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opencc-by-nc-sa-4.0Dec 2018View details →

Supplementary material to "A dynamic flight model for Slocum gliders and implications for turbulence microstructure measurements" by Merckelbach et al.

Supplementary information to the publication "A dynamic flight model for Slocum gliders and implications for turbulence microstructure measurements"  by Lucas Merckelbach, Anja Berger, Gerd Krahmann, Marcus Dengler and Jeffrey R. Carpenter, Journal of Atmospheric and Oceanic Technology, 2019, 36(2), DOI: 10.1175/JTECH-D-18-0168.1. The supplementary information consists of  the set of glider data and DVL data as used in the manuscript.

opencc-by-4.0Dec 2018View details →

Research data supporting "Surface dynamics and ligand-core interactions of quantum size photoluminescent gold nanoclusters"

Experimental research raw data supporting the publication by Lin, Y. et al, 2018, Surface dynamics and ligand-core interactions of quantum sized photoluminescent gold nanoclusters, Journal of the American Chemical Society. DOI: 10.1021/jacs.8b04436 Molecular simulation data is available upon reasonable request from irene.yarovsky@rmit.edu.au.

opencc-by-4.0May 2019View details →

Raw Data supporting Promoters adopt distinct dynamic manifestations depending on transcription factor context

All source data is provided as MAT-files, which can be opened in Matlab. In total, the source data contain 270 core data files and 540 processed data files. The data for each individual promoter is stored in a different directory and the 9 promoters are: <ul> <li> ALD3 </li> <li> DCS2 </li> <li> DDR2 </li> <li> HXK1 </li> <li> RTN2 </li> <li> TKL2 </li> <li> SIP18 </li> <li> pSIP18_mut6 (also referred to as mutant A4) </li> <li> pSIP18_mut21 (also referred to as mutant D6) </li> </ul> The data for the first 7 promoters was previously reported in (Hansen and O’Shea, 2013), though in an unnormalized form. That is, it was previously reported as a concentration per cell in arbitrary fluorescence units (AU). In the present manuscript, we have calibrated the data to obtain absolute abundances, such that the MAT-files now contain both the old AU concentration as well as absolute abundances, i.e. number of YFP molecules per cell. The calibration was performed as described in (Huang et al., 2016). Similarly, the data for the last 2 promoters (A4 and D6) was previously reported in its unnormalized form in (Hansen and O’Shea, 2015) and it is here also reported in the form of absolute abundances.   The MAT-files containing the raw data have the suffix “_size.mat”. The name of the MAT files describes the experiment. If the file name contains “DM”, then it is a single pulse. Thus, “SIP18_DM_40min_275nM_size.mat” refers to a single 40 min pulse with 275 nM 1-NM-PP1 for the SIP18 promoter. Similarly if the file name contains “FM”, e.g. “RTN2_FM_8_5min_690nM_size.mat” then it refers to eight 5 min pulses separated by 5 min intervals at 690 nM for the RTN2 promoter. Finally, if the file name contains “FM4”, e.g.  “TKL2_FM4_15minINT_690nM_size.mat” then the experiment was four 5 min pulses separated by 15 min intervals at 690 nM for the TKL2 promoter. The concentration is the concentration of 1-NM-PP1 that was used and 100 nM, 275 nM, 690 nM and 3mM refers to approximately, 25%, 50%, 75% and 100% Msn2 activation. For full experimental details please see (Hansen and O’Shea, 2013; Hansen et al., 2015).   The “_size.mat” MAT-files contain the following variables: <ul> <li> cell_size_pixels</li> <li> CFP</li> <li> CFP_molecules</li> <li> CFP_raw</li> <li> inhibitor_conc</li> <li> MSN2_raw</li> <li> MSN2_RFP</li> <li> pulse_parameters • time</li> <li> YFP</li> <li> YFP_molecules</li> <li> YFP_raw</li> </ul> CFP, CFP_molecules, CFP_raw and YFP, YFP_molecules, YFP_raw are Nx64 matrices, where each row N correspond to a different cell and the 64 columns correspond to the 64 experimentally measured timepoints corresponding to the “time” vector running from -5 min to 152.5 min in increments of 2.5 min and the 1NM-PP1 inhibitor was added at time 0. “CFP_raw” and “YFP_raw” contains raw, uncorrected data, so without photobleaching correction and background subtraction. “CFP” and “YFP” contain corrected data in arbitrary fluorescence units (AU) and report on the concentration (i.e. size normalized). Finally, “CFP_molecules” and “YFP_molecules” contains the total number of CFP and YFP molecules per cell (i.e. this is not a concentration, but the absolute abundance). The area of each cell at each timepoint can be found in the matrix “cell_size_pixels”. Since the cells are live and growing, this will tend to increase during the experiments. Occasionally large fluctuations can occur due to errors in cell segmentation or due to division. For full details on the image analysis and cell segmentation, please see (Hansen and O’Shea, 2013; Hansen et al., 2015).   The variables “inhibitor_conc” and “pulse_parameters” refer to the type of experiment and is also given by the name. “inhibitor_conc”  gives the 1NMPP1 concentration: 100 nM, 275 nM, 690 nM or 3000 nM. “pulse_parameters” contains either 2 or 3 elements and given the dynamical pulse sequence parameters. Column 1 contains the number of pulses and column 2 the duration of the pulses. Column 3 gives the interval between the pulses if more than one pulse is used – otherwise column 3 is zero.   Moreover, on a more technical note it should be noted that the signal-to-noise of the CFP reporter is worse than the YFP reporter. Therefore, we always use the YFP reporter for quantitative analysis. Furthermore, the two other MAT-files “…MSN2.mat” and “…YFP.mat” contain processed data. Please see the ReadMe file on the code for a full description and how these were derived.   Finally, Supplementary Table 1 contains the model-inferred parameters for each promoter and condition.     References Hansen, A.S., and O’Shea, E.K. (2013). Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression. Mol. Syst. Biol. Hansen, A.S., and O’Shea, E.K. (2015). Cis Determinants of Promoter Threshold and Activation Timescale. Cell Rep. Hansen, A.S., Hao, N., and OShea, E.K. (2015). High-throughput microfluidics to control and measure signaling dynamics in single yeast cells. Nat. Protoc. Huang, L., Pauleve, L., Zechner, C., Unger, M., Hansen, A.S., and Koeppl, H. (2016). Reconstructing dynamic molecular states from single-cell time series. J. R. Soc. Interface.

