cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.825676.v1
title: A video and photographic study of aggregation, swimming and respiratory behaviour changes in the Grey Nurse Shark (<i>Carcharias taurus</i>) in response to the presence of SCUBA divers

description: The Grey Nurse Shark (<i>Carcharias taurus</i>) is a popular attraction for shark eco-tourism using SCUBA. The species is also ‘globally Vulnerable’ (IUCN 2008. List of Threatened Species. www.iucnredlist.org/). Magic Point (off Maroubra) in Sydney is favoured by recreational SCUBA divers wishing to observe these sharks. The objective of this study was to experimentally test the level of the activities of recreational SCUBA divers on shark behaviour. This study assessed the shark responses to diver group size (4, 8 and 12), time of day (am, noon and pm) and diver distance from the sharks (3 m and 6 m). The study found that diver activity does affect the aggregation, swimming and respiratory behaviour of sharks at this site, albeit at short-term levels. Diver group size had no significant effect on shark aggregation, but the proximity of divers to the sharks was crucial. Shark distribution in the cave changed significantly in the presence of divers at 3 m distance from the cave, but stayed unchanged at 6 m. This was particularly apparent in the presence of large groups of 12 divers at 3 m distance when sharks increased their swim speed and ventilation mechanism from ‘active’ to ‘RAM’ ventilation. Such change coincided with a sudden decrease in ventilation frequency. Our research suggests that these effects are short-term and that sharks resume their behaviour once the divers retreat. If divers abide by the current code of practice for diving at this site, it is unlikely that their activities will substantially impact Grey Nurse Sharks in the long term.
DOI: 10.6084/m9.figshare.825678.v1
title: Drivers of <i>Pinus sylvestris</i> L. regeneration following small, high-severity fire in a dry, inner-alpine valley

description: In dry, inner-alpine valleys, regeneration of Scots pine after large, high-severity fires is limited by seed dispersal distance. When dispersal limitations are relaxed (small fires), colonization dynamics of Scots pine remain unclear. Our aims were (1) to assess the regeneration niche of Scots pine seedlings following small fires in a dry, inner-alpine valley and (2) to measure the influence of competition, drought, fertility, and soil pH on pine colonization. We sampled pine seedlings in six high-severity fires (1962–2006), where distance from the unburned edge was
DOI: 10.6084/m9.figshare.825680.v2
title: Distribution range and ecological niche of <i>Primula marginata</i> Curtis (Primulaceae)

description: The distribution range of <i>Primula marginata</i> Curtis (Primulaceae) has never been fully characterized. In the present study, authors did a revision of the distribution range using herbaria material, database records and <i>in situ</i> populations' check-up. <i>P. marginata</i> was confirmed extending from Cottian to Maritime and Ligurian Alps, with few outlier occurrences in the northern Apennines. The localities previously reported from northern Piedmont (Val d'Ossola) were not confirmed. Maximum entropy model (Maxent) was used to simulate the potential distribution of <i>P. marginata</i> under current climate conditions. According to the distribution modelling performed, the species prefers rocky calcareous habitats mainly at high elevations, with abundant precipitation, but low moisture retention at soil level and marked temperature range between winter and summer seasons. The potential distribution area drawn by Maxent seemed to describe <i>P. marginata</i> at its maximum extension, and any future climate changes might cause limitations for the survival of the species.
DOI: 10.6084/m9.figshare.825678.v3
title: Drivers of <i>Pinus sylvestris</i> L. regeneration following small, high-severity fire in a dry, inner-alpine valley

description: In dry, inner-alpine valleys, regeneration of Scots pine after large, high-severity fires is limited by seed dispersal distance. When dispersal limitations are relaxed (small fires), colonization dynamics of Scots pine remain unclear. Our aims were (1) to assess the regeneration niche of Scots pine seedlings following small fires in a dry, inner-alpine valley and (2) to measure the influence of competition, drought, fertility, and soil pH on pine colonization. We sampled pine seedlings in six high-severity fires (1962–2006), where distance from the unburned edge was
DOI: 10.6084/m9.figshare.825678.v2
title: Drivers of <i>Pinus sylvestris</i> L. regeneration following small, high-severity fire in a dry, inner-alpine valley

description: In dry, inner-alpine valleys, regeneration of Scots pine after large, high-severity fires is limited by seed dispersal distance. When dispersal limitations are relaxed (small fires), colonization dynamics of Scots pine remain unclear. Our aims were (1) to assess the regeneration niche of Scots pine seedlings following small fires in a dry, inner-alpine valley and (2) to measure the influence of competition, drought, fertility, and soil pH on pine colonization. We sampled pine seedlings in six high-severity fires (1962–2006), where distance from the unburned edge was
DOI: 10.6084/m9.figshare.825670
title: Pectinoidea (Mollusca: Bivalvia) from Iceland

description: The Icelandic pectinoid fauna is reviewed, based on material from the benthic survey programme BIOICE and 17 species are recorded. <i>Similipecten oskarssoni</i> is proposed as a replacement name for <i>Pecten groenlandicus</i> var. <i>minor</i> Locard, 1898 (Propeamussiidae), which is considered a valid species. Lectotypes are designated for <i>Pecten groenlandicus</i> var. <i>minor</i> and <i>Pecten frigidus</i> Jensen, 1904 (Pectinidae). <i>Cyclopecten ambiannulatus</i> Schein, 1989, <i>Parvamussium propinquum</i> (Smith, 1885), <i>Catillopecten eucymatus</i> (Dall, 1898), and <i>Aequipecten opercularis</i> (Linnaeus, 1758) were previously not known from the Icelandic fauna. All species are figured and described and distinguishing characters are discussed. The distribution in Scandinavian and North Atlantic waters is revised based on the collections in SMNH. The low frequency of juvenile specimens of <i>A. opercularis</i>, <i>Mimachlamys varia</i> and <i>Pecten maximus</i> may indicate that Scandinavian populations are the result of very occasional recruitment.
DOI: 10.6084/m9.figshare.825670.v1
title: Pectinoidea (Mollusca: Bivalvia) from Iceland

description: The Icelandic pectinoid fauna is reviewed, based on material from the benthic survey programme BIOICE and 17 species are recorded. <i>Similipecten oskarssoni</i> is proposed as a replacement name for <i>Pecten groenlandicus</i> var. <i>minor</i> Locard, 1898 (Propeamussiidae), which is considered a valid species. Lectotypes are designated for <i>Pecten groenlandicus</i> var. <i>minor</i> and <i>Pecten frigidus</i> Jensen, 1904 (Pectinidae). <i>Cyclopecten ambiannulatus</i> Schein, 1989, <i>Parvamussium propinquum</i> (Smith, 1885), <i>Catillopecten eucymatus</i> (Dall, 1898), and <i>Aequipecten opercularis</i> (Linnaeus, 1758) were previously not known from the Icelandic fauna. All species are figured and described and distinguishing characters are discussed. The distribution in Scandinavian and North Atlantic waters is revised based on the collections in SMNH. The low frequency of juvenile specimens of <i>A. opercularis</i>, <i>Mimachlamys varia</i> and <i>Pecten maximus</i> may indicate that Scandinavian populations are the result of very occasional recruitment.
DOI: 10.6084/m9.figshare.825664
title: Light on the structural communication in Ras GTPases

description: The graph theory was combined with fluctuation dynamics to investigate the structural communication in four small G proteins, Arf1, H-Ras, RhoA, and Sec4. The topology of small GTPases is such that it requires the presence of the nucleotide to acquire a persistent structural network. The majority of communication paths involves the nucleotide and does not exist in the unbound forms. The latter are almost devoid of high-frequency paths. Thus, small Ras GTPases acquire the ability to transfer signals in the presence of nucleotide, suggesting that it modifies the intrinsic dynamics of the protein through the establishment of regions of hyperlinked nodes with high occurrence of correlated motions. The analysis of communication paths in the inactive (S<sup>GDP</sup>) and active (S<sup>GTP</sup>) states of the four G proteins strengthened the separation of the Ras-like domain into two dynamically distinct lobes, i.e. lobes 1 and 2, representing, respectively, the N-terminal and C-terminal halves of the domain. In the framework of this separation, interfunctional states and interfamily differences could be inferred. The structure network undergoes a reshaping depending on the bound nucleotide. Nucleotide-dependent divergences in structural communication reach the maximum in Arf1 and the minimum in RhoA. In Arf1, the nucleotide-dependent paths essentially express a communication between the G box 4 (G4) and distal portions of lobe 1. In the S<sup>GDP</sup> state, the G4 communicates with the N-term, while, in the S<sup>GTP</sup> state, the G4 communicates with the switch II. Clear differences could be also found between Arf1 and the other three G proteins. In Arf1, the nucleotide tends to communicate with distal portions of lobe 1, whereas in H-Ras, RhoA, and Sec4 it tends to communicate with a cluster of aromatic/hydrophobic amino acids in lobe 2. These differences may be linked, at least in part, to the divergent membrane anchoring modes that would involve the N-term for the Arf family and the C-term for the Rab/Ras/Rho families.
DOI: 10.6084/m9.figshare.825659
title: A histidine-kinase <i>cheA</i> gene of <i>Pseudomonas pseudoalcaligens</i> KF707 not only has a key role in chemotaxis but also affects biofilm formation and cell metabolism

description: A histidine-kinase <i>cheA</i> gene in <i>Pseudomonas pseudoalcaligenes</i> KF707 plays a central role in the regulation of metabolic responses as well as in chemotaxis. Non-chemotactic mutants harboring insertions into the <i>cheA</i> gene were screened for their ability to form biofilms in the Calgary biofilm device. Notably, ≥95% decrease in the number of cells attached to the polystyrene surface was observed in <i>cheA</i> mutants compared to the KF707 wild-type biofilm phenotype. The ability to form mature biofilms was restored to wild-type levels, providing functional copies of the KF707 <i>cheA</i> gene to the mutants. In addition, phenotype micro-arrays and proteomic analyses revealed that several basic metabolic activities and a few periplasmic binding proteins of <i>cheA</i> mutant cells differed compared to those of wild-type cells. These results are interpreted as evidence of a strong integration between chemotactic and metabolic pathways in the process of biofilm development by <i>P. pseudoalcaligenes</i> KF707.
DOI: 10.6084/m9.figshare.825660
title: Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant

description: To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus <i>Ideonella</i> was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species.
DOI: 10.6084/m9.figshare.825664.v1
title: Light on the structural communication in Ras GTPases

description: The graph theory was combined with fluctuation dynamics to investigate the structural communication in four small G proteins, Arf1, H-Ras, RhoA, and Sec4. The topology of small GTPases is such that it requires the presence of the nucleotide to acquire a persistent structural network. The majority of communication paths involves the nucleotide and does not exist in the unbound forms. The latter are almost devoid of high-frequency paths. Thus, small Ras GTPases acquire the ability to transfer signals in the presence of nucleotide, suggesting that it modifies the intrinsic dynamics of the protein through the establishment of regions of hyperlinked nodes with high occurrence of correlated motions. The analysis of communication paths in the inactive (S<sup>GDP</sup>) and active (S<sup>GTP</sup>) states of the four G proteins strengthened the separation of the Ras-like domain into two dynamically distinct lobes, i.e. lobes 1 and 2, representing, respectively, the N-terminal and C-terminal halves of the domain. In the framework of this separation, interfunctional states and interfamily differences could be inferred. The structure network undergoes a reshaping depending on the bound nucleotide. Nucleotide-dependent divergences in structural communication reach the maximum in Arf1 and the minimum in RhoA. In Arf1, the nucleotide-dependent paths essentially express a communication between the G box 4 (G4) and distal portions of lobe 1. In the S<sup>GDP</sup> state, the G4 communicates with the N-term, while, in the S<sup>GTP</sup> state, the G4 communicates with the switch II. Clear differences could be also found between Arf1 and the other three G proteins. In Arf1, the nucleotide tends to communicate with distal portions of lobe 1, whereas in H-Ras, RhoA, and Sec4 it tends to communicate with a cluster of aromatic/hydrophobic amino acids in lobe 2. These differences may be linked, at least in part, to the divergent membrane anchoring modes that would involve the N-term for the Arf family and the C-term for the Rab/Ras/Rho families.
DOI: 10.6084/m9.figshare.825656
title: The Canadian total diet study design: 1992–1999

description: This paper describes the design of the fourth phase of the Canadian total diet study, conducted for the period 1992–1999. During this phase, complete sets of foods were purchased from eight cities (from one of them twice). For each of the sets, individual foods were prepared as for consumption into about 140 different food composites at Kemptville College, homogenised and bottled. Water from Kemptville, Ontario, was used for the preparation of the foods. The composites were stored frozen at −20°C and then analysed in the Food Research Division for chlorinated dioxins and dibenzofurans, pesticides, PCBs and trace elements. The analytical results were combined with average food consumption values for different age/sex groups, and dietary intakes were calculated. The design of the total diet study provided information to achieve the following goals: (a) background concentrations of the chemicals in the 140 different food composites, (b) average dietary intakes of the chemicals by the population and by different age/sex groups, (c) percent contribution of individual foods and food groups to the dietary intakes, (d) identification of individual contaminated foods and (e) identification of trends in human exposure with time.
DOI: 10.6084/m9.figshare.825657
title: Dioxins, furans and non-<i>ortho</i>-PCBs in Canadian total diet foods 1992–1999 and 1985–1988

description: In the period from 1985 to 1999, about 600 samples of total diet foods from Canadian cites were analysed for dioxins, furans and non-<i>ortho</i>-PCBs. Toxic equivalent (TEQ) concentrations on a lipid basis were found to be the highest in dairy and beef products followed by poultry and pork. These levels decreased over the 15-year period of sampling, particularly those for fluid milk, less so for poultry and pork and little or no change for beef. Calculation of the human daily intake for the years 1985–1988 showed values a little less than 1 pg of TEQ<sub>2005</sub> polychlorinated dibenzo-<i>p</i>-dioxin/polychlorinated dibenzofuran per kg body weight, falling progressively to less than 0.5 pg of TEQ in 1999. These estimates are lower than the 2.3 pg of TEQ currently recommended by the WHO. The main categories of foods contributing to the TEQ were animal meats and dairy products, with lesser amounts from fish and other foods.
DOI: 10.6084/m9.figshare.825660.v1
title: Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant

description: To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus <i>Ideonella</i> was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species.
DOI: 10.6084/m9.figshare.825657.v1
title: Dioxins, furans and non-<i>ortho</i>-PCBs in Canadian total diet foods 1992–1999 and 1985–1988

description: In the period from 1985 to 1999, about 600 samples of total diet foods from Canadian cites were analysed for dioxins, furans and non-<i>ortho</i>-PCBs. Toxic equivalent (TEQ) concentrations on a lipid basis were found to be the highest in dairy and beef products followed by poultry and pork. These levels decreased over the 15-year period of sampling, particularly those for fluid milk, less so for poultry and pork and little or no change for beef. Calculation of the human daily intake for the years 1985–1988 showed values a little less than 1 pg of TEQ<sub>2005</sub> polychlorinated dibenzo-<i>p</i>-dioxin/polychlorinated dibenzofuran per kg body weight, falling progressively to less than 0.5 pg of TEQ in 1999. These estimates are lower than the 2.3 pg of TEQ currently recommended by the WHO. The main categories of foods contributing to the TEQ were animal meats and dairy products, with lesser amounts from fish and other foods.
DOI: 10.6084/m9.figshare.825659.v1
title: A histidine-kinase <i>cheA</i> gene of <i>Pseudomonas pseudoalcaligens</i> KF707 not only has a key role in chemotaxis but also affects biofilm formation and cell metabolism

description: A histidine-kinase <i>cheA</i> gene in <i>Pseudomonas pseudoalcaligenes</i> KF707 plays a central role in the regulation of metabolic responses as well as in chemotaxis. Non-chemotactic mutants harboring insertions into the <i>cheA</i> gene were screened for their ability to form biofilms in the Calgary biofilm device. Notably, ≥95% decrease in the number of cells attached to the polystyrene surface was observed in <i>cheA</i> mutants compared to the KF707 wild-type biofilm phenotype. The ability to form mature biofilms was restored to wild-type levels, providing functional copies of the KF707 <i>cheA</i> gene to the mutants. In addition, phenotype micro-arrays and proteomic analyses revealed that several basic metabolic activities and a few periplasmic binding proteins of <i>cheA</i> mutant cells differed compared to those of wild-type cells. These results are interpreted as evidence of a strong integration between chemotactic and metabolic pathways in the process of biofilm development by <i>P. pseudoalcaligenes</i> KF707.
DOI: 10.6084/m9.figshare.825653
title: Multi-class determination of anthelmintics in soil and water by LC-MS/MS

description: The translocation of antiparasitic drugs from animal excrement through soil and water to crops and forages and their recycling to food-producing animals is a potential concern with respect to the contamination of the food chain. To facilitate the investigation of this problem, an LC-MS/MS method for selected anthelmintics in soil and water was developed. The soil sample preparation involved a simple solvent extraction and dispersive clean-up technique. The method was validated at 10, 20 and 40 µg kg<sup>−1</sup> for levamisole, fenbendazole, fenbendazole sulphoxide and fenbendazole sulphone and at 20, 40 and 80 µg kg<sup>−1</sup> for eprinomectin. LOQs were 10 µg kg<sup>−1</sup> for the first four compounds and 20 µg kg<sup>−1</sup> for eprinomectin. The overall mean recoveries ranged from 76.1% to 89% for loamy soils and from 79.9% to 96.9% for sandy soils. Analysis of water samples was performed by extraction/concentration on an Oasis-HLB (Aschaffenburg, Germany) cartridge. Validation was performed at 0.25, 0.5 and 1.0 µg l<sup>−1</sup>. The LOQ for all compounds was 0.25 µg l<sup>−1</sup>. Method recovery (and RSD) varied between 35.4% (28) for eprinomectin and 125.1% (16) for fenbendazole sulphone. The validated methods were applied to soil and water samples in a study on the behaviour of anthelmintic drugs in a soil-plant-water system (manuscript on “transport investigation of antiparasitic drugs based on a lysimeter experiment” in preparation).