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7,327 results for “pathways”
Five thousand randomly generated modular biosynthetic pathways visualised by RAIChU
<p>We randomly generated 5000 modular biosynthetic pathways to test our visualisation software RAIChU: Reaction Analysis through Illustration of Chemical Units.</p>
Decarbonization pathways promote improvements in cement quality and reduce the environmental impact of China's cement industry
<p>The data show the results of the papre "Decarbonization pathways promote improvements in cement quality and reduce the environmental impact of China’s cement industry".</p>
Key results and plot files for the paper "Diversity of biomass usage pathways to achieve emissions targets in the European energy system"
<p>Key results and plot files for the paper:</p> <p>Millinger, M., Hedenus, F., Zeyen, E. <em>et al.</em> Diversity of biomass usage pathways to achieve emissions targets in the European energy system. <em>Nat Energy</em> <strong>10</strong>, 226–242 (2025). https://doi.org/10.1038/s41560-024-01693-6</p>
A High-quality Genome Assembly of Pseudocydonia sinensis Uncovers Uique Phenylpropanoid Pathways
<p>Filename Description Format<br>Pseudocydonia_sinensis.cds.fasta Coding sequence file, with each entry representing the nucleotide sequence of a gene. FASTA<br>Pseudocydonia_sinensis.prot.fasta Protein sequence file, with each entry corresponding to the amino acid sequence of a transcript. FASTA<br>Pseudocydonia_sinensis.annotation.gff3 Genome feature annotation file, describing the locations of genes, exons, and other genomic features. GFF3<br>Pseudocydonia_sinensis.genome.fasta Genome sequence file, providing the complete nucleotide sequence of the genome. FASTA<br>ARK.pep.fa Protein sequence file containing the deduced ancestral protein sequences for the Rosaceae karyotype. FASTA<br>ARK.gff Simplified GFF file formatted specifically for WGDI toolkit. Contains seven columns: chromosome, gene ID, start, end, strand, order, and gene ID. This file represents the positional and structural information of reconstructed ancestral genes in the Ancestral Rosaceae Karyotype. GFF3(7-columns)</p>
Supplementary Data: Industrial sector pathways to a well-below 2ºC world: a global integrated assessment perspective
<p>Supplementary Material for the study titled<em> Industrial sector pathways to a well-below 2ºC world: a global integrated assessment perspective</em>. <em> </em></p>
Datasets: Carbon sources and pathways for citrate secreted by human prostate cancer cells determined by NMR tracing and metabolic modeling
<p>Zipped NMR datasets:</p> <p>data1 LNCaP medium with [U-<sup>13</sup>C<sub>4</sub>]aspartate</p> <p>data2 LNCaP medium with [1,6-<sup>13</sup>C<sub>2</sub>]glucose</p> <p>data3 LNCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data4 VCaP medium with [1,6-<sup>13</sup>C<sub>2</sub>]glucose</p> <p>data5 VCaP medium with [U-<sup>13</sup>C<sub>4</sub>]aspartate -glucose +pyruvate</p> <p>data6 VCaP medium with [5-<sup>13</sup>C]glutamine</p> <p>data7 VCaP medium with [2-<sup>13</sup>C]pyruvate -glucose +aspartate</p> <p>data8 VCaP medium with [5-<sup>13</sup>C]glutamine</p> <p>data9 VCaP medium with [5-<sup>13</sup>C]glutamine</p> <p>data10 VCaP medium with [5-<sup>13</sup>C]glutamine</p> <p>data11 LNCaP and VCaP medium with and without zinc(II)</p> <p>data12 LNCaP and VCaP medium with and without zinc(II)</p> <p>data13 LNCaP and VCaP medium with and without zinc(II)</p> <p>data14 LNCaP medium with [U-<sup>13</sup>C<sub>4</sub>]aspartate -glucose +pyruvate</p> <p>data15 LNCaP medium with [5-<sup>13</sup>C]glutamine</p> <p>data16 LNCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data17 LNCaP medium with [5-<sup>13</sup>C]glutamine</p> <p>data18 VCaP medium with [1,6-<sup>13</sup>C<sub>2</sub>]glucose</p> <p>data19 VCaP medium with [1,6-<sup>13</sup>C<sub>2</sub>]glucose</p> <p>data20 VCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data21 LNCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data22 LNCaP medium with [2-<sup>13</sup>C]pyruvate +citr. Spiking</p> <p>data23 LNCaP medium with [5-<sup>13</sup>C]glutamine</p> <p>data24 LNCaP medium with [5-<sup>13</sup>C]glutamine</p> <p>data25 LNCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data26 VCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data27 VCaP medium with [2-<sup>13</sup>C]pyruvate -glucose +aspartate</p> <p>data28 VCaP medium with [U-<sup>13</sup>C<sub>4</sub>]aspartate -glucose +pyruvate</p> <p>data29 LNCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data30 LNCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data31 LNCaP medium with [2-<sup>13</sup>C]pyruvate</p> <p>data32 VCaP medium with [2-<sup>13</sup>C]pyruvate -glucose +aspartate</p> <p>data33 VCaP medium with [U-<sup>13</sup>C<sub>4</sub>]aspartate -glucose +pyruvate</p> <p>data34 VCaP medium with [U-<sup>13</sup>C<sub>4</sub>]aspartate -glucose +pyruvate</p> <p>data35 LNCaP medium with [U-<sup>13</sup>C<sub>4</sub>]aspartate</p> <p>data36 VCaP medium with [U-<sup>13</sup>C<sub>4</sub>]aspartate -glucose +pyruvate</p> <p>data37 LNCaP medium with [5-<sup>13</sup>C]glutamine + citr. spiking</p>
BridgeDb: pathway identifier mapping database derived from Wikidata
<p>First release of a BridgeDb pathway identifier mapping database. Currently supports Wikidata and WikiPathways identifiers. CCZero.</p> <pre><code>[INFO]: Database finished. INFO: old database is Wikidata 1.0.0 (build: 20211211) INFO: new database is Wikidata 1.0.0 (build: 20211211) INFO: Number of ids in Wd (Wikidata): 905 (unchanged) INFO: Number of ids in Wp (WikiPathways): 900 (unchanged) INFO: new size is 2 Mb (changed +0.0%) INFO: total number of identifiers is 1805 INFO: total number of mappings is 1810 </code></pre> <p> </p>
Global Transportation Demand Dataset using the Shared Socioeconomic Pathways (SSPs) Scenario Framework
<p>We use historical data for the land-based passenger (in passenger-kilometers (km)) across 38 countries and freight transport (in tonne-km) for 43 countries between 1990 and 2018 from the Transport Outlook of the International Transport Forum (ITF) transport database, to investigate the key drivers of transport energy demand <em><strong>source</strong>: ITF. (2019). ITF Transport Outlook 2019. ITF Transport Outlook 2019. <a href="https://www.oecd-ilibrary.org/transport/itf-transport-outlook-2019_transp_outlook-en-2019-en">https://www.oecd-ilibrary.org/transport/itf-transport-outlook-2019_transp_outlook-en-2019-en</a></em></p> <p>We collect the historical socioeconomic variables from the World Bank’s global open data bank <em><strong>source</strong>: World Bank. (2020). Data Bank: World Development Indicators. <a href="https://databank.worldbank.org/source/world-development-indicators">https://databank.worldbank.org/source/world-development-indicators</a></em></p> <p>For this scenario analysis, we rely on the shared socioeconomic pathways (SSPs) from the IIASA database (Riahi et al., 2017). <em><strong>source: </strong>Riahi, K., van Vuuren, D. P., Kriegler, E., Edmonds, J., O’Neill, B. C., Fujimori, S., … Tavoni, M. (2017). The Shared Socioeconomic Pathways and their energy, land use, and greenhouse gas emissions implications: An overview. Global Environmental Change, 42, 153–168. <a href="https://doi.org/10.1016/j.gloenvcha.2016.05.009">https://doi.org/10.1016/j.gloenvcha.2016.05.009</a> Available Online: <a href="https://tntcat.iiasa.ac.at/SspDb/dsd?Action=htmlpage&page=about">https://tntcat.iiasa.ac.at/SspDb/dsd?Action=htmlpage&page=about</a></em></p> <p>The lack of data disaggregated by country and end-use sector in countries of interest was a significant drawback in the data collection process. We make a crucial assumption in this modeling exercise that historical demand profiles in developing countries track the global average per capita transport trends. Therefore, the resulting estimates are indicative and must be interpreted within this analysis's scope given the future is unknown and highly uncertain.</p> <p> </p> <p> </p> <p> </p> <p> </p>
Data from: The evolutionary pathways for local adaptation in mountain hares
<p><span>Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole-genome sequencing, we identify genetic signatures of local adaptation in mountain hares (<i>Lepus timidus</i>) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. We recovered full mitochondrial DNA sequences from whole-genome sequencing data and used it to recontruct the evolutionary relationships among mountain hare haplotypes.</span></p>
Topographic deep neural networks predict the functional organization of the primate ventral visual pathway
