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7,327 results for “Pathway”
Data of "Fully automated pipeline for the fiber tractography of the anterior optic pathway in patients with sellar and parasellar tumors and analysis of the microstructural alterations"
<p>This dataset contains the numerical data used for the analysis described in the paper "<strong><span>Fully automated pipeline for the fiber tractography of the anterior optic pathway in patients with sellar and parasellar tumors and analysis of the microstructural alterations</span></strong>", Gramegna LL et al.</p> <p>chiasma_displacement.xlsx contains the value in mm of the vertical displacement of the chiasm for each subject (see the paper for the methodological procedure of the evaluation).</p> <p>parameters_along_tract.xlsx contains for each subject (Exam): the condition (Cond, 0=healthy control, 1=patient), whether they experienced complete or partial resolution of symptoms after surgical treatment (Responder), the corresponding area along the anterior optic pathway (Zone), the sampling point among the 45 that the anterior optic pathway was divided into (Bin), the microstructural parameter considered (Measure) and its corresponding value (Value).</p>
WGCNA_clusterProfiler_pathway_enrichment
<p>Pathway enrichment analysis results using clusterProfiler with genes from WGCNA modules differentially expressed in APOE2 expressing microglia. </p>
GETV Activates the Ras/Raf/MEK/ERK Pathway through ROS, Mediating Autophagy in Leydig Cells
<p>This is a reproduction package for the paper "GETV Activates the Ras/Raf/MEK/ERK Pathway through ROS, Mediating Autophagy in Leydig Cells" by Fengqin Li, <span>L</span>ishuang <span>D</span>eng, <span>T</span>ong <span>X</span>u, <span>L</span>ei <span>X</span>u, <span>Zh</span>iwen <span>X</span>u, <span>Siyuan Lai</span>, <span>Yanru Ai</span>, <span>Y</span>anqun <span>W</span>ang, <span>G</span>uangwen <span>Y</span>an, <span>L</span>ing <span>Z</span>hu(2024).</p>
Single-cell transcriptome-based analysis reveals hub genes and key pathways in acute B-lymphoblastic leukemia
<p><span>急性</span><span>B </span><span>淋巴细胞白血病(</span><span>Acute B Lymphoblastic Leukemia B-ALL</span><span>)发病机制复杂,与基因突变和信号通路的异常密切相关。本研究旨在对</span><span>B-ALL</span><span>患者的基因表达和信号通路进行系统分析,我们期望揭示疾病发生和发展的分子机理,为临床治疗提供新的靶点。</span><span>在</span><span>GSE130116</span><span>数据集中,通过使用特定标记基因鉴定</span><span>B</span><span>细胞亚型。应用高维加权基因共表达网络分析(</span><span>high-definition Weighted Gene Co-expression Network Analysis hdWGCNA</span><span>)对单细胞</span><span><span>RNA</span></span><span><span>测序(</span><span>single-cell RNA sequencing</span><span> <span> </span>scRNA-seq</span></span><span><span>)</span></span><span>数据进行细胞亚群聚类和基因模块关联,结合伪时间轨迹分析,以确定与</span><span>B-ALL</span><span>相关的关键细胞状态和基因模块。基因组富集分析识别与基因模块相关的生物过程。使用用于活性推断的通路响应基因(</span><span>Pathway RespOnsive GENes for activity inference PROGENy</span><span>)软件包用于基于单细胞转录组数据推断通路活性。分析伪时序变化中的关键基因,并用</span><span>FindMarkers</span><span>函数进行差异表达分析,识别不同伪时间状态中显著变化的基因。</span></p>
Elucidating cisplatin resistance mechanisms in squamous cervical cancer: Proteomic insights into intracellular DNA repair pathways while exploring the horizons of omics-driven drug repurposing
<p>The following dataset consists of mass spectrometry-based-DIA global proteomics data of HPV16+ cervical cancer cell lines.</p>
Supporting data for 'Key structural features, thermodynamics and kinetics along the pathway between active and inactive forms of thrombin'
<p>This data set contains the raw data used for the preparation of the manuscript 'Key structural features, thermodynamics and kinetics along the pathway between active and inactive forms of thrombin'. It is separated into following parts:</p> <ul> <li>X-ray: Data used in the analysis of the PDB structures of thrombin, including a list of the PDB IDs, results of the PCA and values of the introduced features in the structures.</li> <li>cMD: Input parameters, topologies and starting coordinates of the five classical MD simulation that are based on different PDB structures, resulting trajectories, projection on X-ray PCA, RMSD values and values of the introduced features during the simulations.</li> <li>TMD: Input parameters, topologies and starting coordinates of the Targeted MD simulations, resulting trajectories, projection on X-ray PCA, RMSD values and values of the introduced features during the simulations.</li> <li>Seeded-Sims: Input parameters, topologies and starting coordinates of classical MD simulations that are started from cluster representatives of the TMD simulations and resulting trajectories.</li> <li>MSM: Values of the introduced features of the trajectories started from the TMD seeds, results of the TICA and of the denity-based clustering, representative structures of the states E, I1, I2 and E* and distribution of the introduced features in these states.</li> </ul> <p>A more detailed description of the included files can be found in the <em>README</em> files in each folder. Additional information about software versions can also be found there.</p>
