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0.40543 | e87a84dea201461f966dc9b17e819b7a | 2wT flow diagram for ART retention [43] | PMC9882492 | nihpp-2023.01.09.23284326v1-f0001.jpg |
0.549558 | c64b95943a4f43dca6806bce937c2a55 | 2wT actions completed by HCWs | PMC9882492 | nihpp-2023.01.09.23284326v1-f0002.jpg |
0.420084 | 82493d56c4fc4fc5b619e1563eb70026 | Experiment design and tasks flow | PMC9883942 | 12909_2022_3996_Fig1_HTML.jpg |
0.45339 | 9e44f260ca9f41cbbe2262e911203024 | Information about ROH, inbreeding coefficient (FROH), LD decay, and effective population size. A The number of ROH segments in different length categories. B The distribution of the length and number of ROH in different individual. The X-axis denotes the number of ROHs per chromosome and the Y-axis represents the average percentage (%) of each chromosome covered by ROH (red lines). C Violin plot of genomic inbreeding coefficient in two sheep populations. D Linkage disequilibrium decay (LD decay) in two breeds. E Estimated effective population sizes (Ne) over time for two breeds. F Analysis of common genes of two Tibetan sheep breeds ROH island | PMC9883975 | 12864_2023_9146_Fig1_HTML.jpg |
0.432569 | c03894958efb4de2ac223a797c8e0cc1 | Manhattan plot of incidence of each SNP in the ROH across individuals. The abscissa represents the chromosome number of sheep and the dashed line represents the 35% threshold | PMC9883975 | 12864_2023_9146_Fig2_HTML.jpg |
0.431778 | 4cebf41d4e0c438183bd9ae3b2895959 | Population relationship and structural analysis of OL sheep and PO sheep varieties. A Principal component analysis was performed on 20 sheep. B Maximum likelihood tree reconstruction using RAxML and GTRGAMMA models. C Whole-genome mixing ratio of K = 2 in 20 sheep of two breeds | PMC9883975 | 12864_2023_9146_Fig3_HTML.jpg |
0.393549 | ea6c47f523224b58bbb76dde859ff2d9 | Analysis of the signatures of positive selection in the genome of samples. Genomic landscape of the Fst values and π ratio values. A Using Fst and π ratio methods to determine the genomic Manhattan selection feature map and global map of selection signals. B&C GO and KEGG heatmap selected analyzed by Fst and π ratio. The top 1% was chosen as the significant threshold for Fst and π ratio. D The venn map of selected genes combining Fst and π ratio with the parameters determined by top1% | PMC9883975 | 12864_2023_9146_Fig4_HTML.jpg |
0.416183 | 8c547777f8104b0ea71e7eaf894078ba | Methionine sulfoxidation impairs TDP-43’s PLD phase separation by reshaping its structure.A Cartoon representation of the domain architecture of TDP-43 (top). The disordered PLD (region 274–414) is represented by a purple line. PLD primary structure, with the Met residues highlighted in red (bottom). The double α-helices are limited by orange boxes. B Turbidity measurements showing concentration- and salt-dependent LLPS for the PLD. C Differential Interference Contrast (DIC) microscopy images showing liquid condensates formed by the PLD in the specified conditions. Scale bars correspond to 25 μM. D LLPS of MetO PLD in the corresponding samples (circles), compared to unmodified PLD (gray stars), as measured by the area under the turbidity curves after 24 h of incubation. Gray broken line corresponds to the averaged LLPS of unmodified PLD. E Detailed region of the overlay of the 15N-HSQC spectra from de-mixed PLD (purple) and MetO PLD (green) showing the large shifts for the Met moieties upon methionine sulfoxidation. MetO cross peaks are highlighted in red. F Comparison of the NMR signal intensity of unmodified PLD (purple) and MetO PLD (green) upon de-mixing shows a reduced broadening in the region 305-345 for MetO PLD. The preceding region (280–305) is also partially broadened in both proteins. The plot at the bottom shows the hydrophobicity of the PLD. G Secondary chemical shifts (ΔCα-ΔCβ) analysis for 300 μM PLD (top), 25 μM PLD (middle), and 300 μM MetO PLD (bottom). In these plots, positive values indicate acquisition of α-helical conformations, while negative values correspond to β-strand structures. Each plot shows the overlay with the structural propensities at 300 μM (broken purple line) for comparison. The schematic cartoon at the top highlights the two α-helices (in cylinders) and β-strands (arrows) formed in the PLD. Met residues are located with asterisks. For clarity, Met residues were removed from the MetO PLD plot (bottom) due to the strong shifts upon oxidation (Supplementary Fig. 5B). Unless otherwise stated, turbidimetry and microscopy samples (B–D) contained 150 mM KCl. NaCl in B–D refers to 150 mM NaCl. NMR samples (E–G) contained 10 mM KCl. | PMC9884275 | 41467_2023_36023_Fig1_HTML.jpg |
0.398181 | 4e24efbf0a7b46f2a7e328ff571d170c | MetO PLD forms distinct fibrillar aggregates.A Amyloid aggregation kinetics as measured by ThT fluorescence. Samples contained either 150 mM KCl or 150 mM NaCl, as noted. B Representative electron micrographs showing fibrils formed by 50 μM PLD and MetO PLD aged for 20 days. Scale bars correspond to 200 nm. C Atomic force microscopy topographic characterization of the fibrils formed by 100 μM PLD (left) and 100 μM MetO PLD (right) samples aged for 4 months. PLD fibrils show variable diameters along their length. Scale bars correspond to 400 nm. Heat-color height scale is 5 nm. Samples in B and C contained 150 mM KCl. | PMC9884275 | 41467_2023_36023_Fig2_HTML.jpg |
0.431045 | 520664a8b04f4a83b5f6e7dd26473bd2 | Methionine sulfoxidation promotes significant disorder in the PLD.A Longitudinal (R1, top), transverse (R2, middle) rate constants, and heteronuclear (1H)-15N NOE (bottom) relaxation parameters were obtained for MetO PLD309 at 600 MHz. The values of all relaxation parameters indicate that the protein is highly dynamic. B Secondary chemical shifts (ΔCα-ΔCβ) for MetO PLD309. C J-coupling assessment of the secondary structure propensities for MetO PLD309. Values around 4 Hz indicate α-helix formation, while values around 8 Hz are typical of β-strand structures. D Structural ensemble of the 20 conformers of MetO PLD309 with the lowest conformational energy as calculated by CYANA (left), compared to the ensemble of ten conformers of a comparable PLD fragment (PDB code 2n3x, right). The lowest energy structure is displayed on top of the corresponding ensemble, with the rest of the conformers shown in transparent representation. Structures were aligned onto the structured elements. Met residues are highlighted in red stick representation. Gray broken lines in A, B plots indicate the boundaries of the two α-helices present in the PLD, while light red bars mark the location of Met residues. Diagrams on top of the plots (A, B) represent the α-helix formed in MetO PLD309 (green cylinder). | PMC9884275 | 41467_2023_36023_Fig3_HTML.jpg |
0.442972 | 82ae9b32689d4a1d9f9adfabeba04e34 | The interplay with chaperones and co-chaperones is mediated by the double α-helix of the PLD.A Turbidity measurements of the PLD in presence of the indicated chaperones (all in 1:2 molar ratios). Error bars are not included in the PLD plot (black dots) for clarity. B DIC microscopy image of the condensates formed by 20 μM PLD in complex with HSP72 after 48 h of incubation at 25 °C. C NMR signal intensity plots of 25–35 μM PLD in complex with the indicated chaperones (all in 1:2 molar ratios). For comparison, the plots are overlaid with the data corresponding to de-mixed PLD (300 μM PLD, broken purple line, Fig. 1F) and HSP72 interaction (orange broken line). D NMR intensity plots for MetO PLD in the presence of the chaperones (green bars) in comparison to the unmodified PLD:chaperone interactions in identical molar ratios (broken lines). E LLPS of 20 μM PLD in the presence of HSP72 and/or JDPs represented as the area under the curve of the turbidity measurements after 24 h. Vertical broken lines separate the three JDP classes (A, B, and C, indicated on top). F DIC microscopy image of the condensates formed by 20 μM PLD in complex with HSP72:DNAJB1 after 3 h of incubation at 25 °C. G NMR signal intensity plots for the interaction of 25–35 μM PLD with JDPs (all in 1:2 molar ratios). In each plot, the broken line represents the interaction of the PLD with HSP72 and the corresponding JDPs (all in 1:2:2 molar ratios). H LLPS of 20 μM PLD in presence of HSP90 and the specified co-chaperones as measured by turbidity. I LLPS of 20 μM MetO PLD in the presence of the specified chaperones and co-chaperones. For simplicity, the plots in C, D, and G show the reverse of the NMR signal decay. The gray broken line in E, H, and I represents the average turbidity of 20 μM PLD, for comparison. Scale bars (B, F) correspond to 25 μM. Turbidimetry and microscopy samples (A, B, E, F, H, I) contained 150 mM KCl, whereas NMR samples (C, D, G) contained 10 mM KCl. | PMC9884275 | 41467_2023_36023_Fig4_HTML.jpg |
0.45935 | eb45e4f8091145b6b1f37cfeadd297c1 | MetO impairs CK1δ phosphorylation.A Western blot immunoblotting results for the phosphorylation of the PLD using pS410 (bottom) antibody. CK1δ incubation times are indicated. Band at 14 kDa corresponds to unphosphorylated PLD, and phosphorylation is revealed as an increase in the molecular weight. On top, the same samples are subjected to SDS-PAGE, for comparison. Phosphorylated PLD is undetected in the gel due to aggregation. MetO samples are noticeably detained during migration in the gel. B NMR signal intensity decay plots after 24 h of incubation at 25 °C for 40 μM phosphoPLD (top) and phospho MetO PLD (bottom). The decay in intensity observed in phosphoPLD is attributed to sample precipitation. Broken gray lines locate Ser resides and golden lines locate Met residues. C Kinetics of amyloid fibril formation as measured by ThT fluorescence for 20 μM PLD samples. D Reverse of the NMR intensity plots for 40 μM phosphoPLD (bottom, blue) and phospho MetO PLD (top, magenta) in the presence of HSP72 (all in 1:2 molar ratios). For comparison, the plots are overlaid to the data for PLD:HSP72 interaction (bottom, orange line, corresponding to Fig. 4C) and MetO PLD:HSP72 (top, green line, corresponding to Fig. 4D) in identical molar ratios. | PMC9884275 | 41467_2023_36023_Fig5_HTML.jpg |
0.390931 | fcff99f033db426b93a4a2a045ed58d8 | Mechanistic model for the role of the modifications in the PLD in TDP-43 pathogenicity.TDP-43 PLD phase separation is strictly controlled by HSP70 and JDPs, whose interaction is mediated by structured elements present in the PLD. A liquid-to-solid transition will promote aggregate and fibril formation. Under oxidative stress, methionine sulfoxidation of the PLD will promote structural changes that will abrogate chaperone control and impact PLD phase separation, leading to the formation of alternative mature amyloid fibrils. While CK1δ phosphorylation promotes the aggregation of the PLD and hampers its recognition by HSP70, phosphorylation of soluble PLD is prevented after methionine sulfoxidation. Overall, modifications in the PLD trigger metamorphism which determines chaperone recognition, with impact on TDP-43’s pathophysiology. | PMC9884275 | 41467_2023_36023_Fig6_HTML.jpg |
0.557292 | 5055761ccf67442bb7c969840d77696d | Assessment of cell viability of HCT116 and HT29 exposed with different concentration of TMA. Cytotoxicity of TMA was evaluated by MTT assay (A. HCT116, (B) HT29), luminescent assay (C. HCT116, D) HT29) and LDH assay (E). Cells were treated with or without different concentrations of TMA for 24 h, 48 h and 72 h. Cellular viability (A, B) and membrane integrity (E) were analyzed colorimetrically following treatment with TMA. Below 5 mM TMA exposure, there is no significant increase in LDH release compared to control group. Luminescence was measured for measuring ATP level (C, D). Untreated control is considered as 100%. Difference of average values between untreated and treated cells were tested using one way ANOVA. All tested subjects showed significant decrease in viability at higher concentration of TMA while 10 mM TMA at 72 h proved most cytotoxic to cells. Significance was calculated in comparision to control. The results (mean±SEM) were obtained from 3 independent experiments. Error bars represent standard error from three independent experiments. *indicates significantly different values compared to control group (P<0.05)** indicates significantly different values compared to control group (P<0.001). ***indicates significantly different values compared to control group (P<0.0001). | PMC9885123 | fimmu-13-1101429-g001.jpg |
0.466165 | a6c8dafa63a34ff9bc5fa1511df48fd2 | Detection of apoptosis and oxidative stress induced by superoxide radicals. Effect of TMA on HCT116 (A, E), HT29 (B, F) cells was checked by flow cytometry. (A–C) are representative flow cytometric dot plot showing the percentage of viable cells (annexin V-FITC-, PI-), early apoptotic cells (annexin V-FITC+, PI-), late apoptotic cells (annexin V-FITC+, PI+) and necrotic cells (annexin V-FITC-, PI+). Results are plotted as no. of apoptotic cells (annexin V-FITC+, PI-) which shows significant increase in apoptosis with increase in concentration of TMA (B, D). Negative control cells were treated with solvent only. TMA induces production of anion superoxide radical in both cell lines, (E). HCT116 and (F). HT29. HCT116 and HT29 cells were treated with 5 mM and 10 mM TMA for 48 h. Difference of average values between untreated and treated cells were tested using paired student’s t-test. Both cell lines showed significant increase in apoptosis and ROS production particularly 10 mM TMA proved most toxic to cells. The exposure of TMA led to an increase in fluorescence intensity in both cell lines thereby, shifting histogram towards right (G). The results (mean±SEM) were obtained from 3 independent experiments. *indicates significantly different values compared to control group (P<0.05). ***indicates significantly different values compared to control group (P<0.0001). | PMC9885123 | fimmu-13-1101429-g002.jpg |
0.396572 | 47fc4bc8f12a400f9d3b6d84f182f047 | Bright field images of HCT116 (A) and HT29 (B) showing changes in cellular morphology, detachment from surface, decreased no. with increase in TMA concentration and time of exposure. Decrease in cell viability was observed after exposure (C). ** indicates significant decrease in cell viability compared to control group (P<0.001). | PMC9885123 | fimmu-13-1101429-g003.jpg |
0.381027 | d2e3956efe60473e86e51b572685b83c | Clonogenic assay. TMA inhibits colony formation of (A) HCT116 and (B) HT29 cells. Evaluation of colony forming ability in HCT116 and HT29 cell line exposed to various concentrations of TMA for 48 h. TMA inhibits the colony forming ability of HCT116 in a concentration dependent manner. Results were plotted as no. of colonies formed after 14 days (shown right to the colony images). Negative control cells were treated with cell culture water only. Difference of average values between untreated and treated cells were tested using paired student’s t-test. All tested subjects showed significant decrease in viability while 10 mM TMA proved most cytotoxic to cells. The results (mean±SEM) were obtained from 3 independent experiments. *indicates significantly different values compared to control group (P<0.05). | PMC9885123 | fimmu-13-1101429-g004.jpg |
0.366776 | e04c4f4f2b964bb292fdf5df817e5797 | Comet assay. Comet assay was performed to evaluate genotoxicity induced by TMA. Cells were treated with different concentrations of TMA for 48 h. Representative images at X200 magnification shows that TMA causes DNA damage in dose dependent manner as shown in (A) HCT116 cells treated with and without TMA and (B) HT29 cells treated with and without TMA. 1, 2, 3, and 4 represent control, 2.5 mM, 5 mM and 10 mM treatment respectively. DNA damage was enumerated using the OpenComet software tool in imageJ software (https://imagej.net/software/fiji/ ) as shown in (C) HCT116 and (D) HT29 respectively. Results were plotted as comet parameters. Both cell lines showed significant DNA damage at 10 mM TMA. The results (mean±SEM) were obtained from 3 independent experiments. *indicates significantly different values compared to control group (P<0.05) **indicates significantly different values compared to control group (P<0.001). | PMC9885123 | fimmu-13-1101429-g005.jpg |
0.634544 | 18871de819e748d6bbd62a2fab782527 | Effect of TMA on cell cycle progression. Evaluation of cell cycle HCT116 (A) and HT29 (B) cells were treated with various concentrations of TMA for 48 h. Untreated cells were considered as negative control. (A) and (B) showed the quantification of cell cycle distribution. TMA induced cell cycle arrest. 1, 2, 3, and 4 represent control, 1.25 mM, 5 mM and 10 mM treatment respectively. The distribution of various phase of HCT116 and HT29 cells are represented in (C, D) Difference of average values between untreated and treated cells were tested using one-way ANOVA. The results (mean±SEM) were obtained from 3 independent experiments. *indicates significantly different values compared to control group (P<0.05). | PMC9885123 | fimmu-13-1101429-g006.jpg |
