cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.907153
title: Manipulation of epilithic biofilm and metabolism measurements

description: The aim of this project was to study the role of the different constituents of epilithic biofilm (photosynthetic organisms vs bacteria only) in the metabolism of temperate rocky shores. We sampled rock chips from a mid-intertidal sandstone area, measured the surface area covered in biofilm and placed them in a cold room (8-10 °C) under constant irradiance (PAR: 400 - 700 nm) at 290 μmolphotons.m-2.h-1 in glass containers with filtered seawater. After a 2h acclimatisation phase, we took fluorescence measurements following a 15 min dark adaptation (Fv/Fm) and then applied the following treatments (see Figure for layout): 10 mg.L-1 Simazine in 1.0 μm filtered seawater (herbicide), 25 mg.L-1 Streptomycin and 50 mg.L-1 ampicillin in 1.0 μm filtered seawater (antibiotic), 1.0 μm filtered seawater (control). 5 rockchips were placed in separate compartments in of treatment and left to incubate for 4 hours udner constant irradiance. Rock chips were then emersed again and Fv/Fm measurements taken as described above. Samples were then placed back in filtered seawater in darkness for overnight recovery and the Fv/Fm measurements taken again to see test for any longer-term effect of the treatments. The same protocol was repeated several times to ensure repeatability of the effect of the treatments. This protocol did result in consistent signficant negative effect of the Simazine on the photosynthetic capacity of the biofilm. The effect of the antibiotic mixture, however was not so consistent and could not be used reliably to significantl affect the bacteria of the biofilm. Also, it was not possible to establish by an alternative method the proportion of live/dead bacteria: it was hoped that flow cytometry should be able to provide this information but lack of available expertise did not allow to take this through. Finally, the aim was to measure the metabolism of the rock chips after treatment in the lab using a small incubating chamber and an oxygen probe. A glass chamber was design with a flat lid with a 'chimeney' in its center where the probe could be inserted. The lid was sealled to the chamber with silicon grease and the probe surrounded in parafilm to make the chamber airtight (see Figure). a magntic stirrer was placed in the chamber to avoid the formation of boundary layers. Metabolism measurements were then performed by measuring the change in oxygen concentration with time under light (for net primary productivity) and under darkness (for respiration). The setup, however, did allow allow for appropriate measurements: even though the measurements were performed in the cold room, the water temperature did not remain constant or was much higher than environmental conditions. There were also problems of water saturation that could not be resolved. Clearly, the effect of the treatments could be further explored but a more complex setup is needed to be able to perform appropriate laboratory measurements of oxygen metabolism.
DOI: 10.6084/m9.figshare.907179.v2
title: Serotonergic chemosensory neurons modify the C. elegans immune response by regulating G-protein signaling in epithelial cells

description: This paper describes a role for the neurotransmitter serotonin in regulating the <em>C. elegans</em> cellular immune response
DOI: 10.6084/m9.figshare.907153.v1
title: Manipulation of epilithic biofilm and metabolism measurements

description: The aim of this project was to study the role of the different constituents of epilithic biofilm (photosynthetic organisms vs bacteria only) in the metabolism of temperate rocky shores. We sampled rock chips from a mid-intertidal sandstone area, measured the surface area covered in biofilm and placed them in a cold room (8-10 °C) under constant irradiance (PAR: 400 - 700 nm) at 290 μmolphotons.m-2.h-1 in glass containers with filtered seawater. After a 2h acclimatisation phase, we took fluorescence measurements following a 15 min dark adaptation (Fv/Fm) and then applied the following treatments (see Figure for layout): 10 mg.L-1 Simazine in 1.0 μm filtered seawater (herbicide), 25 mg.L-1 Streptomycin and 50 mg.L-1 ampicillin in 1.0 μm filtered seawater (antibiotic), 1.0 μm filtered seawater (control). 5 rockchips were placed in separate compartments in of treatment and left to incubate for 4 hours udner constant irradiance. Rock chips were then emersed again and Fv/Fm measurements taken as described above. Samples were then placed back in filtered seawater in darkness for overnight recovery and the Fv/Fm measurements taken again to see test for any longer-term effect of the treatments. The same protocol was repeated several times to ensure repeatability of the effect of the treatments. This protocol did result in consistent signficant negative effect of the Simazine on the photosynthetic capacity of the biofilm. The effect of the antibiotic mixture, however was not so consistent and could not be used reliably to significantl affect the bacteria of the biofilm. Also, it was not possible to establish by an alternative method the proportion of live/dead bacteria: it was hoped that flow cytometry should be able to provide this information but lack of available expertise did not allow to take this through. Finally, the aim was to measure the metabolism of the rock chips after treatment in the lab using a small incubating chamber and an oxygen probe. A glass chamber was design with a flat lid with a 'chimeney' in its center where the probe could be inserted. The lid was sealled to the chamber with silicon grease and the probe surrounded in parafilm to make the chamber airtight (see Figure). a magntic stirrer was placed in the chamber to avoid the formation of boundary layers. Metabolism measurements were then performed by measuring the change in oxygen concentration with time under light (for net primary productivity) and under darkness (for respiration). The setup, however, did allow allow for appropriate measurements: even though the measurements were performed in the cold room, the water temperature did not remain constant or was much higher than environmental conditions. There were also problems of water saturation that could not be resolved. Clearly, the effect of the treatments could be further explored but a more complex setup is needed to be able to perform appropriate laboratory measurements of oxygen metabolism.
DOI: 10.6084/m9.figshare.907133
title: V-REGION mutation levels of IGH rearrangements of known isotype

