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7,327 results for “pathways”
Spring and latch dynamics can act as control pathways in ultrafast systems
<p><span>Ultrafast movements propelled by springs and released by latches are thought limited to energetic adjustments prior to movement and seemingly cannot adjust once movement begins. Even so, across the tree of life, ultrafast organisms navigate dynamic environments and generate a range of movements, suggesting unrecognized capabilities for control. We develop a framework of control pathways leveraging the non-linear dynamics of spring-propelled, latch-released systems. We analytically model spring dynamics and develop reduced-parameter models of latch dynamics to quantify how they can be tuned internally or through changing external environments. Using Lagrangian mechanics, we test feedforward and feedback control implementation via spring and latch dynamics. We establish through empirically-informed modeling that ultrafast movement can be controllably varied during latch release and spring propulsion. A deeper understanding of the interconnection between multiple control pathways, and the tunability of each control pathway, in ultrafast biomechanical systems presented here has the potential to expand the capabilities of synthetic ultra-fast systems and provides a new framework to understand the behaviors of fast organisms subject to perturbations and environmental non-idealities.</span></p>
Tracing pathways from high-resolution tractography, transcription, and temporal dimensions
<p>The neural circuits supporting human cognition are topics of enduring interest. The lack of tools available to map circuits has precluded our ability to trace the evolution of the human connectome. We harnessed high-resolution connectomic, anatomic, and transcriptomic data to develop enhanced tools to test for modifications in developmental programs across species. We found corresponding ages across species and transcriptionally define neurons with stereotypical projections in humans and macaques. We used these data to test for modifications in frontal cortex circuit. Frontal cortex circuitry development is extended in primates, which is concomitant with an expansion in cortico-cortical pathways compared with mice in adulthood. These parameters varied little across humans and macaques. We identify a collection of conserved features in frontal cortex circuits in studied primates. We demonstrate that the integration of transcriptional and connectomic data across temporal dimensions is a robust approach to trace the evolution of connections in primates. This dataset contains scripts as well as diffusion MR scans of mouse brains.</p>
Dynamic antagonism between key repressive pathways maintains the placental epigenome (source data and custom code)
<p>DNA and Histone-3 Lysine 27 methylation typically function as repressive modifications and operate within distinct genomic compartments. In mammals, the majority of the genome is kept in a DNA methylated state, whereas the Polycomb Repressive Complexes regulate the CpG-rich promoters of developmental genes. In contrast to this general framework, the extraembryonic lineages display noncanonical, globally intermediate DNA methylation levels that includes disruption of local Polycomb domains. To better understand this unusual landscape’s molecular properties, we genetically and chemically perturbed major epigenetic pathways in mouse Trophoblast Stem Cells (TSCs). We find that the extraembryonic epigenome reflects ongoing and dynamic de novo methyltransferase recruitment, which is continuously antagonized by Polycomb to maintain intermediate, locally disordered methylation. Despite its disorganized appearance, our data point to a highly controlled equilibrium between counteracting repressors within extraembryonic cells, one that can seemingly persist indefinitely without bistable features typically seen for embryonic forms of epigenetic regulation.</p> <p> </p>
Data from: Seed dormancy revisited: dormancy-release pathways and environmental interactions
<p>1. Many internal (inherent) and environmental (imposed) factors control seed dormancy and germina-tion from which we can derive three basic dormancy-release pathways: Maternal structures and embryo physiology control inherent dormancy that is broken by various types of scarification and physiological changes, followed by imposed-dormancy release when replaced by certain 'standard' environmental conditions that stimulate germination (pathway 1); imposed dormancy prevails even if inherent dorman-cy is broken or not applicable that is released when replaced by certain 'standard' environmental condi-tions which stimulate germination (pathway 2); release from inherent dormancy by light/dark or cold stratification is contingent on existing presence of certain 'standard' environmental conditions that stim-ulate germination (pathway 3).