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Redoxin systems and their measurement  In the thioredoxin system, oxidized ...
Published: 15 February 2024
Figure 1 Redoxin systems and their measurement In the thioredoxin system, oxidized thioredoxin (TrxSS) is reduced by thioredoxin reductase (TR) and upon reduction (TrxSH) can then reduce protein disulfides (PSS) ( A ). In the GSH/glutaredoxin system ( B ), disulfides and glutathionylated proteins... More about this image found in Redoxin systems and their measurement In the thioredoxin system, oxidized ...
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Redoxin redox states and rates are interlinked  The fluxes (or rates) throu...
Published: 15 February 2024
Figure 2 Redoxin redox states and rates are interlinked The fluxes (or rates) through redoxin systems, and the reduced and oxidized redoxin isoforms, are usually not measured together in experimental studies. However, computational models for the thioredoxin system ( A ) [ 90 ], GSH/glutaredoxin ... More about this image found in Redoxin redox states and rates are interlinked The fluxes (or rates) throu...
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Computational models can enhance the analyses of redoxin systems  Computati...
Published: 15 February 2024
Figure 3 Computational models can enhance the analyses of redoxin systems Computational approaches integrate and organize in vitro and cellular data on redoxin systems into quantitative models of these systems. These models can be used to analyze these data, clarify contradictions, and generate... More about this image found in Computational models can enhance the analyses of redoxin systems Computati...
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Network structure for metabolic oscillations  A schematic representation fo...
Published: 11 January 2024
Figure 1 Network structure for metabolic oscillations A schematic representation for the glycolytic pathway (blue arrows), its co-factors, and the link to oxidative metabolism (red arrows). The schema represents the yeast case; in muscle and cancer cells pyruvate is reduced to lactate. More about this image found in Network structure for metabolic oscillations A schematic representation fo...
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ATP versus F6P phase plane plot of models and experimental data of glycolyt...
Published: 11 January 2024
Figure 2 ATP versus F6P phase plane plot of models and experimental data of glycolytic oscillations in yeast cells Black dots and circles indicate experimental data reported in [ 1 ] (Richard) and [ 18 ] (Eschrich) respectively. The solid grey line shows the trajectory according to the fitted sin... More about this image found in ATP versus F6P phase plane plot of models and experimental data of glycolyt...
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ATP versus NADH phase plane plot of models and experimental data of glycoly...
Published: 11 January 2024
Figure 3 ATP versus NADH phase plane plot of models and experimental data of glycolytic oscillations in yeast cells Black dots indicate experimental data from [ 1 ]. Coloured curves were obtained by simulating the indicated models as available from the JWS Online model database [ 73 , 74 ]. Model... More about this image found in ATP versus NADH phase plane plot of models and experimental data of glycoly...
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Exemplary overview of LC-MS mechanism and resulting mass chromatogram  In t...
Published: 24 November 2023
Figure 1 Exemplary overview of LC-MS mechanism and resulting mass chromatogram In the chromatographic separation (top left) a mixture of compounds, represented by the different colors, elutes through the column. The differential interactions of the compounds with the mobile and stationary phases ... More about this image found in Exemplary overview of LC-MS mechanism and resulting mass chromatogram In t...
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Diagram representing tandem MS experiments  Diagram representing tandem MS ...
Published: 24 November 2023
Figure 2 Diagram representing tandem MS experiments Diagram representing tandem MS experiments in ( A ) DDA, and ( B ) DIA modes. The different geometric forms in the isolation chart represent a mixture of different ion populations and how they are transferred through the device on the different ... More about this image found in Diagram representing tandem MS experiments Diagram representing tandem MS ...
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Ordinal, nominal and binary factor (categorical) variables  Binary factor v...
Published: 25 October 2023
Figure 1 Ordinal, nominal and binary factor (categorical) variables Binary factor variables are a special case which may be consider either ordinal or nominal depending on the variable. Artwork by @allison_horst. More about this image found in Ordinal, nominal and binary factor (categorical) variables Binary factor v...
