A user guide for the online exploration and visualization of PCAWG data.

The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we provide a user's guide to the five publicly available online data exploration and visualization tools introduced in the PCAWG marker paper. These tools are ICGC Data Portal, UCSC Xena, Chromothripsis Explorer, Expression Atlas, and PCAWG-Scout.

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2.

The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.

The UCSC Cancer Genomics Browser: update 2015.

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover and share their research observations.

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.

The Cancer Genomics Hub (CGHub) is the online repository of the sequencing programs of the National Cancer Institute (NCI), including The Cancer Genomics Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE) and the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects, with data from 25 different types of cancer. The CGHub currently contains >1.4 PB of data, has grown at an average rate of 50 TB a month and serves >100 TB per week.

Effect of thermal treatment and frozen storage on lipid decomposition of light and dark muscles of saithe (Pollachius virens).

Lipid decomposition of saithe (Pollachius virens) light and dark muscles was monitored during frozen storage at -25°C of raw (up to 18 months) and cooked products. Samples were cooked after 0, 6 and 12 months raw storage then refrozen and stored at -25°C for 12 months to determine the stability of cooked-then-stored samples. Fatty acid profiles, formation of hydroperoxides (PV), thiobarbituric acid reactive substances (TBARS), fluorescence compounds (OFR) and free fatty acids (FFA) were evaluated throughout the storage for all samples.

Effects of temperature during frozen storage on lipid deterioration of saithe (Pollachius virens) and hoki (Macruronus novaezelandiae) muscles.

Lipid deterioration of two lean fish species, saithe (Pollachius virens) and hoki (Macruronus novaezelandiae), during frozen storage at -20 and -30°C (up to 18months) was studied. Lipid composition, lipid oxidation and hydrolysis, and sensory attributes were evaluated on both light and dark muscles of the fish species. Results showed significant lipid deterioration with extended storage time, but lower storage temperature showed significantly more preservative effects.

Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser.

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) offers interactive visualization and exploration of TCGA genomic, phenotypic, and clinical data, as produced by the Cancer Genome Atlas Research Network.

The UCSC Cancer Genomics Browser: update 2013.

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a set of web-based tools to display, investigate and analyse cancer genomics data and its associated clinical information.

Glycidyl esters in refined palm (Elaeis guineensis) oil and related fractions. Part II: practical recommendations for effective mitigation.

In a previous work, it was shown that at high temperatures (up to 280°C) glycidyl esters (GE) are formed from diacylglycerols (DAG) via elimination of free fatty acid (FFA). In the present study, the impact of DAG content and temperature on the formation of GE using a model vacuum system mimicking industrial edible oil deodorization is investigated. These deodorization experiments confirmed that the formation of GE from DAG is extensive at temperatures above 230-240°C, and therefore, this value should be considered as an upper limit for refining operations.

Factors impacting the formation of monochloropropanediol (MCPD) fatty acid diesters during palm (Elaeis guineensis) oil production.

Recently, organic and inorganic chlorinated compounds were detected in crude and commercially refined palm oils. Further, the predominant formation mechanism of monochloropropanediol (MCPD) diesters at high temperatures (>170-180°C) was revealed. The present study involved the development and comparison of solutions to mitigate MCPD diester levels in oils from various stages of palm oil production.

Formation mechanisms of monochloropropanediol (MCPD) fatty acid diesters in refined palm (Elaeis guineensis) oil and related fractions.

Monochloropropanediol (MCPD) fatty acid esters are process contaminants generated during the deodorisation of edible oils. In particular, MCPD diesters are found in higher abundance in refined palm oil than other edible oils. In the present study, a series of model reactions mimicking palm oil deodorisation has been conducted with pure acylglycerols in the presence or absence of either organic or inorganic chlorine-containing compounds.

The UCSC Cancer Genomics Browser: update 2011.

The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data.

Antioxidant properties of extracts obtained from raw, dry-roasted, and oil-roasted US peanuts of commercial importance.

Raw, skinless peanut kernels from US commercial production lines were dry- and oil-roasted according to standard industrial practices. Eighty percent (v/v) methanolic extracts from the peanut cultivars were prepared and characterized by RP-HPLC: five predominant compounds were found comprising free p-coumaric acid and potential p-coumaric acid derivatives, as elucidated by DAD-UV spectra with comparisons to those of commercial standards. A Spanish high-oleic peanut possessed the greatest naturally-occurring level of p-coumaric acid and its derivatives, followed by a high-oleic Runner, a normal Runner, and a Virginia peanut.