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485 results for “pathway analysis”
Fig. 2 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers
Fig. 2. Effect of pH on the activity of partially purified enzymes from Mucuna pruriens. The assay was performed using 50 mM catechol and 30 mM L-tyrosine as substrates for the PPO and TH enzyme activity, respectively. Four different buffers with their optimal buffering capacity in the pH range of 3–10 were used in separate assays.
Fig. 7 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers
Fig. 7. Homology modelling and secondary structure prediction of PPO enzyme from Mucuna pruriens (a) Predicted secondary structure of PPO (b) Phyre2 protein model for PPO with 3D model dimensions (in Å) (X:49.941 Y:64.463 Z:57.979). Image colored by rainbow N → C terminus (c) Three dimensional SWISS protein model for PPO enzyme with two active copper binding ligands (copper ions bridging oxygen moiety is illustrated as small yellow spheres highlighted in the box), conserved histidine residues and metal complex interactions (in dotted lines). Chain A for Ligand 1: H.183, H.204, H.213, F.367, H.371; metal interactions: A:H.183, A:H.204, A:H.213. Chain A for Ligand 2: H.337, H.341, F.367, H.370, H.371; metal interactions: A:H.337, A:H.341, A:H.371). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
Fig. 6. The 1800 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers
Fig. 6. The 1800 bp amplicon of full-length PPO cDNA obtained after deducing the 5′and 3′ ends through RACE analysis. Lane 1- 1 Kb DNA marker, Lane 2 and 3 the amplicon in duplicate after amplification using gene specific primers.
Analysis of Visual Pathways in Glaucoma Patients Using a 3tesla-MRI
ClinicalTrials.gov study NCT01621841. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Post-stroke Pathway: Analysis and Link With One Year Sequelae in a French Cohort of Stroke Patients
ClinicalTrials.gov study NCT03865173. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Landscape genomics and pathway analysis to understand genetic adaptation of South African indigenous goat populations
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Data from: Pathways of cryptic invasion in a fish parasite traced using coalescent analysis and epidemiological survey
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Transcriptomic analysis reveals potential candidate pathways and genes involved in toxin biosynthesis in true toads
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Data from: Making a queen: an epigenetic analysis of the robustness of the honey bee (Apis mellifera) queen developmental pathway
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Data from: Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways
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Data from: Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway
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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
<p><b>Objective: </b>To compare NHS organisations testing pathways for patients with suspected COVID-19 in the community versus standard hospital testing practices</p> <p><b>Perspective</b>: NHS commissioners and services</p> <p><b>Methods</b>: During the containment phase of the Covid-19 pandemic we developed a community model pathway for Covid-19 testing in Wales with testing teams undertaking swabbing for Covid-19 in individuals usual place of residence. We undertook a cost-minimisation analysis comparing the costs to the NHS in Wales of community testing for COVID-19 versus standard hospital testing practices and ambulance conveyancing. We analysed data from patients with suspected COVID-19 between January and February 2020 and applied assumptions of costs from national contractual and reference costs for ambulances, staffing and transportation with market costs at the time of publication.</p> <p><b>Results</b>: 177 patients with suspected COVID-19 underwent community testing via local NHS organisations between January and February 2020 with a mean age of 46.1 (IQR 27.5-56.3). This was 92% of total patients who were tested for Covid-19 during this period. We estimate, compared to standard hospital testing practices cash savings in improved productivity for the NHS of £152,190 during this time period, in addition to further non-monetised benefits for hospital and ambulance flow.</p> <p><b>Conclusions</b>: Community testing for COVID-19 in Wales is now an established pathway and continues to bring benefits for patients, local healthcare organisations and the NHS. Further application of this model in other settings and to other infectious diseases may herald promising returns.</p>
Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera
<p>Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific and dynamic patterns of evolution for hearing and sound producing organs. In the suborder Ensifera, we infer that forewing-based stridulation and tibial tympanal ears co-evolved, but in the suborder Caelifera, abdominal tympanal ears first evolved in a non-sexual context, and later co-opted for sexual signalling when sound producing organs evolved. However, we find little evidence that the evolution of hearing and sound producing organs increased diversification rates in those lineages with known acoustic communication.</p>
Data from: Range-wide population genomics of the Mexican fruit fly: towards development of pathway analysis tools
Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction-site associated DNA sequencing, and then developed and demonstrated a panel of highly-differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genome-wide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly-differentiated SNPs that were able to recreate the genome-wide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.