opencc-by-4.0Oct 2022View details →

Investigation of the behavior of dioxadet molecules in water by molecular dynamics

A set of files for all-atom molecular dynamic simulations of a dioxadet molecule in water for four parametrizations obtained with a number of tools: ATBuilder, Amber tools, and Swiss Parameters.

opencc-by-4.0Oct 2022View details →

Data for "Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics"

We provide the raw data for the paper "Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics". The files hold time tagged and time resolved single photon data from experiments on immobilized structures as well on free diffusion structures. The files have PicoQuant's .ptu files-format. Additionally we provide the python scripts used to analyze these data sets.

opencc-by-4.0Oct 2022View details →

Supporting data for "Nuclear quantum effects on zeolite proton hopping kinetics explored with machine learning potentials and path integral molecular dynamics"

Supporting data for "<a href="https://www.nature.com/articles/s41467-023-36666-y">Nuclear quantum effects on zeolite proton hopping kinetics explored with machine learning potentials and path integral molecular dynamics</a>" by M. Bocus, R. Goeminne, A. Lamaire, M. Cools-Ceuppens, T. Verstraelen and V. Van Speybroeck, Nature Communications, 2023, 14, 1008. This dataset contains examples of input files, submission and analysis scripts to train and use a machine learning potential based on the Schnet architecture for the proton hopping reaction in the H-CHA zeolite. The complete DFT training set, obtained by unbiasing the forces printed by CP2K (with PLUMED coupling), is stored as extended xyz files in the folders DFT/A-B/training_data.xyz where A=1-3 and A<B<5. More details on the folder architecture can be found in the README.md file.

Source Data for Crowdsourcing Bridge Dynamic Monitoring with Smartphone Vehicle Trips

This data accompanies the study "Crowdsourcing Bridge Dynamic Monitoring with Smartphone Vehicle Trips" published in (Nature) Communications Engineering. This paper focuses on using large and inexpsensive datasets for obtaining information on the dynamics of bridges. In this study, data is collected by smartphones in moving vehicles as the cross over a bridge, in three distinct applications. Smartphone data was collected in controlled field experiments and uncontrolled Uber rides on a long-span suspension bridge in the USA (The Golden Gate Bridge) and an analytical method was developed to accurately recover modal properties. The method was also successfully applied to partially-controlled crowdsourced data collected on a short-span highway bridge in Italy. The results suggest that larve and inexpensive datasets collected by smartphones could play a role in monitoring the health of existing transportation infrastructure. The data provided includes the source data for the figures in the publication as well as the "controlled data" referenced in the study.