Coghlan-et-al.-2024_benthic-pelagic-energy-pathways-lizard-island
<p><strong>PLEASE NOTE: these data form part of a PhD project with chapters still pending. For permission to use the data contact me: amy.<a href="mailto:coghlan@utas.edu.au">coghlan@utas.edu.au</a>.</strong></p> <p><strong><span>Related publication:</span></strong><span> Beyond pelagic subsidies: benthic primary production also fuels coral reef fish communities</span></p> <p><strong><span>Authors:</span></strong><span> Amy Rose Coghlan<sup>1</sup>*; Heidi Pethybridge<sup>2</sup>; Asta Audzijonyte<sup>1, 3</sup>; Rick D. Stuart-Smith<sup>1</sup>; Chris Harrod<sup>4</sup>; Elizabeth A. Brewer<sup>2</sup>; Julia Blanchard<sup>1, 3</sup></span></p> <p><strong><span> </span></strong></p> <p><strong><span>Affiliations:</span></strong><span> <sup>1 </sup>Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia.</span></p> <p><sup><span>2</span></sup><span> Commonwealth Scientific and Industrial Research Organization (CSIRO), Hobart, Tasmania Australia.</span></p> <p><sup><span>3</span></sup><span>Centre for Marine Socioecology, University of Tasmania, Hobart, Tasmania, Australia</span></p> <p><sup><span>4</span></sup><span>Scottish Centre for Ecology and the Natural Environment, School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, G63 0AW, UK.</span></p> <p><strong><span> </span></strong></p> <p><strong><span>Corresponding author:</span></strong><span> Amy Rose Coghlan (email: </span><a href="mailto:amy.coghlan@utas.edu.au"><span>amy.coghlan@utas.edu.au</span></a><span>)</span></p> <p><span><strong>PLEASE NOTE: these data form part of a PhD project with chapters still pending. For permission to use the data contact me: amy.<a href="mailto:coghlan@utas.edu.au">coghlan@utas.edu.au</a>.</strong></span></p>
Time series transcriptomes resolve metabolic pathways underlying crocin's anti-cancer activity | Dataset: sequencing reads (controls); Kallisto counts/TPMs
<p>This repository is deprecated. Controls are now here: https://zenodo.org/records/13822024 and the Kallisto and ShinyGO analyses are here: https://zenodo.org/records/15804191</p> <p> </p> <p>Liver cancer can be treated with natural products, including saffron. The exact mechanism for the components of saffron, including crocin, to eliminate malignancy in HCC cells is not known. We used response screening from time series transcriptomic datasets to decipher the underlying mechanisms responsible for crocin’s anti-cancer activity. We treated HCC cells with 1 and 2 mM crocin for 2, 6, 12, and 24 hours and examined transcriptomic profiles at each timepoint compared to controls. The effect size was strongest at two hours and 1 mM crocin; later timepoints and the 2 mM dose showed similar responses, but the overall effect was diminished after two hours post-treatment. We observed the upregulation of transcripts for fatty acid oxidation enzymes, mitochondrial carnitine transpoart systems, bile acid synthesis, and cholesterol metabolism to varying degrees at all timepoints tested after crocin treatment. Pathway enrichment analyses showed that pathways for DNA damage checkpoint activation and senescence induction were upregulated while a variety of pro-proliferation pathways were downregulated. We saw 52 genes involved in non-alcoholic fatty liver disease down-regulated after 24 hours post-treatment (enrichment FDR p = 8 x 10<sup>8</sup>), indicating a reversal of many pathways promoting carcinogenesis after crocin treatment. The significant upregulation of senescence and autophagy genes was contrasted with the significant down-regulation of spliceosomal machinery genes at all time points after crocin treatment. Interestingly, the cell fate-protecting PAX transcription factor was significantly upregulated while ELK oncogenes were downregulated after crocin treatment. Overall, the data outline an intricate cellular response leading to HCC spliceosome repression and induced senescence after crocin treatment. Our findings help to explain the cancer-fighting effects of saffron and outline an example of antioxidant ‘swamping’ in cancer cells by natural products.</p>