0.470542 | 987c15379d2244218c05ca8a21225604 | Length of large intestine of mice of Negative control (A), Vehicle control (B), TMA given intraperitoneally (C) and TMA given intrarectally (D). Graph showing the length of intestine and spleen in different groups (E, F) respectively. *p<0.05. | PMC9885123 | fimmu-13-1101429-g007.jpg |
0.430177 | e9a43fd55a404cec85b979c030ae601d | Micrographs of the colon (A-D) and histological score of all groups (E). H & E sections of colon from mice exposed to TMA intraperitoneally (C) and intrarectally (D) or negative control (A) or vehicle control (B) are shown. Severe inflammation characterized by severe cellular infiltration persisted in the colon of mice exposed to TMA intrarectally (D) compared to negative and vehicle control. Black star point to cellular infiltration, red star points to damaged muscularis, yellow star points to increased lumen and red triangle points to distorted crypts. The histology scores for the inflammation of these groups are summarized in (E). The histological score showed a significant increase in inflammation after TMA exposure. *p<0.05. | PMC9885123 | fimmu-13-1101429-g008.jpg |
0.465337 | a6706c6fe7da410ab7eb0174fe0da696 | Micrographs of the rectum (A-D) and histological score of all groups (E). H & E sections of rectum from mice exposed to TMA intraperitoneally (IP) (C) and intrarectally (IR) (D) or negative control (A) or vehicle control (B) are shown. Severe inflammation characterized by severe cellular infiltration persisted in the colon of mice exposed to TMA intrarectally (D) compared to negative and vehicle control. The histology scores for the inflammation of these groups are summarized in (E). Black star points to cellular infiltration and black arrow represents crypt distortion in TMA exposed mice rectum. The histological score showed a significant increase in inflammation after TMA exposure. *p<0.05. | PMC9885123 | fimmu-13-1101429-g009.jpg |
0.43516 | a87ca28506eb4a4689bd1845cd644357 | The ileum resected during operation | PMC9885642 | 12872_2023_3066_Fig1_HTML.jpg |
0.494726 | 091f1df852e245c38893e801383ba550 | An isolated tibial tuberosity fracture without rotation of the fractured bone fragment was observed on preoperative x-rays (A-B). | PMC9885693 | aott-56-6-416_f001.jpg |
0.424384 | 5d98b6cf5bb44e779efe2a03715f04c6 | Exposed tibial tuberosity fracture site. Comminution is observed in the lateral aspect of the cortical bone. | PMC9885693 | aott-56-6-416_f002.jpg |
0.458962 | d9067f64b7204bf5ab686cee255ac211 | The center of the bone fragment is marked (arrow). | PMC9885693 | aott-56-6-416_f003.jpg |
0.44706 | cf9d4b5b4a714a2681fe5014e94d82f1 | Preliminary reduction with Ethibond was done (A). Ethibond wrapped around the patellar tendon (asterisk). The crossing point of both threads passes through the point previously marked at the center of the bone fragment (arrow). The location where the suture anchors will be inserted is marked at a distance of 1-2 cm distal from the fracture site among the locations where the thread passes (arrowheads). The preliminary reduction was done with 2 Fibertapes (B). | PMC9885693 | aott-56-6-416_f004.jpg |
0.453895 | 3ed5dc82c20c41e38e3601643f011e46 | The final fixation was done with 2 knotless suture anchors. Four strands of Fibertapes fix the bone fragments and patellar tendon (asterisk), preventing further displacement. | PMC9885693 | aott-56-6-416_f005.jpg |
0.408789 | c5f2e67f31754a27b1d994e0e0cec571 | Intraoperative fluoroscopic evaluation with the knee fully extended (A), flexed at 120˚ (B). | PMC9885693 | aott-56-6-416_f006.jpg |
0.431656 | ff4d863e9df0436fbc9764cb2d4d5d43 | At 4 weeks postoperatively, the patient achieved an active straight leg raise without an extension lag (A) and near full range of motion (B). | PMC9885693 | aott-56-6-416_f007.jpg |
0.446235 | 5b44f86a3d8f430ab215aa3f7ea5eab9 | Follow-up x-rays. Postoperative x-rays (A-B). x-rays 5 months postoperatively (C-D). Near-complete bone union was achieved. x-rays 1 year after surgery (E-F). | PMC9885693 | aott-56-6-416_f008.jpg |
0.427065 | a6343037ba6d4b45ae9a786f078f3179 | Spectral characteristics of human GBM in comparison to non-tumor brain: A Preprocessed spectra and mean spectra B mean difference of GBM and non-tumor spectra C Intensities of selected IR bands for non-tumor and GBM. Points represent spectroscopic measurements (non-tumor: multiple measurements on 39 patient’s biopsies; GBM: one measurement was performed on each biopsy), black line indicates the median. Significant difference ***P < 0.001 (Mann–Whitney test) | PMC9886632 | 11060_2022_4204_Fig1_HTML.jpg |
0.406758 | 4416b9588acf473ca86b9245f0178381 | Classification of GBM versus non-tumor specimens A Developed data analysis strategy that is compatible with future clinical exploitation (PCA: principal component analysis, LDA: Linear discriminant analysis) B Classification result for non-tumor samples and GBM (primary disease, samples independent of the training set). Multiple measurements on the same sample were performed for non-tumor tissue. C Difference spectra to non-tumor of recurrent GBM (red) and primary disease GBM (gray) D Classification result for specimens of recurrent GBM. The probability of class assignment is shown for each patient in a color code | PMC9886632 | 11060_2022_4204_Fig2_HTML.jpg |
0.471688 | 35980abbd4f3481c8d3b8f18d6c5f290 | Difference spectra to non-tumor brain tissue and classification results for different types of brain tumors. Difference spectra of the brain tumor type (red) are shown in comparison to the difference spectrum of GMB and non-tumor tissue (gray), respectively. The classification result shows the probability of class assignment for each patient in a color code. The primum of brain metastases is indicated | PMC9886632 | 11060_2022_4204_Fig3_HTML.jpg |
0.43463 | 22889cc3bfc8471380de3a41b3703ac6 | Flowchart of identifying a polyamine-related signature and six novel prognostic biomarkers in oral squamous cell carcinoma. | PMC9887031 | fmolb-10-1073770-g001.jpg |
0.427473 | 7a2ac630ae3c42b297cf645f9baaf3d6 | Overview of genetic and prognostic information of polyamine regulators in OSCC. (A) Boxplot of 17 polyamine regulators expression in OSCC and its adjacent normal tissue. (B) Waterfall plot of the polyamine regulators altered in OSCC samples. (C) Interaction of the polyamine regulators. Size of each cell represents the survival effect of each gene. Red represents a positive correlation, whereas blue indicates a negative correlation. (D) PPI network map showed the interaction of the 17 polyamine regulators. | PMC9887031 | fmolb-10-1073770-g002.jpg |
0.455189 | e8f94bebb76f4036adae2014a718c2db | Construction of two polyamine-related gene (PARG) clusters in OSCC patients. (A) Consensus clustering of OSCC patients. (B) OS curves of OSCC patients in two PARG clusters. (C) Heatmap of 17 polyamine regulator expression in two clusters. (D) Quantity of immunological infiltration cells as determined by ssGSEA between PARG clusters. (E) Heatmap of GSVA in the KEGG pathway between PARG clusters. | PMC9887031 | fmolb-10-1073770-g003.jpg |
0.438016 | 4f30bb2cc73f4b2f804a6d4cd8bd0662 | Functional annotation of 17 polyamine regulators using GO terms and the KEGG pathway. GO (A) and KEGG (B) analyses of the identified genes. | PMC9887031 | fmolb-10-1073770-g004.jpg |
0.434603 | a6e8f28df53f478bb1c8c63a828931e3 | Identification of polyamine-related differentially expressed gene (PARDEG) clusters. (A) Consensus clustering of OSCC patients based on PARDEGs. (B) Comparison of the three cluster survival probability of OSCC patients. (C) Polyamine marker expression in three clusters. | PMC9887031 | fmolb-10-1073770-g005.jpg |
0.43269 | dfc610bbb64c41c89f9794ebcbd19d8c | Stepwise identification of PARG risk signature of the model. (A) Cross-validation for tuning parameter selection in the proportional hazards model. (B) LASSO coefficient of the PARDEGs. (C) Forest plot of the univariate Cox regression analysis in DEGs. (D) Forest plot of the multivariate Cox regression analysis in DEGs. | PMC9887031 | fmolb-10-1073770-g006.jpg |
