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7,327 results for “pathways”
Input datasets for modeling snapshot structures of the NPC post mitotic assembly pathway
<p>This folder contains a reference coarse-grained model of the mature NPC and electron microscopy density maps that are used to restrain snapshot structures in the NPC assembly pathway model. These data sets are used to parameterize the native contact model and restrain the overall shape of NPC pre-pores at each snapshot along the assembly pathway. This data is provided in preparation of the PDB-dev deposition of the assembly pathway, accession to be determined.</p>
Disentangling the interrelated abiotic and biotic pathways linking landscape composition and crop production
<p><span>Landscape composition and its related functional agrobiodiversity (FAB) was severely simplified during the last decades. As landscape composition is expected to influence the interrelated microclimate and arthropod community at different scales, this simplification might have led to a decline in multiple agro-ecosystem services, with potential impacts for the growth of crops with different demands from the environment. </span></p> <p><span>To study landscape-scale effects on multi-crop yield and herbivory in combination with its potential drivers, including functional arthropod community and microclimate, we used standardised 1 m² mini-gardens planted with ten different vegetable crops as phytometers. The gardens were installed at locations varying in surrounding landscape composition and </span><span>the vegetables were selected to have contrasting requirements in terms of growing conditions, pollination services, and susceptibility to pests. Monitoring of the mini-gardens was performed in 2018 and 2019 in Flanders (Belgium). </span></p> <p><span>We found no relationship between landscape composition in a 500 meter radius and crop yield. Considering possible mechanisms, we found that an increasing share of woody vegetation (> 3 m high) in the surrounding landscape is important to buffer the temperature and soil moisture variation in the mini-gardens. The share of agricultural land use and urban green (< 3 m high) is, respectively, positively and negatively related with the activity-density of natural enemies and pollinators. The growth of different crops responded differently to higher temperature ranges and we found no relation between natural enemies and herbivory. In conclusion, these abiotic and biotic pathways did not cause an overall relationship between landscape composition and yield.</span></p>
Native and invaded plant communities alter tick exposure risk via different mechanistic pathways
<p>Plant invasions may alter vector-borne disease risk by modifying microclimates that influence vector survival, or by changing habitat conditions that determine reservoir host use. Here, we evaluated multiple mechanistic pathways by which plant invasion may alter vector-borne disease risk using the common disease vector lone star tick (<em>Amblyomma americanum</em>) and the widespread invasive cogongrass (<em>Imperata cylindrica</em>) in the southeastern USA. Ticks survived over 50% longer in invaded than native plant species dominated communities, likely due to lower temperature and higher humidity conditions. However, wildlife host activity was higher in native than invaded plant species dominated communities. As a result, host-seeking tick abundances were similar between invaded and native areas, albeit through different mechanisms: longer survival maintained tick abundances in invaded areas while greater host use maintained tick abundance in native areas. Multiple, potentially off-setting mechanistic pathways should be considered when evaluating possible effects of invasive plants on vector-borne disease risk.</p>
Figure 3–Figure Supplement 4 of the paper 'A Feed-forward Pathway Drives LRRK2 kinase Membrane Recruitment and Activation'