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Boxplot of taster genotype and weekly coffee consumption (cups per week)  t...
Published: 25 October 2023
Figure 6 Boxplot of taster genotype and weekly coffee consumption (cups per week) tt genotype represents non-tasters, Tt weak tatsers and TT strong tasters for thiourea-containing compounds More about this image found in Boxplot of taster genotype and weekly coffee consumption (cups per week) t...
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Density plot of a normal distribution  The  Z -value ( Z -score) is the num...
Published: 25 October 2023
Figure 8 Density plot of a normal distribution The Z -value ( Z -score) is the number of standard deviations a value departs from the mean, so the mean has a value of zero. Vertical dashed lines highlight one standard deviation above and below the mean. Vertical solid lines highlight two standa... More about this image found in Density plot of a normal distribution The Z -value ( Z -score) is the num...
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Histograms of 1000 observations sampled from three distributions commonly o...
Published: 25 October 2023
Figure 9 Histograms of 1000 observations sampled from three distributions commonly observed in biology with their parameters stated above each plot First a normal histogram with mean of 10 and standard deviation of 2, second a Poisson distribution with mean of 3 and finally a Bernoulli (binary) ... More about this image found in Histograms of 1000 observations sampled from three distributions commonly o...
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Diagram showing how total variation (sums of squares) in our response varia...
Published: 25 October 2023
Figure 11 Diagram showing how total variation (sums of squares) in our response variable is partitioned between what can be explained by our explanatory variable and what is left unexplained The variation we explain can be added to the variation left unexplained to calculate total variation. Thi... More about this image found in Diagram showing how total variation (sums of squares) in our response varia...
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Diagram showing how total variation (sums of squares) in our response varia...
Published: 25 October 2023
Figure 12 Diagram showing how total variation (sums of squares) in our response variable is partitioned between what can be explained by our explanatory variable and what is left unexplained First, the variation in our response variable is calculated by sum of squares (Total SS), the deviance fo... More about this image found in Diagram showing how total variation (sums of squares) in our response varia...
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Visual illustration of how a General Linear Model works with a numerical ex...
Published: 25 October 2023
Figure 13 Visual illustration of how a General Linear Model works with a numerical explanatory variable (regression), i.e. quantifying whether variation in coffee consumption can be explained by age First, the variation in our response variable is calculated by sums of squares (Total SS), the de... More about this image found in Visual illustration of how a General Linear Model works with a numerical ex...
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Illustrative plot of how coefficients are estimated by the GLM  The numeric...
Published: 25 October 2023
Figure 16 Illustrative plot of how coefficients are estimated by the GLM The numerical coefficients shown have been taken directly from the summary output of the model shown in Figure 15 . More about this image found in Illustrative plot of how coefficients are estimated by the GLM The numeric...
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The structure of our model showing the linear equation and replacing with c...
Published: 25 October 2023
Figure 17 The structure of our model showing the linear equation and replacing with coefficients from our model to predict mean weekly coffee consumption for each TAS2R38 taster genotype The top row shows the general structure of a model with a three-level factor explanatory variable, the middle... More about this image found in The structure of our model showing the linear equation and replacing with c...
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Histogram of the residuals from our General Linear Model  They should be no...
Published: 25 October 2023
Figure 19 Histogram of the residuals from our General Linear Model They should be normally distributed and appear similar to a bell-shaped curve. Our residuals are not perfectly normally distributed, but they are fairly evenly spread around a central peak at zero and we could conclude they are f... More about this image found in Histogram of the residuals from our General Linear Model They should be no...
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Main immunomodulatory mechanisms elicited by RT in the TME  Focal radiation...
