Cluster analysis of multiplex ligation-dependent probe amplification data in choroidal melanoma.

PurposeTo determine underlying correlations in multiplex ligation-dependent probe amplification (MLPA) data and their significance regarding survival following treatment of choroidal melanoma (CM).MethodsMLPA data were available for 31 loci across four chromosomes (1p, 3, 6, and 8) in tumor material obtained from 602 patients with CM treated at the Liverpool Ocular Oncology Center (LOOC) between 1993 and 2012. Data representing chromosomes 3 and 8q were analyzed in depth since their association with CM patient survival is well-known. Unsupervised k-means cluster analysis was performed to detect latent structure in the data set. Principal component analysis (PCA) was also performed to determine the intrinsic dimensionality of the data. Survival analyses of the identified clusters were performed using Kaplan-Meier (KM) and log-rank statistical tests. Correlation with largest basal tumor diameter (LTD) was investigated.ResultsChromosome 3: A two-cluster (bimodal) solution was found in chromosome 3, characterized by centroids at unilaterally normal probe values and unilateral deletion. There was a large, significant difference in the survival characteristics of the two clusters (log-rank, p<0.001; 5-year survival: 80% versus 40%). Both clusters had a broad distribution in LTD, although larger tumors were characteristically in the poorer outcome group (Mann-Whitney, p<0.001). Threshold values of 0.85 for deletion and 1.15 for gain optimized the classification of the clusters. PCA showed that the first principal component (PC1) contained more than 80% of the data set variance and all of the bimodality, with uniform coefficients (0.28±0.03). Chromosome 8q: No clusters were found in chromosome 8q. Using a conventional threshold-based definition of 8q gain, and in conjunction with the chromosome 3 clusters, three prognostic groups were identified: chromosomes 3 and 8q both normal, either chromosome 3 or 8q abnormal, and both chromosomes 3 and 8q abnormal. KM analysis showed 5-year survival figures of approximately 97%, 80%, and 30% for these prognostic groups, respectively (log-rank, p<0.001). All MLPA probes within both chromosomes were significantly correlated with each other (Spearman, p<0.001).ConclusionsWithin chromosome 3, the strong correlation between the MLPA variables and the uniform coefficients from the PCA indicates a lack of evidence for a signature gene that might account for the bimodality we observed. We hypothesize that the two clusters we found correspond to binary underlying states of complete monosomy or disomy 3 and that these states are sampled by the complete ensemble of probes. Consequently, we would expect a similar pattern to emerge in higher-resolution MLPA data sets. LTD may be a significant confounding factor. Considering chromosome 8q, we found that chromosome 3 cluster membership and 8q gain as traditionally defined have an indistinguishable impact on patient outcome

Investigations towards incorporation of Eu3+ and Cm3+ during ZrO2 crystallization in aqueous solution

Nuclear energy provides a widely applied carbon-reduced energy source. Following operation, the spent nuclear fuel (SNF), containing a mixture of radiotoxic elements such as transuranics, needs to be safely disposed of. Safe storage of SNF in a deep geological repository (DGR) relies on multiple engineered and natural retention barriers to prevent environmental contamination. In this context, zirconia (ZrO2) formed on the SNF rod cladding, could be employed as an engineered barrier for immobilization of radionuclides via structural incorporation. This study investigates the incorporation of Eu3+ and Cm3+, representatives for trivalent transuranics, into zirconia by co-precipitation and crystallization in aqueous solution at 80 °C. Complementary structural and microstructural characterization has been carried out by powder X-ray diffraction (PXRD), spectrum imaging analysis based on energy-dispersive X-ray spectroscopy in scanning transmission electron microscopy mode (STEM-EDXS), and luminescence spectroscopy. The results reveal the association of the dopants with the zirconia particles and elucidate the presence of distinct bulk and superficially incorporated species. Hydrothermal aging for up to 460 days in alkaline media points to great stability of these incorporated species after initial crystallization, with no indication of phase segregation or release of Eu3+ and Cm3+ over time. These results suggest that zirconia would be a suitable technical retention barrier for mobilized trivalent actinides in a DGR

IoT based implemented comparison analysis of two well-known network platforms for smart home automation

