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opencc-by-4.0Dec 2023View details →

Dataset for Active shortening simultaneous to normal faulting based on GNSS, geophysical and geological data: The seismogenic Ventas de Zafarraya Fault (Betic Cordillera). Tectonics

Dataset for "Active shortening simultaneous to normal faulting based on GNSS, geophysical and geological data: The seismogenic Ventas de Zafarraya Fault (Betic Cordillera)" Tectonics File "hypoDD_10_300.reloc.txt" compile all the relocated seismicity in the study area. Files "810_.NEU, 811_.NEU, 812_.NEU, 813_.NEU, 814_.NEU, 815_.NEU,  and 816_.NEU" presents the time series data of GNSS sites of the Zafarraya network.

opencc-by-4.0Dec 2023View details →

Supplementary Information: RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity

The Simulation_files folder contains initial coordinates, input files and output coordinates of the Molecular Dynamics (MD) simulations of wild type and mutants of the Apdp peptide in the ribosome ( region of 35 Å around the peptide). The Uncharged_N-terminal_residues folder includes residue topologies (.rtp file) and hydrogen data bank (.hdb) of the uncharged terminal Alanine and Proline (used for modelling Ala134 and Pro134). The Figures folder contains rmsd, distances, rmsf values, and projections on the most dominant conformational modes sampled by the Ala 132 backbone atoms obtained from the MD trajectories.

openmit-licenseDec 2023View details →

Small Test Suites for Active Automata Learning: Supplemental Material

Supplemental material for the paper: Small Test Suites for Active Automata Learning. Submitted to TACAS 2024.

opencc-by-4.0Dec 2023View details →

Self-efficacy to Regulate physical activity

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dryad32/100

Data from: Molecular docking and dynamics studies to identify novel active compounds targeting potential breast cancer receptor proteins from an indigenous herb Euphorbia thymifolia Linn

Breast cancer has become most prevalent disease and their incidence has doubled in Indian scenario. Targeted therapy with the novel compounds derived from plants could be the promising approach for the development of drugs. Euphorbia thymifolia L is a widely growing tropical herb which has been reported for its various ethnopharmacological properties, including anticancer properties. The aim of the present study was to identify the active phytocompounds present in the methanolic extract using an In-silico approach. The methanolic extract of E. thymifolia (ME.ET) was subjected to GC-MS analysis and the identified compounds were docked with potential protein targets implicated in breast cancer such as ERK1, AKT, EGFR/HER2, ER, MELK, PLK1, PTK6. Compounds with good docking score were further subjected to dynamics study to understand the protein ligand binding stability, ligand pathway calculation, molecular mechanics energies combined with Poisson-Boltzmann (MM/PBSA) calculation using Schrodinger suite. Out of 219 unique phytocompounds subjected to docking, two compounds namely, 3,6,9,12-tetraoxatetradecane-1,14-diyl dibenzoate (TTDB) and succinic acid, 2-(dimethylamino)ethyl 4-isopropylphenyl ester (SADPE) showed good docking score. Molecular dynamics study showed high affinity and low binding energy for TTDB with HER2, ERK1 and SADPE with ER. Hence this is the first study to identify and report active compounds from E.thymifolia linn. Further invitro and invivo anticancer studies can be performed to confirm these results and understand the molecular mechanism by which TTDB and SADPE exhibit anticancer activity against breast cancer.

opencc-zeroJan 2024View details →

dryad32/100

Density-dependent effects of parasitism on the activity of a benthic engineer species: potential impact on ecosystem functioning

While parasitism is a common lifestyle on Earth, its importance for the functioning of marine ecosystems has been overlooked for a long time. In particular, parasites have significant potential to influence central ecological processes through their impacts on hosts that serve as ecosystem engineers. Using an ex-situ experimental approach, we explored the effects of trematode parasites on the engineering bioturbation activity of a common and abundant bivalve along European Atlantic soft-bottom coastlines, the peppery furrow shell Scrobicularia plana, as well as knock-on effects for nutrient exchanges at the sediment-water interface. Trematodes negatively impacted the host's ability to transport sediment particles and solutes in a density-dependent way with parasite burden explaining 22–31% of the inter-individual variability. This could be explained by parasitism impairing the bivalve physiological state and ability to burrow as we observed a decrease in the condition index and the burrowing depth of the bivalves with an increase in the number of parasites they host. In contrast, the influence of S. plana on benthic biogeochemical fluxes did not vary significantly according to parasitic burden over a short time scale. Here, we focused on the effects of trematode parasites on the sole behaviour of S. plana and thus excluded other macrofaunal organisms. We should next test whether trematodes modulate the structure and functioning of benthic communities dominated by S. plana to better understand and quantify the engineering role of parasites in soft-bottom coastal environments.

opencc-zeroJan 2024View details →

dryad32/100

A global analysis of field body temperatures of active squamates in relation to climate and behaviour

