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29,897 results for “activism”
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
<p>The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.</p>
Original data for publication: The Atomically Precise Gold/Captopril Nanocluster Au25(Capt)18 Gains Anticancer Activity by Inhibiting Mitochondrial Oxidative Phosphorylation
<p> Original data for publication: The Atomically Precise Gold/Captopril Nanocluster Au<sub>25</sub>(Capt)<sub>18</sub> Gains Anticancer Activity by Inhibiting Mitochondrial Oxidative Phosphorylation, ACS Applied Materials & Interfaces</p>
Migraine monoclonal antibodies against CGRP change brain activity depending on ligand or receptor target – an fMRI study
<p>Background: Monoclonal antibodies (mAbs) against calcitonin gene-related peptides (CGRP) are novel treatments for migraine prevention. Based on a previous functional imaging study which investigated the CGRP receptor mAb (erenumab), we hypothesized that (i) the CGRP ligand mAb galcanezumab would alter central trigeminal pain processing; (ii) responders to galcanezumab treatment would show specific hypothalamic modulation in contrast to non-responders; and (iii) the ligand and the receptor antibody differ in brain responses.</p> <p>Methods: Using an established trigeminal nociceptive functional magnetic imaging paradigm, 26 migraine patients were subsequently scanned twice: before and 2–3 weeks after administration of galcanezumab.</p> <p>Results: We found that galcanezumab decreases hypothalamic activation in all patients and that the reduction was stronger in responders than in non-responders. Contrasting erenumab and galcanezumab showed that both antibodies activate a distinct network. We also found that pre-treatment activity of the spinal trigeminal nucleus (STN) and coupling between the STN and the hypothalamus covariates with the response to galcanezumab.</p> <p>Conclusions: These data suggest that despite relative impermeability of the blood-brain barrier for CGRP mAb, mAb treatment induces certain and highly specific brain effects which may be part of the mechanism of their efficacy in migraine treatment.</p> <p>Funding: This work was supported by the German Ministry of Education and Research (BMBF) of ERA-Net Neuron under the project code BIOMIGA (01EW2002 to AM) and by the German Research Foundation (SFB936-178316478-A5 to AM). The funding sources did not influence study conduction in any way. </p> <p>Clinical trial number: The basic science study was preregistered in the Open Science Framework (https://osf.io/m2rc6).</p>
Dataset from Microbial bile salt hydrolase activity influences gene expression profiles and gastrointestinal maturation in infant mice
<p>Files from Intestinal Alkaline Phosphatase, Ki-67, and apoptosis (TUNEL) from colon samples. RT-qPCR dCT values of genes analyzed in colon, small intestine, liver and colon organoids</p>
Population and single dopamine neuron activity during classical conditioning
<p>We trained naive or trained mice to associate odor cues with outcome (water, air puff or no outcome), and recorded dopamine cell body activity in the vetral tegmental area (VTA), dopamine axon activity in the ventral striatum (VS) or dopamine release in VS with optic fiber fluorometry (photometry). In different set of mice, single dopamine neuron activiy was recorded with 2-photon microscope. In some of these mice, we reversed odor-outcome contingency so that an odor that was associated with no outcome or air puff became associated with water reward. Licking pattern was also recorded.</p>
Computational models from: Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer
<p>Computational models, compressed molecular dynamics (MD) simulation trajectories, and sample input files for "Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer". An early version of this manuscript is available as a preprint here: https://www.biorxiv.org/content/10.1101/2022.03.16.484661v1</p>
Thunderstorm activity over the Qinghai–Tibet Plateau indicated by the combined data of the FY-2E geostationary satellite and WWLLN
<p>This dataset is for the article titled "Thunderstorm activity over the Qinghai–Tibet Plateau indicated by the combined data of the FY-2E geostationary satellite and WWLLN" which is being submitted to the Remote Sensing for review. </p> <p><strong>Abstract: </strong>Thunderstorm activity over the Qinghai–Tibet Plateau (QTP) has important climatic effects and disaster impacts. Using the thunderstorm feature dataset (TFD) established based on the black body temperature (TBB) and cloud classification (CLC) products of the Fengyun-2E (FY-2E) geostationary satellite, as well as the lightning data of the World Wide Lightning Location Network (WWLLN), the temporal and spatial distributions and some cloud properties of the thunderstorms over the QTP were analyzed. Approximately 93.9% and 82.7% of thunderstorms over the QTP occur from May to September and from 12 to 21 o'clock local time, and the corresponding peaks are in August and at 14:00, respectively. There are three centers featuring frequent thunderstorms in the southeast, south-central, and southwest regions of the QTP. The average thunderstorm cloud area (the region with TBB ≤ −32℃) is 1.8 × 10<sup>4</sup> km<sup>2</sup>. Approximately 32.9% of thunderstorms have strong convective cells (SCCs) composed of areas with TBB ≤ −52℃.The average number and area ratio of SCCs are 3.6 and 25.4%, respectively, and their spatial distribution is given. The average cloud area and the number and area ratio of SCCs of extreme-lightning thunderstorms (thunderstorms with the top 10% of lightning numbers) are approximately 30.0, 3.9, and 1.5 times those of normal thunderstorms. The spatial distribution of the thunderstorm activity is quite different from that of lightning activity given by the Lightning Imaging Sensor (LIS) and Optical Transient Detector (OTD) over the northeastern and southwestern QTP, which may mean that the convection intensity, cloud structure, and charge structure of the thunderstorms over the QTP are different between different regions and seasons.</p>
DATASET: Palaeoenvironmental framing of the O Areal Roman saltworks and related anthropogenic activities in north-western Iberia
<p>Palynological and geochemical dataset of two pedo-sedimentary profiles (P3-6-I and P3-6-II) of the manuscript: <em>Palaeoenvironmental framing of the O Areal Roman saltworks and related anthropogenic activities in north-western Iberia</em>.</p>
Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure
Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. As shown previously (Souque et al, 2021), the integron can generate under stress combinatorial variation in resistance cassette expression by cassette re-shuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here we test this hypothesis by selecting for increased piperacillin resistance populations of <em>P.aeruginosa</em> with a mobile integron containing a hard-to-mobilise beta-lactamase cassette to minimize the potential for adaptive cassette re-shuffling. We found that integron activity can both decrease overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations, albeit at a cost of reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes.