<p>Raw immunoblotting and quantitation data for Figure 3–Figure Supplement 4 of the paper "A Feed-forward Pathway Drives LRRK2 kinase Membrane Recruitment and Activation" (Edmundo G. Vides, Ayan Adhikar, Claire Y. Chiang, Pawel Lis, Elena Purlyte, Charles Limouse, Justin L. Shumate, Elena Spínola-Lasso, Herschel S. Dhekne, Dario R. Alessi, and Suzanne R. Pfeffer)</p> <p><strong>File descriptions:</strong></p> <p><strong>Figure 3–Figure Supplement 4A</strong><br> <strong>Fig.3.S4A_700(tRab10;tLRRK2)_High.tif </strong>- Licor scan (channel 700) showing total Rab10 and total LRRK2 blots; high contrast<br> Panel 1 - top left membrane<br> Panel 2 - top right membrane<br> Panel 3 - bottom left membrane<br> Panel 4 - bottom right membrane</p> <p><strong>Fig.3.S4A_700(tRab10;tLRRK2)_Low.tif</strong> - Licor scan (channel 700) showing total Rab10 and total LRRK2 blots; low contrast<br> Panel 1 - top left membrane<br> Panel 2 - top right membrane<br> Panel 3 - bottom left membrane<br> Panel 4 - bottom right membrane</p> <p><strong>Fig.3.S4A_800(pRab10;pLRRK2)_High.tif</strong> - Licor scan (channel 800) showing Rab10 pT73 and LRRK2 pS935 blots; high contrast<br> Panel 1 - top left membrane<br> Panel 2 - top right membrane<br> Panel 3 - bottom left membrane<br> Panel 4 - bottom right membrane</p> <p><strong>Fig.3.S4A_800(pRab10;pLRRK2)_Low.tif</strong> - Licor scan (channel 800) showing Rab10 pT73 and LRRK2 pS935 blots; high contrast<br> Panel 1 - top left membrane<br> Panel 2 - top right membrane<br> Panel 3 - bottom left membrane<br> Panel 4 - bottom right membrane</p> <p><strong>Fig.3.S4A_HA.tif </strong>- ChemiDoc Scan (ECL) showing HA blot</p> <p><strong>Figure 3–Figure Supplement 4B</strong></p> <p><strong>Fig.3.S4B_700(tRab10;tLRRK2)_High.tif </strong>- Licor scan (channel 700) showing total Rab10 and total LRRK2 blots; high contrast<br> Panel 1 - top left membrane<br> Panel 2 - top right membrane<br> Panel 3 - bottom left membrane<br> Panel 4 - bottom right membrane</p> <p><strong>Fig.3.S4B_700(tRab10;tLRRK2)_Low.tif</strong> - Licor scan (channel 700) showing total Rab10 and total LRRK2 blots; low contrast<br> Panel 1 - top left membrane<br> Panel 2 - top right membrane<br> Panel 3 - bottom left membrane<br> Panel 4 - bottom right membrane</p> <p><strong>Fig.3.S4B_800(pRab10;pLRRK2)_High.tif</strong> - Licor scan (channel 800) showing Rab10 pT73 and LRRK2 pS935 blots; high contrast<br> Panel 1 - top left membrane<br> Panel 2 - top right membrane<br> Panel 3 - bottom left membrane<br> Panel 4 - bottom right membrane</p> <p><strong>Fig.3.S4B_800(pRab10;pLRRK2)_Low.tif </strong>- Licor scan (channel 800) showing Rab10 pT73 and LRRK2 pS935 blots; high contrast<br> Panel 1 - top left membrane<br> Panel 2 - top right membrane<br> Panel 3 - bottom left membrane<br> Panel 4 - bottom right membrane</p> <p><strong>Fig.3.S4B_HA.tif </strong>- ChemiDoc Scan (ECL) showing HA blot</p> <p><strong>Fig.3.S4_immunoblotting_numerical_data.xlsx</strong> - Excel sheet containing raw quatitation values from Licor scans as well as calculated pRab10/Rab10 ratios (values used in Figure 3C and 3D)</p>
Insulin sensitivity in mesolimbic pathways predicts and improves with weight loss in older dieters
<p><span>Central insulin is involved in the regulation of hedonic feeding. Insulin resistance in overweight has recently been shown to reduce the inhibitory function of insulin in the human brain, but how this affects future weight management is unclear. Also unknown is the role of central insulin sensitivity on eating behavior of older people, who are highly vulnerable to hyperinsulinemia and in whom neural target systems of insulin action undergo age-related changes. Here, fifty overweight, pre-diabetic elderly participated in a double-blind, placebo-controlled pharmacological fMRI study before and after randomization to a 3-month caloric restriction or active waiting group. We show that treatment outcome in dieters can be predicted by baseline measures of individual intranasal insulin (INI) inhibition of value signals in the ventral tegmental area related to sweet food liking as well as, independently, by peripheral insulin sensitivity. At follow-up, both INI inhibition of hedonic value signals in the nucleus accumbens and whole-body insulin sensitivity improved with weight loss. These data highlight the critical role of central insulin function in mesolimbic systems for future weight management in humans and directly demonstrate that neural insulin function can be improved by weight loss even in older age, which may be essential for preventing metabolic disorders in later life.</span></p>
A seasonal analysis of aerosol NO3- sources and NOx oxidation pathways in the Southern Ocean marine boundary layer
<p>This dataset includes coarse mode atmopsheric nitrate concentration and isotopic composition from the Southern Ocean marine boundary layer in summer (2018/19), winter (2019) and spring (2019). Environmental data (temperature, SLP and relative humidity) are also included.</p>
Implication of the myo-inositol pathway in behavioral alterations of infected threespine sticklebacks
