Patterns of BAP1 protein expression provide insights into prognostic significance and the biology of uveal melanoma

Uveal melanoma (UM) is a rare aggressive intraocular tumour with a propensity for liver metastases, occurring in ∼50% of patients. The tumour suppressor BAP1 is considered to be key in UM progression. Herein, we present the largest study to date investigating cellular expression patterns of BAP1 protein in 165 UMs, correlating these patterns to prognosis. Full clinical, histological, genetic, and follow‐up data were available for all patients. BAP1 gene sequencing was performed on a subset of 26 cases. An independent cohort of 14 UMs was examined for comparison. Loss of nuclear BAP1 (nBAP1) protein expression was observed in 54% (88/165) UMs. nBAP1 expression proved to be a significant independent prognostic parameter: it identified two subgroups within monosomy 3 (M3) UM, which are known to have a high risk of metastasis. Strikingly, nBAP1‐positiveM3 UMs were associated with prolonged survival compared to nBAP1‐negative M3 UMs (Log rank, p = 0.014). nBAP1 protein loss did not correlate with a BAP1 mutation in 23% (6/26) of the UMs analysed. Cytoplasmic BAP1 protein (cBAP1) expression was also observed in UM: although appearing ‘predominantly diffuse’ in most nBAP1‐negative UM, a distinct ‘focal perinuclear’ expression pattern – localized immediately adjacent to the cis Golgi – was seen in 31% (18/59). These tumours tended to carry loss‐of‐function BAP1 mutations. Our study demonstrates loss of nBAP1 expression to be the strongest prognostic marker in UM, confirming its importance in UM progression. Our data suggest that non‐genetic mechanisms account for nBAP1 loss in a small number of UMs. In addition, we describe a subset of nBAP1‐negative UM, in which BAP1 is sequestered in perinuclear bodies, most likely within Golgi, warranting further mechanistic investigation

Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma

Uveal melanoma (UM) has well-characterised somatic copy number alterations (SCNA) in chromosomes 1, 3, 6 and 8, in addition to mutations in GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, SF3B1 and EIF1AX, most being linked to metastatic-risk. To gain further insight into the molecular landscape of UM, we designed a targeted next-generation sequencing (NGS) panel to detect SCNA and mutations in routine clinical UM samples. We compared hybrid-capture and amplicon-based target enrichment methods and tested a larger cohort of primary UM samples on the best performing panel. UM clinical samples processed either as fresh-frozen, formalin-fixed paraffin embedded (FFPE), small intraocular biopsies or following irradiation were successfully profiled using NGS, with hybrid capture outperforming the PCR-based enrichment methodology. We identified monosomy 3 (M3)-UM that were wild-type for BAP1 but harbored SF3B1 mutations, novel frameshift deletions in SF3B1 and EIF1AX, as well as a PLCB4 mutation outside of the hotspot on exon 20 coinciding with a GNAQ mutation in some UM. We observed samples that harboured mutations in both BAP1 and SF3B1, and SF3B1 and EIF1AX, respectively. Novel mutations were also identified in TTC28, KTN1, CSMD1 and TP53BP1. NGS can simultaneously assess SCNA and mutation data in UM, in a reliable and reproducible way, irrespective of sample type or previous processing. BAP1 and SF3B1 mutations, in addition to 8q copy number, are of added importance when determining UM patient outcome

Multicenter external validation of the liverpool uveal melanoma prognosticator online: An OOG collaborative study

Uveal melanoma (UM) is fatal in ~50% of patients as a result of disseminated disease. This study aims to externally validate the Liverpool Uveal Melanoma Prognosticator Online V3 (LUMPO3) to determine its reliability in predicting survival after treatment for choroidal melanoma when utilizing external data from other ocular oncology centers. Anonymized data of 1836 UM patients from seven international ocular oncology centers were analyzed with LUMPO3 to predict the 10-year survival for each patient in each external dataset. The analysts were masked to the patient outcomes. Model predictions were sent to an independent statistician to evaluate LUMPO3’s performance using discrimination and calibration methods. LUMPO3’s ability to discriminate between UM patients who died of metastatic UM and those who were still alive was fair-to-good, with C-statistics ranging from 0.64 to 0.85 at year 1. The pooled estimate for all external centers was 0.72 (95% confidence interval: 0.68 to 0.75). Agreement between observed and predicted survival probabilities was generally good given differences in case mix and survival rates between different centers. Despite the differences between the international cohorts of patients with primary UM, LUMPO3 is a valuable tool for predicting all-cause mortality in this disease when using data from external centers

Investigation of Adhesion and Tribological Behavior of Borided AISI 310 Stainless Steel

