Coupled-mode theory for periodic side-coupled microcavity and photonic crystal structures

We use a phenomenological Hamiltonian approach to derive a set of coupled mode equations that describe light propagation in waveguides that are periodically side-coupled to microcavities. The structure exhibits both Bragg gap and (polariton like) resonator gap in the dispersion relation. The origin and physical significance of the two types of gaps are discussed. The coupled-mode equations derived from the effective field formalism are valid deep within the Bragg gaps and resonator gaps.Comment: 13 pages, 6 figure

Gamma-smooth muscle actin expression is associated with epithelial-mesenchymal transition and stem-like properties in hepatocellular carcinoma

BACKGROUND AND AIMS: The prognosis of hepatocellular carcinoma (HCC) is hampered by frequent tumour recurrence and metastases. Epithelial-Mesenchymal Transition (EMT) is now recognized as a key process in tumour invasion, metastasis and the generation of cancer initiating cells. The morphological identification of EMT in tumour samples from the expression of novel mesenchymal markers could provide relevant prognostic information and aid in understanding the metastatic process. METHODS: The expression of Smooth Muscle Actins was studied using immunofluorescence and immunohistochemistry assays in cultured liver cells during an induced EMT process and in liver specimens from adult and paediatric HCC series. RESULTS: We report here that in HCC cell lines treated with TGF-beta and in HCC specimens, the expression of alphaSMA, a known mesenchymal marker of EMT, could never be detected. In addition, our in vitro studies identified the enteric form of SMA, gammaSMA, as being a marker of EMT. Moreover, this SMA isoform was expressed in 46% of 58 tumours from 42 adult HCC patients and in 90% of 16 tumours from 12 paediatric HCC patients. Interestingly, this expression was significantly correlated with poor tumour differentiation and progenitor cell features characterized by the expression of EpCAM and K19. CONCLUSION: Taken together, our results support the conclusion that gammaSMA expression in HCC is strongly correlated with the EMT process, HCC aggressiveness and the identification of cancer stem cells. This correlation suggests that gammaSMA represents a novel and powerful marker to predict HCC progression

Mathematical Modelling as a Proof of Concept for MPNs as a Human Inflammation Model for Cancer Development

<p><b>Left:</b> Typical development in stem cells (top panel A) and mature cells (bottom panel B). Healthy hematopoietic cells (full blue curves) dominate in the early phase where the number of malignant cells (stipulated red curves) are few. The total number of cells is also shown (dotted green curves). When a stem cell mutates without repairing mechanisms, a slowly increasing exponential growth starts. At a certain stage, the malignant cells become dominant, and the healthy hematopoietic cells begin to show a visible decline. Finally, the composition between the cell types results in a takeover by the malignant cells, leading to an exponential decline in hematopoietic cells and ultimately their extinction. The development is driven by an approximately exponential increase in the MPN stem cells, and the development is closely followed by the mature MPN cells. <b>Right:</b> B)The corresponding allele burden (7%, 33% and 67% corresponding to ET, PV, and PMF, respectively) defined as the ratio of MPN mature cells to the total number of mature cells.</p

Desterke et al, 2020, Heterogeneity of macrophage immunoproteasome activation during lung COVID19 disease

This study describe the activation of immunoproteasome components in M1 polarized macrophages at lung level during COVID19 disease. - Supplemental table 1:Table of genes implicated in MHC class I antigen presentation and found up regulated in COVID19 lung depending of SARS-COV2 virus level detected in the tissue - Supplemental Table 2: Genes found to be significant on PSMB8 cell trajectory inside CD14+/CD68+ bronchoalveolar cells from COVID19 patients - Supplemental Table 3 : Table of allele prevalence for 70 most frequent HLA-A,B,C through 20 ethnicities with worldwide distribution (USA NMDP bone marrow registry) - Supplemental Table 5: SARS-COV2 immunopeptidome against MHC class I presentation through 70 most prevalent HLA-A,B,C allele

Desterke et al, 2020, Heterogeneity of macrophage immunoproteasome activation during lung COVID19 disease

This study describe the activation of immunoproteasome components in M1 polarized macrophages at lung level during COVID19 disease. - Supplemental table 1:Table of genes implicated in MHC class I antigen presentation and found up regulated in COVID19 lung depending of SARS-COV2 virus level detected in the tissue - Supplemental Table 2: Genes found to be significant on PSMB8 cell trajectory inside CD14+/CD68+ bronchoalveolar cells from COVID19 patients - Supplemental Table 3 : Table of allele prevalence for 70 most frequent HLA-A,B,C through 20 ethnicities with worldwide distribution (USA NMDP bone marrow registry) - Supplemental Table 5: SARS-COV2 immunopeptidome against MHC class I presentation through 70 most prevalent HLA-A,B,C allele

NR0B2 regulation during Primary Sclerosing Cholangitis defines a metabolic and pre-malignant reprogramming of Cholangiocyte

Supplemental tables associated to manuscript:Supplemental Table 1. Text mining of the 525 ranked genes found in PUBMED with symptom keywords: this Table describes the 525 ranked genes obtained by text mining with the ‘Génie’ algorithm against the three MESH terms: biliary inflammation, biliary fibrosis and biliary stasis. The respective ranks, p-values and PMID identifiers collected for each gene and each MESH term are presented.Supplemental Table 2. Symptom-related genes found to be differentially expressed in livers from primary sclerosing cholangitis patients: Differentially expressed gene analysis results (logarithmic Fold Change, Average Expression and Adjusted p-values) are presented with respective machine learning predictive scores for supervised sample categories from the GSE61256 dataset (PSC versus other liver samples).Supplemental Table 3. Pavlidis Template Matching for FXR dependency in the liver transcriptome. Results of Pavlidis template analysis used to describe the FXR regulation dependency of PSC genes in liver samples from the GSE54557 dataset. For each gene, the R-Pearson correlation coefficient and its respective p-value are presented in this Table. Supplemental Table 4. Best one hundred genes found to be significant in the pseudotime trajectory of Abcb4-/- cholangiocytes. Best one hundred ranked genes found to be significant on the pseudotime cell trajectory of Abcb4-/- cholangiocytes based on the alternative expression of Nr0b2 and Sox9 in GSE168758.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

PPAR-gamma cistrome repression during activation of lung monocyte-macrophages in severe COVID-19. Desterke et al.

Supplemental tables 3, 4, 5 Supplemental S1 Data (R bioinformatics code) for iscience article ISCIENCE-D-20-0141