Link to dataset related to article "The epigenetic enzyme DOT1L orchestrates vascular smooth muscle cell-monocyte crosstalk and protects against atherosclerosis via the NF-κB pathway "
<p>Link to dataset related to article "The epigenetic enzyme DOT1L orchestrates vascular smooth muscle cell-monocyte crosstalk and protects against atherosclerosis via the NF-κB pathway"</p> <p>Abstract</p> <p><strong>Aims: </strong> Histone H3 dimethylation at lysine 79 is a key epigenetic mark uniquely induced by methyltransferase disruptor of telomeric silencing 1-like (DOT1L). We aimed to determine whether DOT1L modulates vascular smooth muscle cell (VSMC) phenotype and how it might affect atherosclerosis in vitro and in vivo, unravelling the related mechanism.</p> <p><strong>Methods and results: </strong> Gene expression screening of VSMCs stimulated with the BB isoform of platelet-derived growth factor led us to identify Dot1l as an early up-regulated epigenetic factor. Mouse and human atherosclerotic lesions were assessed for Dot1l expression, which resulted specifically localized in the VSMC compartment. The relevance of Dot1l to atherosclerosis pathogenesis was assessed through deletion of its gene in the VSMCs via an inducible, tissue-specific knock-out mouse model crossed with the ApoE-/- high-fat diet model of atherosclerosis. We found that the inactivation of Dot1l significantly reduced the progression of the disease. By combining RNA- and H3K79me2-chromatin immunoprecipitation-sequencing, we found that DOT1L and its induced H3K79me2 mark directly regulate the transcription of Nf-κB-1 and -2, master modulators of inflammation, which in turn induce the expression of CCL5 and CXCL10, cytokines fundamentally involved in atherosclerosis development. Finally, a correlation between coronary artery disease and genetic variations in the DOT1L gene was found because specific polymorphisms are associated with increased mRNA expression.</p> <p><strong>Conclusion: </strong> DOT1L plays a key role in the epigenetic control of VSMC gene expression, leading to atherosclerosis development. Results identify DOT1L as a potential therapeutic target for vascular diseases.</p>
Datset related to article "Pathways of follow-up care in an Italian center: retrospective study on patients with gliomas II and III"
<p>Database related to the descriptive statistics used to illustrate the characteristics of the sample and to identify the pathways of follow-up care in an Italian center.</p>
Adolescent stress impairs postpartum social behavior via anterior insula-prelimbic pathway in mice
<p>The custom code has been developed to analyze in vivo calcium imaging data in the study titled "Adolescent stress impairs postpartum social behavior via anterior insula-prelimbic pathway in mice".</p>
In vivo diffusion MRI of optic pathways in 18 healthy mice
<p>The dataset contains manganese enhanced T1- and diffusion-weighted images of optic pathways in 18 healthy mice. All raw (Bruker) and a subset of processed (NIfTI) files are stored.</p><p><strong>Animals</strong><br>Our study was approved by the Institutional Animal Care and Use Committee (IACUC) at NYU Langone Health. All n=18 mice were females, genotype C57BL/6, 7-8 weeks old at baseline and sacrificed within 24 hours after completing the imaging.<br> <br><strong>Data</strong><br>We acquired in vivo MRI using a preclinical wide bore 7T scanner with a four-channel phased array cryogenically cooled receive-only coil (Bruker BioSpin MRI GmbH, Ettlingen, Germany). Prior to imaging, the mice were anesthetized with inhaled isoflurane (3% induction, 1.0-1.5% maintenance). The acquisition protocol consisted of FLASH T1-weighted images at 100µm isotropic resolution (TE/TR = 4.5/30ms) and multishell DWIs at 200µm isotropic resolution (multi-shot multi-slice EPI with 3 readout segments, TE/TR = 27.6/2781ms, L/R phase encoding) sampled in 60 directions distributed on radial lines at b ∈ {250, 1000, 2250, 4000} [s/mm2] interleaved with 5 images at b=0. </p><p>To minimize motion artifacts, we fixed the mice to the holder with a bite bar and a pair of ear bars. Additionally, we used a TTL (Transistor-Transistor Logic) trigger receiving inputs from a pressure pad to account for breathing-related motion artifacts. The expected scan time for the dMRI protocol was 37min. 24sec. The effective scan time with the trigger varied between 60 and 70 minutes.