<p>Recording of presentation at the Neuroscience 2021 annual meeting (held virtually). The abstract follows:</p> <p> </p> <p>The primate ventral visual pathway is organized into functional maps, including pinwheel-like arrangements of orientation-tuned neurons in primary visual cortex (V1) and patches of category-selective neurons in higher visual cortex. While deep convolutional neural networks (DCNNs) trained for object recognition accurately predict neural representations throughout the ventral pathway, they have no spatial layout for features at a given retinotopic location and are thus unable to predict the rich topographic organization of visual cortex. Here, we close this gap by first assigning each DCNN unit a position in a 2D cortical sheet, then training the network to minimize a cost function with two components: one encouraging accurate object recognition, and another favoring correlated responses among nearby units in each model layer (Figure 1A, 1B). </p> <p>We find that training with this composite spatial loss produces brain-like topographic maps in both early and later model layers (Figure 1B). Early layers contain smooth orientation preference maps with pinwheels, clusters of units preferring the same spatial frequency, and color-preference domains resembling V1 “blobs”. In a later layer of the same model, we observe clusters of category-selective units, e.g., face patches, whose spatial organization largely matches that found in primate higher visual cortex. Our model thus leverages local response correlations, which have been linked to theories of wire-length minimization, to accurately predict neuron responses and functional organization throughout the ventral visual pathway. In support of the wire-length minimization hypothesis, we find that our topographic DCNN would require shorter connections than a standard DCNN to support connections between similarly-tuned neurons within early (38% reduction) and later (31% reduction) model layers (Figure 1D). These results suggest that the functional organization of visual cortex can be explained by two constraints: the need to perform object recognition and pressure for local populations of neurons to have correlated responses.</p>
Results for Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast
<p>This dataset contains the original results for the paper "Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast". To reproduce all figures in this paper, this dataset is required. The scripts can be found in Github (https://github.com/SysBioChalmers/pcSecYeast)</p>
Data from: Mycorrhizal symbiosis pathway and edaphic fertility frame root economics space among tree species
<p><span>The root economics space (RES) is multidimensional and largely shaped by belowground biotic and abiotic influences. However, how root-fungal symbioses and edaphic fertility drive this complexity remains unclear. </span></p> <p><span>Here, we measured absorptive root traits of 112 tree species in temperate and subtropical forests of China, including traits linked to functional differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) hosts. </span></p> <p><span>Our data, from known mycorrhizal tree species, revealed a 'fungal-symbiosis' dimension distinguishing AM from ECM species. This divergence likely resulted from the contrasting mycorrhizal evolutionary development of AM versus ECM associations. Increased root tissue cortical space facilitates AM symbiosis, whereas increased root branching favors ECM symbiosis. Irrespective of mycorrhizal type, a 'root-lifespan' dimension reflecting aspects of root construction cost and defense was controlled by variation in specific root length and root tissue density, which was fully independent of root nitrogen content. Within this function-based RES, we observed a substantial covariation of axes with soil phosphorus and nitrate levels, highlighting the role played by these two axes in nutrient acquisition and conservation. </span></p> <p><span>Overall, our findings demonstrate the importance of</span><span> evolved mycorrhizal symbiosis pathway and edaphic fertility in framing the </span><span>RES</span><span>, and</span> <span>provide theoretical and mechanistic insights into the complexity of root economics.</span></p>
Meta data file for the paper "Characterising the silver particle generator; a pathway towards standardising silver aerosol generation" https://doi.org/10.1016/j.jaerosci.2022.105978
<p>The attached file contains meta data that were used for the figures shown in the paper "Characterising the silver particle generator; a pathway towards standardising silver aerosol generation" by Tobias Hammer et al., https://doi.org/10.1016/j.jaerosci.2022.105978</p> <p>The new commercial silver particle generator (SPG; an updated version of the prototype that was analyzed in the aforementioned study) will be analyzed in summer 2022</p>
