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7,228 results for “Modules”
Proteomics data for "Gut Microbial Beta-Glucuronidases Influence Endobiotic Homeostasis and Are Modulated by Diverse Therapeutics"
<p>Proteomics data used to generate results in "Gut Microbial Beta-Glucuronidases Influence Endobiotic Homeostasis and Are Modulated by Diverse Therapeutics" as published in <em>Cell Host and Microbe</em>. <a href="https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(24)00138-0">Manuscript Link</a></p>
Enhanced modulation of streamflow flash droughts by reservoir operations in India
Open the record for dataset details and reuse information.
Uncertainty in Pedestrian Decision-Making in Urgent Scenarios Modulates Multi-Level Neural Hierarchies from Perception to Execution
<p><span>In urgent traffic scenarios, pedestrians exhibit decision-making uncertainty, significantly influencing safe interaction dynamics with automated vehicles. However, the inherent mechanisms of such decision behavior remain inadequately understood. To address this gap, we designed dynamic interactive stimulus experiments to replicate pedestrian-vehicle interactions in urgent scenarios, incorporating spatiotemporal pressure and introducing substantial penalties for decision failures. We employed multimodal data analysis, including behavioral data, electroencephalography (EEG) and eye-tracking data, to investigate the influence of urgency on uncertainty in decision-making and the underlying multi-level neural processes. Our findings demonstrate that as the urgency of the stimulus increases, humans adjust their decision objectives, resulting in an initial decrease followed by an increase in decision uncertainty when dealing with more urgent stimuli. Specifically, urgency augments top-down perceptual processes during the early perception stage. <span>Such a mechanism implies an enhanced dependence on prior experiences for perceptual </span></span><span><span><span>decision<span>-making in high-urgency situations. </span></span></span></span><span>While urgency accelerated motion preparation time during the decision-execution stage, it is noteworthy that the culmination of evidence accumulation (represented by the CPP peak) manifested later than the actual response. These results suggest that insufficient perceptual information and evidence accumulation may increase decision-making uncertainty. Our experimental study unveils a correlation between human decision-making uncertainty and scenario urgency, particularly within a defined urgency range. </span></p>
Unraveling the Mechanism and Modulation of Activation Barriers in Uncatalyzed Anhydride Covalent Bond Exchange
<p><span>This folder contains the DFT-optimized geometries (in .xyz format together with the gas-phase energy, E) accompanying the paper</span></p> <p><span>"Unraveling the Mechanism and Modulation of Activation Barriers in Uncatalyzed Anhydride Covalent Bond Exchange"</span></p> <p><span>Where conformers occur, they are always named from the lowest Gibbs energy to the highest in ascending order from c1 (sometimes omitted), c2, c3, ...</span></p> <p><span>/MAA_and_PNA/ -- DFT structures from the study of anhydride exchange beween methacrylic anhydride (MAA) and 4-pentenoic anhydride (PNA)</span></p> <p><span><span> </span>|----/acid_catalysis/ -- DFT structures from M06-2X/def2-SVP level of theory optimization in gas phase for acid catalyzed mechanism</span></p> <p><span><span> </span>|----/gas_def2/ -- DFT structures from M06-2X/def2-SVP level of theory optimization in gas phase</span></p> <p><span><span> </span>|----/gas_def2_irc/ -- IRC movies of the TS for the concerted mechanism with and without acid at M06-2X/def2-SVP level of theory in gas phase</span></p> <p><span><span> </span>|----/gas_pople/ -- DFT structures from M06-2X/6-31G+(d) level of theory optimization in gas phase</span></p> <p><span><span> </span>|----/solv_opt/ -- DFT structures from SMD(CHCl3)-M06-2X/def2-SVP level of theory optimization in implicit chloroform solvent phase</span></p> <p><span>/UDC3/ -- DFT structures from the study of anhydride self-exchange beween UDC3 monomers, individual folders therein contains individual (un)substituted UDC3 systems</span></p> <p> </p>