CESM 1.2 climate model simulation output for: The Essential Role of Westerly Wind Bursts in ENSO Dynamics and Extreme Events Quantified in Model 'Wind Stress Shaving' Experiments

Westerly wind bursts (WWBs)—brief but strong westerly wind anomalies in the equatorial Pacific—are believed to play an important role in El Niño Southern Oscillation (ENSO) dynamics, but quantifying their effects is challenging. Here, we investigate the cumulative effects of WWBs on ENSO characteristics, including the occurrence of extreme El Niño events, via modified coupled model experiments within Community Earth System Model (CESM1) in which we progressively reduce the impacts of wind stress anomalies associated with model-generated WWBs. In these "wind stress shaving" experiments we limit momentum transfer from the atmosphere to the ocean above a preset threshold, thus "shaving off" wind bursts. To reduce the tropical Pacific mean state drift, both westerly and easterly wind bursts are removed, although the changes are dominated by WWB reduction. As we impose progressively stronger thresholds, both ENSO amplitude and the frequency of extreme El Niño decrease, and ENSO becomes less asymmetric. The warming center of El Niño shifts westward, indicating less frequent and weaker Eastern Pacific (EP) El Niño events. Removing most of wind bursts-related wind stress anomalies reduces ENSO amplitude by 22%. The essential role of WWBs in the development of extreme El Niño events is revealed in the suppressed eastward migration of the western Pacific warm pool and hence a weaker Bjerknes feedback under wind shaving. Overall, our results reaffirm the importance of WWBs in shaping the characteristics of ENSO and its extreme events and imply that WWB changes with global warming could influence future ENSO.

Droplet digital PCR (ddPCR) as a tool for investigating dynamics of cryptic symbionts

Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions is critical for understanding symbiont-host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking and hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected and high host densities were found to have lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.

Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas: An assessment of population connectivity and ocean dynamics

Biophysical models are a powerful tool for assessing population connectivity of marine organisms that broadcast spawn. Albula vulpes is a species of bonefish that is an economically and culturally important sportfish found throughout the Caribbean and that exhibits genetic connectivity among geographically distant populations. We created ontogenetically relevant biophysical models for bonefish larval dispersal based upon multiple observed spawning events in Abaco, The Bahamas in 2013, 2018, and 2019. Biological parameterizations were informed through active acoustic telemetry, CTD casts, captive larval rearing, and field collections of related albulids and anguillids. Ocean conditions were derived from the Regional Navy Coastal Ocean Model American Seas dataset. Each spawning event was simulated 100 times using the program Ichthyop. Ten thousand particles were released at observed and putative spawning locations and were allowed to disperse for the full 71-day pelagic larval duration for A. vulpes. Settlement densities in defined settlement zones were assessed along with interactions with oceanographic features. The prevailing Northern dispersal paradigm exhibited strong connectivity with Grand Bahama, the Berry Islands, Andros, and self-recruitment to lower and upper Abaco. Ephemeral gyres and flow direction within Northwest and Northeast Providence Channels were shown to have important roles in larval retention to the Bahamian Archipelago. Larval development environments for larvae settling upon different islands showed few differences and dispersal was closely associated with the thermocline. Settlement patterns informed the suggestion for expansion of conservation parks in Grand Bahama, Abaco, and Andros, and the creation of a park in Eleuthera and the Berry Islands to protect fisheries. Further observation of spawning events and the creation of biophysical models will help to maximize protection for bonefish spawning locations and nursery habitat, and may help to predict year-class strength for bonefish stocks throughout the Greater Caribbean.

