cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7313642.v1
title: ALL RAW DATA FOR : Pathological mutations differentially affect the self-assembly and polymerisation of the the immune system signaling adaptor molecule MyD88

description: The fluorescence time-traces obtained for the full-length MYD88, mutants of MYD88 and the separate domains of MyD88 from single molecule fluorescence spectroscopy. For TIR domain alone the fluctuations of intensity around the average value are limited, for the death domain, small bursts of intensities can be detected. These fluorescence peaks correspond to entries of single protein complexes, increasing the local number of proteins for a brief period of time. The amplitude and duration of the deviations from average are linked to the number of proteins co-diffusing in a single complex and the physical size of the diffusion complex. For full-length MyD88, we observe extremely bright and long-diffusing bursts of fluorescence. The simplest analysis to quantify the presence of protein complexes is to calculate the average brightness of the diffusing species, calculated from the measured intensity values (I) as B=〖(Standard deviation (I))〗^2/(average (I)). FCS data in solution. Values are from repeated dilution experiments with the various protein concentrations and corresponding brightness values obtained plotted. NS &gt;0.9999, ***P=0.0001, ****P&lt;0.0001
DOI: 10.7284/126691
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise RR1712 using a Hawaii UHDAS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126700
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR1712 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126704
title: Expendable Probe data collected during research cruise RR1712 using a Turo Quoll instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126692
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1712 using a Furuno GP-150 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7313606
title: Verbose community analysis results. from Biological interactions mediate context and species-specific sensitivities to salinity

description: Toxicants have both sub-lethal and lethal effects on aquatic biota, influencing organism fitness and community composition. However, toxicant effects within ecosystems may be altered by interactions with abiotic and biotic ecosystem components, including biological interactions. Collectively this generates the potential for toxicant sensitivity to be highly context dependent, with significantly different outcomes in ecosystems than laboratory toxicity tests predict. We experimentally manipulated stream macroinvertebrate communities in 32 mesocosms to examine how communities from a low-salinity site were influenced by interactions with those from a high-salinity site across a gradient of salinity. Relative to those from the low-salinity site, organisms from the high-salinity site were expected to have greater tolerance and fitness at higher salinities. This created the potential for both salinity and tolerant-sensitive organism interactions to influence communities. We found that community composition was influenced by both direct toxicity and tolerant-sensitive organism interactions. Taxon and context-dependent responses included: (i) direct toxicity effects, irrespective of biotic interactions; (ii) effects that were owing to the addition of tolerant taxa, irrespective of salinity; (iii) toxicity dependent on sensitive-tolerant taxa interactions; and (iv) toxic effects which that were increased by interactions. Our results reinforce that ecological processes require consideration when examining toxicant effects within ecosystems.This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
DOI: 10.7284/126694
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1712 using a Ashtech ADU2 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7313606.v1
title: Verbose community analysis results. from Biological interactions mediate context and species-specific sensitivities to salinity

description: Toxicants have both sub-lethal and lethal effects on aquatic biota, influencing organism fitness and community composition. However, toxicant effects within ecosystems may be altered by interactions with abiotic and biotic ecosystem components, including biological interactions. Collectively this generates the potential for toxicant sensitivity to be highly context dependent, with significantly different outcomes in ecosystems than laboratory toxicity tests predict. We experimentally manipulated stream macroinvertebrate communities in 32 mesocosms to examine how communities from a low-salinity site were influenced by interactions with those from a high-salinity site across a gradient of salinity. Relative to those from the low-salinity site, organisms from the high-salinity site were expected to have greater tolerance and fitness at higher salinities. This created the potential for both salinity and tolerant-sensitive organism interactions to influence communities. We found that community composition was influenced by both direct toxicity and tolerant-sensitive organism interactions. Taxon and context-dependent responses included: (i) direct toxicity effects, irrespective of biotic interactions; (ii) effects that were owing to the addition of tolerant taxa, irrespective of salinity; (iii) toxicity dependent on sensitive-tolerant taxa interactions; and (iv) toxic effects which that were increased by interactions. Our results reinforce that ecological processes require consideration when examining toxicant effects within ecosystems.This article is part of the theme issue ‘Salt in freshwaters: causes, ecological consequences and future prospects’.
DOI: 10.6084/m9.figshare.7313597
title: FIGURE 4 RAW DATA MYD88 MUTANT TRACES