</p> <p>2. On-plant seed storage (serotiny) and frugivorous seeds are recognized here as representing special types of physical dormancy, as their properties are consistent with those of hard diaspores. Warm stratification does not require seeds to be moist as it is just a physical response. Heat may promote germination of non-hard, as well as hard, seeds as it may also increase their permeability.</p> <p>3. Levels of germination gauge the net effect of inherent- and imposed-dormancy release so that it only possible to identify the extent of inherent-dormancy release when conditions for germination are optimal (imposed dormancy has been annulled). While imposed dormancy may be protracted after inherent dormancy is broken by heat or chilling during the dry or cold seasons, release from both states may effectively coincide if smoke chemicals or light are received during the (wet) growing sea-son.</p> <p>4. We suggest reserving the term secondary dormancy for seeds that return to (inherent or imposed) dormancy due to changed environmental conditions. Under seasonal climates, fluctuations in envi-ronmental conditions can lead to secondary dormancy and even dormancy cycling.</p> <p>5. We recognize four types of functional interactions between any two environmental factors that induce inherent-dormancy release: binary interactions are either ineffective, only one effective, non-additive or additive/synergistic. Two environmental stimuli that individually break dormancy but have no additive effect must be affecting the same process; this was demonstrated here for some interac-tions between heat and smoke.</p> <p>6. The three dormancy-release pathways, together with internal, seasonal and stochastic interact ions, are coordinated by the non-dormant seed to ensure maximum germination under optimal conditions. To ignore any aspect outlined here leads to an impoverished understanding of the disparate seed ecol-ogy of species adapted to different stressful and disturbance-prone habitats.</p>
Distinct representations of innate and learned threats within the thalamic-amygdala pathway
<p>Behavioral flexibility and timely reactions to salient stimuli are essential for survival. The subcortical thalamic-basolateral amygdala (BLA) pathway serves as a shortcut for salient stimuli ensuring rapid processing. Here, we show that BLA neuronal and thalamic axonal activity mirror the defensive behavior evoked by an innate visual threat as well as an auditory learned threat. Importantly, perturbing this pathway compromises defensive responses to both forms of threats, in that animals fail to switch from exploratory to defensive behavior. Despite the shared pathway between the two forms of threat processing, we observed noticeable differences. Blocking beta-adrenergic receptors impair the defensive response to the innate but not the learned threats. This reduced defensive response, surprisingly, is reflected in the suppression of the activity exclusively in the BLA, as the thalamic input response remains intact. Our side-by-side examination highlights the similarities and differences between innate and learned threat-processing, thus providing new fundamental insights.</p>
Pathways of methane removal in the sediment and water column of a seasonally anoxic eutrophic marine basin - dataset
<p>Dataset used in the article: "Pathways of methane removal in the sediment and water column of a seasonally anoxic eutrophic marine basin", Zygadlowska et al., 2023.</p>
Data from: Solanum lycopersicum CLASS-II KNOX genes regulate fruit anatomy via gibberellin-dependent and independent pathways
<p>The pericarp is the predominant tissue determining the structural characteristics of most fruits. However, the molecular and genetic mechanisms controlling pericarp development remain only partially understood. Previous studies have identified that CLASS-II KNOX genes regulate fruit size, shape, and maturation in Arabidopsis thaliana and Solanum lycopersicum. Here we characterized the roles of the Solanum lycopersicum CLASS-II KNOX (TKN-II) genes in pericarp development via a detailed histological, anatomical, and karyotype analysis of the TKN-II knockdown (35S:amiR-TKN-II) fruits. We identify that 35S:amiR-TKN-II pericarps contain more cells around their equatorial perimeter and fewer cell layers than the control. In addition, the cell sizes but not the ploidy levels of these pericarps were dramatically reduced.</p> <p>Further, we demonstrate that fruit shape and pericarp layer number phenotypes of the 35S:amiR-TKN-II fruits can be overridden by the procera mutant, known to induce a constitutive response to the plant hormone gibberellin. However, neither the procera mutation nor exogenous gibberellin application can fully rescue the reduced pericarp width and cell size phenotype of 35S:amiR-TKN-II pericarps. Our findings establish that TKN-II genes regulate tomato fruit anatomy, acting via gibberellin to control fruit shape but utilizing a gibberellin-independent pathway to control the size of pericarp cells.</p>
Modeling Decarbonization Pathways in the Power Sector in Developing Countries: The case of Colombia (EMP-LAC 2023) - Dataset