Lipid-driven SRC self-association modulates its transformation capacity
<p>Data Type: SPR data, sensorgrams with reference flow cell correction.</p> <p>Data format: Comma-delimited text file </p> <p>Data Type: AFM raw data </p> <p>Data format: Binary files jpk format</p>
Computational dataset, scripts and models for 'Lipid shape as a membrane activity modulator of a model antimicrobial peptide'
<p>Analysis scripts and computational models used in the manuscript 'Lipid shape as a membrane activity modulator of a model antimicrobial peptide', by Marcin Makowski, Octávio L. Franco, Nuno C. Santos and Manuel N. Melo.</p>
Feeding-state dependent neuropeptidergic modulation of reciprocally interconnected inhibitory neurons biases sensorimotor decisions in Drosophila
<p>Raw and source data related to the study "Feeding-state dependent neuropeptidergic modulation of reciprocally interconnected inhibitory neurons biases sensorimotor decisions in Drosophila"</p> <p>Please not that protein-deprived (pd) and sucrose annotation are used interchangeabley in the dataset</p> <p> </p>
Open data for publication Reconstruction of Ice Surface upon Acetone Adsorption: An in-situ ATR-IR Modulation Excitation Spectroscopy Study
<p>Original data for publication "Reconstruction of Ice Surface upon Acetone Adsorption: An in-situ ATR-IR Modulation Excitation Spectroscopy Study". Original data used for the Figures.</p>
Data from: Microsaccades as a marker not a cause for attention-related modulation
<p>Recent evidence suggests that microsaccades are causally linked to the attention-related modulation of neurons – specifically, that microsaccades towards the attended location are required for the subsequent changes in firing rate. These findings have raised questions about whether attention-related modulation is due to different states of attention as traditionally assumed or might instead be a secondary effect of microsaccades. Here, in two rhesus macaques, we tested the relationship between microsaccades and attention-related modulation in the superior colliculus, a brain structure crucial for allocating attention. We found that attention-related modulation emerged even in the absence of microsaccades, was already present prior to microsaccades towards the cued stimulus, and persisted through the suppression of activity that accompanied all microsaccades. Nonetheless, consistent with previous findings, we also found significant attention-related modulation when microsaccades were directed towards, rather than away from, the cued location. Thus, in contrast to the prevailing hypothesis, microsaccades are not necessary for attention-related modulation, at least not in the superior colliculus. They do, however, provide an additional marker for the state of attention, especially at times when attention is shifting from one location to another.</p>
DeMal: Module Decomposition of Malware Based on Community Discovery
<p>See README.md</p>
Three‐dimensional soil heterogeneity modulates responses of grassland mesocosms to an experimentally imposed drought extreme
<p>Heterogeneity is an intrinsic characteristic of soils, which regulates plant diversity and ecosystem functioning. However, whether soil heterogeneity also modulates responses of plant communities to climate change, including climate extremes, remains largely an open question. Here, we explore responses of plant communities to drought extremes across four levels of spatial soil heterogeneity, with cell sizes varying from very small to very large, i.e. 0, 12, 24 and 48 cm. These were created in mesocosms by alternating nutrient-rich and nutrient-poor substrate in three dimensions. A seed mixture of 24 grassland species was evenly sown on each mesocosm in spring. In late summer, a three-week drought was imposed with a rainout shelter. During the drought, soil water content at the mesocosm scale decreased more at intermediate (12 and 24 cm) than at small or large (0 and 48 cm) cell sizes, which was reflected in increased senescence and drought-induced heat stress. These responses could be traced to greater plant biomass coupled with higher water demand at those intermediate cell sizes, likely related to between-cell access to nutrients and effects of diversity and community composition. Our results indicate that soil heterogeneity can modulate the impact of drought extremes on plant communities, though more research is needed on the transition between intermediate and extreme cell sizes, where heterogeneity effects seem to change most. We propose that soil heterogeneity be considered more explicitly in studies of changing precipitation regimes.</p>