The force response of muscles to activation and length perturbations depends on length history
<p>Recent studies have demonstrated that muscle force is not determined solely by activation under dynamic conditions, and that length history has an important role in determining dynamic muscle force. Yet, the mechanisms for how muscle force is produced under dynamic conditions remain unclear. To explore how muscle force production is determined under dynamic conditions, we investigated the effects of muscle stiffness, activation, and length perturbations on muscle force. First, submaximal isometric contraction was established for whole soleus muscles. Next, the muscles were actively shortened at three velocities. During active shortening, we measured muscle stiffness at L<sub>0 </sub>and<sub> </sub>the force response to time-varying activation and length perturbations. We found that muscle stiffness increased with activation but decreased as shortening velocity increased. The slope of the relationship between maximum force and activation amplitude differed significantly among shortening velocities. Also, the intercept and slope of the relationship between length perturbation amplitude and maximum force decreased with shortening velocities. As shortening velocities were related with muscle stiffness, the results suggest that length history determines muscle stiffness and the history-dependent muscle stiffness influences the contribution of activation to muscle force and the contribution of length perturbations to muscle force. A three-parameter viscoelastic model that included a linear spring and linear damper in parallel with tunable history-dependent spring stiffness proportional to measured muscle stiffness predicted history-dependent muscle force with high accuracy. The results and simulations support the hypothesis that muscle force under dynamic conditions can be accurately predicted as the force response of a history-dependent viscoelastic material to length perturbations.</p>
A feed-forward pathway drives LRRK2 kinase membrane recruitment and apparent activation
<p>Activating mutations in the Leucine Rich Repeat Kinase 2 (LRRK2) cause Parkinson's disease and activated LRRK2 phosphorylates a subset of Rab GTPases. Moreover, Golgi-associated Rab29 can recruit LRRK2 to the surface of the Golgi and activate it there for both auto- and Rab substrate phosphorylation. Here we define the precise Rab29 binding region of the LRRK2 Armadillo domain between residues 360-450 and show that this site, termed "Site #1", can also bind additional LRRK2 substrates, Rab8A and Rab10. Moreover, we identify a distinct, N-terminal, higher affinity interaction interface between LRRK2 phosphorylated Rab8 and Rab10 termed "Site #2", that can retain LRRK2 on membranes in cells to catalyze multiple, subsequent phosphorylation events. Kinase inhibitor washout experiments and mutation analysis demonstrate that rapid recovery of kinase activity in cells depends on the ability of LRRK2 to associate with phosphorylated Rab reaction products. Reconstitution of purified LRRK2 recruitment onto planar lipid bilayers decorated with Rab10 protein demonstrates cooperative association of only active LRRK2 with phospho-Rab10-containing membrane surfaces. These experiments reveal a feed-forward pathway that provides spatial control and apparent membrane activation of LRRK2 kinase activity.</p>
Taking up and terminating leisure-time physical activity over the life course: The role of life events in the familial and occupational life domains
<p>Dataset used for the analyses in the following publication:</p> <p>Lenze, L., Klostermann, C., Lamprecht, M. & Nagel, S. (2021). Taking up and terminating leisure-time physical activity over the life course: The role of life events in the familial and occupational life domains. <em>International Journal of Environmental Research and Public Health</em>, <em>18</em>, 9809. https://doi.org/10.3390/ijerph18189809</p>
Stigma, Activity Monitoring, and Pain (StAMP) study
<p>Original and cleaned data, analysis scripts (R scripts), and script outputs for the StAMP study.</p>
Earthworms increase the potential for enzymatic bio-activation of biochars made from co-pyrolyzing animal manures and plastic wastes
<p>We assessed the enzymatic activation of four different biochars produced from pyrolyzing swine manure and poultry litter, and by co-pyrolyzing these livestock residues with agricultural spent mulch plastic film wastes (plastichars). Enzymatic activation consisted of incubating biochars in soil inoculated with earthworms (<em>Lumbricus terrestris</em>), which acted as biological vectors to facilitate retention of extracellular enzymes onto biochar surface. The activity of carboxylesterase ‒a pesticide-detoxifying enzyme‒ was measured in non-bioturbed soils (reference), linings of the burrows created by earthworms, casts (feces) and biochar particles recovered from the soil.</p>
Microwave-activated gates between a fluxonium and a transmon qubit
<p>Numerical data and figures generators for the paper A. Ciani, B. Varbanov, N. Jolly, C. Andersen, B. Terhal "Microwave-activated gates between a fluxonium and a transmon qubit" </p>
Chiral flow in a binary mixture of two-dimensional active disks - Supplementary Data