description: Immunoglobulin heavy chain rearrangements were sequences from PBMCs of 8 individuals using IGHC primers for all isotypes bar IgE. Each indivdual has a unique label 'Subject' identifier of the format NSXXX. Sequencing was carried out on the 454 pyrosequencing platform and rearranged immunoglobulin heavy chain sequences were partitioned against germline IGHV, IGHD and IGHJ using iHMMune-align. The datasets for each individual has been filtered to remove non-productive rearrangements (frame shift of the IGHJ or stop codons), those with greater than 45 IGHV mutations, sequences which contained indels in the V or J, and those with ambiguities. Within each data only unique sequences were reatained (100% identical) with a 'read copy no.' assigned to track the underlying copies of a sequence. Clonally-related sequences within each subject's dataset were also identified. Following germline reversion of all non-CDR3 nucleotide positions, sequence were clustered using the vmatch package (http://www.vmatch.de/) allowing up to 3 differences. A single representative for each cluster (representing a likely clonal set) was retained within the dataset. Representative sequences were selected based on the sequence with the highest copy number, or in cases where sequences shared the highest copy number, the least mutated sequence. If a cluster spanned multiple isotypes then a representative for each isotype was kept. Clusters are identified by a label that includes the subject in which the cluster was identified. Sequences that weren't part of a cluster as labelled with the subject identifier and "na". Where a cluster spans multiple isotypes the 'Span multiple isotypes' column is set to TRUE. Replacement (R) and silent (S) mutation counts for complementarity determining regions (CDRs) and framework regions (FR) were determined for each sequence. CDR definitions that take the outer limits of the Kabat and IMGT systems were used. Where more than one mutation occurred within a single codon, all independent pathways to the final mutational outcome were considered and the R and S counts were weighted accordingly. For sequences with an Mv (total V-REGION mutation from codon 25 through 104, that is, excluding the CDR3 contribution of the V-REGION) greater than zero the proportion of total mutations that represent R in CDRs (CDR1 and CDR2) was calculated. These values were used in the analysis of antigen selection between sequences of different isotypes. V-REGION mutation frequencies and CDR3 amino acid sequences and lengths are included.
DOI: 10.6084/m9.figshare.907150.v1
title: PL-MOOC Design Team Questions (draft)

description: This instrument is designed to audit MOOC courses for SRL provision.
DOI: 10.6084/m9.figshare.907133.v1
title: V-REGION mutation levels of IGH rearrangements of known isotype

description: Immunoglobulin heavy chain rearrangements were sequences from PBMCs of 8 individuals using IGHC primers for all isotypes bar IgE. Each indivdual has a unique label 'Subject' identifier of the format NSXXX. Sequencing was carried out on the 454 pyrosequencing platform and rearranged immunoglobulin heavy chain sequences were partitioned against germline IGHV, IGHD and IGHJ using iHMMune-align. The datasets for each individual has been filtered to remove non-productive rearrangements (frame shift of the IGHJ or stop codons), those with greater than 45 IGHV mutations, sequences which contained indels in the V or J, and those with ambiguities. Within each data only unique sequences were reatained (100% identical) with a 'read copy no.' assigned to track the underlying copies of a sequence. Clonally-related sequences within each subject's dataset were also identified. Following germline reversion of all non-CDR3 nucleotide positions, sequence were clustered using the vmatch package (http://www.vmatch.de/) allowing up to 3 differences. A single representative for each cluster (representing a likely clonal set) was retained within the dataset. Representative sequences were selected based on the sequence with the highest copy number, or in cases where sequences shared the highest copy number, the least mutated sequence. If a cluster spanned multiple isotypes then a representative for each isotype was kept. Clusters are identified by a label that includes the subject in which the cluster was identified. Sequences that weren't part of a cluster as labelled with the subject identifier and "na". Replacement (R) and silent (S) mutation counts for complementarity determining regions (CDRs) and framework regions (FR) were determined for each sequence. CDR definitions that take the outer limits of the Kabat and IMGT systems were used. Where more than one mutation occurred within a single codon, all independent pathways to the final mutational outcome were considered and the R and S counts were weighted accordingly. For sequences with an Mv (total V-REGION mutation from codon 25 through 104, that is, excluding the CDR3 contribution of the V-REGION) greater than zero the proportion of total mutations that represent R in CDRs (CDR1 and CDR2) was calculated. These values were used in the analysis of antigen selection between sequences of different isotypes.
DOI: 10.6084/m9.figshare.907016
title: Research of kinematic characteristics of basic attacking technical action young wrestlers freestyle