Data from: Auditory functional magnetic resonance imaging in dogs – normalization and group analysis and the processing of pitch in the canine auditory pathways
Background: Functional magnetic resonance imaging (fMRI) is an advanced and frequently used technique for studying brain functions in humans and increasingly so in animals. A key element of analyzing fMRI data is group analysis, for which valid spatial normalization is a prerequisite. In the current study we applied normalization and group analysis to a dataset from an auditory functional MRI experiment in anesthetized beagles. The stimulation paradigm used in the experiment was composed of simple Gaussian noise and regular interval sounds (RIS), which included a periodicity pitch as an additional sound feature. The results from the performed group analysis were compared with those from single animal analysis. In addition to this, the data were examined for brain regions showing an increased activation associated with the perception of pitch. Results: With the group analysis, significant activations matching the position of the right superior olivary nucleus, lateral lemniscus and internal capsule were identified, which could not be detected in the single animal analysis. In addition, a large cluster of activated voxels in the auditory cortex was found. The contrast of the RIS condition (including pitch) with Gaussian noise (no pitch) showed a significant effect in a region matching the location of the left medial geniculate nucleus. Conclusion: By using group analysis additional activated areas along the canine auditory pathways could be identified in comparison to single animal analysis. It was possible to demonstrate a pitch-specific effect, indicating that group analysis is a suitable method for improving the results of auditory fMRI studies in dogs and extending our knowledge of canine neuroanatomy.
Supplementary Spreadsheet S1. Canonical pathway using IPA analysis
<p>Supplementary Spreadsheet S1. Canonical pathway using IPA analysis</p>
Data from: Systems analysis of adaptive responses to MAP Kinase pathway blockade in BRAF mutant melanoma
Fifty percent of cutaneous melanomas are driven by activated BRAFV600E, but tumors treated with RAF inhibitors, even when they respond dramatically, rapidly adapt and develop resistance. Thus, there is a pressing need to identify the major mechanisms of intrinsic and adaptive resistance and develop drug combinations that target these resistance mechanisms. In a combinatorial drug screen on a panel of 12 treatment-naïve BRAFV600E mutant melanoma cell lines of varying levels of resistance to mitogen-activated protein kinase (MAPK) pathway inhibition, we identified the combination of PLX4720, a targeted inhibitor of mutated BRaf, and lapatinib, an inhibitor of the ErbB family of receptor tyrosine kinases, as synergistically cytotoxic in the subset of cell lines that displayed the most resistance to PLX4720. To identify potential mechanisms of resistance to PLX4720 treatment and synergy with lapatinib treatment, we performed a multi-platform functional genomics analysis to profile the genome as well as the transcriptional and proteomic responses of these cell lines to treatment with PLX4720. We found modest levels of resistance correlated with the zygosity of the BRAF V600E allele and receptor tyrosine kinase (RTK) mutational status. Layered over base-line resistance was substantial upregulation of many ErbB pathway genes in response to BRaf inhibition, thus generating the vulnerability to combination with lapatinib. The transcriptional responses of ErbB pathway genes are associated with a number of transcription factors, including ETS2 and its associated cofactors that represent a convergent regulatory mechanism conferring synergistic drug susceptibility in the context of diverse mutational landscapes.
Pan-cancer study on variants of canonical miRNA biogenesis pathway components: A pooled analysis
<p>Updated version of 10.5281/zenodo.7248080</p>
Pan-cancer study on variants of canonical miRNA biogenesis pathway components: A pooled analysis
<p>Supplementary Tables S30-S36</p>
Fig. 1 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers
Fig. 1. The proposed hypothetical pathway for catecholamine biosynthesis in Mucuna pruriens.
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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.