The developments of the internet of things (IoT) technologies fascinated the universe and provided great opportunities to introduce these innovations in smart house networks. Smart home automation is highly required these days. Smart home automation is a collection of electronic devices connected to monitor and control in the market home appliance remotely. However, it is still needed to design a friendly and reliable system since the system mainly depends on the devices used and the environment of the network. NETPI and BLYNK are IoT frameworks used for hardware-agnostic with smartphones, websites, private clouds, system security, data mining, and deep learning. The results confirmed that NETPI provides flexibility to deal with several NODEMCU controllers in a single control framework. The proposed system shows its applicability in monitoring and controlling home appliances remotely

Whole-genome microarray detects deletions and loss of heterozygosity of chromosome 3 occurring exclusively in metastasizing uveal melanoma

PURPOSE. To detect deletions and loss of heterozygosity of chromosome 3 in a rare subset of fatal, disomy 3 uveal melanoma (UM), undetectable by fluorescence in situ hybridization (FISH). METHODS. Multiplex ligation-dependent probe amplification (MLPA) with the P027 UM assay was performed on formalinfixed, paraffin-embedded (FFPE) whole tumor sections from 19 disomy 3 metastasizing UMs. Whole-genome microarray analyses using a single-nucleotide polymorphism microarray (aSNP) were performed on frozen tissue samples from four fatal disomy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 years' metastasis-free survival. RESULTS. Two metastasizing UMs that had been classified as disomy 3 by FISH analysis of a small tumor sample were found on MLPA analysis to show monosomy 3. No ubiquitous gene deletions of chromosome 3 were seen in the remaining 17 metastasizing disomy 3 UMs by MLPA. aSNP analysis revealed 95 deleted genes and 16 genes with loss of heterozygosity (LOH) on chromosome 3 in the disomy 3 metastasizing UMs that were not deleted or showing LOH in the nonmetastatic tumors. CONCLUSIONS. MLPA can detect monosomy 3 cell populations in FFPE whole tumor sections previously missed by FISH performed on small tumor samples. Consistent deletion and LOH of genes on chromosome 3 occur in metastasizing disomy 3 UM and are detectable by aSNP analysis. Ninety-five genes were found to be deleted, and 16 genes showed LOH exclusively in disomy 3 metastasizing UM, suggesting a potential role for these genes in UM metastasis. (Invest Ophthalmol Vis Sci. 2010;51:4884 -4891) DOI:10.1167/iovs.09-5083 U veal melanoma (UM), the most common primary intraocular cancer in adults, is fatal in almost 50% of patients, because of metastatic spread often involving the liver. Chemotherapy of metastases has limited success 1,2 and disseminated disease is fatal in 92% of patients within 2 years of diagnosis. Clinical and histopathologic risk factors for UM metastasis include large basal tumor diameter (LBD), ciliary body involvement, epithelioid cytomorphology, extracellular matrix periodic acid-Schiff-positive (PAS ϩ ) loops, and high mitotic count. 3,4 Prescher et al. 3,6 -10 Consequently, fluorescence in situ hybridization (FISH) detection of chromosome 3 using a centromeric probe became routine practice for UM prognostication; however, 5% to 20% of disomy 3 UM patients unexpectedly develop metastases. We hypothesize that disomy 3 UMs that metastasize do so by the same mechanisms as metastasizing monosomy 3 UMs. However, instead of loss of a single copy of chromosome 3 facilitating this process, specific genes are deleted on chromosome 3 that are essential to an early progression to metastasis, not commonly seen in disomy 3 UM. The purpose of our study was to identify key MSGs that are deleted exclusively in a rare subset of UMs that metastasized despite apparent disomy 3 on FISH testing. We investigated whether deletions of chromosome 3 could be detected using either multiplex ligationdependent probe amplification (MLPA) or a single-nucleotide polymorphism microarray (aSNP; SNP 6.0; Affymetrix, Santa Clara, CA). Knowledge of such deletions on chromosome 3 may allow more accurate prognostication, increase understanding of the natural history of UM, and help identify aberrant cell signaling pathways that may be amenable to therapy. MATERIALS AND METHODS Tumor Samples Fresh primary UM samples were routinely obtained at the Royal Liverpool University Hospital between 2001 and 2007 and analyzed by FISH for chromosome 3 copy number. Of these UMs, formalin-fixed, paraffin-embedded (FFPE) tumor samples were available in our archive for 34 disomy 3 UMs that were known to have metastasized (Di3M-UM). Nineteen of these samples were selected for MLPA studies, as they provided sufficient extracted DNA (700 ng) for quality control PCR and analysis by MLPA in triplicate. Four snap-frozen Di3M-UM samples from patients with fatal metastasis within 5 years of diagnosis and samples from three disomy 3 surviving UM (Di3S-UM) patients with no detectable metastases after a minimum of 5 years since diagnosis were used for aSNP analysis. Personalized survival curves were generated for all three patients with disomy 3 nonmetastasizing UM using the Cox proportional hazards model. The model predicts survival up to 8 years after diagnosis and specifies 95% CI based on the following information: age at treatment, sex, ciliary body involvement, largest basal From th