description: Purpose. Іdentified temporal characteristic structures basic attacking technicians action young wrestlers freestyle different qualifications. Material. The study involved 38 boys engaged in freestyle wrestling. Held analysis specially scientifically literature evidenced about that exists objective necessity at decisions question concerning study biomechanical speciality technicians wrestlers freestyle for working technology formation sports technicians athlete during pre-basic training. Results. Identified biomechanical characteristics defined kinematic structure of the temporal and spatial-temporal characteristics of the basic techniques. Shown variability of the individual phases of the basic techniques. Conclusions. Research duration preparatory, basic and final phases basic attacking technical action at stand young wrestlers freestyle different qualifications testifies about her variability and ambiguous at each studied technical action.
DOI: 10.6084/m9.figshare.907016.v1
title: Research of kinematic characteristics of basic attacking technical action young wrestlers freestyle

description: Purpose. Іdentified temporal characteristic structures basic attacking technicians action young wrestlers freestyle different qualifications. Material. The study involved 38 boys engaged in freestyle wrestling. Held analysis specially scientifically literature evidenced about that exists objective necessity at decisions question concerning study biomechanical speciality technicians wrestlers freestyle for working technology formation sports technicians athlete during pre-basic training. Results. Identified biomechanical characteristics defined kinematic structure of the temporal and spatial-temporal characteristics of the basic techniques. Shown variability of the individual phases of the basic techniques. Conclusions. Research duration preparatory, basic and final phases basic attacking technical action at stand young wrestlers freestyle different qualifications testifies about her variability and ambiguous at each studied technical action.
DOI: 10.6084/m9.figshare.907150.v2
title: (instrument) Design Team Questions (draft)

description: This instrument is designed to audit MOOC courses for SRL provision.
DOI: 10.6084/m9.figshare.904926
title: Readme file for .xls files

description: This is a readme file for the raw data files for the publication, "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus".
DOI: 10.6084/m9.figshare.904933
title: Lipid force field comparison

description: 10 current molecular dynamics forcefields of phospholipids compared against NMR data of headgroup order parameters. These simulation data are an outcome of an open collaborative effort taking place at nmrlipids.blogspot.fi.
DOI: 10.6084/m9.figshare.904925
title: Pollen viability data

description: Raw pollen viability data for the paper, <br>"Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus", to be published in G3.
DOI: 10.6084/m9.figshare.904926.v1
title: Readme file for .xls files

description: This is a readme file for the raw data files for the publication, "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus".
DOI: 10.6084/m9.figshare.904927
title: Raw data for "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus"

description: Raw data for the publication, "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus". G3:Genes, Genomes, Genetics. Early Online 27 January 2014. doi: 10.1534/g3.113.008441 http://www.g3journal.org/content/early/2014/01/22/g3.113.008441.full.pdf+html Authors: Jennifer Modliszewski and John Willis
DOI: 10.6084/m9.figshare.904917
title: KPMD.fasta

description: Fasta file of the PAGIT assembled genome for strain KPMD
DOI: 10.6084/m9.figshare.904918
title: KPMD.gbk

description: Genbank file of annotated KPMD strain
DOI: 10.6084/m9.figshare.904924
title: All phenotypic data (other than pollen viability)

description: Data for the paper, "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus"
DOI: 10.6084/m9.figshare.904927.v2
title: Raw data for "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus"

description: Raw data for the publication, "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus". G3:Genes, Genomes, Genetics. Early Online 27 January 2014. doi: 10.1534/g3.113.008441 http://www.g3journal.org/content/early/2014/01/22/g3.113.008441.full.pdf+html Authors: Jennifer Modliszewski and John Willis
DOI: 10.6084/m9.figshare.904924.v1
title: All phenotypic data (other than pollen viability)