<p><span>Threespine stickleback (<em>Gasterosteus</em> <em>aculeatus</em>) infected with the tapeworm <em>Schistocephalus</em> <em>solidus</em> display impairments in their anti-predator responses. They also have increased expression of the gene encoding the IMPase 1 enzyme in their brains, which is part of a key step in <em>myo</em>-inositol synthesis. IMPase 1 and <em>myo</em>-inositol levels are the targets of lithium treatment in patients with bipolar disorder. Although promising candidates, we do not know if IMPase 1 and <em>myo</em>-inositol are directly implicated in the changes in risky behaviors measured in <em>Schistocephalus</em>-infected fish. Understanding the molecular mechanisms directly or indirectly involved in these behavioral alterations is crucial to understand the evolution of host-parasite interactions. Here, we increased <em>myo</em>-inositol levels of uninfected fish and inhibited IMPase 1 activity in infected fish to test the prediction that it would decrease and increase their anti-predator behaviour, respectively. We found that uninfected fish with increased <em>myo</em>-inositol levels (by injecting exogenous <em>myo</em>-inositol or by inducing endogenous production using an osmotic challenge) did not decrease their anti-predator responses. However, infected fish treated with lithium chloride had some of their anti-predator behaviors restored, but not all. They spent less time swimming close to the surface, swam a shorter distance, had a higher latency to feed, and spent more time frozen after a predator attack. Our results suggest that the target of lithium treatment is implicated in the risky behaviors of infected fish and supports the idea that the parasite-associated alteration in behavior has a multifactorial nature.</span></p>
Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma
<p>This repository contains signalling to metabolic pathways interconnecting (S-M) protein-protein interaction (PPI) paths. The repository consists of two file:</p> <p><a href="https://zenodo.org/api/files/61dbb365-104e-4c41-ad0a-79f4c657bbee/S-M_paths_z-score_greater_equal_1.txt">S-M_paths_z-score_greater_equal_1.txt </a>: It contains all the S-M paths having z-score >= 1.</p> <p><a href="https://zenodo.org/api/files/61dbb365-104e-4c41-ad0a-79f4c657bbee/S-M_paths_z-score_greater_equal_3.txt">S-M_paths_z-score_greater_equal_3.txt </a>: It contains all the S-M paths having z-score >=3</p>
Poet's Pathway Commemorative Plaque Draft
The plaque marks the start of a commemorative path called "The Poet's Pathway" at Brittania Beach in Ottawa, Ontario and honours the first confederate poets in the region. A poem by Emily Pauline Johnson, An Indigenous confederation time poet, is displayed on the plaque. For more about what the plaque commemorates, visit: http://poetspathway.ca/a_britannia.htm located at: 45⁰21'54"N 75⁰ 48'18"W. Source: Objaverse 1.0 / Sketchfab
Optical coherence tomography of the macular ganglion cell layer in children with neurofibromatosis type 1 is a useful tool in the assessment for optic pathway gliomas
<p><span>To investigate whether the ganglion cell layer assessed by OCT is a reliable measure to identify and detect relapses of symptomatic OPGs in children with NF1.</span></p>
Case study input data set for article "Stochastic planning of energy system transformation pathways under uncertain industry demands"
<p>The data set contains input data for the model EMPRISE of Fraunhofer Institute for Energy Economics and Energy System Technology IEE. </p>
Pacific salmon in the Canadian Arctic highlight a range-expansion pathway for sub-Arctic fishes
<p>The R code and data to support the manuscript "Pacific salmon in the Canadian Arctic highlight a range-expansion pathway for sub-Arctic fishes" published by Dunmall & Langan et al. 2024 in Global Change Biology. Briefly, this study investigated the mechanisms behind variable, rising catches of Pacific salmon by subsistence fishers in the Canadian Arctic. Detailed descritptions of the data and the performed analyses are provided in the associated manuscript.</p>
Data from: Elephant pathway use in a human-dominated landscape
