost 60% of the World Health Organisation (WHO) guideline and exceeded the European Food Safety Authority (EFSA) guideline. Nickel and manganese intake was higher in younger children than reported in international studies. Modelling based on the 95% percentile of dietary consumption exceeded the respective guidelines or upper level of intake for several of the metals studied. The findings from this study support the need for further investigation into the exposure of children to metals from diet and the health implications of exposure.
DOI: 10.6084/m9.figshare.1243691.v2
title: Effective two-phase <i>p</i>-median approach for the balanced cell formation in the design of cellular manufacturing system

description: In this paper, we present an effective two-phase <i>p</i>-median approach for the balanced cell formation (CF) in the design of cellular manufacturing system. In phase 1, the <i>p</i>-median mathematical model of machine CF, which adopts a linear integer programming formulation, is developed. Our formulation uses a new similarity coefficient based on the generalised nonbinary part-machine incidence matrix (PMIM) which incorporates realistic manufacturing aspects such as setup time, processing time, operation sequences and lot size of parts and duplicate machine types. In phase 2, a systematic part assignment procedure based on the new classification scheme of part types is established in pursuit of balancing the workload among machine cells. New efficiency measures for evaluating the quality of the binary and nonbinary PMIM-based block diagonal solutions are proposed to judge the degree of cell load imbalance. Computational experiments with moderately intermediate-sized data-sets selected from the literature show effectiveness of our two-phase <i>p</i>-median approach for the balanced CF.
DOI: 10.6084/m9.figshare.1243691.v1
title: Effective two-phase <i>p</i>-median approach for the balanced cell formation in the design of cellular manufacturing system

description: In this paper, we present an effective two-phase <i>p</i>-median approach for the balanced cell formation (CF) in the design of cellular manufacturing system. In phase 1, the <i>p</i>-median mathematical model of machine CF, which adopts a linear integer programming formulation, is developed. Our formulation uses a new similarity coefficient based on the generalised nonbinary part-machine incidence matrix (PMIM) which incorporates realistic manufacturing aspects such as setup time, processing time, operation sequences and lot size of parts and duplicate machine types. In phase 2, a systematic part assignment procedure based on the new classification scheme of part types is established in pursuit of balancing the workload among machine cells. New efficiency measures for evaluating the quality of the binary and nonbinary PMIM-based block diagonal solutions are proposed to judge the degree of cell load imbalance. Computational experiments with moderately intermediate-sized data-sets selected from the literature show effectiveness of our two-phase <i>p</i>-median approach for the balanced CF.
DOI: 10.6084/m9.figshare.1243675
title: Increased dipicolinic acid production with an enhanced <i>spoVF</i> operon in <i>Bacillus subtilis</i> and medium optimization

description: Dipicolinic acid (DPA) is a multi-functional agent for cosmetics, antimicrobial products, detergents, and functional polymers. The aim of this study was to design a new method for producing DPA from renewable material. The <i>Bacillus subtilis spoVF</i> operon encodes enzymes for DPA synthase and the part of lysine biosynthetic pathway. However, DPA is only synthesized in the sporulation phase, so the productivity of DPA is low level. Here, we report that DPA synthase was expressed in vegetative cells, and DPA was produced in the culture medium by replacement of the <i>spoVFA</i> promoter with other highly expressed promoter in <i>B. subtilis</i> vegetative cells, such as <i>spoVG</i> promoter. DPA levels were increased in the culture medium of genetically modified strains. DPA productivity was significantly improved up to 29.14 g/L in 72 h culture by improving the medium composition using a two-step optimization technique with the Taguchi methodology.
DOI: 10.6084/m9.figshare.1243677.v2
title: Metals in commonly eaten groceries in Western Australia: a market basket survey and dietary assessment

description: Children’s dietary exposure to metals has received limited attention in Australia. This study undertook a market basket survey and analysed 253 food and beverages for metals. These data were used in conjunction with recent average diet data for children in Western Australia to model dietary metals exposure, with mean metals intakes calculated for boys and girls aged 8, 12, 13 and 16 years. Results show that for some metals, including cadmium, nickel and manganese, dietary intake guidelines have been exceeded in younger children. The mean modelled cadmium intake in children aged 8 years was almost 60% of the World Health Organisation (WHO) guideline and exceeded the European Food Safety Authority (EFSA) guideline. Nickel and manganese intake was higher in younger children than reported in international studies. Modelling based on the 95% percentile of dietary consumption exceeded the respective guidelines or upper level of intake for several of the metals studied. The findings from this study support the need for further investigation into the exposure of children to metals from diet and the health implications of exposure.
DOI: 10.6084/m9.figshare.1243676.v1
title: Characterization and expression analyses of two plastidic enolase genes in rice

