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485
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ShareScore release 0.9.0
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485 results for “pathway analysis”
Spectroscopic Analysis of Vibronic Relaxation Pathways in Molecular Spin Qubit [Ho(W5O18)2]9–: Sparse Spectra Are Key
<p>Vibrations play a prominent role in magnetic relaxation processes of molecular spin qubits as they couple to spin states, leading to the loss of quantum information. Direct experimental determination of vibronic coupling is crucial to understand and control the spin dynamics of these nano-objects, which represent the limit of miniaturization for quantum devices. Herein, we measure the magneto-infrared properties of the molecular spin qubit system Na<sub>9</sub>[Ho(W<sub>5</sub>O<sub>18</sub>)<sub>2</sub>]·35H<sub>2</sub>O. Our results place significant constraints on the pattern of crystal field levels and the vibrational excitations allowing us to unravel vibronic decoherence pathways in this system. We observe field-induced spectral changes near 63 and 370 cm<sup>–1</sup> that are modeled in terms of odd-symmetry vibrations mixed with <em>f</em>-manifold crystal field excitations. The overall extent of vibronic coupling in Na<sub>9</sub>[Ho(W<sub>5</sub>O<sub>18</sub>)<sub>2</sub>]·35H<sub>2</sub>O is limited by a modest coupling constant (on the order of 0.25) and a transparency window in the phonon density of states that acts to keep the intramolecular vibrations and <em>M</em><sub>J</sub> levels apart. These findings advance the understanding of vibronic coupling in a molecular magnet with atomic clock transitions and suggest strategies for designing molecular spin qubits with improved coherence lifetimes.</p>
Analysis of Mother-child Interaction and Regulation of Candidate Genes of Stress Signaling Pathways in Mature Infants
ClinicalTrials.gov study NCT03926923. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Auditory functional magnetic resonance imaging in dogs – normalization and group analysis and the processing of pitch in the canine auditory pathways
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Data from: Range-wide population genomics of the Mexican fruit fly: towards development of pathway analysis tools
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Data from: Impact of a novel community testing pathway for people with suspected COVID-19 in Wales: a cost-minimisation analysis
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Data from: Invasive plants differentially affect soil biota through litter and rhizosphere pathways: a meta-analysis
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Data from: Systems analysis of adaptive responses to MAP Kinase pathway blockade in BRAF mutant melanoma
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Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera
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Data from: Proteomic analysis reveals a predominant NFE2L2 (NRF2) signature in the canonical pathway and upstream regulator analysis of Leishmania-infected macrophages
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Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice
Background: mRNA interactions with each other and other signaling molecules define different biological pathways and functions. Researchers have been investigating various tools to analyze these types of interactions. In particular gene co-expression network methods have proved useful in finding and analyzing these molecular interactions. Many different analytical pipelines to identify these interactions networks have been proposed with the aim of identifying an optimal partition of the network where the individual modules are neither too small to make any general inference or too large to be biologically interpretable. Results: In this study we propose a new pipeline to perform gene co-expression network analysis. The proposed pipeline uses WGCNA a widely used software to perform different aspects of gene co-expression network analysis and modularity maximization algorithm to analyze novel RNA-Seq data to understand the effects of low-dose 56Fe ion irradiation on the formation of hepatocellular carcinoma in mice. The network results along with experimental validation show that using WGCNA combined with Modularity provide a more biologically interpretable network in our dataset. Our pipeline showed better performance than the existing clustering algorithm in WGCNA in finding modules and identified a module with mitochondrial subunits that are supported by mitochondrial complex assay. Conclusions: We present a pipeline that can reduce the problem of parameter selection with the existing algorithm in WGCNA for comparable RNA-Seq datasets which may assist in future research to discover novel mRNA interactions and their downstream molecular effects. C57BL16 males were placed into 2 treatment groups and received the following irradiation treatments at Brookhaven National Laboratories (Long Island NY): 600 MeV/n 56Fe (0.2 Gy) and no irradiation. Left liver lobes were collected at 30 60 120 270 and 360 days post-irradiation flash frozen and stored at -80 xc2 xb0C until they could be processed for RNA-Seq. Livers were sampled by taking two 40-micron thick slices using a cryotome at -20 xc2 xb0C. This allowed multiple sampling of the tissue without the tissue going through multiple freeze/thaw cycles. Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific Waltham MA) and rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina San Diego CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500. Reads were aligned to the mouse GRCm38 reference genome using the STAR alignment program version 2.5.3a with the recommended ENCODE options. The -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file. Total number of reads used in analysis varies between 23-35 millions of reads.
Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis
GEO Series GSE90081. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis
GEO Series GSE80532. Yersinia pseudotuberculosis IP 32953; Yersinia pseudotuberculosis. 16 samples. Type: Expression profiling by array.
Transcriptome analysis to investigate the oncogenic TGF-β-Smad-Snail signaling pathway
GEO Series GSE90024. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Next Generation Sequencing Facilitates Quantitative Analysis of IL-2-STAT5 pathway change in the WT or PD-L1-/- HCT recipients with or without anti-IL-2 treatment
GEO Series GSE149026. Mus musculus. 22 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomics driven metabolic pathway analysis reveals similar metabolic alterations in diet- and chemical-induced mouse NASH model and human
GEO Series GSE230639. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas
GEO Series GSE291551. Homo sapiens; Mus musculus. 11 samples. Type: Expression profiling by high throughput sequencing.
Glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H: a combined fluxomics and transcriptomics analysis
GEO Series GSE42223. Gluconobacter oxydans 621H. 3 samples. Type: Expression profiling by array.
RNA sequencing analysis for cellular metabolic pathway in MARCHF6 Knock-Out HeLa cell lines
GEO Series GSE173282. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
High throughput phenotypic screen and transcriptional analysis identify new compounds, targets and pathways for macrophage reprogramming I
GEO Series GSE144989. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing.
Integrated transcriptomic analysis of Trichosporon asahii uncovers the core genes and pathways of fluconazole resistance
GEO Series GSE106454. Trichosporon asahii var. asahii CBS 2479; Trichosporon asahii var. asahii CBS 8904. 10 samples. Type: Expression profiling by high throughput sequencing.
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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.