<p>Habitat loss and fragmentation are one of the biggest threats facing wildlife today. Understanding the role of wildlife pathways in connecting resource areas is key to maintain landscape connectivity, reduce the impacts of habitat loss and help address human-wildlife conflict. In this study, we used sign surveys and camera trapping to understand the fine scale movement of elephants moving between a protected area and agricultural zone in the Masai Mara, Kenya. We used Generalised Linear Models to determine factors driving high frequency of pathway use by elephants. Our results showed strong seasonal trends in pathway use, with peaks coinciding with the dry season. However, no correlations between rainfall and pathway use were found. Temporal patterns of pathway use indicate that elephants use risk avoidance strategies by moving between the two areas at times of low human disturbance. Spatial analysis revealed that the most frequently used pathways were closer to farms, saltlicks and forest and those that had a higher percentage of forest cover. Our models also showed a positive relationship between pathway use and the number of elephant crop raiding incidents, highlighting that pathways can play a role in human-elephant conflict. As habitat loss continues, pathways may become more important for linking resources. However, they are also likely to facilitate movement into farmland. The results from this study provide an opportunity for planned management activities to ensure connectivity and to mitigated conflict.</p>
Dataset used in publication titled " Dependence of climate and carbon cycle response in net zero emission pathways on the magnitude and duration of positive and negative emission pulses"
<p>Essential model data use to produce figures and tables for the publication titled " Dependence of climate and carbon cycle response in net zero emission pathways on the magnitude and duration of positive and negative emission pulses"</p>
FHIRed MOTU data. FHIR-standardized data collection on the clinical rehabilitation pathway of trans-femoral amputation patients.
<h3>Dataset presented in the article "MOTU on FHIR: A 10-year data collection on the clinical rehabilitation pathway of 1006 trans-femoral amputees".</h3> <p>Data has been anonymised prior the publication. The data has been standardized in Fast Healthcare Interoperability Resources (FHIR) data standard. </p> <p>This work has been conducted within the framework of the MOTU++ project (PR19-PAI-P2).</p> <p>This research was co-funded by the Complementary National Plan PNC-I.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector” D.D. 931 of 06/06/2022, DARE - DigitAl lifelong pRevEntion initiative, code PNC0000002, CUP: (B53C22006450001) and by the Italian National Institute for Insurance against Accidents at Work (INAIL) within the MOTU++ project (PR19-PAI-P2).</p> <p>Authors express their gratitude to all the AlmaHealthDB Team.</p> <h2>Instruction MOTU-to-FHIR Importer</h2> <div> <div> <p>The repository includes a Docker Compose setup for importing the MOTU dataset into a HAPI FHIR server, formatted as NDJSON following the HL7 FHIR R4 standards.</p> <h3>Prerequisites</h3> <p>Before you begin, ensure you have the following installed:</p> <ul> <li><a href="https://www.docker.com/get-started/">Docker </a></li> <li><a href="https://docs.docker.com/compose/install/">Docker Compose</a></li> <li><a href="https://www.python.org/downloads/">Python >=3.7</a> </li> <li><a href="https://pypi.org/project/requests/">Requests Python Library</a></li> </ul> </div> <div> <h3>How to run</h3> <ol> <li>First, unzip the <code>dataset</code> directory containing the NDJSON files.</li> <li>Open a terminal or command prompt in the root directory of this repository.</li> <li>Run the command <code>docker-compose up</code> in the terminal to start the Docker containers.</li> <li>Once the containers are up and running, open another terminal window in the root directory of this repository.</li> <li>Run the command <code>python main.py</code> in the terminal to start the data import process.</li> <li>After the import process is complete, you can access the HAPI FHIR server by opening a web browser and navigating to <a href="http://localhost:8082" target="_blank" rel="nofollow noreferrer noopener">http://localhost:8082</a>.</li> </ol> <p> </p> </div> </div>
Data from: Transcriptional profiling of lung macrophages following ozone exposure in mice identifies signaling pathways regulating immunometabolic activation
<p>Macrophages play a key role in ozone-induced lung injury by regulating both the initiation and resolution of inflammation. These distinct activities are mediated by pro-inflammatory and anti-inflammatory/pro-resolution macrophages which sequentially accumulate in injured tissues. Macrophage activation is dependent, in part, on intracellular metabolism. Herein, we used RNA-sequencing (seq) to identify signaling pathways regulating macrophage immunometabolic activity following exposure of mice to ozone (0.8 ppm, 3 hr) or air control. Analysis of lung macrophages using an Agilent Seahorse showed that inhalation of ozone increased macrophage glycolytic activity and oxidative phosphorylation at 24 and 72 hr post exposure. An increase in the percentage of macrophages