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deidentified clinformatics data mart database cdm  (Optum Inc)

 
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    Optum Inc deidentified clinformatics data mart database cdm
    Deidentified Clinformatics Data Mart Database Cdm, supplied by Optum Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/deidentified clinformatics data mart database cdm/product/Optum Inc
    Average 86 stars, based on 1 article reviews
    deidentified clinformatics data mart database cdm - by Bioz Stars, 2026-05
    86/100 stars

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    Amino acid auxotrophy experiments of E. faecium DO. (A) Mean final optical density (OD) of E. faecium DO in the absence of single amino acids from the <t>CDM-LAB.</t> Bar chart showing final mean OD values after 24 hours incubation. Each bar represents the mean OD of three biological replicates ± SD for a condition where single amino acid was omitted. Cultures with a final OD < 0.1 are marked in red; those with a final OD > 0.3 are marked in blue; and ambiguous growth (OD between 0.1 and 0.3) is color-coded in green. A repeated one-way ANOVA test was performed to compare growth (final average OD 600 ) across amino acid omissions. Results were significantly different ( p value = 0.0024, ≤ 0.05). This was followed by Tukey’s multiple comparisons post hoc test. (B) Repeated passaging of cultures grown in the absence of lysine, phenylalanine, and tyrosine, respectively, results in adaptation to omissions. (C) Individual comparison of each amino acid between the experimental results of the amino acid leave-out experiments (EXP) and the simulation results of the model iDR479 (GEM). Purple squares indicate growth, and green squares indicate no-growth
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    Amino acid auxotrophy experiments of E. faecium DO. (A) Mean final optical density (OD) of E. faecium DO in the absence of single amino acids from the CDM-LAB. Bar chart showing final mean OD values after 24 hours incubation. Each bar represents the mean OD of three biological replicates ± SD for a condition where single amino acid was omitted. Cultures with a final OD < 0.1 are marked in red; those with a final OD > 0.3 are marked in blue; and ambiguous growth (OD between 0.1 and 0.3) is color-coded in green. A repeated one-way ANOVA test was performed to compare growth (final average OD 600 ) across amino acid omissions. Results were significantly different ( p value = 0.0024, ≤ 0.05). This was followed by Tukey’s multiple comparisons post hoc test. (B) Repeated passaging of cultures grown in the absence of lysine, phenylalanine, and tyrosine, respectively, results in adaptation to omissions. (C) Individual comparison of each amino acid between the experimental results of the amino acid leave-out experiments (EXP) and the simulation results of the model iDR479 (GEM). Purple squares indicate growth, and green squares indicate no-growth

    Journal: bioRxiv

    Article Title: The first digital twin of Enterococcus faecium metabolism reproduces high-throughput phenotyping data

    doi: 10.64898/2026.05.01.720924

    Figure Lengend Snippet: Amino acid auxotrophy experiments of E. faecium DO. (A) Mean final optical density (OD) of E. faecium DO in the absence of single amino acids from the CDM-LAB. Bar chart showing final mean OD values after 24 hours incubation. Each bar represents the mean OD of three biological replicates ± SD for a condition where single amino acid was omitted. Cultures with a final OD < 0.1 are marked in red; those with a final OD > 0.3 are marked in blue; and ambiguous growth (OD between 0.1 and 0.3) is color-coded in green. A repeated one-way ANOVA test was performed to compare growth (final average OD 600 ) across amino acid omissions. Results were significantly different ( p value = 0.0024, ≤ 0.05). This was followed by Tukey’s multiple comparisons post hoc test. (B) Repeated passaging of cultures grown in the absence of lysine, phenylalanine, and tyrosine, respectively, results in adaptation to omissions. (C) Individual comparison of each amino acid between the experimental results of the amino acid leave-out experiments (EXP) and the simulation results of the model iDR479 (GEM). Purple squares indicate growth, and green squares indicate no-growth

    Article Snippet: Model validation for carbon source utilization was conducted via growth simulation in a CDM-LAB containing all AAs but lacking glucose, which exactly mirrors the conditions of experimental Biolog carbon utilization assays.

    Techniques: Incubation, Passaging, Comparison

    Color-coded matrix with the predicted essential genes in defined medium and rich medium and their corresponding subsystem (B) Venn diagram illustrating the shared/unique essential genes between the two conditions (defined and rich medium). (C) Comparison between gene essentiality results in iDR479 model and experimental data in a simulated rich medium (when all the exchanges are open), the model achieved 86.7% concordance compared with the experimental results of Tn-seq study of MDR E. faecalis MMH594. (D) Comparison between gene essentiality results in iDR479 model and experimental data in a defined medium (CDM-LAB), the model achieved 74.1% concordance compared with the experimental results of Tn-seq study of MDR E. faecalis MMH594.

    Journal: bioRxiv

    Article Title: The first digital twin of Enterococcus faecium metabolism reproduces high-throughput phenotyping data

    doi: 10.64898/2026.05.01.720924

    Figure Lengend Snippet: Color-coded matrix with the predicted essential genes in defined medium and rich medium and their corresponding subsystem (B) Venn diagram illustrating the shared/unique essential genes between the two conditions (defined and rich medium). (C) Comparison between gene essentiality results in iDR479 model and experimental data in a simulated rich medium (when all the exchanges are open), the model achieved 86.7% concordance compared with the experimental results of Tn-seq study of MDR E. faecalis MMH594. (D) Comparison between gene essentiality results in iDR479 model and experimental data in a defined medium (CDM-LAB), the model achieved 74.1% concordance compared with the experimental results of Tn-seq study of MDR E. faecalis MMH594.

    Article Snippet: Model validation for carbon source utilization was conducted via growth simulation in a CDM-LAB containing all AAs but lacking glucose, which exactly mirrors the conditions of experimental Biolog carbon utilization assays.

    Techniques: Comparison