0.474386 | d86d4aa72fd644f2b3aa87b73923fbc7 | Correlation between the risk score and overall survival of OSCC patients in the training, validation, and the whole cohort. (A–C) Overall survival (OS) of the high-risk group was significantly shorter than that of the low-risk group. (D–F) ROC curve and the areas under the curve for predicting a 1-, 3-, and 5-year OS in OSCC patient. (G–I) Heatmap of six genes’ expression in the training, test, and total cohorts. (J–O) Based on the polyamine-related risk score, groups are distributed. Scatterplot showed the variations in OSCC patients' survival rates between high-risk and low-risk categories. | PMC9887031 | fmolb-10-1073770-g007.jpg |
0.423456 | eef87a963d3147bdacfc61511d09e08a | Comparison of the effectiveness of risk scores in different groups. (A) Sankey plot shows the OSCC patients’ distribution in different states of our analyses. (B) Risk score in A and B clusters related to PARGs. (C) Risk score in A, B, and C clusters divided by the PARDEG cluster-related genes. (D) High- and low-risk groups expressed PARGs significantly different. | PMC9887031 | fmolb-10-1073770-g008.jpg |
0.374703 | 9a214c31352c4a7298791d053b7feca2 | Correlation between the risk score and the immune cell infiltration by ssGSEA (A) memory B cells, (B) naive B cells, (C) resting dendritic cells, (D) M0 macrophages, (E) activated mast cells, (F) resting mast cells, (G) resting NK cells, (H) activated memory CD4+ T cells, (I) CD8+ T cells, (J) follicular helper T cells, (K) gamma delta T cells, and (L) regulatory T cells. | PMC9887031 | fmolb-10-1073770-g009.jpg |
0.4172 | d8c6a715b7064fc6890b30d6d80f9294 | Exploration of risk scores and tumor mutation burden. (A) High-risk score tumors were markedly correlated with a higher TMB (p = 4e−06, Student’s t-test). (B) There was a positive correlation between risk scores and TMB (p = 1.7e−07). Tumor mutation landscape in high-risk (C) and low-risk (D) score groups of OSCC patients were presented in the waterfall plots. | PMC9887031 | fmolb-10-1073770-g010.jpg |
0.517322 | a7e37a3ac43c4632838333529d2c7abf | Sensitivity of low- and high-risk patients to four common chemotherapy agents. The y-axis represents 50% inhibitory concentration (IC50). (A) Cisplatin, (B) docetaxel, (C) doxorubicin, and (D) paclitaxel. | PMC9887031 | fmolb-10-1073770-g011.jpg |
0.425082 | c3f744a20a6047bc9a510e4e4f4f9273 | Six genes’ expression and its correlation with immune cells and chemotherapy. (A) Expression of six genes constructed the model. (B) RNA expression level of six genes in 12 pairs of tumor and normal adjacent tissues from OSCC patients. (C) Correlation between each TME infiltration cell 22 type and each regulator constructing the model using Spearman’s analysis. (D) Top 16 chemotherapy correlated to the six genes. | PMC9887031 | fmolb-10-1073770-g012.jpg |
0.525743 | 5dc1fed49fff4f8fb809cc1f37461930 | Schematic presentation of gastrointestinal tract reconstruction after total gastrectomy end-to-end hand-sewn esophagojejunostomy (A), end-to-side circular stapled esophagojejunostomy (B). The figure was created by author Karolina Majewska using GoodNotes 5 application, Time Base Technology Limited, © 2011–2022 GoodNotes Limited. | PMC9887901 | medscimonit-29-e938759-g001.jpg |
0.449278 | e1533199d6584bdda16b452d4fb5ed90 | American Joint Committee on Cancer (AJCC) staging comparison between stapler and hand-sewn esophago-jejunal anastomosis. | PMC9887901 | medscimonit-29-e938759-g002.jpg |
0.514357 | a204722c9e884d78a50a6675f10f09a8 | Disease-Specific Survival (DSS) comparison between stapler and hand-sewn esophago-jejunal anastomosis. | PMC9887901 | medscimonit-29-e938759-g003.jpg |
0.535084 | 5e4a326295a8425993a5e97ba000c62d | Disease-Free Survival (DFS) comparison between stapler and hand-sewn esophago-jejunal anastomosis. | PMC9887901 | medscimonit-29-e938759-g004.jpg |
0.370901 | 18a1063d9f5e4f1ead0aaaeb29fcc042 | SARS-CoV-2 infections by (A) absolute numbers over time and (B) by incidence rates over study centre. Note: the first nationwide lockdown came into force on 22 March and included a ban on gatherings of more than two people not living in the same household. Futher measures included travel restrictions and the closure of schools, daycare centres and non-essential businesses (eg, pubs and cultural institutions). N=108 960 persons. | PMC9888438 | SJWEH-48-446-g001.jpg |
0.408498 | 6d1293296ed3477a81eb122be8807595 | Risk for SARS-CoV-2 infection (1 February–31 August 2020) among different groups of essential workers in comparison to non-essential workers. Incidence rate ratios obtained from robust Poisson regression analysis (person-time at risk specified as an exposure variable to control for different observation times). Estimations were adjusted for age group (in five-year increments), sex, migration background, study centre, weekly working hours, self-employment, occupational skill level (5th digit of the KldB-2010), and supervisory/leadership role (4th digit of the KldB-2010). N=108 960 employed individuals. | PMC9888438 | SJWEH-48-446-g002.jpg |
0.425695 | b36d4d61fa3e4e12ae248ea6ec7071cc | Acute dissection in the distal right internal carotid artery in a 45-year-old woman. The contrast-enhanced CT angiography examination initially revealed a narrowing of the distal extracranial segment of the right ICA (arrow in a). Note the absence of an atherosclerotic plaque. While a surrounding soft tissue density could be seen on close examination of the affected artery segment on a professional display, this is often difficult to appreciate. The narrowing is further illustrated on the curved MPR image (arrow in b), which can be compared with the normal left ICA (c). Due to its ability to visualize blood degradation products, MR is for carotid dissection clearly superior to CT to detect wall hemorrhage. While this can be seen on a TOF sequence (arrow in d), a T1-weighted fat-suppressed sequence remains the method of choice to detect the thrombosed false lumen in acute carotid dissection (arrow in e) | PMC9889425 | 330_2022_9025_Fig10_HTML.jpg |
0.432228 | e6443b7ba540437a94d30ed64ba8a1c1 | Acute dissection in the supra-bulbar left internal carotid artery (ICA) in a 28-year-old man due to fibromuscular dysplasia, presenting with an acute stroke. The CT angiography examination performed on the day of the acute event reveals a sub-occlusive narrowing of the supra-bulbar left ICA (arrow in a), with a large eccentrically located thrombosed part (asterisk in a), containing a large proximal pseudo-aneurysm (arrowhead in a). Note the complete absence of atherosclerosis in the carotid bulb. On the follow-up examination performed three weeks after the acute event, the thrombus has largely resolved, revealing the typical strings-of-beads sign of fibromuscular dysplasia which was the underlying condition leading to the acute dissection. Fibromuscular dysplasia should always be considered when investigating stroke in young patients | PMC9889425 | 330_2022_9025_Fig11_HTML.jpg |
0.476157 | bf200f1a039a480eae20e3531a0b9d65 | Near-occlusion in the internal carotid artery bulb due to an extensive embolic and now thrombosed fragment. The correct term for this sub-occluded lumen with the collapse of the distal portion of the ICA is “near-occlusion” and not “99% stenosis.” In this case, the distal portion of the ICA as the denominator for the quantification of the degree of stenosis should not be used | PMC9889425 | 330_2022_9025_Fig1_HTML.jpg |
0.493539 | 110c1a38d3db473b9548b3021a99cb00 | Differences in degree of stenosis between NASCET and ESCT. In this patient, a large mostly calcified plaque can be found in the bulb of the internal carotid artery. However, the luminal diameter remains unchanged compared with a reference diameter beyond the carotid bulb (red lines), resulting in a 0% NASCET-stenosis. However, this does not equal the absence of carotid disease. Conversely, the ESCT-measured stenosis is 52%, as the outer diameter of the carotid bulb (blue solid and dashed line) as reference diameter meter reflects the current situation. In situations like this, a detailed reporting of plaque location and characteristics is essential to accurately describe the findings beyond the degree of luminal narrowing | PMC9889425 | 330_2022_9025_Fig2_HTML.jpg |