Eremohaplomydas, Haplomydas, and Lachnocorynus dichotomous, pathway key in SDD-format
<p>Dichotomous, pathway key to genera Eremohaplomydas, Haplomydas, and Lachnocorynus (Diptera: Mydidae) developed with Lucid Builder v4 in XML Structure of Descriptive Data (SDD) format.</p>
Intramolecular Hydroxyl Nucleophilic Attack Pathway by a Polymeric Water Oxidation Catalyst with Single Cobalt Sites
<p>Exploring efficient water oxidation catalysts (WOCs) is the primary challenge in converting renewable energy into fuels. Here we report a molecularly well-defined heterogeneous WOC with Aza-fused-π-conjugated-microporous-polymer (Aza-CMP) coordinated single cobalt sites (Aza-CMP-Co). The single cobalt sites in Aza-CMP-Co exhibited superior activity under alkaline and near-neutral conditions. Moreover, the molecular nature of the isolated catalytic sites makes Aza-CMP-Co a reliable model for studying the heterogeneous water oxidation mechanism. By combining the experimental and theoretical results, a pH-dependent nucleophilic attack pathway for O-O bond formation was proposed. Under alkaline conditions, the intramolecular hydroxyl nucleophilic attack (IHNA) process that the adjacent -OH group nucleophilically attacks Co<sup>4+</sup>=O was identified as the rate-determining step. The process leads to lower activation energy and boosted kinetics than that of the intermolecular water nucleophilic attack pathway. This study provides significant insights into the crucial function of electrolyte pH in water oxidation catalysis and enhancement of the water oxidation activity by regulating the IHNA pathway.</p>
Transcriptomic analysis reveals potential candidate pathways and genes involved in toxin biosynthesis in true toads
<p>Synthesized chemical defenses have broadly evolved across countless taxa and are important in 30 shaping evolutionary and ecological interactions within ecosystems. However, the underlying 31 genomic mechanisms by which these organisms synthesize and utilize their toxins are relatively 32 unknown. Herein, we use comparative transcriptomics to uncover potential toxin synthesizing 33 genes and pathways, as well as interspecific patterns of toxin synthesizing genes across ten 34 species of North American true toads (Bufonidae). Upon assembly and annotation of the ten 35 transcriptomes, we explored patterns of relative gene expression and possible protein-protein 36 interactions across the species to determine what genes and/or pathways may be responsible for 37 toxin synthesis. We also tested our transcriptome dataset for signatures of positive selection to 38 reveal how selection may be acting upon potential toxin producing genes. We assembled high 39 quality transcriptomes of the bufonid parotoid gland, a tissue not often investigated in other 40 bufonid related RNAseq studies. We found several genes involved in metabolic and biosynthetic 41 pathways (e.g. steroid biosynthesis, terpenoid backbone biosynthesis, isoquinoline biosynthesis, 42 glucosinolate biosynthesis) that were functionally enriched and/or relatively expressed across the 43 ten focal species that may be involved in the synthesis of alkaloid and steroid toxins, as well as 44 other small metabolic compounds that cause distastefulness in bufonids. We hope that our study 45 lays a foundation for future studies to explore the genomic underpinnings and specific pathways 46 of toxin synthesis in toads, as well as at the macroevolutionary scale across numerous taxa that 47 produce their own defensive toxins.</p>
Carbon loss pathways in degraded peatlands: Repository dataset
<p>The data on the following sheets is associated with the paper:</p> <p> </p> <p>Evans, M.G., Alderson, D.M., Evans, C.D., Stimson, A., Goulsbra, C., Allott,T.E.H., Worrall, F., Crouch, T., Walker, J., Garnett, M.H., Rowson, J. (2022). Carbon Loss Pathways in Degraded Peatlands: New Insights from Radiocarbon Measurements of Peatland Waters. </p> <p> </p> <p>The data are organised according to the figures within the paper, with the data for each figure corresponding to an individual datasheet. The methods for data collection can be found in the associated manuscript.</p> <p> </p> <p>For further information please contact Martin Evans (martin.g.evans@manchester.ac.uk) or Danielle Alderson (danielle.alderson@manchester.ac.uk).</p> <p> </p> <p>Figures 1, 7 and 11 either do not contain data or are visual model outputs and are therefore not included. </p> <p> </p>