Data from: Self-myofascial release decreased pain intensity and improved conditioned pain modulation response in patients with myofascial pain syndrome: a single-blind RCT study
<p>Objective: The present study investigated the effects of self-myofascial release (SMFR) on pain perception, myofascial trigger point (MTrP) activity, and conditioned pain modulation (CPM) response in patients with myofascial pain syndrome (MPS).</p> <p>Methods: A total of 32 MPS patients with a visual analog scale (VAS) score greater than 30/100 mm were enrolled and randomly assigned to 3 groups of 4 weeks of intervention – A) SMFR with a 60 s period (n=11), B) SMFR with a 30 s period (n=10) and C) conventional myofascial release (MFR) performed by the physiotherapist (n=11). Pressure pain threshold (PPT), VAS, resting-state electromyography amplitude (rAEMG) and conditioned pain modulation response (CPM-R) were assessed before, 1 week, 2 weeks and 4 weeks during the intervention.</p> <p>Results: Compared with baseline, VAS and rAEMG levels in were significantly decreased, while the PPT and CPM-R values were significantly increased in all groups after 4 weeks' intervention without significant difference between groups.</p> <p>Conclusion: Both SMFR and MFR techniques with a single pressing duration of 60s and 30s had significant therapeutic effects on chronic myofascial pain, with the decrease of VAS and rAEMG, the increase of PPT and CPM-R values, indicating that SMFR could activate and restore the function of descending pain modulation.</p>
Data of "Modulating Electric Field Distribution by Alkali Cations for CO2 Electroreduction in Strongly Acidic Medium"
<p>Data of the paper "Modulating Electric Field Distribution by Alkali Cations for CO2 Electroreduction in Strongly Acidic Medium"</p>
Predator community and resource use jointly modulate the inducible defense response in body height of crucian carp
<p>Phenotypic plasticity can be expressed as changes in body shape in response to environmental variability. Crucian carp (<i>Carassius carassius</i>), a widespread cyprinid, displays remarkable plasticity in body morphology and increases body depth when exposed to cues from predators, suggesting the triggering of an anti-predator defense mechanism. However, these morphological changes could also be related to resource use and foraging behavior, as an indirect effect of predator presence. In order to determine whether phenotypic plasticity in crucian carp is driven by a direct or indirect response to predation threat, we compared twelve fish communities inhabiting small lakes in southeast Norway grouped by four categories of predation regimes: no predator fish, or brown trout (<i>Salmo trutta</i>), perch (<i>Perca fluviatilis</i>) or pike (<i>Esox lucius</i>) as main piscivores. We predicted the body shape of crucian carp to be associated with the species composition of predator communities, and that the presence of efficient piscivores results in a deeper body shape. We use stable isotope analyses to test if this variation in body shape was related to a shift in individual resource use – i.e., littoral rather than pelagic resource use would favor the development of a specific body shape - or other environmental characteristics. The results showed that increasingly efficient predator communities induced progressively deeper body shape, larger body size and lower population densities. Predator maximum gape size and individual trophic position were the best variables explaining crucian carp variation in body depth among predation categories, while littoral resource use did not have a clear effect. The gradient in predation pressure also corresponded to a shift in lake productivity. These results indicate that crucian carp have a fine-tuned morphological defense mechanism against predation risk, triggered by the combined effect of predator presence and resource availability.</p>