opencc-by-4.0Oct 2021View details →

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors

Raw fast SPT data for Hypoxia-Inducible Factors: HIF2a_HIF1b_KIN_Clones.zip corresponds to Figure 2A-C and Figure 2-Figure supplement 2A-B, contains fast SPT data for Halo-HIF-2α KIN clone A31 and clone B50, Halo-HIF-1β KIN clone A21 and clone B89. HIF1b_with_HIF2a_overexpression.zip corresponds to Figure 2D-E and Figure 2-Figure supplement 2C, contains fast SPT data for: Halo-HIF-1β KIN clone A21, Halo-HIF-1β KIN clone A21 with HIF-2α stably over-expressed, and Halo-HIF-1β KIN clone A21 with a dimerization mutant form of HIF-2α (R171A/V192D) stably over-expressed. Belzutifan_dosage.zip corresponds to Figure 3-Figure supplement 1, contains fast SPT data for: Halo-HIF-2α KIN clone A31, treated with 0.0002 uM,  0.002 uM, 0.005 uM, 0.01 uM, 0.02 uM, and 0.2 uM of Belzutifan. HIF1b_with_HIFa_chimera_overexpression_and_Belzutifan.zip corresponds to Figure 3 and Figure 3-Figure supplement 2, contains fast SPT data for: Parental Halo-HIF-1β KIN clone A21 cells and cells stably over-expressing either a certain form of HIF-α (WT or domain swap), treated with either Belzutifan or DMSO.  HIFa_domain_swap.zip corresponds to Figure 4 and Figure 4-Figure supplement 2, contains fast SPT data for: Halo-HIF-2α KIN clone A31, WT 786-O cells stably express V5-Halo-HIF-2α with an L30 promoter, WT 786-O cells stably express V5-Halo-HIF-2α/1α with an L30 promoter, WT 786-O cells stably express V5-Halo-HIF-1α with an L30 promoter, and WT 786-O cells stably express V5-Halo-HIF-1α/2α with an L30 promoter.   DBD_mutant.zip corresponds to Figure 5A-C, contains fast SPT data for: WT 786-O cells stably express V5-Halo-HIF-2α with an L30 promoter, WT 786-O cells stably express a DBD mutant form of V5-Halo-HIF-2α (R27E) with an L30 promoter, WT 786-O cells stably express V5-Halo-HIF-1α with an L30 promoter, and WT 786-O cells stably express a DBD mutant form of V5-Halo-HIF-1α (R30E) with an L30 promoter. Dimerization_mutant.zip corresponds to Figure 5D-F, contains fast SPT data for: WT 786-O cells stably express V5-Halo-HIF-2α with an L30 promoter, WT 786-O cells stably express a dimerization mutant form of V5-Halo-HIF-2α (R171A/V192D) with an L30 promoter, WT 786-O cells stably express V5-Halo-HIF-1α with an L30 promoter, and WT 786-O cells stably express a dimerization mutant form of V5-Halo-HIF-1α (R170A/V191D) with an L30 promoter.

opencc-by-4.0Mar 2022View details →

Dynamic rewiring of electrophysiological brain networks during learning

This space is dedicated to the dataset used in the manuscript "Dynamic rewiring of electrophysiological brain networks during learning" under peer-reviewing process.

opencc-by-4.0Nov 2022View details →

Molecular dynamics simulation of the permeation of 5ALA across the lipid bilayers of the stratum corneum

Input and output files for US-REST3 MD simulations of the permeation of 5ALA across a lipid bilayer representative of the lipid bilayers of the stratum corneum. Each folder corresponds to US-REST3 and conventional US calculations performer at different distances between the permeant and the centre of mass of the lipid bilayer.

opencc-by-4.0Nov 2022View details →

Molecular dynamics simulation of the permeation of Me-5ALA across the lipid bilayers of the stratum corneum

Input and output files for US-REST3 MD simulations of the permeation of Me-5ALA across a lipid bilayer representative of the lipid bilayers of the stratum corneum. Each folder corresponds to US-REST3 and conventional US calculations performer at different distances between the permeant and the centre of mass of the lipid bilayer.

Molecular dynamics simulations in: High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter

Transporters of the Nramp (Natural resistance-associated macrophage protein) family import divalent transition metal ions into cells of most organisms. By supporting metal homeostasis, Nramps prevent disorders related to metal insufficiency or overload. Previous studies revealed that Nramps take on a LeuT fold and identified the metal-binding site. We present high- resolution structures of Deinococcus radiodurans Nramp in three stable conformations of the transport cycle revealing that global conformational changes are supported by distinct coordination geometries of its physiological substrate, Mn2+, across conformations and conserved networks of polar residues lining the inner and outer gates. A Cd2+-bound structure highlights differences in coordination geometry for Mn2+ and Cd2+. Measurements of metal binding using isothermal titration calorimetry indicate that the thermodynamic landscape for binding and transporting physiological metals like Mn2+ is different and more robust to perturbation than for transporting the toxic Cd2+ metal.