0.435836 | d9d14eb21eec43f4b6d9fe6b4c495a32 | Various examples of arterial remodeling are illustrated. First, two examples of inward/negative remodeling are shown (a, b). The outer diameter of the artery (red dotted line) remains in both examples unchanged. In both cases, the lumen is narrowed (green dotted line) due to a plaque (asterisk), indicating negative/inward remodeling. However, due to the concentric morphology of the plaque in panel a, the narrowed lumen remains in a central position, representing concentric remodeling. Conversely, in panel b the luminal narrowing is eccentric. Panels c and d illustrate outward/positive eccentric remodeling, where the outer perimeter of the artery, outlined by the red dotted line, is increased due to plaque formation with eccentric luminal narrowing. The positive remodeling example illustrates the notion that significant plaque can be present but still produce only mild stenosis (only 25% NASCET-calculated stenosis in this case) with a mostly outward protruding plaque. NASCET: North American Symptomatic Carotid Endarterectomy Trial | PMC9889425 | 330_2022_9025_Fig3_HTML.jpg |
0.426775 | 97a35ca1d26049008e53de10a7ff4a45 | Varying presentation of carotid plaques with different ratios of calcified and non-calcified components (a–d). The different panes illustrate several plaque configurations ranging from a completely non-calcified (a) to an extensively and exclusively calcified plaque (d) with different calcified/non-calcified ratios in between (b, c). Note that, independently of the plaque composition and the degree of luminal stenosis, panel a and b reveal additional ulcerations (asterisk), a plaque feature with prognostic implications which must certainly be mentioned in the report. These examples further illustrate the notion that the description of carotid plaques must extend beyond mere calculation of luminal stenosis, mentioning all relevant plaque features to provide the most complete disease assessment | PMC9889425 | 330_2022_9025_Fig4_HTML.jpg |
0.466065 | 885a856a29ce4bb0baa9926d22fbcbe8 | Illustration of the “rim”-sign on contrast-enhanced CT. The axial CT-image at the level of the internal carotid artery reveals only minimal small calcifications in the right ICA (arrowhead in a), and a plaque with calcified and non-calcified components in the left ICA (arrow in b). Close examination of this plaque reveals a small semicircular rim of adventitial calcifications at the periphery of the plaque (<2 mm thickness) with a larger (>2 mm) non-calcified plaque component bordering the lumen. This plaque phenotype is known as a positive “rim”-sign, a feature associated with the presence of intraplaque hemorrhage and as such with higher stroke risk. Reporting of this type of plaque is significant, as the luminal narrowing is only moderate and by itself according to NASCET criteria considered non-significant | PMC9889425 | 330_2022_9025_Fig5_HTML.jpg |
0.422862 | c079e437a27a4f449dcaefc894fe584e | Intraplaque hemorrhage (IPH) demonstrated on MR in a 74-year-old man with a left-sided stroke. This case of intraplaque hemorrhage clearly demonstrates the T1-shortening effect of methemoglobin generated from erythrocyte degradation, illustrated as an intralesional hyperintense signal (arrows in a, b) in the left internal carotid artery (asterisk in a), as shown in CUBE (a) and MPRAGE-sequences (b). For additional evaluation of luminal repercussion, a contrast-enhanced MR angiography sequence was executed, revealing a severe luminal narrowing with a focal ulceration (arrow in c). The presence of plaque ulceration and intraplaque hemorrhage are two important features in this case that provide additional clinically and prognostically relevant information on top of the mentioned luminal narrowing. CUBE: General Electric proprietary name for a 3D fast spin echo sequence; MPRAGE: magnetization-prepared 180° radio-frequency pulses and rapid gradient echo | PMC9889425 | 330_2022_9025_Fig6_HTML.jpg |
0.398799 | 1d70a7baa8cb4d72878b73c036283b8d | Floating thrombus in the supra-bulbar right internal carotid artery. A large eccentric non-calcified thrombus is clearly seen, on cross-sectional CTA images appearing as a central non-enhancing thrombus surrounded by a (semi-)circular enhancing lumen, the so-called “donut”-sign (arrow in a). A coronal CTA image further reveals the irregular outer border of this floating thrombus (arrow in b), indicative of a higher risk for distal emboli. This is further illustrated by an axial diffusion-weighted MR-image of the same patient revealing a recent ischemic infarct in the distribution region of the right media cerebral artery | PMC9889425 | 330_2022_9025_Fig7_HTML.jpg |
0.409194 | 4ac09c0ae35d4b1f9233caa466c047e0 | Carotid web in the right internal carotid artery. A semi-circular non-calcified thin lesion is seen protruding in the lumen from the posterior wall of the artery (arrow in a). No calcification or thrombus can be seen, as further illustrated in the detailed image (b). Some authors consider a carotid web to be a variant of fibromuscular dysplasia. A carotid web may induce flow stasis with thrombus formation, hence increasing the risk of stroke | PMC9889425 | 330_2022_9025_Fig8_HTML.jpg |
0.474156 | bd14c30d9972439ca8a8ed1c167231f9 | Curved MPR image of neo-intimal hyperplasia in a carotid stent, producing significant proximal luminal narrowing. CT offers exquisite anatomical detail, highlighting complications like the mentioned intima hyperplasia and guiding as such further treatment and potential re-intervention | PMC9889425 | 330_2022_9025_Fig9_HTML.jpg |
0.414593 | c076dfbb5ef048ab8cfc94f2e6ca1b6c | The extended interface of FANCI's ubiquitin with FANCD2 is required for enhanced protection against USP1‐UAF1
AInteractions of FANCI and FANCD2 with the ubiquitin conjugated to the other ID2 subunit, in DNA‐bound IUbD2, IUbD2Ub (PDB: 6VAE), ID2Ub (PDB: 6VAF) and IUbD2Ub (PDB: 6VAE) structures (Wang et al, 2020). Dotted straight lines indicate hydrogen bonding. Both FANCD2 and FANCI interact with ubiquitin's hydrophobic I44 patch (residues L8, I44, H68 and V70; all labelled in highlighted‐yellow font) and additionally with residues F45 to G47 of ubiquitin. However, the ubiquitin conjugated to FANCI has a more extensive interface with FANCD2. This extended interface is formed by interactions of FANCD2 α10 ‐ α13 helices (predominant interacting residues highlighted in boxes) with residues R74, T9 and K11 of ubiquitin (shown in black font). The ubiquitin‐FANCD2 interface may be further extended via interactions between residues K33 and E34 of ubiquitin with K165 and R174 of FANCD2, as shown in IUbD2Ub‐DNA structure. For direct comparison of corresponding interactions, the same orientation for all ubiquitins (both FANCI‐conjugated and FANCD2‐conjugated) was achieved by aligning: ID2Ub‐DNA and IUbD2Ub‐DNA structures to the ubiquitin of IUbD2‐DNA structure, and subsequently, the IUbD2Ub‐DNA structure to the ubiquitin of ID2Ub‐DNA structure as well.BClustal O multiple sequence alignment of human, mouse, rat, chicken, frog and zebrafish FANCD2 amino‐acid sequences, focused on a region encompassing α11‐13 helices of FANCD2 in human IUbD2‐DNA structure (helical regions shown on top). Identical residues among various species are highlighted red, whereas residues in positions displaying 83% similarity/identity are shown in red font. Residues of FANCD2 interacting with FANCI's ubiquitin in both IUbD2‐DNA and IUbD2Ub‐DNA structures (extended FANCD2‐ubiquitin interface) are indicated with blue circles.C, DAlanine mutagenesis of key FANCD2's residues (H209, V243 and P244) participating in the extended FANCD2‐ubiquitin interface (IUbD2‐DNA and IUbD2Ub‐DNA structures), results in enhanced FANCI deubiquitination by USP1‐UAF1. (C) FANCI deubiquitination by USP1‐UAF1 (incubation with 50 nM USP1‐UAF1 for 30 min at room temperature) in the presence of DNA and, in the absence or presence of wild‐type (D2WT) or mutant (D2H209A,VP243AA) FANCD2. Replicate residual ubiquitination values (three technical replicates) and statistically significant changes (t‐test and one‐way ANOVA test with Bonferroni correction) are shown. (D) FANCI was ubiquitinated with DyLight‐680 labelled ubiquitin (IUb‐DL680) and its deubiquitination by USP1‐UAF1 (incubation with 100 nM USP1‐UAF1 for 20 min at room temperature), was assessed at increasing concentrations (20, 200 or 200 nM) of, either wild‐type (D2WT), or mutant (D2H209A,VP243AA) FANCD2. Experiment was repeated three times (technical replicates), and the fold change in residual FANCI ubiquitination was determined by normalisation to the mean intensity of IUb‐DL680 at 20 nM FANCD2 (average from six values, for both D2WT and D2H209A,VP243AA). Mean (with range) fold‐increase values and statistically significant changes upon FANCD2 mutation for each FANCD2 concentration (t‐test and two‐way ANOVA test with Bonferroni correction) are shown.