</p><p>Immediately after the baseline scans, while the mice remained under isoflurane-induced general anesthesia, we administered intravitreally manganese chloride (MnCl2) solution to the left (nleft=8) or the right eye (nright=10). We began by injecting 1.0µl of 0.1M MnCl2 (Mice 1–2), which we eventually lowered to 0.5µl (Mice 3–18) without any observable loss in contrast enhancement. Finally, 21±4 hours after injection, we repeated the exact same FLASH T1 acquisition to obtain follow-up MEMRI scans. </p><p><strong>Image processing</strong><br>In our DWI postprocessing pipeline, we executed the MRtrix3 implementations of the Marchenko-Pastur PCA denoising (<i>dwidenoise</i>), Gibbs ringing (<i>mrdegibbs</i>) and B1 field inhomogeneity artifacts removal (<i>dwibiascorrect ants</i>). After that, we interpolated the DWIs to 100µm isotropic resolution such that they would match the voxel size of the anatomical images. Then, we registered the follow-up MEMRI scans to the corresponding b=0 images using 3-dimensional rigid body transformation implemented in: <i>antsRegistrationSyN.sh </i></p><p><strong>Acknowledgements</strong><br>The authors would like to thank Orin Mishkit, Zakia Ben Youss Gironda, Orlando Aristizabal, and Youssef Wadghiri from the NYU Langone Health Preclinical Imaging Laboratory for their invaluable help.</p><p>This project was supported in part by the National Institutes of Health (NIH, R01 EB028774, R01 EB029306, and R01 NS082436). It was performed under the rubric of the Center for Advanced Imaging Innovation and Research (CAI2R, https://www.cai2r.net), a NIBIB Biomedical Technology Resource Center (NIH P41 EB017183), and at the NYU Langone Health Preclinical Imaging Laboratory, a shared resource partially supported by the NIH/SIG 1S10OD018337-01, the Laura and Isaac Perlmutter Cancer Center Support Grant NIH/NCI 5P30CA016087.</p>
SCALABLE - Social-ecological pathways and gender perspectives for future conservation of biocultural mountain agro-ecosystems - Deliverable 1.1: Database of social perceptions towards impacts and threats
<p><strong>D1.1: Database of social perceptions towards impacts and threats</strong></p> <p><strong>.- Social database in case study 1: Almócita, Almería, Spain</strong></p> <p>This dataset contains the results from a social survey targeting rural local communities over their perceptions on rural abandonment. Respondents were asked about: a) relation with the rural area and human-nature connectedness; b) perception toward rural abandonment and drivers of change; c) specific activities that in the municipality are carried out to face rural abandonment and how those activities are connected and promote different human well-being components. A final section of the survey compiled socio-demographic information to allow the characterization of the respondents. The survey was carried out by face-to-face and the data compilation was using tablets and manually. </p> <p>In this upload you can find 2 files:</p> <p>1- Database: this file contains the dataset with all the valid responses to the survey. blank spaces mean that the question was left unanswered by the respondents.</p> <p>2- Document of the face-to-face survey with all the questions and panels used for the social sampling: a) panel of drivers of change; b) panel of activities; and c) panel of contributions.</p> <p><strong>.- Social database in case study 2: Purchena, Almería, Spain</strong></p> <p>This dataset contains the results from a social survey targeting rural local communities over their perceptions on human-nature connections and their dimensions, as well as factors for reconnecting with rural areas. Respondents were asked about: a) human-nature connectedness in a rural areas; b) dimensions of human-nature connectedness; and c) reconnection with nature. A final section of the survey compiled socio-demographic information to allow the characterization of the respondents. The survey was carried out by face-to face and online, and the data compilation was manually. </p> <p>In this upload you can find 2 files:</p> <p>1- Database: this file contains the dataset with all the valid responses to the survey. blank spaces mean that the question was left unanswered by the respondents.</p> <p>2- Document of the face-to-face survey with all the questions used for the social sampling.</p>
SCALABLE - Social-ecological pathways and gender perspectives for future conservation of biocultural mountain agro-ecosystems - Deliverable 2.1: Spatially explicit database on biocultural practices and their associated ecosystem services