miR-1285-3p targets TPI1 to regulate the glycolysis metabolism signaling pathway of Tibetan sheep Sertoli cells
<p><span>Glycolysis in sertoli cells (SCs) can provide energy substrates for the development of spermatogenic cells. Triose phosphate isomerase 1 (TPI1) is one of the key catalytic enzymes involved in glycolysis. However, the biological function of TPI1 in SCs and its role in glycolytic metabolic pathways are poorly understood. On the basis of previous research, we isolated primary SCs from Tibetan sheep and overexpressed <em>TPI1</em> gene to determine its effect on the proliferation, glycolysis, and apoptosis of SCs. Secondly, we investigated the relationship between <em>TPI1</em> and miR-1285-3p, and whether miR-1285-3p regulates the proliferation and apoptosis of SCs, and participates in glycolysis by targeting <em>TPI1</em>. Results showed that overexpression of <em>TPI1</em> increased the proliferation rate and decreased apoptosis of SCs. In addition, overexpression of <em>TPI1</em> altered glycolysis and metabolism signaling pathways and significantly increased the amount of the final product lactic acid. Further analysis showed that miR-1285-3p inhibited <em>TPI1</em> by directly targeting its 3'untranslated region. Overexpression of miR-1285-3p suppressed the proliferation of SCs, and this effect was partially reversed by restoration of <em>TPI1</em> expression. In summary, this study shows that the miR-1285-3p/TPI1 axis regulates glycolysis in SCs. These findings add to our understanding of the regulation of spermatogenesis in sheep and other mammals.</span></p>
Supplementary material 2 from: Sirbu C, Miu IV, Gavrilidis AA, Gradinaru SR, Niculae IM, Preda C, Oprea A, Urziceanu M, Camen-Comanescu P, Nagoda E, Sirbu IM, Memedemin D, Anastasiu P (2022) Distribution and pathways of introduction of invasive alien plant species in Romania. NeoBiota 75: 1-21. https://doi.org/10.3897/neobiota.75.84684
Appendix S2. Altitudinal range of invasive and potentially invasive alien plant species recorded in Romania
Network Theme: Digital and data-driven blood monitoring and analytics for patient centred care pathways - Dr Weizi (Vicky) Li (Henley Business School, University of Reading)
<p>This video is the fifth talk from our Future Blood Testing Network Plus Launch that took place on the 23/11/2021.</p> <p>Network Theme: Digital and data-driven blood monitoring and analytics for patient centred care pathways - Dr Weizi (Vicky) Li (Henley Business School, University of Reading).</p> <p>Bio: Dr Weizi (Vicky) Li is the PI of the Future Blood Testing Network, an Associate Professor of Informatics and Digital Health, Deputy Director in Informatics Research Centre, Henley Business School, University of Reading. She is an interdisciplinary researcher focusing on using informatics, data science, machine learning, and digital information systems to solve real-world healthcare challenges. She is the academic lead of a large collaborative project of Improving the Quality of Healthcare through an Integrated Clinical Pathway Management Approach and Cloud based Digital Data Integration Platform, which was awarded ESRC O2RB Excellence in Impact Award in 2018 for her research impact on healthcare quality improvement. She is the academic lead of machine learning based decision support system for outpatient management which has successfully been implemented in Royal Berkshire NHS Foundation Trust and has received Research Engagement and Impact award in 2020. She has been PI on projects funded by ESRC, EPSRC, The Health Foundation, NHS and companies, working on data-driven decision support systems that use real-world data (under privacy preserving framework) from multiple sources including Electronic Patient Record in acute, community hospital and primary care settings, remote health monitoring and patient reported outcomes to develop novel technologies (including AI based methods) to support clinical and operational decision makings in patient pathway.</p> <p>Further details on this event can be found at: https://futurebloodtesting.org/event/23-11-21-future-blood-testing-network-launch/</p> <p>This video is an output from the Future Blood Testing Network which is funded by EPSRC under Grant Number EP/W000652/1</p> <p>YouTube Link: https://youtu.be/egINC9hJifI</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.