<p>Supplementary data for the paper: "Chiral flow in a binary mixture of two-dimensional active disks"</p> <p> </p> <ol> <li>*_raw_trajectories.pkl.xz files contain tracking data for each experiment as a pickled Pandas DataFrame object (xz compression) in pixel units (particle diameter=77px)</li> <li>*_w.pkl.xz files contain self-rotation velocity for each experiment as a pickled Pandas DataFrame object (xz compression) in rad/s</li> <li>experiments_properties.dat is a summary table containing the average fields (including vorticity and kinetic energy) for all experiments. Also subdivided by species.</li> </ol>
Following Darwin's footsteps: Evaluating the impact of an activity designed for elementary school students to link historically important evolution key concepts on their understanding of natural selection
<p>While several researchers have suggested that evolution should be explored from the initial years of schooling, little information is available on effective resources to enhance elementary school students' level of understanding of evolution by natural selection (LUENS). For the present study, we designed, implemented and evaluated an educational activity planned for fourth graders to explore concepts and conceptual fields that were historically important for the discovery of natural selection. Observation field notes and students' productions were used to analyse how the students explored the proposed activity. Additionally, an evaluation framework consisting of a test, the evaluation criteria and the scoring process was applied in two fourth-grade classes to estimate elementary school students' LUENS before and after engaging in the activity. Our results suggest that our activity allowed students to effectively link all of the key concepts in the classroom and produced a significant increase in their LUENS. These results indicate that our activity had a positive impact on students' understanding of natural selection. They also reveal that additional activities and minor fine-tuning of the present activity are required to further support students' learning about the concept of differential reproduction. We also observed a low level of teleological predictions for both pre- and post-tests. --</p>
Not Only Systemin Prosystemin Harbors Other Active Regions Able to Protect Tomato Plants
<p>Prosystemin is a 200-amino acid precursor expressed in Solanaceae plants which releases at the C-terminal part a peptidic hormone called Systemin in response to wounding and herbivore attack. We recently showed that Prosystemin is not only a mere scaffold of Systemin but, even when deprived of Systemin, is biologically active. These results, combined with recent discoveries that Prosystemin is an intrinsically disordered protein containing disordered regions within its sequence, prompted us to investigate the N-terminal portions of the precursor, which contribute to the greatest disorder within the sequence. To this aim, PS1-70 and PS1-120 were designed, produced, and structurally and functionally characterized. Both the fragments, which maintained their intrinsic disorder, were able to induce defense-related genes and to protect tomato plants against <em>Botrytis cinerea</em> and <em>Spodoptera littoralis</em> larvae. Intriguingly, the biological activity of each of the two N-terminal fragments and of Systemin is similar but not quite the same and does not show any toxicity on experimental non-targets considered. These regions account for different anti-stress activities conferred to tomato plants by their overexpression. The two N-terminal fragments identified in this study may represent new promising tools for sustainable crop protection.</p>
Supplementary Material 1 : Monitoring Hydrothermal Activity Using Major and Trace Elements in Low-Temperature Fumarolic Condensates, The Case of La Soufriere de Guadeloupe Volcano, by Inostroza et al.
<p>Supplementary Material 1 - Monitoring hydrothermal activity using major and trace elements in low-temperature fumarolic condensates, the case of La Soufriere de Guadeloupe volcano, by Manuel Inostroza, Séverine Moune, Roberto Moretti, Vincent Robert, Magali Bonifacie, Elodie Chilin-Eusebe, Arnaud Burtin, Pierre Burckel</p>
Optogenetic activation of striatal D1R and D2R cells differentially engages downstream connected areas beyond the basal ganglia
<p>This dataset supports the Cell Reports publication entitled '<em>Optogenetic activation of striatal D1/D2 medium spiny neurons differentially engages downstream connected areas beyond the basal ganglia</em>' (https://doi.org/10.1016/j.celrep.2021.110161). Please refer to this publication for detailed information. </p> <p>The dataset contains functional (GE-BOLD) and anatomical (T1-weighted) scans of a total of 34 subjects (Cre-mouse lines Drd1-Cre, Drd2-Cre, A2A-Cre, and wildtype mice) in NIFTI format, multiplied by 10. The 'StimulationProtocol' text file specifies the precise onset (in seconds) and duration (in seconds) of the optogenetic stimulation during a 480 seconds functional scan. The 'SubjectDetails' file lists the subject IDs, their gender, their genotype, the number of functional scans, and whether they have an associated anatomical scan.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.