in the S phase of the cell cycle was observed 24 hr post ozone. RNA-seq revealed significant enrichment of pathways involved in innate immune signaling and cytokine production among differentially expressed genes at both 24 and 72 hr after ozone, while pathways involved in cell cycle regulation were upregulated at 24 hr and intracellular metabolism at 72 hr. An interaction network analysis identified tumor suppressor 53 (TP53), E2F family of transcription factors (E2Fs), Cyclin Dependent Kinase Inhibitor 1A (CDKN1a/p21), and Cyclin D1 (CCND1) as upstream regulators of cell cycle pathways at 24 hr and TP53, nuclear receptor subfamily 4 group a member 1 (NR4A1/Nur77), and estrogen receptor alpha (ESR1/ERα) as central upstream regulators of mitochondrial respiration pathways at 72 hr. These results highlight the complex interaction between cell cycle, intracellular metabolism, and macrophage activation which may be important in the initiation and resolution of inflammation following ozone exposure.</p>
Recording of the webinar "Six Pathways to Smart Certification of BioBased Systems" in the frame of the 3-CO project
<p>In this webinar on 7th June 2024 six different Horizon Europe projects presented themselves to the public: 3-CO (as the organiser), BioReCer, SUSTRACK and the BIOBASEDCERT Cluster (Star4bbs, Harmonitor, Sustcert4Biobased).</p> <p>Speakers were: Maarit Haltunen (3-CO), Pedro Villanueva Rey (BioReCer), Gülsah Yilan (SUSTRACK), Costanza Rossi, Luana Ladu, Iris Vural Gürsel (Cluster).</p> <p>Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Research Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.</p>
Topology testing and demographic modeling illuminate a novel speciation pathway in the Greater Caribbean Sea following the formation of the Isthmus of Panama
<p>Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here we conduct range-wide sampling for Pederson's cleaner shrimp (<em>Ancylomenes</em> <em>pedersoni</em>), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates x 45 evolutionary models x 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 million years ago. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.</p>
Dynamic interplay of cNHEJ and MMEJ pathways of DNA double-strand break repair during embryonic development in zebrafish.
<p><span>Fastq sequences from zebrafish embryos corresponding to 9 amplicons sequenced by </span><span>Illumina MiSeq. DNA sample were obtained from non-treated wildtype controls (ctrl) or from wildtype (WT), polq mutants, lig3 mutant or lig4 mutant injected with Cas9 protein and a pool of 5 or 4 different sgRNA (numbered from 1#1 to 5#2). Each target site corresponds to one amplicon. </span></p>
A machine learning framework for extracting information from biological pathway images in the literature
<p><strong>466 target chemicals_selected chemicals:</strong></p> <p>Target chemicals satisfying the criteria for biochemical reactions not covered by MetaNetX and KEGG.</p> <p> </p> <p><strong>466 target chemicals_statistics:</strong><br>Numbers of MetaCyc reactions, papers, and pathway images collected for 466 target chemicals from the bio-based chemicals map (Jang et al., Trends in Biotechnology, 2023).</p> <p> </p> <p><strong>arrow detection_bounding box labels:</strong><br>Bounding box labels for 6,471 images in the training and validation datasets and 100 images in the test dataset. The corresponding images are available in "arrow detection_training and validation datasets.zip".</p> <p> </p> <p><strong>arrow detection_test dataset:</strong></p> <p>Test dataset for arrow detection using Faster R-CNN model. A total of 100 images have been prepared from 89 papers searched through PubMed Central (PMC).</p> <p> </p> <p><strong>arrow detection_training and validation datasets:</strong></p> <p>Training and validation datasets for arrow detection using Faster R-CNN model. A total of 6,471 images have been prepared, including 2,332 images from five different sources and 4,139 augmented images.</p> <p> </p> <p><strong>EBPI outputs:</strong></p> <p>Reaction information extracted using EBPI from 49,846 biological pathway images across 466 target chemicals.</p> <p> </p> <p><strong>text classification_training, validation and test datasets:</strong></p> <p>Dataset for text classification using BioBERT. A total of 59,370 terms have been prepared, including 15,101 “gene” terms, 21,417 “protein” terms, and 22,852 “others” terms by combining the data from MetaCyc and the PaddleOCR results from the papers.</p>
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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.