description: To verify the presence of enolase related to the chloroplastic glycolysis in rice, database search was carried out and identified seven putative enolase genes in the rice genome. Among them, <i>OsEno1</i> and <i>OsEno3</i> encode long proteins with N-terminal extensions. GFP protein fusions of these N-terminal extensions were both targeted to plastids of onion epidermal cell. Promoter::<i>GUS</i> analysis showed that <i>OsEno3</i> was highly expressed in young developing leaves, but its expression was drastically decreased during leaf development and greening. On the other hand, the expression of <i>OsEno1</i> was low and detected in limited portions such as leaf sheath at the tiller base. Recombinant OsEno1 protein showed enolase activity with a pH optimum at pH 8.0, whereas OsEno3 did not exhibit detectable activity. Although it remains obscure if OsEno3 encodes a functional enolase <i>in vivo</i>, our results demonstrate that the entire glycolytic pathway does not operate in rice chloroplasts.
DOI: 10.6084/m9.figshare.1243677.v1
title: Metals in commonly eaten groceries in Western Australia: a market basket survey and dietary assessment

description: Children’s dietary exposure to metals has received limited attention in Australia. This study undertook a market basket survey and analysed 253 food and beverages for metals. These data were used in conjunction with recent average diet data for children in Western Australia to model dietary metals exposure, with mean metals intakes calculated for boys and girls aged 8, 12, 13 and 16 years. Results show that for some metals, including cadmium, nickel and manganese, dietary intake guidelines have been exceeded in younger children. The mean modelled cadmium intake in children aged 8 years was almost 60% of the World Health Organisation (WHO) guideline and exceeded the European Food Safety Authority (EFSA) guideline. Nickel and manganese intake was higher in younger children than reported in international studies. Modelling based on the 95% percentile of dietary consumption exceeded the respective guidelines or upper level of intake for several of the metals studied. The findings from this study support the need for further investigation into the exposure of children to metals from diet and the health implications of exposure.
DOI: 10.6084/m9.figshare.1243675.v1
title: Increased dipicolinic acid production with an enhanced <i>spoVF</i> operon in <i>Bacillus subtilis</i> and medium optimization

description: Dipicolinic acid (DPA) is a multi-functional agent for cosmetics, antimicrobial products, detergents, and functional polymers. The aim of this study was to design a new method for producing DPA from renewable material. The <i>Bacillus subtilis spoVF</i> operon encodes enzymes for DPA synthase and the part of lysine biosynthetic pathway. However, DPA is only synthesized in the sporulation phase, so the productivity of DPA is low level. Here, we report that DPA synthase was expressed in vegetative cells, and DPA was produced in the culture medium by replacement of the <i>spoVFA</i> promoter with other highly expressed promoter in <i>B. subtilis</i> vegetative cells, such as <i>spoVG</i> promoter. DPA levels were increased in the culture medium of genetically modified strains. DPA productivity was significantly improved up to 29.14 g/L in 72 h culture by improving the medium composition using a two-step optimization technique with the Taguchi methodology.
DOI: 10.6084/m9.figshare.1243676.v3
title: Characterization and expression analyses of two plastidic enolase genes in rice

description: To verify the presence of enolase related to the chloroplastic glycolysis in rice, database search was carried out and identified seven putative enolase genes in the rice genome. Among them, <i>OsEno1</i> and <i>OsEno3</i> encode long proteins with N-terminal extensions. GFP protein fusions of these N-terminal extensions were both targeted to plastids of onion epidermal cell. Promoter::<i>GUS</i> analysis showed that <i>OsEno3</i> was highly expressed in young developing leaves, but its expression was drastically decreased during leaf development and greening. On the other hand, the expression of <i>OsEno1</i> was low and detected in limited portions such as leaf sheath at the tiller base. Recombinant OsEno1 protein showed enolase activity with a pH optimum at pH 8.0, whereas OsEno3 did not exhibit detectable activity. Although it remains obscure if OsEno3 encodes a functional enolase <i>in vivo</i>, our results demonstrate that the entire glycolytic pathway does not operate in rice chloroplasts.
DOI: 10.6084/m9.figshare.1243671
title: MERS data June 4, 2014