In the present study, the effects of the boriding process on adhesion and tribological properties of AISI 310 steel were investigated. Boriding was performed in a solid medium consisting of Ekabor-II powders at 1123 and 1323K for 2 and 6 h. The boride layer was characterized by optical microscopy, the X-ray diffraction technique and the micro-Vickers hardness tester. The X-ray diffraction analysis of the boride layers on the surface of the steels revealed the existence of FexBy, CrxBy and NixBy compounds. Depending on the chemical composition of substrates, the boride layer thickness on the surface of the AISI 310 steel was found to be 56.74 μm. The hardness of the boride compounds formed on the surface of the AISI 310 steel ranged from 1658 to 2284 HV0,1, whereas the Vickers hardness value of the untreated steel AISI 310 was 276 HV0,1. The wear tests were carried out in a ball-disc arrangement under a dry friction condition at room temperature with an applied load of 10N and with a sliding speed of 0.3 m/s, at a sliding distance of 1000m. The wear surfaces of the steel were analyzed using an SEM microscopy and X-ray energy dispersive spectroscopy EDS. It was observed that the wear rate of unborided and borided AISI 310 steel ranged from 4.57 to 71.42 mm3/Nm

A genetic programming approach to development of clinical prediction models: A case study in symptomatic cardiovascular disease

BACKGROUND:Genetic programming (GP) is an evolutionary computing methodology capable of identifying complex, non-linear patterns in large data sets. Despite the potential advantages of GP over more typical, frequentist statistical approach methods, its applications to survival analyses are rare, at best. The aim of this study was to determine the utility of GP for the automatic development of clinical prediction models. METHODS:We compared GP against the commonly used Cox regression technique in terms of the development and performance of a cardiovascular risk score using data from the SMART study, a prospective cohort study of patients with symptomatic cardiovascular disease. The composite endpoint was cardiovascular death, non-fatal stroke, and myocardial infarction. A total of 3,873 patients aged 19-82 years were enrolled in the study 1996-2006. The cohort was split 70:30 into derivation and validation sets. The derivation set was used for development of both GP and Cox regression models. These models were then used to predict the discrete hazards at t = 1, 3, and 5 years. The predictive ability of both models was evaluated in terms of their risk discrimination and calibration using the validation set. RESULTS:The discrimination of both models was comparable. At time points t = 1, 3, and 5 years the C-index was 0.59, 0.69, 0.64 and 0.66, 0.70, 0.70 for the GP and Cox regression models respectively. At the same time points, the calibration of both models, which was assessed using calibration plots and the generalization of the Hosmer-Lemeshow test statistic, was also comparable, but with the Cox model being better calibrated to the validation data. CONCLUSION:Using empirical data, we demonstrated that a prediction model developed automatically by GP has predictive ability comparable to that of manually tuned Cox regression. The GP model was more complex, but it was developed in a fully automated way and comprised fewer covariates. Furthermore, it did not require the expertise normally needed for its derivation, thereby alleviating the knowledge elicitation bottleneck. Overall, GP demonstrated considerable potential as a method for the automated development of clinical prediction models for diagnostic and prognostic purposes

Investigation of tribological behaviour of plasma paste boronized of AISI 8620, 52100 and 440C steels

370-376In the present study, AISI 8620, 52100 and 440C steels were plasma paste boronized (PPB) by using 100% borax paste. PPB process was carried out in a dc plasma system at temperature of 700 and 800<span style="font-family:Symbol; mso-ascii-font-family:" times="" new="" roman";mso-hansi-font-family:"times="" roman";="" mso-ansi-language:en-us;mso-char-type:symbol;mso-symbol-font-family:symbol"="" lang="EN-US">°C for 3 and 5 h in a gas mixture of 70%H2-30%Ar under a constant pressure of 4 mbar. Wear tests of the bearing steels were performed using a ball-on-disc test device. The applied loads on the ball were 5 and 20 N and the sliding time was 60 min for each test. Wear tests were carried out in the unlubricated and lubrication conditions at room temperature in air. Wear volume of the disc specimen was determined from the cross-sectional area of the wear track, obtained perpendicularly to the sliding direction. Worn surfaces of the samples were PPB characterized by scanning electron microscopy and the results were compared with those obtained for plasma paste boronized specimens. </span

Evaluation of 2,4-D removal via activated carbon from pomegranate husk/polymer composite hydrogel: Optimization of process parameters through face centered composite design

A new type of polymer composite hydrogel was prepared by introducing activated carbons from pomegranate husk into poly ((2-dimethylamino) ethyl methacrylate) network. The removal of 2,4-dichlorophenoxyacetic acid (2,4-D) from aqueous solution was studied with respect to pH of the media, initial 2,4-D concentration and activated carbon content into the polymeric network. Face centered composite design (FCCD) through response surface methodology (RSM) was used for designing the experiments as well as for studying the effects of the process parameters. A quadratic model and a two factor interaction design model were developed for the removal of 2,4-D and adsorption capacity, respectively. The optimum pH of the pesticide solution, activated carbon content into the polymeric network and initial concentration of 2,4-D were found as 3, 2.5 wt% and 100mg/L. 63.245% and 68.805 (mg/g) for the removal of 2,4-D and adsorption capacity were obtained by using Simplex optimization method. Furthermore, the surface characteristics of the adsorbent prepared under optimized conditions were examined by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR). © 2015, Korean Institute of Chemical Engineers, Seoul, Korea