Aim: Squamate fitness is affected by body temperature, which in turn is influenced by environmental temperatures and, in many species, by exposure to solar radiation. The biophysical drivers of body temperature have been widely studied, but we lack an integrative synthesis of actual body temperatures experienced in the field, and their relationships to environmental temperatures, across phylogeny, behaviour, and climate. Location: Global (25 countries on six continents) Taxa: Squamates (210 species, representing 25 families) Methods: We measured body temperatures during activity for 20,231 individuals, and examined how body temperatures vary with substrate and air temperatures across taxa, climates, and behaviours (basking and diel activity). Results: Heliothermic lizards had the highest body temperatures and those most weakly correlated with substrate and air temperatures. Body temperatures of non-heliothermic diurnal lizards were similar to heliotherms in relation to air temperature but to nocturnal species in relation to substrate temperatures. Diurnal snake and non-heliothermic lizard body temperatures were more strongly correlated to air and substrate temperatures than in heliotherms. Correlation parameters of all diurnal squamates vary with mean annual temperatures, especially in heliotherms, so that the thermal relations of the various categories are disparate in cold climate but convergent in warm climate. Non-heliotherms and nocturnal body temperatures are better explained by substrate temperature than by air temperature. Body temperature distributions become left-skewed in warmer-bodied species, especially in colder climate. Main conclusions: Differences in squamate body temperatures, their environmental relationships, and frequency distributions are globally influenced by behavioural and climatic factors. Differences between behavioural categories are smaller in warm climates where environmental temperatures are generally favourable, but heliotherm body temperature remained consistently higher than all others.

opencc-zeroFeb 2024View details →

opencc-by-4.0Mar 2023View details →

JNK Activation Correlates with Cognitive Impairment and Alteration of the Post-Synaptic Element in the 5xFAD AD Mouse Model

The c-Jun N-terminal kinases (JNKs) are a family of proteins that, once activated by stress stimuli, can alter neuronal functions and survival. The JNK cascade plays a crucial role in the post-synaptic neuronal compartment by altering its structural organization and leading, at worst, to an overall impairment of neuronal communication. Increasing evidence suggests that synaptic impairment is the first neurodegenerative event in Alzheimer’s disease (AD). To better elucidate this mechanism, we longitudinally studied 5xFAD mice at three selected time points representative of human AD symptom progression. We tested the mice cognitive performance by using the radial arm water maze (RAWM) in parallel with biochemical evaluations of post-synaptic enriched protein fraction and total cortical parenchyma. We found that 5xFAD mice presented a strong JNK activation at 3.5 months of age in the post-synaptic enriched protein fraction. This JNK activation correlates with a structural alteration of the post-synaptic density area and with memory impairment at this early stage of the disease that progressively declines to cause cell death. These findings pave the way for future studies on JNK as a key player in early neurodegeneration and as an important therapeutic target for the development of new compounds able to tackle synaptic impairment in the early phase of AD pathology

opencc-by-4.0Jul 2023View details →

Collective dynamics and pair-distribution function of active Brownian ellipsoids

Supplemental data for the following manuscript: Stephan Bröker, Michael te Vrugt, Raphael Wittkowski, "Collective dynamics and pair-distribution function of active Brownian ellipsoids"

Supplementary Figure 6 stimulus induced brain activity data

This data set shows brain activity in response to an airpuff stimulus applied to the right whiskers. A 2 s, 3 Hz airpuff stimulus is applied to the right whiskers 20 times. This data was collected using a CMOS camera that costs approximately $750. Wide field images of the mouse brain at four different wavelengths are provided as .tif files. Processed data are included in a .h5 file that contains relative changes in neuronal calcium activity, extracellular acetylcholine, oxyhemoglobin, and deoxyhemoglobin. A trigger file recorded by the data acquisition system shows the timing of measurements and stimuli. This data was used to produce the stimulus response parts of supplementary figure 6 in the following article. Doran, P., Fomin-Thunemann, N., Tang, R., Zimmerman, B., Kilic, K., Kura, S., Fisher, H., Chabbot, G., Herbert, J., Jiang, J., Sakadzic, S., Boas, D., Devor, A., Chen, I., & Thunemann, M. (2023). Widefield in vivo imaging system with two fluorescence and two reflectance channels, a single sCMOS detector, and shielded illumination. bioRxiv. <a href="https://doi.org/https:/doi.org/10.1101/2023.11.07.566086do">https://doi.org/https://doi.org/10.1101/2023.11.07.566086do</a>

Supplementary Figure 6 spontaneous brain activity data

This data set contains a single ten-minute run of spontaneous brain activity. This data was collected using a CMOS camera that costs approximately $750. Wide field images of the mouse brain at four different wavelengths are provided as .tif files. Processed data are included in a .h5 file that contains relative changes in neuronal calcium activity, extracellular acetylcholine, oxyhemoglobin, and deoxyhemoglobin. A video of the mouse face and a recording from an accelerometer placed under the mouse are also included. A trigger file recorded by the data acquisition system shows the timing of measurements. This data was used to produce the spontaneous activity part of supplementary figure 6 in the following article. Doran, P., Fomin-Thunemann, N., Tang, R., Zimmerman, B., Kilic, K., Kura, S., Fisher, H., Chabbot, G., Herbert, J., Jiang, J., Sakadzic, S., Boas, D., Devor, A., Chen, I., & Thunemann, M. (2023). Widefield in vivo imaging system with two fluorescence and two reflectance channels, a single sCMOS detector, and shielded illumination. bioRxiv. <a href="https://doi.org/https:/doi.org/10.1101/2023.11.07.566086do">https://doi.org/https://doi.org/10.1101/2023.11.07.566086do</a>