Published: 28 September 2023
Figure 1 Main immunomodulatory mechanisms elicited by RT in the TME Focal radiation therapy (RT) has been shown to impose various immunologically relevant changes to the tumor microenvironment (TME) that may influence local and systemic cancer control. ( A ) On the one hand, focal RT has been sho... More about this image found in Main immunomodulatory mechanisms elicited by RT in the TME Focal radiation...
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Relationships between T cell subsets in the TME and tdLN  Naïve T cells are...
Published: 28 September 2023
Figure 1 Relationships between T cell subsets in the TME and tdLN Naïve T cells are activated in the tdLN expressing PD-1 while maintaining expression of TCF7 in a partially activated, stem-like state. These stem-like T cells migrate to the TME inhabiting cDC rich niches where further stimulation... More about this image found in Relationships between T cell subsets in the TME and tdLN Naïve T cells are...
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Models for TAM polarization  The dichotomy of the conventionally defined ‘M...
Published: 28 September 2023
Figure 1 Models for TAM polarization The dichotomy of the conventionally defined ‘M1’ and ‘M2’ macrophage polarization program, as pro- (M1) and anti- (M2) inflammatory stages of their phenotypic program, has served as a valuable framework for understanding and classifying the extremes of TAM phe... More about this image found in Models for TAM polarization The dichotomy of the conventionally defined ‘M...
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Evidence of TAM heterogeneity and nest formation in the Pv niche  Represent...
Published: 28 September 2023
Figure 2 Evidence of TAM heterogeneity and nest formation in the Pv niche Representative image of a frozen section of tumor from the spontaneous MMTV-PyMT murine model of breast cancer [ 66 ], stained with DAPI (nuclei;blue) and antibodies against F4/80 (magenta), LYVE-1 (red) and CD31 (green).... More about this image found in Evidence of TAM heterogeneity and nest formation in the Pv niche Represent...
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Development of PvTAMs  Summary of the developmental pathways of PvTAMs high...
Published: 28 September 2023
Figure 3 Development of PvTAMs Summary of the developmental pathways of PvTAMs highlighted in the manuscript text. TIE2 + PvTAMs can arise from TIE2 expressing monocytes recruited from the peripheral blood. TIE2 + PvTAMs are retained in the Pv niche through their interaction with angiopoietin-2... More about this image found in Development of PvTAMs Summary of the developmental pathways of PvTAMs high...
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PvTAM functions in the TME  Summary of the functions of PvTAMs highlighted ...
Published: 28 September 2023
Figure 4 PvTAM functions in the TME Summary of the functions of PvTAMs highlighted in the manuscript text. PvTAMs can facilitate intravasation of Mena + tumor cells into the circulation, where PvTAMs express EGF and tumor cells express CSF1 and participate in a cross-communication axis, which re... More about this image found in PvTAM functions in the TME Summary of the functions of PvTAMs highlighted ...
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A typical immunopeptidomics-based neoantigen discovery workflow  Tumour-spe...
Published: 28 September 2023
Figure 1 A typical immunopeptidomics-based neoantigen discovery workflow Tumour-specific mis-sense variants are identified by comparative whole exome sequencing of tumour tissue samples. Variant gene transcripts may be confirmed by RNAseq, then neoantigens are predicted using HLA typing data and ... More about this image found in A typical immunopeptidomics-based neoantigen discovery workflow Tumour-spe...
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Graphical representation of reported changes to function of CD4 +  T cells,...
Published: 28 September 2023
Figure 1 Graphical representation of reported changes to function of CD4 + T cells, CD8 + T cells, and DCs in response to αPD-L1 immunotherapy Distinct from direct effect on CD8 + T cells, immunotherapy can act via CD4 + T cells and DCs to support CD8 + T-cell function via cytokine productio... More about this image found in Graphical representation of reported changes to function of CD4 + T cells,...
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Graphical representation showing how αPD-L1 immunotherapy can modulate intr...
