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Additional file 2:Evidence of subclonal heterogeneity from RNA-Seq data across a collection of melanoma samples. Allelic imbalance along each gene demonstrates subclonal heterogeneity. The score of the non-reference nucleotide has been calculated as 0.5- | 0.5 - (#B/(#B+#A)) |, where #A and #B are the numbers of reads hosting the reference and non-reference nucleotide respectively. However, all the reported genes have a multimodal distribution of B-allele frequencies along at least one exon. The B-allele frequencies close to 0.5 have been marked in grey, B-alleles that significantly deviate from this cluster are considered acquired somatic mutations (black) and can be explained by subclonal heterogeneity. Vertical bars represent 95% confidence intervals. All non-reference nucleotides shown are supported by at least 100 reads. Vertical dashed lines mark the boundaries between exons in the transcript. (PDF 46 KB)

Additional file 1:Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies. Comparing the M-Measure-based approach to a state-of-the-art CNA algorithm by testing their ability to identify de novo aberrations in SNP-array signals from an evolving tumor at two time points. (DOC 820 KB)

Wine is a product of grape juice fermentation by yeast. Terroir is a term that encompasses all environmental factors and interactions at a specific geographical site, resulting in the development of regional-specific microbial strains and differences in grape phenotypes. The objectives of this study were to determine the distribution of vineyard-associated wine yeast strains, identify potential regional-specific wine yeast strains and characterize the flavonoid profile of Pinot Noir grapes among three different sub-regions in the Okanagan Valley (OV), a major wine region in British Columbia, Canada, in the 2017 vintage. Grape samples were collected from thirteen vineyards among three sub-regions of the OV, namely Kelowna (KE), Naramata-Penticton (NP) and Oliver-Osoyoos (OO), within a week prior to the winery harvesting date, which occurred between September 2017 and October 2017. Vineyard-associated S. cerevisiae and S. uvarum on the grape samples were enriched and isolated from spontaneous fermentations conducted in the lab. The isolates were genotyped by microsatellite analysis. Regional-specific wine yeast strains were differentiated from commercial wine yeast strains using Bruvo’s genetic distance. The anthocyanin and flavonol profiles of Pinot Noir grapes were analyzed by HPLC/UV-vis/MS and the tannin profile was analyzed by a spectrophotometric method. In total, 10 commercial S. cerevisiae strains, 22 potentially indigenous S. cerevisiae strains, 2 previously isolated S. uvarum strains from OV, 1 previously isolated S. uvarum strain from Hornby Island and 2 newly discovered S. uvarum strains were isolated in this study. S. cerevisiae strains is genetically more closely related within each sub-region as compared to between sub-regions. The population structure of the S. cerevisiae strains was significant at the regional level. The anthocyanin content were significantly lower in Pinot Noir grapes isolated from OO as compared to KE. Furthermore, the relative abundance of methoxylated anthocyanin and flavonol compounds were higher in Pinot Noir grapes collected in OO as compared to KE. Therefore, the flavonoid profile of Pinot Noir grapes was significantly affected by sub-regional terroirs. Further research is required to determine how regional-specific wine yeast strains and the flavonoid profile of Pinot Noir grapes affect the quality of wine production in the OV.

More than ten years after the initial description of the humoral theory of transplantation by Dr. Paul I. Terasaki, the significance of humoral alloimmunity in liver transplantation has yet to be clearly defined. The liver allograft has an inherent tolerogenic capacity which confers its resistance to cell-mediated as well as antibody-mediated rejection. Nevertheless, the protection against alloimmunity is not complete, and antibody-mediated tissue injury can occur in the liver graft under specific circumstances. In this article the evidence on the clinicopathologic effects of donor-specific alloantibodies in liver transplantation will be examined and interpreted in parallel with lessons learned from renal transplantation. The unique anatomic and immunologic features of the liver will be reviewed to gain new insights into the complex interactions between humoral immune system and the liver allograft.

Assessments of physiological parameters before, during and after ischemia (MCAO) in control and PSR pre-treated rats. Figure S1. Representative TTC-stained brain slices for sham and MCAO rats, with the latter animals divided into 4 groups that were pre-treated with vehicle, 1.1 g/kg, 2.2 g/kg or 5.5 g/kg PSR. Figure S2. Representative TTC-stained brain slices for sham and MCAO rats, with the latter animals divided into 4 groups that were post-treated with vehicle, 1.1 g/kg, 2.2 g/kg or 5.5 g/kg PSR. (DOCX 3065 kb)

Acadia and University Apartments of the University of British Columbia (UBC) are home to some 800 families. Each month there is a heavy influx and efflux of families due to the temporary nature of the housing. As a result, it’s difficult to ensure composting awareness and practice remains steady among residents. To increase awareness of composting at UBC, and specifically in the Acadia Family Residences and University Apartments, we designed an informational article about composting, a survey for the residents of Acadia to evaluate their composting awareness and habits, and a children’s activity page. The adult information page, the survey, and the children’s activity page were added to the April edition of Acadia’s monthly newsletter and distributed April 1st, 2007. Upon return of our surveys (April 8th, 2007), it was determined that the majority of the residents were interested in improving composting practices in their residence. We collaborated with Carol Young, the Residence Life Manager at Acadia Family Housing, to provide practical solutions to increase the awareness and incidence of composting at this housing unit. We would recommend that upcoming students continue to strengthen this relationship and work together with Ms. Young to further facilitate composting at Acadia and University Apartments. We believe this is a relatively untapped population that can aid in increasing composting and decreasing waste at the University of British Columbia. Disclaimer: “UBC SEEDS provides students with the opportunity to share the findings of their studies, as well as their opinions, conclusions and recommendations with the UBC community. The reader should bear in mind that this is a student project/report and is not an official document of UBC. Furthermore readers should bear in mind that these reports may not reflect the current status of activities at UBC. We urge you to contact the research persons mentioned in a report or the SEEDS Coordinator about the current status of the subject matter of a project/report.”

Additional file of Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies

Additional file of Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies