cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4235564.v1
title: LOC_ID coding in deployment files

description: Details of coding used in SPACECAP input files. In input files LOC_IDs must be represented as sequential numbers. This file shows which LOC_IDs correspond to which camera station numbers.
DOI: 10.6084/m9.figshare.4235561.v1
title: ANIMAL_ID coding in capture files

description: Details of coding used in SPACECAP input files. In input files ANIMAL_IDs must be represented as sequential numbers. This file shows which ANIMAL_IDs correspond to which individual animals.
DOI: 10.6084/m9.figshare.4235549
title: Trees for seagrass paper

description: This zipfile contains three phylogenetic trees in PDF format. These show the relationship of our Shewanella, Vibrio, and Colwellia isolates to their close relatives. The alignments were generated using the Ribosomal Database Project and the trees were inferred using FastTree.<br>
DOI: 10.6084/m9.figshare.4235546
title: SPACECAP input files

description: Zip archive containing SPACECAP input files for 24 surveys of leopard population density in the Soutpansberg Mountains, South Africa from 2012 to 2016. For each survey (for dates see article) the archive contains a - capture history file "capture_sXX.csv" - trap deployment file "deployment_sXX.csv" - potential home range centres file "HRC_s01.csv"
DOI: 10.6084/m9.figshare.4235549.v1
title: Trees for seagrass paper

description: This zipfile contains three phylogenetic trees in PDF format. These show the relationship of our Shewanella, Vibrio, and Colwellia isolates to their close relatives. The alignments were generated using the Ribosomal Database Project and the trees were inferred using FastTree.<br>
DOI: 10.6084/m9.figshare.4235357
title: data

description: This repository contains all data related to the manuscript PCOMPBIOL-D-16-00687 entitled "Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study".
DOI: 10.6084/m9.figshare.4235354
title: code

description: This repository contains all the code related to the manuscript PCOMPBIOL-D-16-00687 entitled "Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study".<br>
DOI: 10.6084/m9.figshare.4235357.v1
title: data

description: This repository contains all data related to the manuscript PCOMPBIOL-D-16-00687 entitled "Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study".
DOI: 10.6084/m9.figshare.4235357.v2
title: data

description: This repository contains all data related to the manuscript PCOMPBIOL-D-16-00687 entitled "Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study".
DOI: 10.6084/m9.figshare.4235285
title: Crystallographic Information File from The modulator driven polymorphism of Zr(IV) based metal-organic frameworks

description: Crystallographic data for DUT-126
DOI: 10.6084/m9.figshare.4235357.v3
title: data

description: This repository contains all data related to the manuscript PCOMPBIOL-D-16-00687 entitled "Inferring epidemiological parameters from phylogenies using regression-ABC: a comparative study".
DOI: 10.6084/m9.figshare.4235282
title: Supplementary Material for: Creating Interactions between Tissue-Engineered Skeletal Muscle and the Peripheral Nervous System

description: Effective models of mammalian tissues must allow and encourage physiologically (mimetic) correct interactions between co-cultured cell types in order to produce culture microenvironments as similar as possible to those that would normally occur in vivo. In the case of skeletal muscle, the development of such a culture model, integrating multiple relevant cell types within a biomimetic scaffold, would be of significant benefit for investigations into the development, functional performance, and pathophysiology of skeletal muscle tissue. Although some work has been published regarding the behaviour of in vitro muscle models co-cultured with organotypic slices of CNS tissue or with stem cell-derived neurospheres, little investigation has so far been made regarding the potential to maintain isolated motor neurons within a 3D biomimetic skeletal muscle culture platform. Here, we review the current state of the art for engineering neuromuscular contacts in vitro and provide original data detailing the development of a 3D collagen-based model for the co-culture of primary muscle cells and motor neurons. The devised culture system promotes increased myoblast differentiation, forming arrays of parallel, aligned myotubes on which areas of nerve-muscle contact can be detected by immunostaining for pre- and post-synaptic proteins. Quantitative RT-PCR results indicate that motor neuron presence has a positive effect on myotube maturation, suggesting neural incorporation influences muscle development and maturation in vitro. The importance of this work is discussed in relation to other published neuromuscular co-culture platforms along with possible future directions for the field.
DOI: 10.6084/m9.figshare.4235285.v1
title: Crystallographic Information File from The modulator driven polymorphism of Zr(IV) based metal-organic frameworks

description: Crystallographic data for DUT-126
DOI: 10.6084/m9.figshare.4235180
title: Supplementary_File_2 from Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities

description: Freshwater habitats are of high conservation value and provide a wide range of ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection are so invasive, expensive and labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation of environmental DNA (eDNA) from water based on a simple protocol can be used for assessing biodiversity. We use universal metazoan primers for characterizing water eDNA across horizontal and vertical spatial dimensions in two reservoirs with known species diversity for two key taxa. eDNA obtained directly from 42 samples × 15 ml water (total = 630 ml) per reservoir yielded DNA signatures for more than 500 metazoan species, of which 105 could be identified to species/genus based on DNA barcodes. We show that eDNA can be used to assign each water sample to its reservoir of origin, and that eDNA outperforms conventional survey methods in single-sample richness comparisons, while revealing evidence for hundreds of unknown species that are undetected by conventional bioassessment methods. eDNA also confirms the presence of a recently discovered invasive snail species and provides evidence for the survival of a rare native species of goby not sighted in that habitat since 2007. eDNA thus promises to be a useful addition to the bioassessment toolbox for freshwater systems.
DOI: 10.6084/m9.figshare.4235180.v1
title: Supplementary_File_2 from Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities

description: Freshwater habitats are of high conservation value and provide a wide range of ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection are so invasive, expensive and labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation of environmental DNA (eDNA) from water based on a simple protocol can be used for assessing biodiversity. We use universal metazoan primers for characterizing water eDNA across horizontal and vertical spatial dimensions in two reservoirs with known species diversity for two key taxa. eDNA obtained directly from 42 samples × 15 ml water (total = 630 ml) per reservoir yielded DNA signatures for more than 500 metazoan species, of which 105 could be identified to species/genus based on DNA barcodes. We show that eDNA can be used to assign each water sample to its reservoir of origin, and that eDNA outperforms conventional survey methods in single-sample richness comparisons, while revealing evidence for hundreds of unknown species that are undetected by conventional bioassessment methods. eDNA also confirms the presence of a recently discovered invasive snail species and provides evidence for the survival of a rare native species of goby not sighted in that habitat since 2007. eDNA thus promises to be a useful addition to the bioassessment toolbox for freshwater systems.
DOI: 10.6084/m9.figshare.4235174
title: Supplementary_File_1 from Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities

description: Freshwater habitats are of high conservation value and provide a wide range of ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection are so invasive, expensive and labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation of environmental DNA (eDNA) from water based on a simple protocol can be used for assessing biodiversity. We use universal metazoan primers for characterizing water eDNA across horizontal and vertical spatial dimensions in two reservoirs with known species diversity for two key taxa. eDNA obtained directly from 42 samples × 15 ml water (total = 630 ml) per reservoir yielded DNA signatures for more than 500 metazoan species, of which 105 could be identified to species/genus based on DNA barcodes. We show that eDNA can be used to assign each water sample to its reservoir of origin, and that eDNA outperforms conventional survey methods in single-sample richness comparisons, while revealing evidence for hundreds of unknown species that are undetected by conventional bioassessment methods. eDNA also confirms the presence of a recently discovered invasive snail species and provides evidence for the survival of a rare native species of goby not sighted in that habitat since 2007. eDNA thus promises to be a useful addition to the bioassessment toolbox for freshwater systems.
DOI: 10.6084/m9.figshare.4235174.v1
title: Supplementary_File_1 from Next-generation freshwater bioassessment: eDNA metabarcoding with a conserved metazoan primer reveals species-rich and reservoir-specific communities

description: Freshwater habitats are of high conservation value and provide a wide range of ecosystem services. Effective management requires regular monitoring. However, conventional methods based on direct observation or specimen collection are so invasive, expensive and labour-intensive that frequent monitoring is uncommon. Here, we test whether the evaluation of environmental DNA (eDNA) from water based on a simple protocol can be used for assessing biodiversity. We use universal metazoan primers for characterizing water eDNA across horizontal and vertical spatial dimensions in two reservoirs with known species diversity for two key taxa. eDNA obtained directly from 42 samples × 15 ml water (total = 630 ml) per reservoir yielded DNA signatures for more than 500 metazoan species, of which 105 could be identified to species/genus based on DNA barcodes. We show that eDNA can be used to assign each water sample to its reservoir of origin, and that eDNA outperforms conventional survey methods in single-sample richness comparisons, while revealing evidence for hundreds of unknown species that are undetected by conventional bioassessment methods. eDNA also confirms the presence of a recently discovered invasive snail species and provides evidence for the survival of a rare native species of goby not sighted in that habitat since 2007. eDNA thus promises to be a useful addition to the bioassessment toolbox for freshwater systems.
DOI: 10.6084/m9.figshare.4234940
title: Safety assessment and antimicrobial properties of the lactic acid bacteria strains isolated from polish raw fermented meat products

description: Twenty-one strains of the genus <i>Lactobacillus</i> and the genus <i>Pediococcus</i>, isolated from Polish raw fermented meat products, were examined for the potential probiotic properties: resistance to simulated gastric and intestine conditions, safety assessment, and antimicrobial properties. Strains were resistant to gastric enzymes and low pH (3–6 log CFU/mL decrease) and intestinal enzymes and bile salts (1–3 log CFU/mL decrease). Most strains were resistant to gentamycin, streptomycin, vancomycin, tetracycline, ciprofloxacin, and kanamycin. Three of them (<i>Lb. brevis</i> BAL1, BAL10, and KL5) produced β-glucuronidase, which excludes them from qualifying as safe. Seven strains had the ability to produce bacteriocins or bacteriocin-like substances. Overall, strains <i>Lb. brevis</i> SCH6, <i>Pd. pentosaceus</i> BAL6, and KL14 revealed selected superior characteristics (resistance to the gastrointestinal conditions, safety assessment, and antimicrobial properties) as compared to the other LAB strains investigated, which made them a viable bioprotective culture that can be inoculated in raw fermented meat products as starter cultures.
DOI: 10.6084/m9.figshare.4234940.v2
title: Safety assessment and antimicrobial properties of the lactic acid bacteria strains isolated from polish raw fermented meat products

description: Twenty-one strains of the genus <i>Lactobacillus</i> and the genus <i>Pediococcus</i>, isolated from Polish raw fermented meat products, were examined for the potential probiotic properties: resistance to simulated gastric and intestine conditions, safety assessment, and antimicrobial properties. Strains were resistant to gastric enzymes and low pH (3–6 log CFU/mL decrease) and intestinal enzymes and bile salts (1–3 log CFU/mL decrease). Most strains were resistant to gentamycin, streptomycin, vancomycin, tetracycline, ciprofloxacin, and kanamycin. Three of them (<i>Lb. brevis</i> BAL1, BAL10, and KL5) produced β-glucuronidase, which excludes them from qualifying as safe. Seven strains had the ability to produce bacteriocins or bacteriocin-like substances. Overall, strains <i>Lb. brevis</i> SCH6, <i>Pd. pentosaceus</i> BAL6, and KL14 revealed selected superior characteristics (resistance to the gastrointestinal conditions, safety assessment, and antimicrobial properties) as compared to the other LAB strains investigated, which made them a viable bioprotective culture that can be inoculated in raw fermented meat products as starter cultures.
DOI: 10.6084/m9.figshare.4234940.v1
title: SAFETY ASSESSMENT AND ANTIMICROBIAL PROPERTIES OF THE LACTIC ACID BACTERIA STRAINS ISOLATED FROM POLISH RAW FERMENTED MEAT PRODUCTS

description: Twenty one strains of the genus <i>Lactobacillus</i> and the genus <i>Pediococcus</i>, isolated from Polish raw fermented meat products, were examined for the potential probiotic properties: resistance to simulated gastric and intestine conditions, safety assessment and antimicrobial properties. Strains were resistant to gastric enzymes and low pH (3-6 log CFU/mL decrease) and intestinal enzymes and bile salts (1-3 log CFU/mL decrease). Most strains were resistant to gentamycin, streptomycin, vancomycin, tetracycline, ciprofloxacin and kanamycin. Three of them (<i>Lb. brevis</i> BAL1, BAL10, KL5) produced β-glucuronidase, which excluded them as safe. Seven strains had the ability to produce bacteriocins or bacteriocin-like substances. Overall, strains <i>Lb. brevis</i> SCH6, <i>Pd. pentosaceus</i> BAL6 and KL14 revealed selected superior characteristics (resistance to the gastrointestinal conditions, safety assessment and antimicrobial properties) as compared to the other LAB strains investigated, which made them a viable bioprotective culture that can be inoculated in raw fermented meat products as starter cultures.
DOI: 10.6084/m9.figshare.4234886
title: A decrease in the abundance and strategic sophistication of cleaner fish after environmental perturbations

description: Extreme recent weather events hitting the Great Barrier Reef, i.e., cyclones and the 2016 El Niño enabled us to explore potential consequences on marine cleaning mutualism involving the cleaner fish <i>Labroides dimidiatus</i> (hereafter ‘cleaner’), a key species for fish biodiversity on coral reefs.
DOI: 10.6084/m9.figshare.4234886.v2
title: Climate change has a negative impact on the indo-pacific cleaner wrasse social behavior and abundance

description: Climate change poses a major threat to coral reef ecosystems worldwide. Here, we present the immediate negative effects of recent cyclones and the 2016 El Niño on the abundance of cleaner wrasse <i>Labroides dimidiatus</i> (hereafter ‘cleaner’), a key species for fish biodiversity on coral reefs. We report that 80% of cleaner densities was lost. Consequently, several repercussions on cleaners social behavior were observed. We outline significant decline in the ability of cleaner to manage their own reputation and strategically prioritize certain category of client reef fish, previously documented as key components of cleaner high cognitive performance in the cleaning mutualism. Thus, contemporary climate change may cause diverse and unexpected effects on species abundance and social interactions, possibly due to the loss of more complex cognition.
DOI: 10.6084/m9.figshare.4234886.v3
title: Climate change has a negative impact on fish social behavior and abundance

description: Climate change poses a major threat to coral reef ecosystems worldwide. Here, we present the immediate negative effects of recent cyclones and the 2016 El Niño on the abundance of cleaner wrasse <i>Labroides dimidiatus</i> (hereafter ‘cleaner’), a key species for fish biodiversity on coral reefs. We report that 80% of cleaner densities was lost. Consequently, several repercussions on cleaners social behavior were observed. We outline significant decline in the ability of cleaner to manage their own reputation and strategically prioritize certain category of client reef fish, previously documented as key components of cleaner high cognitive performance in the cleaning mutualism. Thus, contemporary climate change may cause diverse and unexpected effects on species abundance and social interactions, possibly due to the loss of more complex cognition.
DOI: 10.6084/m9.figshare.4234886.v4
title: Climate change has a negative impact on fish social behavior and abundance

description: Climate change poses a major threat to coral reef ecosystems worldwide. Here, we present the immediate negative effects of recent cyclones and the 2016 El Niño on the abundance of cleaner wrasse <i>Labroides dimidiatus</i> (hereafter ‘cleaner’), a key species for fish biodiversity on coral reefs. We report that 80% of cleaner densities was lost. Consequently, several repercussions on cleaners social behavior were observed. We outline significant decline in the ability of cleaner to manage their own reputation and strategically prioritize certain category of client reef fish, previously documented as key components of cleaner high cognitive performance in the cleaning mutualism. Thus, contemporary climate change may cause diverse and unexpected effects on species abundance and social interactions, possibly due to the loss of more complex cognition.
DOI: 10.6084/m9.figshare.4234886.v6
title: A decrease in the abundance and strategic sophistication of cleaner fish after environmental perturbations

description: Extreme recent weather events hitting the Great Barrier Reef, i.e., cyclones and the 2016 El Niño enabled us to explore potential consequences on marine cleaning mutualism involving the cleaner fish <i>Labroides dimidiatus</i> (hereafter ‘cleaner’), a key species for fish biodiversity on coral reefs.
DOI: 10.6084/m9.figshare.4234886.v5
title: A decrease in the abundance and strategic sophistication of cleaner fish after environmental perturbations

description: Extreme recent weather events hitting the Great Barrier Reef, i.e., cyclones and the 2016 El Niño enabled us to explore potential consequences on marine cleaning mutualism involving the cleaner fish <i>Labroides dimidiatus</i> (hereafter ‘cleaner’), a key species for fish biodiversity on coral reefs.
DOI: 10.6084/m9.figshare.4234808
title: Casting the critical regions in nucleotide binding oligomerization domain 2 protein: a signature mediated structural dynamics approach

description: Nucleotide binding oligomerization domain 2 (NOD2), a protein involved in the first line defence mechanism has a pivotal role in innate immunity. Impaired function of this protein is implicated in disorders such as Blau syndrome and Crohn’s disease. Since an altered function is linked to protein’s structure, we framed a systematic strategy to interpret the structure–function relationship of the protein. Initiated with mutation-based pattern prediction and identified a distant ortholog (DO) of NOD2 from which the intra-residue interaction network was elucidated. The network was used to identify hotspots that serve as critical points to maintain the stable architecture of the protein. Structural comparison of NOD2 domains with a DO revealed the minimal number of intra-protein interactions required by the protein to maintain the structural fold. In addition, the conventional molecular dynamics simulation emphasized the conformational transitions at hot spot residues between native NOD2 domains and its respective mutants (G116R, R42W and R54A) structures. The analysis of intra-protein interactions globally and the displacement of residues locally around the mutational site revealed loss of several critical bonds and residues vital for the protein’s function. Conclusively we report, about 10 residues in leucine-rich repeat, 13 residues in NOD and 6 residues in CARD domain are required by the NOD2 to maintain its function. This protocol will help the researchers to achieve for more prospective studies to attest druggable site utility in discovering novel drug candidates.
DOI: 10.6084/m9.figshare.4234808.v1
title: Casting the critical regions in nucleotide binding oligomerization domain 2 protein: a signature mediated structural dynamics approach

description: Nucleotide binding oligomerization domain 2 (NOD2), a protein involved in the first line defence mechanism has a pivotal role in innate immunity. Impaired function of this protein is implicated in disorders such as Blau syndrome and Crohn’s disease. Since an altered function is linked to protein’s structure, we framed a systematic strategy to interpret the structure–function relationship of the protein. Initiated with mutation-based pattern prediction and identified a distant ortholog (DO) of NOD2 from which the intra-residue interaction network was elucidated. The network was used to identify hotspots that serve as critical points to maintain the stable architecture of the protein. Structural comparison of NOD2 domains with a DO revealed the minimal number of intra-protein interactions required by the protein to maintain the structural fold. In addition, the conventional molecular dynamics simulation emphasized the conformational transitions at hot spot residues between native NOD2 domains and its respective mutants (G116R, R42W and R54A) structures. The analysis of intra-protein interactions globally and the displacement of residues locally around the mutational site revealed loss of several critical bonds and residues vital for the protein’s function. Conclusively we report, about 10 residues in leucine-rich repeat, 13 residues in NOD and 6 residues in CARD domain are required by the NOD2 to maintain its function. This protocol will help the researchers to achieve for more prospective studies to attest druggable site utility in discovering novel drug candidates.