Kin recognition in Drosophila: Rearing environment and relatedness can modulate gut microbiota and cuticular hydrocarbon odour profiles
<p>From inbreeding avoidance to kin-selected cooperation, social behaviours are frequently reliant on kin recognition. However, kin recognition mechanisms are costly to evolve and currently not very well understood. Recent evidence suggests that, by altering their host's odour, gut and other host-associated microorganisms may provide a promising avenue for understanding kin recognition. In Drosophila melanogaster, kin recognition can mediate mate choice, sexual conflict and larval competition/cooperation, underscoring its important functional role. As is commonly the case, kin recognition in this species depends on both familiarity (i.e. shared rearing environment) and relatedness, and seems to rely mainly on body odours determined by cuticular hydrocarbons. Here, we investigated the degree to which larval rearing environment and relatedness (full-sibs vs. unrelated) determine co-variation between gut microbiota and cuticular hydrocarbons in D. melanogaster. We found that rearing environment strongly determined both microbiota and cuticular hydrocarbon composition, but that these effects were independent from each other. In contrast, relatedness did not influence microbiota composition, but had a strong influence on microbiota diversity, which in turn covaried significantly with cuticular hydrocarbon composition. Our results show that, in D. melanogaster, odours may convey information about both familiarity and relatedness via an interaction between: a) direct effects of the rearing environment on cuticular hydrocarbons and b) indirect effects of relatedness on cuticular hydrocarbons via gut microbiota diversity.</p>
Data from the article "Modulation of wintertime canopy Urban Heat Island (CUHI) intensity in Beijing by synoptic weather pattern in planetary boundary layer"
<p>The link includes four datasets, "pcttype" is weather typing data, "pblh" is PBLH data, "uhii-UV" is the mean value of CUHII and wind direction UV of all urban stations, and "uhii-sws" is the value of CUHII, wind speed and wind direction of all urban stations.</p>
Supplementary visualisations for "Chronic iEEG recordings and interictal spike rate reveal multiscale temporal modulations in seizure states"
<p>Supplementary file containing patient-specific visualisations of seizure network state progressions and interictal spike rate decompositions for "Chronic iEEG recordings and interictal spike rate reveal multiscale temporal modulations in seizure states."</p> <p>See preprint at https://arxiv.org/abs/2201.11600</p>
Raw single-molecule imaging data for "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription"
<p><strong>Raw single-molecule imaging data for "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription"</strong></p> <p>Shasha Chong<sup>1</sup>, Thomas G.W. Graham<sup>2</sup>, Claire Dugast-Darzacq<sup>2,5</sup>, Gina M. Dailey<sup>2</sup>, Xavier Darzacq<sup>2,5</sup>, Robert Tjian<sup>2,3,4,5</sup>*</p> <p><sup>1 </sup>Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA</p> <p><sup>2 </sup>Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.</p> <p><sup>3 </sup>Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.</p> <p><sup>4</sup><sup> </sup>Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, CA, USA.