<p>Dataset of the project Modeling Decarbonization Pathways in the Power Sector in Developing Countries: The case of Colombia (EMP-LAC 2023) - Dataset</p>
Identification of the atmospheric water sources and pathways responsible for the East Asian summer monsoon rainfall
<p><strong>era_hydro_easm_jul2013_*.csv.gz:</strong> These three files are the raw output from the TRACMASS trajectory model. They stored positions of each trajectory at the start (ini file), during run (run file) and at the end (out file) during July 2013 and has been used for generating Figure 1.</p> <p><strong>mask.nc:</strong> The basin definition in Figure 1 was plotted using this netcdf file.</p> <p><strong>ep_traj_*.gz: </strong>The four zip files corresponds to four summer months (June, July, August, and September) and used to plot Figure 2.</p> <p><strong>ep_traj_basins_*.gz: </strong>The four zip files corresponds to four summer months (June, July, August, and September) and used to plot Figure 3.</p> <p><strong>quantification.gz: </strong>These files were used for quantification provided in Figure 4 and Figure 8.</p> <p><strong>traj_pathways_*.gz: </strong>The two zip files (one for the South Indian Ocean, SIO and another for the Pacific Ocean, PAC) were used to generate Figure 5.</p> <p><strong>traj_rt.gz: </strong>The residence time of atmospheric waters in Figure 6 was created using the files in this zip.</p> <p><strong>traj_age_*.gz: </strong>The two zip files (one for the South Indian Ocean, SIO and another for the Pacific Ocean, PAC) were used to generate Figure 7.</p>
Pathways of glyphosate effects on litter decomposition in grasslands
<p>1. Grasslands store a third of global terrestrial carbon but are vulnerable to carbon loss due to inappropriate livestock grazing. Grasslands management can be improved with a mechanistic understanding of biogeochemical processes that determine carbon storage, such as plant litter decomposition.</p> <p>2. Herbicides, such as glyphosate, are used to improve the quantity and quality of the forage. In the Flooding Pampa, the most extensive cattle-grazed natural grassland and one of the few remnant temperate grasslands in South America, glyphosate is applied to promote <em>Lolium</em> <em>multiflorum</em>, a forage grass associated with a fungal endophyte non-toxic for cattle.</p> <p>3. We studied five mechanistic pathways in which the application of glyphosate can alter litter decomposition. We grouped them into single application pathways, through effects on living plants (1), leaf litter (2) and bare soil (3), and repeated annual application pathways, through legacies on ecosystem properties (4) and through the growth of an annual forage grass with a fungal endophyte (5). Single application pathways were tested in a greenhouse experiment using leaf litter of <em>L. multiflorum</em> and of a native dominant grass. Repeated annual application pathways were tested through a field experiment with 3-year annual glyphosate application using leaf and root litter of <em>L. multiflorum</em> with and without endophyte association.</p> <p>4. Glyphosate application on living plants produced leaf litter with 70% higher nitrogen content and 140% higher decomposition constant than naturally senesced litter. In contrast, glyphosate application on naturally senesced leaf litter reduced decomposition constant by 20%. Glyphosate application on the soil did not affect the decomposition of naturally senesced leaf litter but accelerated the decomposition of the glyphosate-killed plants even more.</p> <p>5. Legacies of repeated annual application of glyphosate resulted in a notable reduction in plant cover (45%) and potential soil respiration (57%), with a consistent acceleration of leaf (53%) and root (18%) litter decomposition. Furthermore, the association of endophytes in <em>L</em>. <em>multiflorum</em> plants reduced leaf litter decomposition by 22%. On the contrary, the association of endophytes did not alter root litter decomposition.</p> <p>6. Glyphosate application on living plants and legacies of repeated application on the ecosystem stimulate litter decomposition, which can result in a net carbon loss from grasslands. In other ecosystems, the net result on decomposition would depend on the relative cover of vegetation, aboveground litter, and bare soil. This study highlights that glyphosate application should be considered when evaluating sustainable management to preserve and enhance soil carbon storage in grasslands.</p>
Data and analysis of proteomic responses to hexokinase-II depletion in GAL80 and gal80Δ Saccharomyces cerevisiae with an engineered sesquiterpene-pathway
