Adaptive Cartesian meshes for atmospheric single-column models: a study using Basilisk 18-02-16

It is well known that the representation of certain atmospheric conditions in climate and weather models can still suffer from the limited grid resolution that is facilitated by modern-day computer systems. Herein we study a simple one-dimensional analogy to those models by using a single-column model description of the atmosphere. The model employs an adaptive Cartesian mesh that applies a high-resolution mesh only when and where it is required. The so-called adaptive-grid model is described, and we report our findings obtained for tests to evaluate the representation of the atmospheric boundary layer, based on the first two GEWEX ABL Study (GABLS) inter-comparison cases. The analysis shows that the adaptive-grid algorithm is indeed able to dynamically coarsen and refine the numerical grid whilst maintaining an accurate solution. This is an interesting result as in reality, transitional dynamics (e.g. due to the diurnal cycle or due to changing synoptic conditions) are the rule rather than the exception.</p

NMD inhibition fails to identify tumour suppressor genes in microsatellite stable gastric cancer cell lines

BACKGROUND: Gastric cancers frequently show chromosomal alterations which can cause activation of oncogenes, and/or inactivation of tumour suppressor genes. In gastric cancer several chromosomal regions are described to be frequently lost, but for most of the regions, no tumour suppressor genes have been identified yet. The present study aimed to identify tumour suppressor genes inactivated by nonsense mutation and deletion in gastric cancer by means of GINI (gene identification by nonsense mediated decay inhibition) and whole genome copy number analysis. METHODS: Two non-commercial gastric cancer cell lines, GP202 and IPA220, were transfected with siRNA directed against UPF1, to specifically inhibit the nonsense mediated decay (NMD) pathway, and with siRNA directed against non-specific siRNA duplexes (CVII) as a control. Microarray expression experiments were performed in triplicate on 4 × 44 K Agilent arrays by hybridizing RNA from UPF1-transfected cells against non-specific CVII-transfected cells. In addition, array CGH of the two cell lines was performed on 4 × 44K agilent arrays to obtain the DNA copy number profiles. Mutation analysis of GINI candidates was performed by sequencing. RESULTS: UPF1 expression was reduced for >70% and >80% in the GP202 and IPA220 gastric cancer cell lines, respectively. Integration of array CGH and microarray expression data provided a list of 134 and 50 candidate genes inactivated by nonsense mutation and deletion for GP202 and IPA220, respectively. We selected 12 candidate genes for mutation analysis. Of these, sequence analysis was performed on 11 genes. One gene, PLA2G4A, showed a silent mutation, and in two genes, CTSA and PTPRJ, missense mutations were detected. No nonsense mutations were detected in any of the 11 genes tested. CONCLUSION: Although UPF1 was substantially repressed, thus resulting in the inhibition of the NMD system, we did not find genes inactivated by nonsense mutations. Our results show that the GINI strategy leads to a high number of false positives

Education on organ donation and transplantation in primary school; teachers' support and the first results of a teaching module

Organ and tissue donation can also involve children. Because of its sensitivity, this topic requires careful decision making. Children have the ability to carefully reflect on this subject and enjoy participating in family discussions about it. Therefore, what children need is proper information. When schools are used to educate children about this subject, information about teacher support for this type of lesson along with its effects on the depth of family discussions is important.A questionnaire was sent to all 7,542 primary schools in the Netherlands. The goal was to gather information on teachers' perspectives about a neutral lesson devoted to organ and tissue donation, and also on the best age to start giving such a lesson. The second part of our study examined the effects of a newly developed lesson among 269 primary school pupils. The school response was 23%. Of these, 70% were positive towards a lesson; best age to start was 10-11 years. Pupils reported 20% more family discussions after school education and enjoyed learning more about this topic. There is significant support in primary schools for a school lesson on organ and tissue donation. Educational programs in schools support family discussions

Children's opinions about organ donation:a first step to assent?

Background: Parents have to decide about organ donation after the death of their child. Although most parents probably would like to respect their child's intentions, parents often are not aware of their child's wishes. This requires insight into children's opinions about donation. Methods: An internet survey that investigated whether Dutch children in the age range of 12 through 15 years had heard about organ donation, what their opinions were on donation and whether the topic had been discussed at home. Questionnaire response rate 38%. Results: Around 99% of 2016 responders had heard about organ donation and about the possibility of becoming a donor, 75% preferred to decide for themselves about donation, 43% had discussed organ donation more than once at home, 66% were willing to donate. The willingness to donate was positively associated with age and socio-economic status. Conclusion: This survey indicates that these children at 12 through 15 years of age are capable and willing to think about organ donation. Thought should be given about how to raise awareness and how to enable parents and children to develop some sort of health literacy concerning the concept of organ donation. Children and their parents should be given adequate opportunities to receive appropriate information, suited to their psychological and moral developmental status

Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

Objective: This study aimed to identify the oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of 20q gain on mRNA expression of genes in this amplicon. Methods: Segmentation of DNA copy number changes on 20q was performed by array CGH (comparative genomic hybridisation) in 34 non-progressed colorectal adenomas, 41 progressed adenomas (ie, adenomas that present a focus of cancer) and 33 adenocarcinomas. Moreover, a robust analysis of altered expression of genes in these segments was performed by microarray analysis in 37 adenomas and 31 adenocarcinomas. Protein expression was evaluated by immunohistochemistry on tissue microarrays. Results: The genes C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5, mapping at 20q, were significantly overexpressed in carcinomas compared with adenomas as a consequence of copy number gain of 20q. Conclusion: This approach revealed C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5 genes to be important in chromosomal instability-related adenoma to carcinoma progression. These genes therefore may serve as highly specific biomarkers for colorectal cancer with potential clinical applications

Reduced genomic tumor heterogeneity after neoadjuvat chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma

Neoadjuvant chemo(radio)therapy followed by surgery is the standard of care for patients with locally advanced resectable esophageal adenocarcinoma (EAC). There is increasing evidence that drug resistance might be related to genomic heterogeneity. We investigated whether genomic tumor heterogeneity is different after cytotoxic chemotherapy and is associated with EAC patient survival. We used arrayCGH and a quantitative assessment of the whole genome DNA copy number aberration patterns (‘DNA copy number entropy’) to establish the level of genomic tumor heterogeneity in 80 EAC treated with neoadjuvant chemotherapy followed by surgery (CS group) or surgery alone (S group). The association between DNA copy number entropy, clinicopathological variables and survival was investigated. DNA copy number entropy was reduced after chemotherapy, even if there was no morphological evidence of response to therapy (p<0.001). Low DNA copy number entropy was associated with improved survival in the CS group (p=0.011) but not in the S group (p=0.396). Our results suggest that cytotoxic chemotherapy reduces DNA copy number entropy, which might be a more sensitive tumor response marker than changes in the morphological tumor phenotype. The use of DNA copy number entropy in clinical practice will require validation of our results in a prospective study