Modeling storm surges in the Belgian coastal area: preliminary work

Water Qualit

A framework to model thermomechanical coupled of fracture and martensite transformation in austenitic microstructures

A fully thermomechanical coupled phase-field (PF) model is presented to investigate the mechanism of austenite-to-martensite phase transformation (MPT) and crack initiation as well as its propagation in pure austenitic microstructures. The latent heat release and absorption involved in the MPT are explicitly taken into account by coupling the PF model with transient latent heat transfer. In order to consider temperature dependency in the PF model for MPT, a temperature-dependent Landau polynomial function, whose parameters are identified using molecular dynamics (MD) simulations, is proposed. Furthermore, the fracture surface energy is approximated based on the second-order PF model and then, the temporal evolution of the damage variable is given by the variational derivative of the total potential free energy of the system with respect to the damage variable. The achieved numerical results demonstrate that the model can be employed to predict the fracture mechanism of austenitic microstructures under a thermomechanical field in a multiphysics environment. The results reveal that the temperature has a tremendous impact on the growth rate of both martensitic variants and consequently on the crack growth path. The key contributions of this work are to shed light on the impact of thermal boundary conditions on the coupled process of MPT, crack initiation and growth

Gene mutations in stool from gastric and colorectal neoplasia patients by next-generation sequencing

AIM To study cancer hotspot mutations by next-generation sequencing (NGS) in stool DNA from patients with different gastrointestinal tract (GIT) neoplasms. METHODS Stool samples were collected from 87 Finnish patients diagnosed with various gastric and colorectal neoplasms, including benign tumors, and from 14 healthy controls. DNA was isolated from stools by using the PSP (R) Spin Stool DNA Plus Kit. For each sample, 20 ng of DNA was used to construct sequencing libraries using the Ion AmpliSeq Cancer Hotspot Panel v2 or Ion AmpliSeq Colon and Lung Cancer panel v2. Sequencing was performed on Ion PGM. Torrent Suite Software v.5.2.2 was used for variant calling and data analysis. RESULTS NGS was successful in assaying 72 GIT samples and 13 healthy controls, with success rates of the assay being 78% for stomach neoplasia and 87% for colorectal tumors. In stool specimens from patients with gastric neoplasia, five hotspot mutations were found in APC, CDKN2A and EGFR genes, in addition to seven novel mutations. From colorectal patients, 20 mutations were detected in AKT1, APC, ERBB2, FBXW7, KIT, KRAS, NRAS, SMARCB1, SMO, STK11 and TP53. Healthy controls did not exhibit any hotspot mutations, except for two novel ones. APC and TP53 were the most frequently mutated genes in colorectal neoplasms, with five mutations, followed by KRAS with two mutations. APC was the most commonly mutated gene in stools of patients with premalignant/benign GIT lesions. CONCLUSION Our results show that in addition to colorectal neoplasms, mutations can also be assayed from stool specimens of patients with gastric neoplasms.Peer reviewe

Simultaneous Underexpression of let-7a-5p and let-7f-5p microRNAs in Plasma and Stool Samples from Early Stage Colorectal Carcinoma: Supplementary Issue: Biomarkers for Colon Cancer

Colorectal cancer (CRC) is the third most common malignancy and the second most common cause of cancer death worldwide. Early detection of CRC can improve patient survival rates; thus, the identification of noninvasive diagnostic markers is urgently needed. MicroRNAs (miRNAs) have extensive potential to diagnose several diseases, including cancer. In this study, we compared the expression pattern of miRNAs from plasma and stool samples of patients with early stages of CRC (I, II) with that of healthy subjects. We performed miRNA profiling using microarrays on plasma and stool samples of eight patients with CRC and four healthy subjects. Seven miRNAs were found to be underexpressed in both plasma and stool samples of patients with CRC versus healthy subjects. Then, we aimed to verify two out of these seven differentially expressed miRNAs (let-7a-5p and let-7f-5p) by quantitative reverse transcriptase polymerase chain reaction on a larger set of plasma and stool samples of 51 patients with CRC and 26 healthy subjects. We confirmed the results of microarray analysis since their expression was significantly lower in stool and plasma samples of patients with CRC. Moreover, receiver operating characteristic curve analysis demonstrated that fecal let-7f expression levels have significant sensitivity and specificity to distinguish between patients with CRC and healthy subjects. In conclusion, if the results are confirmed in larger series of patients, underexpressed let-7a-5p and let-7f-5p miRNAs in both plasma and stool samples of patients with CRC may serve potentially as noninvasive molecular biomarkers for the early detection of CRC.Peer reviewe

Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms

Background: Microbial ecosystems that inhabit the human gut form central component of our physiology and metabolism, regulating and modulating both health and disease. Changes or disturbances in the composition and activity of this gut microbiota can result in altered immunity, inflammation, and even cancer. Aim: To compare the composition and diversity of gut microbiota in stool samples from patient groups based on the site of neoplasm in the gastrointestinal tract (GIT) and to assess the possible contribution of the bacterial composition to tumorigenesis. Methods: We studied gut microbiota by16S RNA gene sequencing from stool DNA of 83 patients, who were diagnosed with different GIT neoplasms, and 13 healthy individuals. Results: As compared to healthy individuals, stools of patients with stomach neoplasms had elevated levels of Enterobacteriaceae, and those with rectal neoplasms had lower levels of Bifidobacteriaceae. Lower abundance of Lactobacillaceae was seen in patients with colon neoplasms. Abundance of Lactobacillaceae was higher in stools of GIT patients sampled after cancer treatment compared to samples collected before start of any treatment. In addition to site-specific differences, higher abundances of Ruminococcus, Subdoligranulum and lower abundances of Lachnoclostridium and Oscillibacter were observed in overall GIT neoplasms as compared to healthy controls Conclusion: Our study demonstrates that the alterations in gut microbiota vary according to the site of GIT neoplasm. The observed lower abundance of two common families, Lactobacillaceae and Bifidobacteriaceae, and the increased abundance of Enterobacteriaceae could provide indicators of compromised gut health and potentially facilitate GIT disease monitoring.Peer reviewe

Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms

Background: Microbial ecosystems that inhabit the human gut form central component of our physiology and metabolism, regulating and modulating both health and disease. Changes or disturbances in the composition and activity of this gut microbiota can result in altered immunity, inflammation, and even cancer.Aim: To compare the composition and diversity of gut microbiota in stool samples from patient groups based on the site of neoplasm in the gastrointestinal tract (GIT) and to assess the possible contribution of the bacterial composition to tumorigenesis.Methods: We studied gut microbiota by16S RNA gene sequencing from stool DNA of 83 patients, who were diagnosed with different GIT neoplasms, and 13 healthy individuals.Results: As compared to healthy individuals, stools of patients with stomach neoplasms had elevated levels of Enterobacteriaceae, and those with rectal neoplasms had lower levels of Bifidobacteriaceae. Lower abundance of Lactobacillaceae was seen in patients with colon neoplasms. Abundance of Lactobacillaceae was higher in stools of GIT patients sampled after cancer treatment compared to samples collected before start of any treatment. In addition to site-specific differences, higher abundances of Ruminococcus, Subdoligranulum and lower abundances of Lachnoclostridium and Oscillibacter were observed in overall GIT neoplasms as compared to healthy controlsConclusion: Our study demonstrates that the alterations in gut microbiota vary according to the site of GIT neoplasm. The observed lower abundance of two common families, Lactobacillaceae and Bifidobacteriaceae, and the increased abundance of Enterobacteriaceae could provide indicators of compromised gut health and potentially facilitate GIT disease monitoring.</p

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection

The response to respiratory viruses varies substantially between individuals, and there are currently no known molecular predictors from the early stages of infection. Here we conduct a community-based analysis to determine whether pre- or early post-exposure molecular factors could predict physiologic responses to viral exposure. Using peripheral blood gene expression profiles collected from healthy subjects prior to exposure to one of four respiratory viruses (H1N1, H3N2, Rhinovirus, and RSV), as well as up to 24 h following exposure, we find that it is possible to construct models predictive of symptomatic response using profiles even prior to viral exposure. Analysis of predictive gene features reveal little overlap among models; however, in aggregate, these genes are enriched for common pathways. Heme metabolism, the most significantly enriched pathway, is associated with a higher risk of developing symptoms following viral exposure. This study demonstrates that pre-exposure molecular predictors can be identified and improves our understanding of the mechanisms of response to respiratory viruses

Eulerian Oil Spills Model Using Finite-Volume Method with Moving Boundary and Wet-Dry Fronts

The world production of crude oil is about 3 billion tons per year. The overall objective of the model in present study is supporting the decision makers in planning and conducting preventive and emergency interventions. The conservative equation for the slick dynamics was derived from layer-averaged Navier-Stokes (LNS) equations, averaged over the slick thickness. Eulerian approach is applied across the model, based on nonlinear shallow water Reynolds-averaged Navier-Stokes (RANS) equations. Depth-integrated standard k-ε turbulence schemes have been included in the model. Wetting and drying fronts of intertidal zone and moving boundary are treated within the numerical model. A highly accurate algorithm based on a fourth-degree accurate shape function has been used through an alternating-direction implicit (ADI) scheme which separates the operators into locally one-dimensional (LOD) components. The solution has been achieved by the application of KPENTA algorithm for the set of the flow equations which constitutes a pentadiagonal matrix. Hydrodynamic model was validated for a channel with a sudden expansion in width. For validation of oil spill model, predicted results are compared with experimental data from a physical modeling of oil spill in a laboratory wave basin under controlled conditions

Enhancing the management response to oil spills in the Tuscany Archipelago through operational modelling

none5siA new approach towards the management of oil pollution accidents in marine sensitive areas is presented in this work. A set of nested models in a downscaling philosophy was implemented, externally forced by existing regional operational products. The 3D hydrodynamics, turbulence and the oil transport/weathering models are all linked in the same system, sharing the same code, exchanging information in real time and improving its ability to correctly reproduce the spill. A wind-generated wave model is also implemented using the same downscaling philosophy. Observations from several sources validated the numerical components of the system. The results obtained highlight the good performance of the system and its ability to be applied for oil spill forecasts in the region. The success of the methodology described in this paper was underline during the Costa Concordia accident, where a high resolution domain was rapidly created and deployed inside the system covering the accident site. © 2014 Elsevier Ltd.noneJaneiro, João*; Zacharioudaki, Anna; Sarhadi, Ehsan; Sepp Neves, Antonio Augusto; Martins, FlávioJaneiro, João*; Zacharioudaki, Anna; Sarhadi, Ehsan; Sepp Neves, Antonio Augusto; Martins, Flávi