</p> <p><sup>5</sup><sup> </sup>CIRM Center of Excellence, University of California, Berkeley, CA. </p> <p>* Lead contact</p> <p><strong>Overview</strong></p> <p>This repository contains 1) movies of endogenously expressed EWS::FLI1-Halo in genome-edited A673 cells acquired using stroboscopic photo-activatable single particle tracking (spaSPT) and 2) images of exogenously expressed mNeonGreen-EWS-NPM1 fusion protein in the above cells before and after spaSPT movies were acquired. The uploaded files include data acquired from 80 live cells on 4 different days. The imaging data, after being processed, were used to generate Figure 4C-E of the manuscript in the title. </p> <p><strong>Method details</strong></p> <p>The genome-edited A673 cells (described in https://www.science.org/doi/10.1126/science.aar2555) with inducible expression of mNeonGreen-EWS-NPM1 were grown on 25 mm circular No. 1.5 cover glasses (Azer Scientific, 200251) that were plasma-cleaned prior to use. We induced the cells with 200 ng/ml of doxycycline for 96 hours, stained the cells with 20 nM PA-JF646 and 200 nM JFX549 HaloTag ligands, and performed single-molecule imaging of EWS::FLI1-Halo on a custom-built Nikon (Nikon Instruments Inc.) TI microscope described in (https://elifesciences.org/articles/25776). We took images with a 100x/NA 1.49 oil-immersion TIRF objective (Nikon apochromat CFI Apo TIRF 100x Oil) under highly inclined and laminated optical sheet (HILO) illumination (https://www.nature.com/articles/nmeth1171) using following laser lines: 488 nm for mNG; 561 nm for JFX549; 405 nm and 633 nm for photo-activation and excitation of PA-JF646, respectively. The incubation chamber maintained a humidified 37°C atmosphere with 5% CO<sub>2</sub> and the objective was similarly heated to 37°C for live-cell experiments. </p> <p>High-concentration JFX549 staining allows visualization of the intracellular distribution of EWS::FLI1-Halo. We chose cells with EWS::FLI1-Halo enriched in the nucleolus to perform spaSPT. The procedure of spaSPT largely follows what is described in (https://elifesciences.org/articles/25776). Both the excitation laser (633 nm) and the photo-activation laser (405 nm) for PA-JF646 were pulsed. Each frame consisted of a 7-ms camera exposure time followed by a ~500 μs camera ‘dead’ time. The excitation laser (633 nm) was pulsed for 1 ms starting at the beginning for the 7 ms camera exposure time. The photo-activation laser (405 nm) was pulsed during the ~500 μs camera ‘dead’ time, minimizing fluorescence background. Each cell was imaged for 20,000 frames corresponding to ~1.5 min. Images of mNeonGreen-EWS-NPM1 were collected with a camera exposure time of 500 ms before and after the acquisition of each spaSPT movie.</p>
Raw confocal imaging and FRAP data for "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription"
<p><strong>Raw confocal imaging and FRAP data of "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription"</strong></p> <p>Shasha Chong<sup>1</sup>, Thomas G.W. Graham<sup>2</sup>, Claire Dugast-Darzacq<sup>2,5</sup>, Gina M. Dailey<sup>2</sup>, Xavier Darzacq<sup>2,5</sup>, Robert Tjian<sup>2,3,4,5</sup>*</p> <p><sup>1 </sup>Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA</p> <p><sup>2 </sup>Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.</p> <p><sup>3 </sup>Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.</p> <p><sup>4</sup><sup> </sup>Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, CA, USA.</p> <p><sup>5</sup><sup> </sup>CIRM Center of Excellence, University of California, Berkeley, CA. </p> <p>* Lead contact</p> <p><strong>Overview</strong></p> <p>This repository contains 1) raw three-color confocal fluorescence images of a transiently expressed protein (mNeonGreen-EWS, mNeonGreen, EGFP-TAF15, EGFP, mNeonGreen-EWS-NPM1, or mNeonGreen-NPM1), endogenously expressed EWS::FLI1-Halo labeled with JFX549 Halo ligand, and intron RNA fluorescence in situ hybridization (FISH) targeting <em>ABHD6</em>, <em>CAV1</em>, or<em> GAPDH </em>in genome-edited A673 cells, 2) raw fluorescence recovery after photobleaching (FRAP) movies of endogenously expressed EWS::FLI1-Halo labeled with TMR Halo ligand in genome-edited A673 cells in the presence and absence of transient expression of mNeonGreen-EWS-NPM1. The imaging data, after being processed, were used to generate Figure 1D-G (also S1A, S3, and S4), 2E-G (also S5A and S7), 3C-E (also S9), 4A, S2, S6, and S8 of the manuscript in the title. </p> <p><strong>Method details</strong></p> <p>1. RNA fluorescence in situ hybridization (FISH)</p> <p>The genome-edited A673 cells (described in https://www.science.org/doi/10.1126/science.aar2555) were plated on 18 mm circular No. 1 cover glasses (VWR VistaVision, 16004-300) and transfected with a protein expression plasmid using Lipofectamine 3000. 