description: Fluorescence time-traces obtained with disease-associated point mutants of the full-length MyD88 protein, as well as the wild-type full-length MyD88 at a protein concentration of 150 nM. Diffusion time (µs) measured by FCS ADDED ALREADY INTO FIGSHARE FILE FIGURE 2 RAW DATA showing the drastic shift in diffusion time when comparing the mutants to the wild-type protein. (C) Fluorescence intensity histogram showing that the L93P point mutation, which is within the DD, in GFP-tagged MyD88 renders the polymerisation propensity similar to the MyD88 TIR<sup> </sup>domain alone. (D) Fluorescence intensity histogram demonstrating that the R196C and L252P point mutations (present within the TIR domain) in the GFP-tagged MyD88 render the polymerisation propensity more similar to the MyD88 DD<sup> </sup>alone. Fluorescence time-traces and intensity histograms in (A), (C) & (D) are representative of 8 independent experiments. Values in (B) are ±SD from these 8 measurements.
DOI: 10.7284/126702
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1712 using a Trimble SPS351 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7313597.v1
title: FIGURE 4 RAW DATA MYD88 MUTANT TRACES

description: Fluorescence time-traces obtained with disease-associated point mutants of the full-length MyD88 protein, as well as the wild-type full-length MyD88 at a protein concentration of 150 nM. Diffusion time (µs) measured by FCS ADDED ALREADY INTO FIGSHARE FILE FIGURE 2 RAW DATA showing the drastic shift in diffusion time when comparing the mutants to the wild-type protein. (C) Fluorescence intensity histogram showing that the L93P point mutation, which is within the DD, in GFP-tagged MyD88 renders the polymerisation propensity similar to the MyD88 TIR<sup> </sup>domain alone. (D) Fluorescence intensity histogram demonstrating that the R196C and L252P point mutations (present within the TIR domain) in the GFP-tagged MyD88 render the polymerisation propensity more similar to the MyD88 DD<sup> </sup>alone. Fluorescence time-traces and intensity histograms in (A), (C) & (D) are representative of 8 independent experiments. Values in (B) are ±SD from these 8 measurements.
DOI: 10.7284/126695
title: Gravimeter data collected during research cruise RR1712 using a Bell BGM-3 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7313570
title: FIGURE 3 RAW DATA MYD88 WT FULL LENGTH DILUTIONS SEEDED

description: Number of photons from time traces from approx 50 MYD88 dilutions with and without MYD88 cherry tagged seeds, raw data analysed in additional files corresponding to (A) Schematic diagram of the principle of two-colour seeding experiments testing the self-replication propensity of full-length MyD88 filaments. Full-length MyD88<sup> </sup>is expressed in an mCherry-tagged version above its supercritical concentration to create filaments, which are gently spun and washed, then sonicated to increase the number of fragments. These “seeds” are then mixed in a sample expressing GFP-tagged full-length MyD88 at sub-critical concentrations. (B) Example of fluorescence time trace for MyD88 at 10 nM concentration. Unseeded sample demonstrating a monomeric time trace profile (above) with the seeded sample (below) showing polymerisation of GFP-MyD88 upon the addition of MyD88 ‘seeds’. (C) The B parameter (brightness) correlating with number of oligomers detected in typical time-traces as a function of protein concentration (nM), with and without “seeds” introduced. The subcritical, supercritical and “meta-stable” zones are labelled. Values are from approx. 50 repeated dilution experiments with the various protein concentrations and corresponding brightness values obtained plotted.
DOI: 10.6084/m9.figshare.7313570.v1
title: FIGURE 3 RAW DATA MYD88 WT FULL LENGTH DILUTIONS SEEDED

description: Number of photons from time traces from approx 50 MYD88 dilutions with and without MYD88 cherry tagged seeds, raw data analysed in additional files corresponding to (A) Schematic diagram of the principle of two-colour seeding experiments testing the self-replication propensity of full-length MyD88 filaments. Full-length MyD88<sup> </sup>is expressed in an mCherry-tagged version above its supercritical concentration to create filaments, which are gently spun and washed, then sonicated to increase the number of fragments. These “seeds” are then mixed in a sample expressing GFP-tagged full-length MyD88 at sub-critical concentrations. (B) Example of fluorescence time trace for MyD88 at 10 nM concentration. Unseeded sample demonstrating a monomeric time trace profile (above) with the seeded sample (below) showing polymerisation of GFP-MyD88 upon the addition of MyD88 ‘seeds’. (C) The B parameter (brightness) correlating with number of oligomers detected in typical time-traces as a function of protein concentration (nM), with and without “seeds” introduced. The subcritical, supercritical and “meta-stable” zones are labelled. Values are from approx. 50 repeated dilution experiments with the various protein concentrations and corresponding brightness values obtained plotted.
DOI: 10.7284/126699
title: HDSS (Hydrographic Doppler Sonar System) data collected during research cruise RR1712 using a SIO HDSS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7313387
title: FIGURE 2 RAW DATA