| PMC9890228 | EMBJ-42-e111898-g001.jpg |
0.456868 | 0ecf9942390e46459174ff4b80deab7c | DNA and FANCD2 protect against FANCI deubiquitination
USP1‐UAF1‐mediated deubiquitination of V5‐FANCI and FANCD2 was assessed in the absence or presence of DNA (51 bp), when ubiquitinated versions of these proteins were in isolation (IUb and D2Ub) or within singly/doubly ubiquitinated ID2 complexes (IUbD2, IUbD2Ub and ID2Ub). At indicated time‐points, aliquots of each reaction were removed and analysed by western blotting using FANCD2 and V5 antibodies.Residual FANCI and FANCD2 ubiquitination following USP1‐UAF1 treatment for 30 min at room temperature. Experiments shown in (A) were performed in triplicate (technical replicates), apart from ID2Ub and D2Ub deubiquitination in the absence of DNA, which were performed twice (and were thus excluded from statistical analysis). Replicate residual ubiquitination values and statistically significant changes (one‐way ANOVA test with Bonferroni correction) are shown. ***P < 0.001.Deletion of N‐terminus (∆N) of USP1 (residues 1–54) results in greatly reduced FANCD2 deubiquitination. Assays were performed in triplicate (technical replicates) as in (A), but all reactions contained DNA. Left: Western blotting of reaction products at zero and 30 min using FANCD2 and V5 antibodies. Right: Residual FANCI and FANCD2 ubiquitination following USP1‐UAF1 treatment for 30 min. Replicate residual ubiquitination values and statistically significant changes (one‐way ANOVA test with Bonferroni correction) are shown. ***P < 0.001.
| PMC9890228 | EMBJ-42-e111898-g002.jpg |
0.511164 | ab386b107c044b52b50adc48c3f6e5e8 | FANCI and FANCD2 target lysine positioning and accessibility in DNA‐bound IUbD2, ID2, ID2Ub and IUbD2Ub structures
The overall accessibility of FANCI's K523 and FANCD2's K561 is shown within IUbD2‐DNA, ID2‐DNA (PDB: 6VAA), ID2Ub‐DNA (PDB: 6VAF) and IUbD2Ub‐DNA (PDB: 6VAE) structures. For clarity DNA was removed from the structures. The corresponding lysines are illustrated as orange spheres. IUbD2, ID2Ub and IUbD2Ub structures were aligned to FANCI of ID2 structure, to allow visualisation of all structures under same orientation.FANCI's K523 and FANCD2's K561 accessible surface areas and buried surface area (both in Å2) are shown in non‐ubiquitinated ID2 complex and upon ubiquitination of the other subunit. These values were determined from associated PDB files using the PDBePISA tool (Krissinel & Henrick, 2007) at https://www.ebi.ac.uk/pdbe/pisa/.
| PMC9890228 | EMBJ-42-e111898-g003.jpg |
0.414955 | 2f40a5e4d22f4699a88b3a27b73a93ab | FANCI ubiquitination supports and maintains a di‐mono‐ubiquitinated ID2 stateModel explaining how the di‐monoubiquitinated ID2 complex is generated and maintained. The UBE2T ubiquitin conjugating enzyme partners with the FA core ubiquitin ligase for ubiquitination of the DNA‐bound FANCI‐FANCD2 (ID2) complex. Of the two proteins subunits of the ID2 complex, FANCD2 is preferentially targeted for ubiquitination. While the resulting complex (ID2Ub‐DNA) is sensitive to USP1‐UAF1 deubiquitination activity, it has a conformation that now favours FANCI ubiquitination. Upon FANCI ubiquitination, the ubiquitin conjugated to FANCD2 gains some degree of resistance towards USP1‐UAF1‐mediated deubiquitination (IUbD2Ub‐DNA complex). Nevertheless, FANCD2's ubiquitin is preferentially targeted for deubiquitination in the IUbD2Ub‐DNA complex. Its removal, though, is counteracted by very fast rates of FANCD2 ubiquitination (in the IUbD2‐DNA complex), which can (re‐)establish the di‐mono‐ubiquitinated state (IUbD2Ub‐DNA). Since the ubiquitin‐on‐FANCI is highly protected against deubiquitination in both IUbD2‐DNA and IUbD2Ub‐DNA complexes, reverting to a non‐ubiquitinated ID2 state is highly disfavoured, once FANCI ubiquitination is established. Arrow lengths are proportional to ubiquitination rates estimated in Fig 3C. ID2‐DNA, ID2Ub‐DNA and IUbD2Ub‐DNA structures shown correspond to PDB entries 6VAA, 6VAF and 6VAE, respectively (Wang et al, 2020). | PMC9890228 | EMBJ-42-e111898-g004.jpg |
0.506162 | 5909a5110b484379b533eca4d531837b | Cryo‐EM density corresponding to the Ubiquitin‐FANCD2 interface in the IUbD2‐DNA structure
The ubiquitin conjugated to FANCI interacts with several residues located in helices α10, α13, α15, α18 and α23 of FANCD2 in IUbD2‐DNA structure. Assessment of the density map (Phenix auto‐sharpened IUbD2‐DNA map) and of the nature and distance between interacting residues, indicate that the ubiquitin of FANCI predominantly interacts with residues located on helices α10 (H209) and α13 (V243 and P244), and on helix α18 (S337, S338, S341, C342) of FANCD2. Interacting residues are indicated and illustrated as sticks. D168 and N206 of FANCD2 (also shown and illustrated as sticks) are positioned in areas corresponding to overlapping density between ubiquitin and FANCD2, but are not sufficiently close to K33 and K11 of ubiquitin, respectively, for a high confidence interaction.Ubiquitin‐FANCD2 interface from a view centred on residues G47, I44, H68, V70 and L8 of ubiquitin.Ubiquitin‐FANCD2 interface from a view centred on residues K283 and S251 of FANCD2.
Data information: Dotted straight lines indicate hydrogen bonding. | PMC9890228 | EMBJ-42-e111898-g005.jpg |
0.425972 | 3fd3e4fb1bfe426eaa2539764a19f34d | Ubiquitination of either of the two ID2 subunits enhances ubiquitination of the other
AComparison of cryo‐EM density distribution among IUbD2‐DNA (Phenix‐auto‐sharpened map), IUbD2Ub‐DNA (EMD‐21138) and ID2Ub‐DNA (EMD‐21138) maps. IUbD2‐DNA and ID2Ub‐DNA maps, as well as IUbD2Ub‐DNA model (PDB: 6VAE) were aligned to IUbD2Ub‐DNA in ChimeraX. A different colour was applied for each of the protein chains of IUbD2Ub‐DNA model (FANsCI: slate blue, Ubiquitin‐on‐FANCI: green, FANCD2: cyan, Ubiquitin‐on‐FANCD2: magenta), while DNA was coloured red. Then each map was coloured according to nearby (within 6 Å) residue colours. Contour levels were adjusted (IUbD2‐DNA: 6.21, IUbD2Ub‐DNA: 0.0194 and ID2Ub‐DNA: 0.0162) to achieve comparable volumes among all displayed maps (ranging from 8.6 to 9.4 × 104 Å3). Arrows indicate regions of poorer density (in IUbD2‐DNA and ID2Ub‐DNA maps) relative to other regions of the map, as well as to equivalent positions in the other two maps.BBoth K561 of FANCD2 and K523 of FANCI become more accessible upon ubiquitination of the other ID2 subunit. Structural comparison of relative accessibility of FANCD2‐K561, upon FANCI ubiquitination (left panel), and of FANCI‐K523, upon FANCD2 ubiquitination (right panel). The relative positions of these lysines upon conjugation with ubiquitin, are also shown for comparison. Residues of the other ID2 subunit within 8 Å distance from the epsilon‐amino‐group of the corresponding lysine are indicated as sticks. The distance to the nearest residue is shown prior and upon ubiquitination of the other ID2 subunit. In either case this increases, upon ubiquitination of the other subunit, further than 10 Å.C, DID2 ubiquitination on FANCI results in increased rate of FANCD2 ubiquitination (B), whereas ID2 ubiquitination on FANCD2 results in increased rate of FANCI ubiquitination (C). Protein complexes were assembled in vitro on ice in the presence of dsDNA (32 bp) and their in vitro ubiquitination at 30°C was subsequently monitored in a time‐course: at indicative time‐points, aliquots of the reaction were removed and analysed by western blotting using FANCD2 and V5 antibodies (Top). For each protein complex, data‐points from three replicate experiments (three technical replicates) were used in fitting to a one‐phase association model (Bottom).
