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  1. 1
    Visualization 1.mp4

    Visualization 1.mp4 by Ilya Golub (9402797)

    Published 2025
    Subjects: “…Optics Modes, Structured Light, and Beam Shaping…”
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  2. 2
    Visualization 2.mp4

    Visualization 2.mp4 by Ilya Golub (9402797)

    Published 2025
    Subjects: “…Optics Modes, Structured Light, and Beam Shaping…”
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  3. 3
    Visualization 3.mp4

    Visualization 3.mp4 by Ilya Golub (9402797)

    Published 2025
    Subjects: “…Optics Modes, Structured Light, and Beam Shaping…”
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  4. 4
    Visualization 4.mp4

    Visualization 4.mp4 by Ilya Golub (9402797)

    Published 2025
    Subjects: “…Optics Modes, Structured Light, and Beam Shaping…”
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  5. 5
    A. Mouse transcriptome non-negative matrix factorization component weights across all time points and conditions. Larger weight values indicate components with upregulated genes dominating. B. Gene set enrichment plot for selected features from each component in panel A. Components 1, 4, and 5 did not exhibit enrichment in these broad terms. C. Number of genes in enriched gene ontology terms related to immunity, signaling, and transcription for each time point and condition. D. Time course transcriptional profiles for mouse genes characteristic to component 3. E. PARFA-seq validation by quantitative PCR and gene expression changes during immortalized bone marrow-derived macrophage infection by <i>T. gondii</i> assessed by quantitative PCR.

    A. Mouse transcriptome non-negative matrix factorization component weights across all time points and conditions. Larger weight values indicate components with upregulated genes do... by Dominykas Murza (22676289)

    Published 2025
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  6. 6
    A. <i>T. gondii</i> gene group changes throughout the time course, expressed as log<sub>2</sub>(fold change) relative to pre-infection tachyzoites (t = 0). Grey area depicts the 95% confidence interval. n value refers to number of genes detected in each group. B. Gene set enrichment plot for most enriched terms from <i>T. gondii</i> transcriptome features at 15 min to 120 min. Five most significant terms are displayed for each database. C and D. Transcriptional profiles of top five upregulated and downregulated <i>T. gondii</i> transcription factors, respectively.

    A. <i>T. gondii</i> gene group changes throughout the time course, expressed as log<sub>2</sub>(fold change) relative to pre-infection tachyzoites (t = 0). Grey area depicts the 95... by Dominykas Murza (22676289)

    Published 2025
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  7. 7
    Oligonucleotides used in this study.

    Oligonucleotides used in this study. by Dominykas Murza (22676289)

    Published 2025
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  8. 8
    A. Library preparation strategy: poly-A(+) RNAs are captured by complementarity to reverse transcription primer, then second strand is synthesized using random hexamers and handles for sequencing are attached through two rounds of PCR. B. Mapped read distribution by species and by biotype. C and D. Principal component analysis of mouse and <i>T. gondii</i> transcriptomes, respectively. E and F. Volcano plots of Live <i>Toxoplasma</i>-infected mouse and <i>T. gondii</i> time points, respectively. To calculate Log<sub>2</sub>(Fold change), every timepoint is compared to corresponding samples (either macrophage or <i>Toxoplasma</i>) before infection (t = 0 min). Most significant and most upregulated transcripts are labelled. Number of significantly (p ≤ 0.05) downregulated and upregulated genes for each time point is given in blue and red, respectively. In F, 24-hour time point, red dots mark ROP

    A. Library preparation strategy: poly-A(+) RNAs are captured by complementarity to reverse transcription primer, then second strand is synthesized using random hexamers and handles... by Dominykas Murza (22676289)

    Published 2025
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  9. 9
    A. Experimental scheme of infection time course and downstream workflow; B. Optimization of tachyzoite concentration to achieve adequate infection rates, with a threshold set at 50% infection efficiency. Error bars represent ± 1 standard deviation. Corresponding MOI values are given for each condition; C. Infection time course micrograph merged from brightfield and green channels. <i>T. gondii</i> exhibits green fluorescence due to stable GFP expression in the strain used. Percentage at the top left indicates infection efficiency (± 1 standard deviation) for each time point.

    A. Experimental scheme of infection time course and downstream workflow; B. Optimization of tachyzoite concentration to achieve adequate infection rates, with a threshold set at 50... by Dominykas Murza (22676289)

    Published 2025
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  10. 10
    Summary of all significant gene enrichment terms for every condition (as combination of sample type and timepoint).

    Summary of all significant gene enrichment terms for every condition (as combination of sample type and timepoint). by Dominykas Murza (22676289)

    Published 2025
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  11. 11
    Impact of different substitution rate category parameters on cluster inference in different mixture datasets.

    Impact of different substitution rate category parameters on cluster inference in different mixture datasets. by August Guang (9975678)

    Published 2025
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  12. 12
    Rates of different base frequencies from different mixture datasets.

    Rates of different base frequencies from different mixture datasets. by August Guang (9975678)

    Published 2025
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  13. 13
    Rates of different gamma relative rate categories from different mixture datasets.

    Rates of different gamma relative rate categories from different mixture datasets. by August Guang (9975678)

    Published 2025
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  14. 14
    Principle Coordinates Analysis (PCoA) projected onto 2 dimensions between pol-wgs mixtures and nFL genome, subset dataset

    Principle Coordinates Analysis (PCoA) projected onto 2 dimensions between pol-wgs mixtures and nFL genome, subset dataset by August Guang (9975678)

    Published 2025
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  15. 15
    Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset.

    Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, full dataset. by August Guang (9975678)

    Published 2025
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  16. 16
    Principle Coordinates Analysis (PCoA) projected onto 2 dimensions between pol-wgs mixtures and nFL genome, full dataset

    Principle Coordinates Analysis (PCoA) projected onto 2 dimensions between pol-wgs mixtures and nFL genome, full dataset by August Guang (9975678)

    Published 2025
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  17. 17
    Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, subset dataset.

    Proportion of clusters recovered between different mixtures of pol and wgs sequences and all wgs based on overlap coefficient, subset dataset. by August Guang (9975678)

    Published 2025
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  18. 18
    Phylogenetic distance between partial pol-wgs mixtures and nFL genome for subset dataset.

    Phylogenetic distance between partial pol-wgs mixtures and nFL genome for subset dataset. by August Guang (9975678)

    Published 2025
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  19. 19
    Adjusted mutual information (AMI) boxplot between phylogenetic clustering of different mixtures of pol and wgs sequences and all wgs, full dataset.

    Adjusted mutual information (AMI) boxplot between phylogenetic clustering of different mixtures of pol and wgs sequences and all wgs, full dataset. by August Guang (9975678)

    Published 2025
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  20. 20
    Phylogenetic distance between partial pol-wgs mixtures and nFL genome for full dataset.

    Phylogenetic distance between partial pol-wgs mixtures and nFL genome for full dataset. by August Guang (9975678)

    Published 2025
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