description: (A) Increase of apparent brightnesses of diffusing species. Values of B parameters obtained for expressions at protein concentrations &gt;150 nM were averaged and normalised to the sfGFP monomer control. Clearly, the data show that only full-length MyD88 (red) is capable of forming large complexes, while the TIR domain (green) or the death domain (blue) form smaller oligomers. Inset: Expansion of the values obtained for TIR and death domains compared to sfGFP control. (B) FCS data in solution. Control based on GFP monomer (black). Correlation curves obtained for the TIR domain (green), death domain (blue) and full-length MyD88 (red). A clear shift in diffusion time can be seen between the full-length protein and the separate domains. FCS curves are representative traces from 3 repeated measurements. (C) Hydrodynamic radius normalised by the sfGFP control (black) calculated for the domains and full-length MyD88, indicating the increase of approximate physical size of the oligomeric species. Values are mean ± SD from 3 repeat measurements.
DOI: 10.6084/m9.figshare.7313321
title: FIGURE 1 ANALYSED RAW DATA

description: . For GFP-tagged MyD88 TIR<sup> </sup>domain, small fluctuations in intensity are recorded around the average fluorescence value, as expected for a low-order oligomer such as a dimer (for example, if 20 proteins are detected simultaneously, the exit/entry of a single protein causes a decrease/increase of signal of only 5%). The GFP-tagged MyD88 DD shows larger bursts of fluorescence correlating with these death domains forming higher-order oligomeric complexes. As seen by the fluorescent time traces, N-terminally GFP tagged full-length MyD88 shows extremely large filamentous polymers of MyD88 diffusing through the confocal volume. (B) The B parameter (Brightness) correlates with the number of oligomers detected in typical time-traces as a function of protein concentration (nM), for the TIR domain (green), DD (blue) and wild-type full length MyD88 (red). Protein concentrations range from 0 to 320 nM. Monomeric GFP (black) is included as a control. Inset: expansion of the signals obtained for the individual domains, over a lower concentration range. Fluorescence Intensity Time traces in (A) are representative traces obtained at &gt;200nM protein concentrations. Values in (B) are from approx. 30 dilution experiments with the various protein concentrations and corresponding brightness values obtained plotted.
DOI: 10.6084/m9.figshare.7313387.v1
title: FIGURE 2 RAW DATA

description: (A) Increase of apparent brightnesses of diffusing species. Values of B parameters obtained for expressions at protein concentrations &gt;150 nM were averaged and normalised to the sfGFP monomer control. Clearly, the data show that only full-length MyD88 (red) is capable of forming large complexes, while the TIR domain (green) or the death domain (blue) form smaller oligomers. Inset: Expansion of the values obtained for TIR and death domains compared to sfGFP control. (B) FCS data in solution. Control based on GFP monomer (black). Correlation curves obtained for the TIR domain (green), death domain (blue) and full-length MyD88 (red). A clear shift in diffusion time can be seen between the full-length protein and the separate domains. FCS curves are representative traces from 3 repeated measurements. (C) Hydrodynamic radius normalised by the sfGFP control (black) calculated for the domains and full-length MyD88, indicating the increase of approximate physical size of the oligomeric species. Values are mean ± SD from 3 repeat measurements.
DOI: 10.7284/126698
title: INS (Inertial Navigation System) data collected during research cruise RR1712 using a iXSea Phins instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7313186
title: FIGURE 1A EXAMPLES OF TIR DEATH DOMAIN AND WILDTYPE FL MYD88

description: Time trace examples of TIR domain, death domain and wild type full length myd88 upon which figure 1A is based. <b>The domains of MyD88 exhibit different oligomerisation propensities, with only the full-length protein forming polymers.</b>
DOI: 10.6084/m9.figshare.7313321.v1
title: FIGURE 1 ANALYSED RAW DATA