description: This is a frozen version of the publicly available dataset used for analyses described in the PLoS Currents Outbreaks article by Fisman, Rivers, Lofgren, and Majumdar on MERS-CoV epidemiology.
DOI: 10.6084/m9.figshare.1243675.v3
title: Increased dipicolinic acid production with an enhanced <i>spoVF</i> operon in <i>Bacillus subtilis</i> and medium optimization

description: Dipicolinic acid (DPA) is a multi-functional agent for cosmetics, antimicrobial products, detergents, and functional polymers. The aim of this study was to design a new method for producing DPA from renewable material. The <i>Bacillus subtilis spoVF</i> operon encodes enzymes for DPA synthase and the part of lysine biosynthetic pathway. However, DPA is only synthesized in the sporulation phase, so the productivity of DPA is low level. Here, we report that DPA synthase was expressed in vegetative cells, and DPA was produced in the culture medium by replacement of the <i>spoVFA</i> promoter with other highly expressed promoter in <i>B. subtilis</i> vegetative cells, such as <i>spoVG</i> promoter. DPA levels were increased in the culture medium of genetically modified strains. DPA productivity was significantly improved up to 29.14 g/L in 72 h culture by improving the medium composition using a two-step optimization technique with the Taguchi methodology.
DOI: 10.6084/m9.figshare.1243650
title: Wessel et al. : Quantification and Qualification of Bacteria Trapped in Chewed Gums

description: Dataset accompanying the paper by Wessel et al. : Quantification and Qualification of Bacteria Trapped in Chewed Gums
DOI: 10.6084/m9.figshare.1243676.v2
title: Characterization and expression analyses of two plastidic enolase genes in rice

description: To verify the presence of enolase related to the chloroplastic glycolysis in rice, database search was carried out and identified seven putative enolase genes in the rice genome. Among them, <i>OsEno1</i> and <i>OsEno3</i> encode long proteins with N-terminal extensions. GFP protein fusions of these N-terminal extensions were both targeted to plastids of onion epidermal cell. Promoter::<i>GUS</i> analysis showed that <i>OsEno3</i> was highly expressed in young developing leaves, but its expression was drastically decreased during leaf development and greening. On the other hand, the expression of <i>OsEno1</i> was low and detected in limited portions such as leaf sheath at the tiller base. Recombinant OsEno1 protein showed enolase activity with a pH optimum at pH 8.0, whereas OsEno3 did not exhibit detectable activity. Although it remains obscure if OsEno3 encodes a functional enolase <i>in vivo</i>, our results demonstrate that the entire glycolytic pathway does not operate in rice chloroplasts.
DOI: 10.6084/m9.figshare.1243671.v1
title: MERS data June 4, 2014

description: This is a frozen version of the publicly available dataset used for analyses described in the PLoS Currents Outbreaks article by Fisman, Rivers, Lofgren, and Majumdar on MERS-CoV epidemiology.
DOI: 10.6084/m9.figshare.1243675.v2
title: Increased dipicolinic acid production with an enhanced <i>spoVF</i> operon in <i>Bacillus subtilis</i> and medium optimization

description: Dipicolinic acid (DPA) is a multi-functional agent for cosmetics, antimicrobial products, detergents, and functional polymers. The aim of this study was to design a new method for producing DPA from renewable material. The <i>Bacillus subtilis spoVF</i> operon encodes enzymes for DPA synthase and the part of lysine biosynthetic pathway. However, DPA is only synthesized in the sporulation phase, so the productivity of DPA is low level. Here, we report that DPA synthase was expressed in vegetative cells, and DPA was produced in the culture medium by replacement of the <i>spoVFA</i> promoter with other highly expressed promoter in <i>B. subtilis</i> vegetative cells, such as <i>spoVG</i> promoter. DPA levels were increased in the culture medium of genetically modified strains. DPA productivity was significantly improved up to 29.14 g/L in 72 h culture by improving the medium composition using a two-step optimization technique with the Taguchi methodology.