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163 results for “tensor”
Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes
<h2>Description</h2> <p>This dataset contains all of the supplementary files necessary to reproduce the findings published in the research article entitled <em>Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes. </em>The scripts necessary for reproducing the published analyses can be found in the <a href="https://github.com/blasks/barnacle-manuscript">GitHub repository associated with the article</a>. Below is the article abstract and a description of the files included in this dataset.</p> <h2>Abstract</h2> <p>Microbes respond to changes in their environment by adapting their physiology through coordinated adjustments to the expression levels of functionally related genes. To detect these shifts in situ, we developed a sparse tensor decomposition method that derives gene co-expression patterns from inherently complex whole community RNA-sequencing data. Application of the method to metatranscriptomes of the abundant marine cyanobacteria <em>Prochlorococcus</em> and <em>Synechococcus</em> identified responses to scarcity of two essential nutrients, nitrogen and iron, including increased transporter expression, restructured photosynthesis and carbon metabolism, and mitigation of oxidative stress. Further, expression profiles of the identified gene clusters suggest that both cyanobacteria populations experience simultaneous nitrogen and iron stresses in a transition zone between North Pacific oceanic gyres. The results demonstrate the power of our approach to infer organism responses to environmental pressures, hypothesize functions of uncharacterized genes, and extrapolate ramifications for biogeochemical cycles in a changing ecosystem.</p> <h2>Legends for data S1 to S11</h2> <h3>Data S1. <em>Prochlorococcus</em> component profiles.</h3> <p>Median weight profiles for each <em>Prochlorococcus</em> component, including list of associated CyCOGs with corresponding gene weight, bootstrap support, and consensus annotation.</p> <h3>Data S2. <em>Synechococcus</em> component profiles.</h3> <p>Median weight profiles for each <em>Synechococcus</em> component, including list of associated CyCOGs with corresponding gene weight, bootstrap support, and consensus annotation.</p> <h3>Data S3. Enrichment analysis.</h3> <p>Significantly enriched KEGG pathways associated with each component, and compiled consensus annotations for each CyCOG.</p> <h3>Data S4. MED4 CyCOGs.</h3> <p>Mapping of <em>Prochlorococcus</em> MED4 genes to associated CyCOGs.</p> <h3>Data S5. Nitrogen and iron acclimation clusters.</h3> <p>CyCOGs, genes, and annotations for clusters associated with acclimation to nitrogen and iron scarcity.</p> <h3>Data S6. Sample metadata.</h3> <p>Metadata file detailing sampling conditions for all metatranscriptomes used in this study.</p> <h3>Data S7. Genome metadata.</h3> <p>Metadata file for CyCOG v6 reference genomes, including updated clade assignments.</p> <h3>Data S8. CyCOG v6 database.</h3> <p>Tarball of CyCOG v6 database, including reference genomes and annotation data.</p> <h3>Data S9. Reference sequence phylogenies.</h3> <p>Tarball of <em>Prochlorococcus</em> and <em>Synechococcus</em> reference genome phylogenies, used to update clade assignments.</p> <h3>Data S10. <em>Prochlorococcus</em> transcript abundance data.</h3> <p>A netCDF file of raw and normalized <em>Prochlorococcus</em> transcript abundance data, aggregated by CyCOG and organized into an `xarray.Dataset' tensor data structure.</p> <h3>Data S11. <em>Synechococcus</em> transcript abundance data.</h3> <p>A netCDF file of raw and normalized <em>Synechococcus</em> transcript abundance data, aggregated by CyCOG and organized into an `xarray.Dataset' tensor data structure.</p>
Diffusion Tensor Imaging in Chronic Inflammatory Demyelinating Polyneuropathy (PIDC)
ClinicalTrials.gov study NCT03460951. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Role of Mesocorticolimbic Pathway in Apathy of Patients With Parkinson's Disease. - Study Using Diffusion Tensor Imaging and Fibres Tracking
ClinicalTrials.gov study NCT01794195. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Evaluation of Complete Median Nerve Transection With Clinical, Electroneuromyographic and Diffusion Tensor Imaging
ClinicalTrials.gov study NCT02672631. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
the Application of Diffusion Tensor Imaging in the Evaluation of Peripheral Neuropathy in ANCA Associated Vasculitis
ClinicalTrials.gov study NCT04923074. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Role of Diffusion Tensor-magnetic Resonance Imaging in Investigating Sensorineural Hearing Loss
ClinicalTrials.gov study NCT06434129. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Diffusion Tensor and Functional Connectivity Imaging in Pediatric Epilepsy: Imaging/Histology Correlation
ClinicalTrials.gov study NCT02846272. IPD Sharing: NO. Countries: 1. Publications: 0.
Real-life Assessement of Safety and Perofmance of the of the "Infinite-Thread®" Permanent Tensor Thread
ClinicalTrials.gov study NCT07195877. IPD Sharing: NO. Countries: 1. Publications: 0.
Can Diffusion Tensor Imaging (DTI) of the Optic Ways Contributes to Predict the 6 Months Prognosis of Optic Neuritis (ON)?
ClinicalTrials.gov study NCT03570385. IPD Sharing: NO. Countries: 1. Publications: 0.
Determining the Extent of Diffusion Tensor Abnormalities in Focal Cortical Dysplasia
ClinicalTrials.gov study NCT00687024. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Development and Validation Phase of Diffusion Tensor Imaging and Arterial Spin Labelling at 3 Tesla Using a Long-term Effort Model Applicable to Skeletal Muscle Characterization.
ClinicalTrials.gov study NCT02018718. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Magnetic Resonance Spectroscopic and Diffusion Tensor Imaging of Adolescents with Autism Spectrum Disorders
ClinicalTrials.gov study NCT01361503. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Diffusion Tensor Imaging Magnetic Resonance Imaging (DTI MRI) as a Correlate to Pain Relief and Facial Numbness in Patients Following Stereotactic Radiosurgical Rhizotomy for Trigeminal Neuralgia
ClinicalTrials.gov study NCT01364272. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Diffusion Tensor (Magnetic Resonance) Imaging and Tractography in Herniation of the Cervical Spine
ClinicalTrials.gov study NCT00599183. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Diffusion Tensor Imaging in Epilepsy With Continuous Spikes and Waves During Sleep
ClinicalTrials.gov study NCT03035513. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Evaluation of Nerve Regeneration After Nerve Transsection Using (Diffusion-tensor Magnetic Resonance Imaging) DTI MR Imaging
ClinicalTrials.gov study NCT01020149. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Pilot Study of Measurement Agreement Between Morphological and Diffusion Tensor Imaging MRI for Pelvic Nerve Cartography
ClinicalTrials.gov study NCT03320343. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Magnetic Resonance Imaging Diffusion Tensor Tractography for Early Osteoarthritis Assessment
ClinicalTrials.gov study NCT03181425. IPD Sharing: NO. Countries: 1. Publications: 0.
Diffusion-tensor Imaging in Brain Tumors Evaluation
ClinicalTrials.gov study NCT05261724. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Diffusion Tensor Imaging in Autism
ClinicalTrials.gov study NCT00382382. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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