Immunohistochemical analysis indicates that the anatomical location of B-cell non-Hodgkin's lymphoma is determined by differentially expressed chemokine receptors, sphingosine-1-phosphate receptors and integrins.

BackgroundThe aim of this study was to elucidate the mechanisms responsible for the location of B-cell non-Hodgkin's lymphoma (B-NHL) at different anatomical sites. We speculated that the malignant B cells in these disorders have the potential for trafficking between blood and secondary lymphoid organs (SLO) or extranodal sites and that their preferential accumulation at different locations is governed by the expression of key molecules that regulate the trafficking of normal lymphocytes.MethodsBiopsy or blood samples from 91 cases of B-NHL affecting SLO (n = 27), ocular adnexae (n = 51) or blood (n = 13) were analysed by immunohistochemistry or flow cytometry for the expression of the following molecules: CCR7, CCL21 and αL (required for the entry of normal lymphocytes into SLO); CXCR4, CXCL12 and α4 (required for entry into extranodal sites); CXCR5, CXCL13 and S1PR2 (required for tissue retention); S1PR1 and S1PR3 (required for egress into the blood). The expression of each of these molecules was then related to anatomical location and histological subtype.ResultsThe expression of motility/adhesion molecules varied widely between individual patient samples and correlated much more strongly with anatomical location than with histological subtype. SLO lymphomas [comprising 10 follicular lymphoma (FL), 8 diffuse large B-cell lymphoma (DLBCL), 4 mantle-cell lymphoma (MCL) and 5 marginal-zone lymphoma (MZL)] were characterised by pronounced over-expression of S1PR2, suggesting that the malignant cells in these lymphomas are actively retained at the site of clonal expansion. In contrast, the malignant B cells in ocular adnexal lymphomas (10 FL, 9 DLBCL, 4 MCL and 28 MZL) expressed a profile of molecules suggesting a dynamic process of trafficking involving not only tissue retention but also egress via S1PR3 and homing back to extranodal sites via CXCR4/CXCL12 and α4. Finally, leukaemic lymphomas (6 FL, 5 MCL and 2 MZL) were characterised by aberrant expression of the egress receptor S1PR1 and low expression of molecules required for tissue entry/retention.ConclusionsIn summary, our study strongly suggests that anatomical location in B-NHL is governed by the differential expression of specific adhesion/motility molecules. This novel observation has important implications for therapeutic strategies that aim to disrupt protective micro-environmental interactions

Small High-Risk Uveal Melanomas Have a Lower Mortality Rate

Our aim was to determine whether size impacts on the difference in metastatic mortality of genetically high-risk (monosomy 3) uveal melanomas (UM). We undertook a retrospective analysis of data from a patient cohort with genetically characterized UM. All patients treated for UM in the Liverpool Ocular Oncology Centre between 2007 and 2014, who had a prognostic genetic tumor analysis. Patients were subdivided into those with small (≤2.5 mm thickness) and large (>2.5 mm thickness) tumors. Survival analyses were performed using Gray rank statistics to calculate absolute probabilities of dying as a result of metastatic UM. The 5-year absolute risk of metastatic mortality of those with small monosomy 3 UM was significantly lower (23%) compared to the larger tumor group (50%) (p = 0.003). Small disomy 3 UM also had a lower absolute risk of metastatic mortality (0.8%) than large disomy 3 UM (6.4%) (p = 0.007). Hazard rates showed similar differences even with lead time bias correction estimates. We therefore conclude that earlier treatment of all small UM, particularly monosomy 3 UM, reduces the risk of metastatic disease and death. Our results would support molecular studies of even small UM, rather than ‘watch-and-wait strategies’