<p>Dataset 1: <a href="https://zenodo.org/api/files/ece3309f-0ca2-4773-b2e3-b1c5c839faa4/GAL80_HXK2_Vs._dhxk2p_20200324_T2_004.xlsx">GAL80_HXK2_Vs._dhxk2p_20200324_T2_004.xlsx</a></p> <p>The comparison between strain ILHA o128R+pJT9RFR (dHxk2p) and ILHA o401R+ pJT9RFR (HXK2) under the conditions with the addition of 1-Naphthaleneacetic acid and in the exponential growth phase and the ethanol growth phase. </p> <p> </p> <p>Dataset 2: <a href="https://zenodo.org/api/files/ece3309f-0ca2-4773-b2e3-b1c5c839faa4/gal80%CE%94_HXK2_Vs._dhxk2p_20200219_T1_004.xlsx">gal80Δ_HXK2_Vs._dhxk2p_20200219_T1_004.xlsx</a></p> <p>The comparison between strain ILHA NLD128-1 (dHxk2p) and ILHA NLD401 (HXK2) under the conditions with the addition of 1-Naphthaleneacetic acid and in the exponential growth phase (EXP) and the ethanol growth phase (ETH). </p> <p> </p>
The indirect pathway of the basal ganglia promotes transient punishment, but not motor suppression
<p>Data and code for manuscript entitled "The indirect pathway of the basal ganglia promotes transient punishment, but not motor suppression"</p>
Assessment of Fast-Track pathway in hip and knee replacement surgery by propensity score matching on patient-reported outcomes
<p>This is the dataset accompanying the publication "Assessment of Fast-Track pathway in hip and knee replacement surgery by propensity score matching on patient-reported outcomes" published on the Diagnostics journal.</p>
Sunda-Sahul floristic exchange and pathways into the Southwest Pacific: New insights from wet tropical forest trees
<p><strong>Aim</strong> Recent investigations on the floristic exchange between Southeast Asia and Australia have shown a clear dispersal directionality bias (West to East) of wet-adapted plant taxa. However, dispersal routes and directions of wet forest taxa into the South Pacific remain insufficiently known. We here aimed to establish the most likely routes and directions of plant dispersal into the Southwest Pacific islands.</p> <p><strong>Location</strong> Southeast Asia, East Asia, Australia, Southwest Pacific.</p> <p><strong>Taxon</strong> <em>Dysoxylum</em> s.l. (Meliaceae). This includes <em>Dysoxylum</em> s.s., <em>Didymocheton</em>, <em>Epicharis</em>, <em>Goniocheton</em>, <em>Pseudocarapa</em> and <em>Prasoxylon</em>.</p> <p><strong>Method</strong> We sampled 75% of the species diversity in <em>Dysoxylum</em> s.l., covering the entire distribution range, all genera and major lineages. Phylogenetic relationships of 149 accessions were reconstructed using Bayesian Evolutionary Analysis and two internal constraints. The dispersal–extinction–cladogenesis variant, founder-event speciation (DEC+J), was used for reconstructing the biogeographic history, and 100 BSMs were simulated.</p> <p><strong>Results</strong> <em>Dysoxylum</em> s.l. originated and firstly diversified in the western part of its current distribution range (incl. Indochina) during the Miocene to Pliocene, followed by an overall eastern range expansion towards Malesia, Australia and the Southwest Pacific in the Pliocene.</p> <p><strong>Main</strong> <strong>conclusions</strong> The south-eastward expansion of lineages into Wallacea and Australia is in temporal agreement with the convergence of the Asian and Australian tectonic plates since the Miocene. Long-distance dispersal is the main mechanism that led to the current distribution. Two dispersal pathways into the Southwest Pacific are identified, (1) through New Guinea and the Solomon Islands to Fiji, and (2) from New Zealand to Fiji. For both routes, Fiji was an important secondary source area for dispersal into the Southwest Pacific.</p>
Cellular uptake of silica particles influences EGFR signaling pathway and is affected in response to EGF
<p><strong>Background:</strong> The human epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that is involved in several key cellular processes such as cell proliferation and differentiation, and it has been linked to the development and progression of various cancers (e.g. breast and lung). Researchers have attempted to improve current cancer-targeted therapies by conjugating molecules on the surface of (nano)particles to efficiently target and inhibit EGFR. However, very few in vitro studies have investigated the effect of particles per se on EGFR signaling and dynamics. Furthermore, the impact of concomitant exposure of particles and EGFR ligands, such as epidermal growth factor (EGF) on cellular uptake efficiency has received little attention. </p> <p><strong>Purpose: </strong>The purpose of this research was to determine the effects of silica (SiO2) particles on EGFR expression and intracellular signaling pathways in A549 lung epithelial cells, in the presence or absence of epidermal growth factor (EGF).</p> <p><strong>Results: </strong>We showed that A549 cells are able to internalize SiO<sub>2</sub> particles with core diameters of 130 nm and 1 µm without affecting cell proliferation or migration. However, both SiO<sub>2</sub> particles interfere with the EGFR signaling pathway by raising the endogenous levels of extracellular signal-regulated kinase (ERK) 1/2. Furthermore, both in the presence and absence of SiO<sub>2</sub> particles, the addition of EGF increased cell migration. EGF also stimulated cellular uptake of 130 nm SiO<sub>2</sub> particles but not 1 µm particles. The increased uptake is primarily associated with EGF-stimulated macropinocytosis.</p> <p><strong>Conclusion: </strong>This study shows that SiO<sub>2</sub> particle uptake interferes with cellular signaling pathways and can be boosted by concurrent exposure to the bioactive molecule EGF. SiO<sub>2</sub> particles, both alone and in combination with the ligand EGF, interfere with EGFR signaling pathway in a size-dependent manner.</p>