<p>This dataset contains the results from participatory mapping workshops with local communities in the municipality of Abrucena, in Almería, Spain. Participatory workshops were carried out divided by gender in different days. In addition, within each workshop, participants were dividing in two different groups. Participants were asked to: a) map past biocultural diversity elements in the region (i.e., practices, knowledge, and traditions); and b) map current biocultural diversity elements (i.e., practices, knowledge and traditions) in the region.</p> <p>In this upload you can find 4 files (shapefiles format):</p> <p>1- Spatial database of past (1950) biocultural diversity elements mapped by women: this file contains the dataset with three different biocultural diversity elements differentiated (TypeBCD): practices, knowledge, traditions.</p> <p>2- Spatial database of current (2022) biocultural diversity elements mapped by women: this file contains the dataset with three different biocultural diversity elements differentiated (TypeBCD): practices, knowledge, traditions.</p> <p>3- Spatial database of past (1950) biocultural diversity elements mapped by men: this file contains the dataset with three different biocultural diversity elements differentiated (TypeBCD): practices, knowledge, traditions.</p> <p>4- Spatial database of current (2022) biocultural diversity elements mapped by men: this file contains the dataset with three different biocultural diversity elements differentiated (TypeBCD): practices, knowledge, traditions.</p>
SCALABLE - Social-ecological pathways and gender perspectives for future conservation of biocultural mountain agro-ecosystems - Deliverable 3.1: Future scenarios developed for the conservation of mountain agro-ecosystems
<p>This dataset contains the results from participatory mapping workshops with local communities in the municipality of Abrucena, in Almería, Spain. Participatory workshops were carried out divided by gender in different days. In addition, within each workshop, participants were dividing in two different groups. Participants were asked to: a) map future biocultural diversity elements in the region (i.e., practices, knowledge, and traditions); and b) identify strategies to reach the ideal future scenario for the conservation of biocultural diversity in the region.</p> <p>In this upload you can find 4 files:</p> <p>1- Database of future scenarios for biocultural diversity identified by women: this file contains the dataset with biocultural diversity elements identified and classified by three categories: practices, knowledge, traditions.</p> <p>2- Database of future strategies to achieve future scenarios for the conservation of biocultural diversity identified by women: first sheet contains the dataset with strategies identified, and actors involved in each strategy. Second sheet contains general observations of the strategies to facilitate the interpretation of the data.</p> <p>3- Database of future scenarios for biocultural diversity identified by men: this file contains the dataset with biocultural diversity elements identified and classified by three categories: practices, knowledge, traditions.</p> <p>4- Database of future strategies to achieve future scenarios for the conservation of biocultural diversity identified by men: first sheet contains the dataset with strategies identified, and actors involved in each strategy. Second sheet contains general observations of the strategies to facilitate the interpretation of the data.</p>
Fig. 4. Possible biogenetic pathway for taipainine D in Isosteroidal alkaloids of Fritillaria taipaiensis and their implication to Alzheimer's disease: Isolation, structural elucidation and biological activity
Fig. 4. Possible biogenetic pathway for taipainine D (4).
Fig. 22. Postulated biogenetic pathway for ochraceopones A-E in Recent studies on terpenoids in Aspergillus fungi: Chemical diversity, biosynthesis, and bioactivity
Fig. 22. Postulated biogenetic pathway for ochraceopones A-E (234–238).
Fig. 4 in Sesquiterpenes from Kadsura coccinea attenuate rheumatoid arthritis-related inflammation by inhibiting the NF-κB and JAK2/STAT3 signal pathways
Fig. 4. Experimental and calculated ECD spectra of compound 1.
Fig. 4 in Impairment of botrydial production in Botrytis cinerea allows the isolation of undescribed polyketides and reveals new insights into the botcinins biosynthetic pathway
Fig. 4. Conformational disposition and NOE effects observed in compound 25.
Fig. 2. Botcinins and cinbotolide isolated from null mutant Bcbot4 in Impairment of botrydial production in Botrytis cinerea allows the isolation of undescribed polyketides and reveals new insights into the botcinins biosynthetic pathway
Fig. 2. Botcinins and cinbotolide isolated from null mutant Bcbot4Δ.
ScienceDex guides
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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.