PEMAHAMAN MASYARAKAT PEDESAAN TERHADAP MANFAAT ASURANSI KESEHATAN DI INDONESIA: LITERATURE REVIEW

Masih minimnya pengetahuan masyarakat yang tinggal di daerah pedesaan terhadap asuransi kesehatan, sehingga masyarakat pedesaan tersebut cenderung kurang untuk menggunakan asuransi daripada masyarakat perkotaan. Masalah pemahaman ini tidak lepas dari karakteristik masyarakat pedesaan itu sendiri yang masih kental unsur agamanya dalam melihat aspek hukum asuransi. Penelitian ini bertujuan untuk menganalisis dan mengetahui sosialisasi seperti apa yang dapat dilakukan secara efektif dan efisien untuk menjangkau semua kelompok dan lapisan masyarakat. Penelitian ini merupakan literature review yang bersumber dari beberapa situs online seperti Google Scholar dan Garuda dengan memasukkan kata kunci “Pemahaman Masyarakat Desa”, “Asuransi Kesehatan”, dan “Manfaat Asuransi”. Kriteria inklusi yang digunakan adalah pemahaman masyarakat pedesaan terhadap manfaat asuransi kesehatan. Hasil yang ditemukan dari peneliti bahwa pemahaman masyarakat terkait asuransi berbeda-beda, beberapa masyarakat pedesaan telah paham tetapi banyak juga yang masih belum paham dan belum menyadari akan pentingnya manfaat asuransi kesehatan. Hal tersebut terjadi karena dipengaruhi oleh beberapa faktor seperti karakteristik individu, lingkungan sekitar, dan minimnya akses pelayanan kesehatan. Sehingga perlu adanya peningkatan edukasi dan sosialisasi kepada masyarakat desa mengenai manfaat asuransi kesehatan guna meningkatkan derajat kesehatan masyarakat

The emotional consequences of novel political identities: Brexit and mental health in the United Kingdom

AbstractFollowing the 2016 EU referendum on Britain's membership in the European Union, many people described themselves as “Leavers” or “Remainers.” Here, we examine the emotional responses associated with Brexit identities using survey data collected from two nationally representative samples of the British public in 2019 (N = 638) and 2021 (N = 2,058). Confirmatory factor analysis indicated that many in both samples had coherent Leave or Remain identities. Remain and, to a lesser extent, Leave identities (regardless of how people actually voted in the referendum) predicted distress about Brexit‐related events and clinical symptoms of depression and anxiety at both time points. Structural equation models suggested that the effect of identities on symptoms was largely mediated by distress about Brexit‐related events. We demonstrate a lasting impact of Brexit on the mental health of UK citizens and show that the formation of novel political identities has been more important in this process than voting behavior.</jats:p

Genetic Associations With Diabetic Retinopathy and Coronary Artery Disease in Emirati Patients With Type-2 Diabetes Mellitus

Aim: Type 2 Diabetes Mellitus (T2DM) is associated with both microvascular complications such as diabetic retinopathy (DR), and macrovascular complications like coronary artery disease (CAD). Genetic risk factors have a role in the development of these complications. In the present case-control study, we investigated genetic variations associated with DR and CAD in T2DM patients from the United Arab Emirates.Methods: A total of 407 Emirati patients with T2DM were recruited. Categorization of the study population was performed based on the presence or absence of DR and CAD. Seventeen Single Nucleotide Polymorphisms (SNPs), were selected for association analyses through search of publicly available databases, namely GWAS catalog, infinome genome interpretation platform and GWAS Central database. A multivariate logistic regression test was performed to evaluate the association between the 17 SNPs and DR, CAD, or both. To account for multiple testing, significance was set at p &lt; 0.00294 using the Bonferroni correction.Results: The SNPs rs9362054 near the CEP162 gene and rs4462262 near the UBE2D1 gene were associated with DR (OR = 1.66, p = 0.001; OR = 1.37, p = 0.031; respectively), and rs12219125 near the PLXDC2 gene was associated (suggestive) with CAD (OR = 2.26, p = 0.034). Furthermore, rs9362054 near the CEP162 gene was significantly associated with both complications (OR = 2.27, p = 0.0021). The susceptibility genes for CAD (PLXDC2) and DR (UBE2D1) have a role in angiogenesis and neovascularization. Moreover, association between the ciliary gene CEP162 and DR was established in terms of retinal neural processing, confirming previous reports.Conclusions: The present study reports associations of different genetic loci with DR and CAD. We report new associations between CAD and PLXDC2, and DR with UBE2D1 using data from T2DM Emirati patients