| PMC9890228 | EMBJ-42-e111898-g006.jpg |
0.455605 | a0015503b6874a35985d5e6ef24f2c5a | FANCIUb‐FANCD2 complex is a DNA clamp
FANCIUb‐FANCD2 (IUbD2) structure bound to double‐stranded DNA. The structure was determined by cryo‐EM, using a 4.1 Å global resolution map. Two different views of the structure are shown. Unmodelled regions (due to poor density) extending 20 amino‐acid stretches are indicated at the bottom.Ubiquitination of either subunit of the ID2 complex results in increased affinity to double‐stranded DNA (dsDNA). Left: Normalised fluorescent changes of IRDye700‐labelled 32 bp DNA (125 nM) when incubated with increasing concentrations (ranging from 1 nM to 2.5 μM) of FANCI (I) or ubiquitinated FANCI (IUb) in the presence of a constant excess concentration (equal to the maximum concentration of I/IUb used) of FANCD2 (D2) or ubiquitinated FANCD2 (D2Ub). As a control, normalised fluorescent changes of IRDye700‐labelled DNA (125 nM) when incubated with increasing concentrations of FANCD2 (ranging from 40 nM to 5 μM) were monitored as well. For each protein/complex, the experiment was conducted 2–4 times (technical replicates) and all data points from the replicate experiments were used for fitting of a one‐site binding model. Right: Apparent ID2, IUbD2 and D2 Kd values (and associated uncertainties, all in nM) for dsDNA measured from model fitting (n: number of binding experiments per protein/complex).
| PMC9890228 | EMBJ-42-e111898-g008.jpg |
0.397039 | 68d7303f367842fabf04a56b4c769d63 | Cryo‐EM analysis and structure modelling of IUbD2‐DNA complex
Example micrograph with scale bar.Example 2D classes. Circular mask is 170 Å in diameter. 2D classes surrounded by a green box correspond to IUbD2‐DNA complex particles, while smaller‐sized 2D classes surrounded by a red box likely correspond to monomeric IUb/D2 proteins.Fourier Shell Correlation (FSC) curves: between the two half maps produced in the final local non‐uniform refinement (shown in blue) and between the refined model and final map (shown in orange).Particle orientation (viewing direction distribution) in the final map. Total number of particles: 139,601.
Top: Locally filtered map coloured by local resolution, viewed from three different angles. Bottom: Corresponding structural model viewed under same orientations.IUbD2‐DNA structure with corresponding map density (locally filtered map), centred on the isopeptide bond between K523 of FANCI and G76 of ubiquitin. Some well‐resolved side‐chains are illustrated as sticks and indicated.Interaction between FANCI and FANCD2 C‐termini with corresponding map density (locally filtered map). A beta‐sheet consisting of a FANCI and a FANCD2 strand is formed (residues 1,285–1,289 of FANCI and residues 1,384–1,388 of FANCD2). This is held in place through hydrophobic and electrostatic interactions with a FANCD2 helix (1,351–1,377 aa). Residues predicted to participate in such interactions are shown as sticks and indicated. Selected side chains, for which there is good density are also shown as sticks. For clarity, adjacent to that region elements of the IUbD2‐DNA structure and map are not shown.IUbD2‐DNA structure centred on DNA. Density corresponding to the 27 bp modelled DNA is shown as orange mesh. Colouring of structure is as in (E–G).
| PMC9890228 | EMBJ-42-e111898-g009.jpg |
0.436231 | a5b39b0cfe664f41ad5fd3c2b0e0880a | FANCD2 deubiquitination progresses at much faster rate than FANCI deubiquitinationFANCIUb‐FANCD2Ub‐DNA complexes were assembled in vitro, and FANCD2Ub and V5‐FANCIUb deubiquitination by USP1‐UAF1 (50 nM final) was monitored at room temperature in a time course: at indicative time‐points, aliquots of each reaction were removed and analysed by western blotting using FANCD2 and V5 antibodies. Experiment was repeated six times (two technical replicates with three different preparations of ubiquitinated FANCI) and FANCI/FANCD2 ubiquitination levels were calculated following quantification of ubiquitinated and non‐ubiquitinated FANCI/FANCD2 bands from the blots. For each protein, all calculated values for all time‐points were used for fitting to a one‐phase decay model. | PMC9890228 | EMBJ-42-e111898-g010.jpg |
0.417171 | 9129ed838b6248899ac2d95869275c40 | IUbD2‐DNA and IUbD2Ub‐DNA structure comparison
The absence of a FANCD2‐conjugated ubiquitin in IUbD2‐DNA structure is associated with a disorder in the N‐terminus of FANCI (residues 1–170), when compared with IUbD2Ub‐DNA structure. The two structures were aligned in Pymol and visualised from the same angle, either on their own (left and centre), or together (right).Helices of FANCI involved in interaction with FANCD2's ubiquitin (IUbD2Ub‐DNA structure; FANCI: blue, Ubiquitin: magenta), are positioned differently when the ubiquitin is removed (IUbD2‐DNA structure; FANCI: orange). IUbD2Ub‐DNA and IUbD2‐DNA structures were fitted to IUbD2‐DNA sharpened map (yellow) and centred on FANCI N‐terminus.Removal of ubiquitin (magenta) from FANCD2 results in slight movements affecting several FANCD2 helices, from α31 (helix where ubiquitin is conjugated) up to α18. FANCD2 helices of IUbD2‐DNA and IUbD2Ub‐DNA are better aligned towards the N‐terminus of FANCD2 (N‐terminally to, and including α18 helix of FANCD2), whereby FANCD2 interacts with the ubiquitin (green) conjugated to FANCI. The structures shown in (A), were centred on the central part of FANCD2.
| PMC9890228 | EMBJ-42-e111898-g012.jpg |
0.42486 | 813310117e924232ab15c1a414bcc1cf | (A) Characterization of GMSCs and in vitro multipotent differentiation. (B) Flow cytometric analysis of the surface markers in GMSCs. (C) Morphology of GMSCs-Exo under TEM. Scale bar: 100 nm. (D) NTA analysis demonstrating the mean diameter of GMSCs-Exo as 135.2 ± 44.3 nm. (E) Western blot analysis showing the expression of CD63 and Tsg101 in GMSCs and GMSCs-Exo. | PMC9890890 | d2na00762b-f1.jpg |
0.518877 | d4553dc8450a47459055ef902d4e0c29 | GMSCs-Exo effects on HUVECs in vitro. (A) Brief schematic diagram of the cell experiment process. (B) CCK-8 analysis of cell proliferation. (C and D) Images and quantitative analysis of HUVECs transwell assay after 24 h. Scale bar: 100 μm. (E and F) Images and quantitative analysis of HUVECs scratch closure test after 12 h. (G–I) Images and quantitative analysis of HUVECs tube formation assay at 6 h. Scale bar: 200 μm. (a) p < 0.05 vs. the control, (b) p < 0.05 vs. HG, (c) p < 0.05 vs. HG+25 μg mL−1 Exo. | PMC9890890 | d2na00762b-f2.jpg |
0.436707 | 6f17ad688be642f484318d700b7bf697 | ICG-001 suppression of HUVECs proliferation, migration, and tube formation abilities through inhibition of the Wnt/β-catenin pathway. (A) Western blotting showing the protein expression of β-catenin, cyclin D3, and N-cadherin treated with HG medium supplemented with GMSCs-Exo and GMSCs-Exo+ICG-001. (B) Quantitative analysis of the protein level of Wnt/β-catenin in the four groups. (C) CCK-8 assay results used to evaluate the cell proliferation of HUVECs treated with HG medium supplemented with GMSCs-Exo and GMSCs-Exo+ICG-001. (D) Transwell assay results used to assess the cell migration of HUVECs. Scale bar: 100 μm. (E) Quantitative analysis of the cell number in the transwell assay. (F) Tube formation assay results used to show the cell capillary network formation of HUVECs. Scale bar: 200 μm. (G) Quantitative analysis of the tube formation assay of HUVECs. (a) p < 0.05 vs. the control, (b) p < 0.05 vs. HG, (c) p < 0.05 vs. HG+Exo. | PMC9890890 | d2na00762b-f3.jpg |
0.397824 | 88f74d516892484d873af0176126c0f6 | (A) Schematic graph of the preparation process and application in animal experiments with PHE@Exo. (B) Zeta potential detection of PHE@Exo in different states: (a) PLGA/nHAP, (b) hydrolyzing PLGA/nHAP, (c) PLGA/nHAP/EPL, (d) PHE@Exo. (C) Laser confocal microscopy observation showing that exosomes could be successfully loaded on PHE. Scale bar: 1 μm. | PMC9890890 | d2na00762b-f4.jpg |