Published: 28 September 2023
Figure 2 Graphical representation showing how αPD-L1 immunotherapy can modulate intratumoural CD8 + T-cell differentiation during treatment Ineffective response may be a result of poor pre-existing response or previous terminal differentiation. Presence of less-differentiated T PEX cells allows... More about this image found in Graphical representation showing how αPD-L1 immunotherapy can modulate intr...
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An overview  of  the IFN-γ signalling pathway  The IFN-γ receptor (IFNGR), ...
Published: 28 September 2023
Figure 1 An overview of the IFN-γ signalling pathway The IFN-γ receptor (IFNGR), a heterodimer of IFNGR1 and IFNGR2, is expressed on the surface of almost all cell types. After IFN-γ binds to IFNGR, it induces the activation of Janus kinase (JAK) 1 and JAK2 while EHBP1L1 is responsible for stab... More about this image found in An overview of the IFN-γ signalling pathway The IFN-γ receptor (IFNGR), ...
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Different mechanisms elicited by IFN-γ to promote resistance to ICBT  IFN-γ...
Published: 28 September 2023
Figure 2 Different mechanisms elicited by IFN-γ to promote resistance to ICBT IFN-γ drives tumour cell dedifferentiation by either up-regulating its stemness or downregulating its neoantigen expression. IFN-γ feedback loops become dysregulated, by either overexpressing the negative regulators LNK... More about this image found in Different mechanisms elicited by IFN-γ to promote resistance to ICBT IFN-γ...
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Current pharmacological approaches to reverse IFN-γ-driven resistance to IC...
Published: 28 September 2023
Figure 3 Current pharmacological approaches to reverse IFN-γ-driven resistance to ICBT Amplifying antigen presentation can be applied to upregulate tumour MHC-I, double-stranded RNA sensing, and NF-κB signalling to augment the T-cell anti-tumour response. Inhibiting TCIRs by JAK1/JAK2 inhibitor (... More about this image found in Current pharmacological approaches to reverse IFN-γ-driven resistance to IC...
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Regulation of NK cell responses against target cells  ( A ) Natural killer ...
Published: 28 September 2023
Figure 1 Regulation of NK cell responses against target cells ( A ) Natural killer (NK) cells express various receptors that transmit activation (A) or inhibitory (I) signals. NK cell response to target cells (being tolerant or triggering apoptosis) is determined by the overall levels of each sig... More about this image found in Regulation of NK cell responses against target cells ( A ) Natural killer ...
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Activation of NK cells by macrophages  Tumour-associated macrophages (TAMs)...
Published: 28 September 2023
Figure 2 Activation of NK cells by macrophages Tumour-associated macrophages (TAMs), tissue-resident macrophages (TRMs) and monocyte-derived macrophages (MDMs) repolarize upon stimulation with IFNγ and/or toll-like receptor (TLR) ligands such as poly I:C and lipopolysaccharide (LPS). Repolarized ... More about this image found in Activation of NK cells by macrophages Tumour-associated macrophages (TAMs)...
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Suppression of NK cells by macrophages  ( A ) Short-term interaction with T...
Published: 28 September 2023
Figure 3 Suppression of NK cells by macrophages ( A ) Short-term interaction with TAMs expressing activating ligands (RAE1, CD48) promotes NK cell activation via activating receptors such as NKG2D and 2B4 (left). However, persistent engagement causes downregulation of activating receptors in NK c... More about this image found in Suppression of NK cells by macrophages ( A ) Short-term interaction with T...
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Current TAM-targeting strategies that potentially enhance NK cell function ...
Published: 28 September 2023
Figure 4 Current TAM-targeting strategies that potentially enhance NK cell function Anti-tumour efficacy of therapeutically infused NK cells could be enhanced by combining with TAM targeting, such as depletion, reprogramming, and disarming (i.e., blocking inhibitory ligands in TAMs). Tables show ... More about this image found in Current TAM-targeting strategies that potentially enhance NK cell function ...
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