description: . For GFP-tagged MyD88 TIR<sup> </sup>domain, small fluctuations in intensity are recorded around the average fluorescence value, as expected for a low-order oligomer such as a dimer (for example, if 20 proteins are detected simultaneously, the exit/entry of a single protein causes a decrease/increase of signal of only 5%). The GFP-tagged MyD88 DD shows larger bursts of fluorescence correlating with these death domains forming higher-order oligomeric complexes. As seen by the fluorescent time traces, N-terminally GFP tagged full-length MyD88 shows extremely large filamentous polymers of MyD88 diffusing through the confocal volume. (B) The B parameter (Brightness) correlates with the number of oligomers detected in typical time-traces as a function of protein concentration (nM), for the TIR domain (green), DD (blue) and wild-type full length MyD88 (red). Protein concentrations range from 0 to 320 nM. Monomeric GFP (black) is included as a control. Inset: expansion of the signals obtained for the individual domains, over a lower concentration range. Fluorescence Intensity Time traces in (A) are representative traces obtained at &gt;200nM protein concentrations. Values in (B) are from approx. 30 dilution experiments with the various protein concentrations and corresponding brightness values obtained plotted.
DOI: 10.6084/m9.figshare.7313087
title: FIGURE 1 RAW DATA MYD88 FL WT DILUTIONS

description: Number of photons from time traces of MYD88 wildtype full length from approx. 30 dilution experiments with the various protein concentrations and corresponding brightness values obtained plotted in additional files
DOI: 10.7284/126703
title: INS (Inertial Navigation System) data collected during research cruise RR1712 using a Kongsberg Seapath 320+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7313087.v1
title: FIGURE 1 RAW DATA MYD88 FL WT DILUTIONS

description: Number of photons from time traces of MYD88 wildtype full length from approx. 30 dilution experiments with the various protein concentrations and corresponding brightness values obtained plotted in additional files
DOI: 10.6084/m9.figshare.7312847
title: FIGURE 1 RAW DATA MYD88 TIR DOMAIN DILUTIONS

description: Number of photons from time traces of approx. 30 dilution experiments of MYD88 TIR domain alone with the various protein concentrations and corresponding brightness values obtained plotted in additional files
DOI: 10.7284/126690
title: Meteorological Station data collected during research cruise RR1712 using a SIO MET-System instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312799
title: FIGURE 1 RAW DATA MYD88 DEATH DOMAIN DILUTIONS

description: Number of photons collected in time traces for approx. 30 dilution experiments of MYD88 death domain alone with the various protein concentrations and corresponding brightness values obtained plotted in additional files
DOI: 10.6084/m9.figshare.7312847.v1
title: FIGURE 1 RAW DATA MYD88 TIR DOMAIN DILUTIONS

description: Number of photons from time traces of approx. 30 dilution experiments of MYD88 TIR domain alone with the various protein concentrations and corresponding brightness values obtained plotted in additional files
DOI: 10.7284/126693
title: Multibeam Echosounder data collected during research cruise RR1712 using a Kongsberg EM122 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312799.v1
title: FIGURE 1 RAW DATA MYD88 DEATH DOMAIN DILUTIONS

description: Number of photons collected in time traces for approx. 30 dilution experiments of MYD88 death domain alone with the various protein concentrations and corresponding brightness values obtained plotted in additional files
DOI: 10.7284/128407
title: Multibeam Echosounder data collected during research cruise RR1712 using a Kongsberg EM122 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126697
title: Winch data collected during research cruise RR1712 using a Markey DUTW-9-11 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126701
title: Winch data collected during research cruise RR1712 using a Markey DUSH-5 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7312637
title: Supplemental table 3 - Aguirre

description: <b>Supplemental Table 3</b>. Adverse Events After 18 Months of Testosterone Therapy
DOI: 10.6084/m9.figshare.7312637.v1
title: Supplemental table 3 - Aguirre

description: <b>Supplemental Table 3</b>. Adverse Events After 18 Months of Testosterone Therapy
DOI: 10.7284/126706
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise RR1713 using a Hawaii UHDAS instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126715
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise RR1713 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126719
title: Expendable Probe data collected during research cruise RR1713 using a Turo Quoll instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126707
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1713 using a Furuno GP-150 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126709
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1713 using a Ashtech ADU2 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126717
title: GNSS (Global Navigation Satellite System) data collected during research cruise RR1713 using a Trimble SPS351 instrument system onboard the platform RV Roger Revelle

description: Original (unprocessed) data collected during a Field_expedition