A new scientific initiative with the Pelagic RAC to develop a management plan for western horse mackerel

This article was originally published by ICES on their website http://www.ices.dk/.The western horse mackerel stock is currently managed by annual TACs covering only part of its distribution area. No stock assessment has been accepted and recent ICES advice has consistently been for status quo catches. In 2006, the Pelagic Regional Advisory Committee asked scientists to help with developing a harvest control rule for the stock that would both meet conservation and stability objectives. An initial questionnaire was circulated to the industry, to elicit feedback on possible management options. A series of Harvest Control Rules were developed. These were tested by simulation and presented to the RAC at a number of meetings. Results will be presented within the ICES advisory process and elsewhere in the scientific literature. This is a developing approach involving scientists and stakeholders in an iterative process. The problems encountered and lessons learned, are discussed

Spatial interplay of lymphocytes and fibroblasts in estrogen receptor-positive HER2-negative breast cancer

In estrogen-receptor-positive, HER2-negative (ER+HER2−) breast cancer, higher levels of tumor infiltrating lymphocytes (TILs) are often associated with a poor prognosis and this phenomenon is still poorly understood. Fibroblasts represent one of the most frequent cells in breast cancer and harbor immunomodulatory capabilities. Here, we evaluate the molecular and clinical impact of the spatial patterns of TILs and fibroblast in ER+HER2− breast cancer. We used a deep neural network to locate and identify tumor, TILs, and fibroblasts on hematoxylin and eosin-stained slides from 179 ER+HER2− breast tumors (ICGC cohort) together with a new density estimation analysis to measure the spatial patterns. We clustered tumors based on their spatial patterns and gene set enrichment analysis was performed to study their molecular characteristics. We independently assessed the spatial patterns in a second cohort of ER+HER2− breast cancer (N = 630, METABRIC) and studied their prognostic value. The spatial integration of fibroblasts, TILs, and tumor cells leads to a new reproducible spatial classification of ER+HER2− breast cancer and is linked to inflammation, fibroblast meddling, or immunosuppression. ER+HER2− patients with high TIL did not have a significant improved overall survival (HR = 0.76, P = 0.212), except when they had received chemotherapy (HR = 0.447). A poorer survival was observed for patients with high fibroblasts that did not show a high level of TILs (HR = 1.661, P = 0.0303). Especially spatial mixing of fibroblasts and TILs was associated with a good prognosis (HR = 0.464, P = 0.013). Our findings demonstrate a reproducible pipeline for the spatial profiling of TILs and fibroblasts in ER+HER2− breast cancer and suggest that this spatial interplay holds a decisive role in their cancer-immune interactions

Low-risk susceptibility alleles in 40 human breast cancer cell lines

Background: Low-risk breast cancer susceptibility alleles or SNPs confer only modest breast cancer risks ranging from just over 1.0 to 1.3 fold. Yet, they are common among most populations and therefore are involved in the development of essentially all breast cancers. The mechanism by which the low-risk SNPs confer breast cancer risks is currently unclear. The breast cancer association consortium BCAC has hypothesized that the low-risk SNPs modulate expression levels of nearby located genes. Methods: Genotypes of five low-risk SNPs were determined for 40 human breast cancer cell lines, by direct sequencing of PCR-amplified genomic templates. We have analyzed expression of the four genes that are located nearby the low-risk SNPs, by using real-time RT-PCR and Human Exon microarrays. Results: The SNP genotypes and additional phenotypic data on the breast cancer cell lines are presented. We did not detect any effect of the SNP genotypes on expression levels of the nearby-located genes MAP3K1, FGFR2, TNRC9 and LSP1. Conclusion: The SNP genotypes provide a base line for functional studies in a well-characterized cohort of 40 human breast cancer cell lines. Our expression analyses suggest that a putative disease mechanism through gene expression modulation is not operative in breast cancer cell lines

Spatial interplay of lymphocytes and fibroblasts in estrogen receptor-positive HER2-negative breast cancer

In estrogen-receptor-positive, HER2-negative (ER+HER2−) breast cancer, higher levels of tumor infiltrating lymphocytes (TILs) are often associated with a poor prognosis and this phenomenon is still poorly understood. Fibroblasts represent one of the most frequent cells in breast cancer and harbor immunomodulatory capabilities. Here, we evaluate the molecular and clinical impact of the spatial patterns of TILs and fibroblast in ER+HER2− breast cancer. We used a deep neural network to locate and identify tumor, TILs, and fibroblasts on hematoxylin and eosin-stained slides from 179 ER+HER2− breast tumors (ICGC cohort) together with a new density estimation analysis to measure the spatial patterns. We clustered tumors based on their spatial patterns and gene set enrichment analysis was performed to study their molecular characteristics. We independently assessed the spatial patterns in a second cohort of ER+HER2− breast cancer (N = 630, METABRIC) and studied their prognostic value. The spatial integration of fibroblasts, TILs, and tumor cells leads to a new reproducible spatial classification of ER+HER2− breast cancer and is linked to inflammation, fibroblast meddling, or immunosuppression. ER+HER2− patients with high TIL did not have a significant improved overall survival (HR = 0.76, P = 0.212), except when they had received chemotherapy (HR = 0.447). A poorer survival was observed for patients with high fibroblasts that did not show a high level of TILs (HR = 1.661, P = 0.0303). Especially spatial mixing of fibroblasts and TILs was associated with a good prognosis (HR = 0.464, P = 0.013). Our findings demonstrate a reproducible pipeline for the spatial profiling of TILs and fibroblasts in ER+HER2− breast cancer and suggest that this spatial interplay holds a decisive role in their cancer-immune interactions

A mathematical model and analytical solution for the fixation of bacteria in biogrout

Biogrout is a new method for soil reinforcement, which is based on microbialinduced carbonate precipitation. Bacteria and reactants are flushed through the soil, resulting in calcium carbonate precipitation and consequent soil reinforcement. Bacteria are crucially important in the Biogrout process since they catalyse the reaction. Hence, to control the process, it is essential to know where the bacteria are located. The bacteria are possibly in suspension but can also be adsorbed or fixated on the matrix of the porous structure. In this article, a model is derived for the placement of bacteria. The model contains three phases of bacteria: bacteria in suspension, adsorbed bacteria and fixed bacteria. An analytical solution is derived for instantaneous reactions between these three phases. The analytical solution is compared to numerical simulations for finite reaction rates. For the numerical simulations the standard Galerkin Finite Element Method is used.Delft Institute of Applied MathematicsElectrical Engineering, Mathematics and Computer Scienc

Bacterial adhesion to inert thermoplastic surfaces

The adhesion of four bacterial species, two strains of each, to four hydrophobic thermoplastics was observed. Image analysis of adherent cells stained with acridine orange provided a rapid, direct and objective means of measuring adhesion to clear, translucent and opaque surfaces by calculating the percentage area of a microscopic field covered by cells (percentage coverage). There was a highly significant correlation (P>0.05) between percentage coverage value and adherent cell count (obtained manually) for both rods and cocci. Bacterial adhesion to thermoplastics appeared to be strain specific and was not related to polymer composition. Highest percentage coverage values were obtained using hydrophobic bacteria, and lowest using hydrophilic bacteria. There was no relationship between the origin of the organisms (culture collections or isolates from biomaterial-associated infections) and their ability to adhere, after cultivation in brain heart infusion broth. Many factors influence this ability: an awareness of all experimental variables is essential