Figure 2 stimulus induced brain activity data

This data set shows brain activity in response to an airpuff stimulus applied to the right whiskers. A 2 s, 3 Hz airpuff stimulus is applied to the right whiskers 20 times. Raw .dat files produced by the camera contain wide field images of the mouse brain collected at four different wavelengths. Processed data are included in a .h5 file that contains relative changes in neuronal calcium activity, extracellular acetylcholine, oxyhemoglobin, and deoxyhemoglobin. A video of the mouse face and a recording from an accelerometer placed under the mouse are also included. A trigger file recorded by the data acquisition system shows the timing of measurements and stimuli. This data was used to produce the stimulus response parts of figure 2 in the following article. Doran, P., Fomin-Thunemann, N., Tang, R., Zimmerman, B., Kilic, K., Kura, S., Fisher, H., Chabbot, G., Herbert, J., Jiang, J., Sakadzic, S., Boas, D., Devor, A., Chen, I., & Thunemann, M. (2023). Widefield in vivo imaging system with two fluorescence and two reflectance channels, a single sCMOS detector, and shielded illumination. bioRxiv. <a href="https://doi.org/https:/doi.org/10.1101/2023.11.07.566086do">https://doi.org/https://doi.org/10.1101/2023.11.07.566086do</a>

Blockage, vandalism, and harassment activities for the cause of climate change mitigation: data deposit

The paper describes a dataset of metadata of 89 blockage, vandalism, and harassment events happening in recent years. The dataset comprises three main categories: 1) Events, 2) Activists, and 3) Consequences. For researchers interested in environmental activism, climate change, and sustainability, the dataset is helpful in studying the effectiveness and appropriateness of strategies to raise public awareness and support. For researchers in the field of security studies and green criminology, the dataset offers resources to study features and impacts of blockage, vandalism, and harassment events. The Bayesian Mindsponge Framework (BMF) analytics was employed to validate the dataset. Consequently, the estimated result aligns with the Mindsponge Theory’s theoretical reasoning.

opennotspecifiedSep 2019View details →

FIG. 1 in Temporal Patterns of Mating Activity in Alpine Newts, Ichthyosaura alpestris

FIG. 1. Number of mating pairs in relation to (A) the time and (B) the day, with 95% credible intervals (dotted lines). The yellow lines show the model prediction for the number of mating pairs while the lights were on; blue lines show the model prediction for lights off. Points show the raw data (yellow: lights on; blue: lights off) and are jittered for better visibility. n = 172 observations on 51 males and 54 females.

opennotspecifiedSep 2022View details →

Fig. 2 in The hydroperoxyl radical scavenging activity of natural hydroxybenzoic acids in oil and aqueous environments: Insights into the mechanism and kinetics

Fig. 2. The optimized structures of TS of the HOO• + HBA reactions following the FHT mechanism in pentyl ethanoate.

opennotspecifiedSep 2022View details →

Fig. 4 in The hydroperoxyl radical scavenging activity of natural hydroxybenzoic acids in oil and aqueous environments: Insights into the mechanism and kinetics

Fig. 4. Calculated log(koverall) at 298.15 K, in the reactions of the HBA with HOO• in water following pH values.

Fig. 6. ITS2 secondary structures showing significant variations between our isolate A in Funiculosone, a substituted dihydroxanthene-1,9-dione with two of its analogues produced by an endolichenic fungus Talaromyces funiculosus and their antimicrobial activity

Fig. 6. ITS2 secondary structures showing significant variations between our isolate A. Talaromyces sp. (MF927596.1*) and B. T. funiculosus (consensus), incompatible base pairs are highlighted in pale red and yellow colour based on their degrees of incompatibility; * indicating own isolate. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Funiculosone, a substituted dihydroxanthene-1,9-dione with two of its analogues produced by an endolichenic fungus Talaromyces funiculosus and their antimicrobial activity

Fig. 5. Maximum Parsimony (MP) tree constructed using 88 ITS rDNA (A) and 58 ITS2 sequences (B) of different Talaromyces spp. showing taxonomic placement of our isolate (indicated by an asterisk).

Fig. 3 in Funiculosone, a substituted dihydroxanthene-1,9-dione with two of its analogues produced by an endolichenic fungus Talaromyces funiculosus and their antimicrobial activity

Fig. 3. ECD spectra of funiculosone, 1 (green line) and mangrovamide J, 2 (pink line). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Funiculosone, a substituted dihydroxanthene-1,9-dione with two of its analogues produced by an endolichenic fungus Talaromyces funiculosus and their antimicrobial activity

Fig. 4. ORTEP view of 2-phase-II showing atomic labeling. Displacement ellipsoids are drawn at the 30% probability level.