24 hours after transfection, we stained the cells with 200 nM JFX549 HaloTag ligand following the protocol described above, fixed the cells, and then proceeded with RNA FISH. To measure nascent transcription levels of <em>ABHD6</em>, <em>CAV1</em>, and <em>GAPDH </em>genes, we performed intron RNA FISH following the published Stellaris RNA FISH protocol for adherent cells (https://biosearchassets.blob.core.windows.net/assets/bti_stellaris_protocol_adherent_cell.pdf) using Quasar 670-labeled FISH probes designed with the online software Stellaris Probe Designer (https://www.biosearchtech.com/support/tools/design-software/stellaris-probe-designer) and purchased from LGC Biosearch Technologies. </p> <p>2. Confocal fluorescence imaging of protein and nucleic acid distribution</p> <p>Two confocal microscopes were used to image intron RNA FISH samples. One is an inverted laser scanning confocal microscope (Zeiss, LSM 710 AxioObserver) equipped with 34-channel spectral detection, a motorized stage, a full incubation chamber maintaining 37°C and 5% CO<sub>2</sub>, a heated stage, an X-Cite 120 illumination source as well as several laser lines (405, 458, 488, 514, 561, 591, 633 nm). Images were acquired with a 40x Plan NeoFluar NA1.3 oil-immersion objective under control of the Zeiss Zen software. The other is an inverted laser scanning confocal microscope with Airyscan super-resolution capability (Zeiss, LSM 900 with Airyscan 2) and equipped with four laser lines (405, 488, 561, 640 nm). Images were acquired with a 40x oil objective (Zeiss Plan-Apochromat 40x/1.3 Oil DIC) in the confocal (CO) mode under control of the Zen software. We acquired z stacks of RNA FISH samples with a slice interval of 0.3 mm. 405 nm, 488 nm, 561 nm, and 633 or 640 nm lasers were used to excite the fluorescence of Hoechst-labeled nuclei, EGFP or mNeonGreen-labeled proteins, JFX549-labeled EWS::FLI1-Halo, and Quasar 670-labeled intron RNA FISH, respectively. Before acquiring any fluorescence image, we carefully set the laser intensity and microscope detectors to make sure that no pixel in the image was saturated. We used proper emission filters for sequential four-color imaging and ensured no bleed-through between the four channels by imaging cell samples that contain only one of the four fluorophores (Hoechst, EGFP or mNeonGreen, JFX549, and Quasar 670) under the four-color imaging settings.</p> <p>3. Fluorescence recovery after photobleaching (FRAP)</p> <p>FRAP was performed on the inverted laser scanning confocal microscope (Zeiss, LSM 710 AxioObserver) described above. The 561 nm laser and the epi-illumination mode were used for FRAP measurements. Images were acquired with a 40x Plan NeoFluar NA1.3 oil-immersion objective. The knock-in A673 cells were grown on glass-bottom (No. 1.5, 14 mm diameter) 35 mm dishes (MatTek, P35G-1.5-14-C). To measure the FRAP dynamics of EWS::FLI1-Halo in the nucleolus, we transfected the knock-in cells with a plasmid encoding mNG-EWS-NPM1 and stained the cells with 500 nM HaloTag TMR ligand (Promega, G8251) following the protocol described above. We acquired 1000 frames at one frame per 0.3 seconds with the first 5 frames acquired before the bleach pulse for the measurement of baseline fluorescence of the bleach spot and the whole nucleus. We chose to photobleach a circular spot with a radius of 1 μm within a nucleolus using the 561 nm laser at maximum intensity. To measure the FRAP dynamics of EWS::FLI1-Halo in the nucleoplasm, we followed the same procedure as above, except that the knock-in cells were not transfected and a circular bleach spot with a radius of 1 μm was chosen within the nucleoplasm of a cell and at least 1 μm from nuclear and nucleolar boundaries. </p>
Inter-spike Intervals Data (Pulsed modulation)
<p>In this dataset you can find the inter-spike intervals experimental data recorded under sinusoidal modulation and a given Idc value for a semiconductor laser under optical feedback and current modulation. The DC pump current ranges from 25.5 to 27.5mA and the modulation amplitude is set constant to 100 (arb units) while the modulation frequency ranges from 1 to 70 MHz.</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.