Supporting Data and Guidance: Modeling policy pathways to maximize renewable energy growth and investment in Democratic Republic of the Congo using OSeMOSYS
<p>This repository contains data files and guidance documents that are supplementary materials to accompany the policy paper "Modeling policy pathways to maximize renewable energy growth and investment in Democratic Republic of the Congo using OSeMOSYS" available on Research Square here: <a href="https://www.researchsquare.com/article/rs-2702275/v1">https://www.researchsquare.com/article/rs-2702275/v1</a></p>
Brazilian Starter Data Kit Update to Support the Paper "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage"
<p>This dataset presents updates on the Brazilian starter data kit, considering current load profile data and specific renewable energy sources production, using public data from official Brazilian power system agents. The dataset contains the input data and respective files to run OSeMOSYS and Flextool, including the utility-scale storage model. Additionally, this dataset contains the results of the study "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage". This study evaluates the increase in variable renewable energy in Brazil and its integration with Storage systems. </p>
CCG: Beyond the Dams: Combatting Hydropower Over-reliance & Securing Pathways for a Low-carbon Future for Laos' Electricity Sector using OSeMOSYS (Open-Source Energy Modelling System)
<p>Seven clicSAND scenario files for <strong>Beyond the Dams: Combatting Hydropower Over-reliance & Securing Pathways for a Low-carbon Future for Laos' Electricity Sector using OSeMOSYS (Open-Source Energy Modelling System).</strong> </p> <p><strong>How to Visualise Results Online and Offline</strong> outline the steps required to re-run the scenarios on OSeMOSYS Cloud</p> <p><strong>Scenario Short Note</strong> outlines the steps to replicate the analysis and rebuild the scenarios</p> <p><strong>Annex - Input Data and Assumptions</strong> listing the data sources and assumptions in the scenarios</p>
Data for: Copper ions inhibit pentose phosphate pathway function in Staphylococcus aureus
<p>To gain a better insight of how Cu ions toxify cells, metabolomic analyses were performed in <em>S. aureus</em> strains that lack the described Cu ion detoxification systems (ΔcopBL <em>ΔcopAZ</em>; <em>cop<sup>-</sup></em>). Exposure of the <em>cop<sup>-</sup></em> strain to Cu(II) resulted in an increase in the concentrations of metabolites utilized to synthesize phosphoribosyl diphosphate (PRPP). PRPP is created using the enzyme phosphoribosylpyrophosphate synthetase (Prs) which catalyzes the interconversion of ATP and ribose 5-phosphate to PRPP and AMP. Supplementing growth medium with metabolites requiring PRPP for synthesis improved growth in the presence of Cu(II). A suppressor screen revealed that a strain with a lesion in the gene coding adenine phosphoribosyltransferase (<em>apt</em>) was more resistant to Cu. Apt catalyzes the conversion of adenine with PRPP to AMP. The <em>apt</em> mutant had an increased pool of adenine suggesting that the PRPP pool was being redirected. Over-production of <em>apt</em>, or alternate enzymes that utilize PRPP, increased sensitivity to Cu(II). Increasing or decreasing expression of <em>prs</em> resulted in decreased and increased sensitivity to growth in the presence of Cu(II), respectively. We demonstrate that Prs is inhibited by Cu ions <em>in</em> <em>vivo</em> and <em>in vitro</em> and that treatment of cells with Cu(II) results in decreased PRPP levels. Lastly, we establish that <em>S. aureus</em> that lacks the ability to remove Cu ions from the cytosol is defective in colonizing the airway in a murine model of acute pneumonia, as well as the skin. The data presented are consistent with a model wherein Cu ions inhibits pentose phosphate pathway function and are used by the immune system to prevent<em> S. aureus</em> infections.</p>
HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways_CAL27_RNAseq_siHUWE1
<p>RNA-seq data from CAL27 cells 3 days after transfection with one of three siRNAs (1, 155 or 969) targeting human HUWE1. si155 corresponds to sequence #2, and si969 corresponds to sequence #3 in Monda et al. <em>Cell Reports</em>. 2023. Each transfection was performed in triplicate and analyzed with paired-end reads.</p> <p>See DOI:10.5281/zenodo.7839090 for the CAL27 siControl dataset.</p> <p>See DOI:10.5281/zenodo.7839102 for the CAL27 siHAPSTR1 dataset.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.