0.404054 | c255c2c4da0946c192685ece4eb34f5a | Diabetic wound-healing examinations in different groups. (A) Surgical procedure for the animal experiments. (B) Representative images of full-thickness skin defects in diabetic mice on days 0, 7, and 14 of the different groups. (C) Quantitative analysis of the wound-closure rates in each group at days 7 and 14 post-surgery (n = 5 in each group). (D) H&E staining of the wound section in each group at day 14 post-surgery. Scale bar: 2 mm. (E) Quantitative analysis of the length of the wound area at day 14 post-surgery. (F) H&E staining of the neo-epithelium thickness at day 14. Scale bar: 10 μm. (G) Masson's trichrome staining of the wound section at day 14. Scale bar: 2 μm. (a) p < 0.05 vs. the control, (b) p < 0.05 vs. exosomes, (c) p < 0.05 vs. PHE. | PMC9890890 | d2na00762b-f5.jpg |
0.4087 | 16af5eeec1574cfe88ffc06ad6b5e162 | Immunofluorescence staining demonstrating the regenerative and angiogenic capacities of HUVECs in vivo. (A and C) Expression of CK-17 in the neo-epithelium after 1 week. (B and D) Thickness of the neo-epithelium after 2 weeks. Red fluorescence for CK17, blue fluorescence for DAPI. (E) Expression of CD34 and VEGF in the neo-epithelium. Red fluorescence for CD34, green fluorescence for VEGF, blue fluorescence for DAPI. (F and G) Quantitative analysis of CD34 and VEGF positive area. (a) p < 0.05 vs. the control, (b) p < 0.05 vs. Exo, (c) p < 0.05 vs. PHE. | PMC9890890 | d2na00762b-f6.jpg |
0.461919 | a628246eacf7423ab87d14e094ac87b3 | Schematic diagram showing GMSCs-Exo accelerating diabetic wound repair through enhancing angiogenesis by activation of the Wnt/β-catenin signaling pathway. | PMC9890890 | d2na00762b-f7.jpg |
0.375102 | 9e4241f28c3341ea8970ef77ec6068b5 | Free energy profile for the reaction of [tBu3PAuAl(NON)] with H2 at the Au (blue line) and the Al (red line) sites. ΔG values refer to the energy of the separated reactants taken as zero. Selected interatomic distances (Å) and bond angles (degrees) are shown with all the stationary point structures. | PMC9890964 | d2sc05815d-f1.jpg |
0.429254 | 1dd0a9d2ab504e60b058461156ea5a47 | Free energy profile for the reaction of [tBu3PMAl(NON)] (M = Cu, Ag) with H2 at the M (blue line) and the Al (red line) sites. ΔG values refer to the energy of the separated reactants taken as zero. Selected interatomic distances (Å) and bond angles (degrees) are shown with all the stationary point structures for the [tBu3PCuAl(NON)] complex (for the [tBu3PAgAl(NON)] complex see Fig. S3 in the ESI†). | PMC9890964 | d2sc05815d-f2.jpg |
0.39293 | c35515adb33e4c0cb3edc887a27ca49c | Results of the NOCV analysis of the [H2]–[tBu3PAuAl(NON)] interaction at TSIV (top) and TSI (bottom). The isosurfaces for the and components for TSIV ((a) and (b), respectively) and TSI ((c) and (d), respectively) are reported together with the associated orbital interaction energy. The charge flux is red → blue. The isovalue is 3me/a03 for all isosurfaces. See Fig. S5–S8 in the ESI† for the complete NOCV analysis. | PMC9890964 | d2sc05815d-f3.jpg |
0.467453 | 0d8a5540c0cf44438b33a68838871363 | (a) Pathways for the homolytic dissociation of the two H-substrate bonds in the singly bridged product [tBu3PAu(μ-H)AlH(NON)] (PCAu) with relative associated energies (kcal mol−1). (b) Spin density (in blue) associated with the [tBu3PAu(μ-H)Al(NON)]˙ (left) and [tBu3PAuAlH(NON)]˙ (right) radicals. The isovalue for the surface is 5me/a03. The most relevant atomic spin polarization values are reported. | PMC9890964 | d2sc05815d-f4.jpg |
0.487418 | 83057ff63a51476cb8cd0a4693dda3eb | Theoretical model. | PMC9891665 | fpsyg-13-1023808-g001.jpg |
0.467072 | 2f04af6a1e3446acbb0675ffce911c04 | Structural equation model results. EI, entrepreneurial intention; EEL, entrepreneurial education learning; EL, experiential learning; ESE, entrepreneurial self-efficacy; SNL, social network learning. | PMC9891665 | fpsyg-13-1023808-g002.jpg |
0.456105 | 0add5a9a8f884be183cde5eafdaebf19 | Structural equation model results: path diagram. EI, entrepreneurial intention; EEL, entrepreneurial education learning; EL, experiential learning; ESE, entrepreneurial self-efficacy; SNL, social network learning. **p < 0.01 and ***p < 0.001. | PMC9891665 | fpsyg-13-1023808-g003.jpg |
0.476404 | 220f17fdcd8a481a8a2aff1450bd51fd | Compressive strength. | PMC9891823 | IJAC2023-2587551.001.jpg |
0.564908 | ffe9e51a8d2d4366b3192bdedffb1a7f | Flexural strength. | PMC9891823 | IJAC2023-2587551.002.jpg |
0.569837 | 23bb392d8107445bb364ab65896290dd | Split tensile strength. | PMC9891823 | IJAC2023-2587551.003.jpg |
0.412282 | 14d4d71ed36749aa97b053f58ee86c2e | Schematic diagram of screw placement. (A) Surgical incision in PS/CBT group. (B) PS/CBT trajectory area coverage. (C) Position of the entry point and screw trajectory (PS—yellow, CBT—red). The screw entry point PS is located at the apex of the herringbone crest and CBT is located at the isthmus of the vertebral arch. | PMC9892841 | fbioe-11-1060059-g001.jpg |
0.425128 | 7d1d81979f7647699a1e7552c068eadf | Three-dimensional simulation models and spine specimen models for posterior internal fixation of T12-S segment lumbar spine. (A) Intact model, (B) L45 PS model, (C) L45CBT model, (D) L4 CBT/L5 PS model, (E) L345 PS model, (F) L34CBT/L45PS model, and (G) L3 CBT-L45 PS model. | PMC9892841 | fbioe-11-1060059-g002.jpg |
0.399892 | 44d9453d900e4e09b5739f8029d5f20c | Flow chart of FEA and IVE. | PMC9892841 | fbioe-11-1060059-g003.jpg |
0.460712 | 24de0c3796914f84a4ea71ae2a7ae6c5 | Spinal composition, constraint setting, and validation. (A) Spinal constraint setting: compression force F, follower load. (B) Spinal constraint setting: S1 fixed constraints. (C) Hybrid placement of screws and “tie” constrains. (D) Comparison of ROM, between this study and the results reported in the previous literature. | PMC9892841 | fbioe-11-1060059-g004.jpg |
0.461286 | bb597e607f3a4c7c96a9575edb16efc9 | Stiffness and overall ROM. (A) Stiffness calculation (force–displacement curve). (B) Comparison of stiffness, between FEMs and IVEs under different conditions. (C) ROM measurement. (D) Comparison of overall ROM, between FEMs and IVEs under different operations. | PMC9892841 | fbioe-11-1060059-g005.jpg |
0.468266 | 95c5e02da1a84f2ca768ceca69e9fa05 | Adjacent-segment ROM and L2-segment ROM. (A) Comparison of adjacent-segment ROM, between postoperative FEMs (blue column) and the intact FEM (purple column). (B) Comparison of L2-segment ROM, between postoperative FEMs (blue column) and the intact FEM (purple column). (C) Comparison of adjacent-segment ROM, between postoperative IVEs (red column) and the intact IVE (green column). (D) Comparison of L2-segment ROM, between postoperative IVEs (red column) and the intact IVE (green column). | PMC9892841 | fbioe-11-1060059-g006.jpg |
0.438582 | 7bf2fae8e4f848099c0c40b70631795c | ROM for each segment between postoperative FEMs and the intact FEM. (A) Flexion–extension conditions. (B) Lateral bending conditions. (C) Axial rotation conditions. | PMC9892841 | fbioe-11-1060059-g007.jpg |
0.427721 | c5348a84ecce403681332a393bef8e9b | The stress value of screw–rod systems in six postoperative FEMs under different conditions. | PMC9892841 | fbioe-11-1060059-g008.jpg |
0.410816 | 57fb0821e8df4011891b37b8b38fcbc3 | The stress distribution of screw–rod systems in six postoperative FEMs under different conditions. According to the indicator diagram, red indicates the stress concentration area, while blue shows the stress dispersion area. | PMC9892841 | fbioe-11-1060059-g009.jpg |
0.445388 | cce0ad938a9349329b56028cb69ea0b6 | Longitudinal associations between WBC count and (a) biologic immunosuppressants, (b) chemotherapy, and (c) oral contraceptives. Asterisks (*) indicate associations passing multiple testing correction (<9.09 × 10−4). | PMC9892923 | cxp-2023-0009-01-4-528605_f1.jpg |
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