description: Data for the paper, "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus"
DOI: 10.6084/m9.figshare.904918.v1
title: KPMD.gbk

description: Genbank file of annotated KPMD strain
DOI: 10.6084/m9.figshare.904927.v1
title: Raw data for "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus"

description: Raw data for the publication, "Near-Absent Levels Of Segregational Variation Suggest Limited Opportunities For The Introduction Of Genetic Variation Via Homeologous Chromosome Pairing In Synthetic Neoallotetraploid Mimulus". Authors: Jennifer Modliszewski and John Willis
DOI: 10.6084/m9.figshare.904917.v1
title: KPMD.fasta

description: Fasta file of the PAGIT assembled genome for strain KPMD
DOI: 10.6084/m9.figshare.904909
title: Data on the responses of neurons and astrocytes to oxidative injury in the presence of insulin-like growth factor I

description: Fig1a) Neuron viability measured as percentage of GFP positive cells cultured ± astrocytes after treatment with H2O2. N: neurons, NA: neurons + astrocytes. Names for each file refer to the related figures in the associated research article. Fig1b) IGF-I measured in the supernatant of neuron or astrocyte cultures treated ± with H2O2. Fig1c) pAKT levels measured in astrocytes transfected with an IGF-IR dominant negative construct (IGF-IR DN) after treatment with IGF-I. Fig1d) Neuron viability measured as percentage of GFP positive cells cultured with astrocytes transfected with IGF-IR DN. Fig2a) pAKT levels in astrocytes treated ± with PPP (picropodophyllin) after treatment with IGF-I. Fig2b) Neuron viability measured as percentage of GFP positive cells treated ± with PPP and H2O2. Fig2c) Neuron viability expressed as percentage of GFP positive cells cultured with astrocytes and treated ± with PPP and H2O2. Fig2d) Neuron viability measured as percentage of GFP positive cells cultured with astrocytes (both cells types from forebrain) and treated ± with PPP and H2O2. Fig2e) Neuron viability measured as percentage of GFP positive cells cultured with astrocytes and treated with IGF-I, H2O2 or both. Fig3a) Neuron death measured as percentage of PI positive cells treated ± with IGF-I and H2O2. Fig3b) Astrocyte survival expressed as percentage of PI negative cells treated ± with IGF-I and H2O2. Fig3c) FOXO activity from astrocytes treated with IGF-I, H2O2 or both. Fig3d) Cell survival expressed as percentage of GFP positive cells for astrocytes transfected with wt or AKT-insensitive mutant FOXO, treated ± with IGF-Iand H2O2. Fig3e) pAKT levels form astrocytes treated with IGF-I I ± H2O2. Fig4a) Mitochondrial O2- measured in astrocytes treated ± with IGF-I and H2O2. Fig4b) Total ROS (reactive oxygen species) measured in astrocytes treated ± with IGF-I and H2O2. Fig5a) Cu/Zn SOD (superoxide dismutase) levels from astrocytes treated with IGF-I, H2O2 or both. Fig5b) Mn SOD levels from astrocytes treated with IGF-I, H2O2 or both. Fig6a) TXNIP levels from astrocytes treated with IGF-I, H2O2 or both. Fig6b) Cell survival from astrocytes transfected with TXNIP shRNA ± H2O2. Fig6c) TXNIP levels from neurons treated with IGF-I, H2O2 or both. Fig6d) TXNIP levels from astrocytes pre-treated with the calcium inhibitor BAPTA in the presence of IGF-I, H2O2 or both. Fig7a) SCF (stem cell factor) mRNA from astrocytes treated with IGF-I, H2O2 or both. Fig7b) Neuron viability measured as percentage of GFP positive cells treated with IGF-I, SCF or both in the presence of H2O2. Fig7c) pERK levels form astrocytes treated with IGF-I, SCF or both ± H2O2. Fig7d) SCF and IGF-I mRNA from control or MCAO (medial cerebral artery occlusion) animal cortex (contralateral or ispsilateral cortex). Fig7e) SCF protein levels from control or MCAO animal cortex (contralateral or ispsilateral cortex). Luminol) Reactive oxygen species (ROS) measurements using luminol (which detects superoxide anions)
DOI: 10.6084/m9.figshare.904908
title: Responses from a survey on leadership and management issues by wildlife reintroduction practitioners

description: Responses of 68 wildlife reintroduction practitioners to a survey (Qualtrics, 2009) on management and leadership aspects of wildlife reintroduction programs. The survey was completed between April-May 2009.