Genet dynamics and its variation among genets of a clonal plant Convallaria keiskei

In clonal plant populations, a number of genetically identical ramets form a genet. While coexisting ramets potentially perform independently, their behaviours not only depend on ages and sizes but are also constrained by genetic background. In this study, genet dynamics and its variability among neighbouring genets were investigated based on the ramet demography of each genet in Convallaria keiskei. Genet dynamics were first formulated as a matrix model with the two components of clonal growth (clonal reproduction) and survival-transitions between ramet size classes. Then, a statistical estimation of the matrix elements was established using three datasets: aboveground demographic censuses, belowground directional rhizomatous connections and genetic identification of ramets. Finally, genet growth rates reflecting both the changes of clonal growth and ramet size growth were estimated and compared for fundamental demographic elements among genets. Over three years of aboveground annual censuses of a 28 × 2 m plot, 2,021 ramets were identified as belonging to 28 genotypes. Belowground excavation detected 515 clonal fragments. Genet growth rate of three dominant genets varied with medians of 1.13, 1.02 and 1.05; 95% credible intervals of the posterior distributions did not overlap between the genet with the largest median and the others. The variation was caused primarily by differences in clonal growth rather than survival-transitions between size classes. Clonal growth by branching was rarer than at the tips but contributed to the maintenance of the genet. Therefore, both clonal growth frequencies and connecting patterns of ramets caused the variation of genet dynamics and established genets persist for a long time through the positive growth rates, which would contribute to maintaining a population. We also conclude that fundamental demographic elements relating to clonal growth traits (the features of individual genets) strongly impact genet dynamics.

Soil N dynamics in mixed and larch forests in northeastern China

We developed a multiple-indicator approach to evaluate differences in soil N availability across sites and between larch monoculture and mixed stands paired at three sites (Daxinganling, Maoershan, and Qingyuan) in northeastern China. The selected indicators were foliar %N, soil C/N, soil inorganic N, foliar δ15N, and δ15N of bulk soil, ammonium, and nitrate in the soil profiles.

Fine-scale temporal dynamics of flower visitors sheds light on the pollination strategy of a dioecious palm in the Ecuadorian Andes

Background: Dioecious plants generally display sexual dimorphism in male and female floral traits, potentially attracting slightly different pollinator communities. The sharing of common floral visitors between male and female flowers and their timing of visits to both sexes is of critical importance to ensure plant's reproductive success. Palm inflorescences are visited by abundant and diverse insect communities, yet the temporal patterns of insect visits on both sexes remain poorly known. Results: We report 59 morphospecies in the arthropod community, dominated by three beetle families: Staphylinidae, Nitidulidae and Curculionidae. Male inflorescences were more abundantly visited than female, but visitors of the later were taxonomically more diverse. Among the 16 pollinator candidates identified, 9 visited both inflorescence sexes synchronously at dusk /night whereas the others did so asynchronously during the day. Conclusion: Our study provides new insights into the pollination mechanism of P. aequatorialis. We found evidence of differential pollinator attraction between floral sexes, which may be explained by the sexual dimorphism of both flowers. Synchronicity in dusk/night visits of both inflorescence sexes suggests a sexual synchronization of the signal used to attract pollinators.

Data for: Ectoparasite population dynamics affected by host body size but not host density or water temperature in a 32-year long time series

Host density, host body size, and ambient temperature have all been positively associated with increases in parasite infection. However, the relative importance of these factors in shaping long-term parasite population dynamics in wild host populations is unknown due to the absence of long-term studies. Here, we examine long-term drivers of gill lice (Copepoda) infections in Arctic charr (Salmonidae) over 32 years. We predicted that host density and body size and water temperature would all positively affect parasite population size and population growth rate. Our results show that fish size was the main driver of gill lice infections in Arctic charr. In addition, Arctic charr became infected at smaller sizes and with more parasites in years of higher brown trout population size. Negative intraguild interactions between brown trout and Arctic charr appear to drive smaller Arctic charr to seek refuge in deeper areas of the lake, thus increasing infection risk. There was no effect of host density on the force of infection, and the relationship between Arctic charr density and parasite mean abundance was negative, possibly due to an encounter-dilution effect. The population densities of host and parasite fluctuated independently of one another. Water temperature had negligible effects on the temporal dynamics of the gill lice population. Understanding long-term drivers of parasite population dynamics is key for research and management. In fish farms, artificially high densities of hosts lead to vast increases in the transmission of parasitic copepods. However, in wild fish populations fluctuating at natural densities, the surface area available for copepodid attachment might be more important than the density of available hosts.