The Role of the UBC Library in Scholarly Research

A discussion paper prepared by the UBC Library’s Working Group on the Role of the Library in Scholarly Research about three distinct yet intertwining roles – a consulting/supportive role; a collaborative role; and, a scholarly professional role.Library, UBCUnreviewedFacult

PET CT Thresholds for Radiotherapy Target Definition in Non-Small-Cell Lung Cancer: How Close are we to the Pathologic Findings?

Purpose: Optimal target delineation threshold values for positron emission tomography (PET) and computed tomography (CT) radiotherapy planning is controversial. In this present study, different PET CT threshold values were used for target delineation and then compared pathologically. Methods and Materials: A total of 31 non-small-cell lung cancer patients underwent PET CT before surgery. The maximal diameter (MD) of the pathologic primary tumor was obtained. The CT-based gross tumor volumes (GTVCT) were delineated for CT window-level thresholds at 1,600 and -300 Hounsfield units (HU) (GTVCT1); 1,600 and -400 (GTVCT2); 1,600 and -450 HU (GTVCT3); 1,600 and -600 HU (GTVCT4); 1,200 and -700 HU (GTVCT5); 900 and -450 HU (GTVCT6); and 700 and -450 HU (GTVCT7). The PET-based GTVs (GTVPET) were autocontoured at 20% (GTV20), 30% (GTV30), 40% (GTV40), 45% (GTV45), 50% (GTV50), and 55% (GTV55) of the maximal intensity level. The MD of each image-based GTV in three-dimensional orientation was determined. The MD of the GTVPET and GTVCT were compared with the pathologically determined MD. Results: The median MD of the GTVCT changed from 2.89 (GTVCT2) to 4.46 (GTVCT7) as the CT thresholds were varied. The correlation coefficient of the GTVCT compared with the pathologically determined MD ranged from 0.76 to 0.87. The correlation coefficient of the GTVCT1 was the best (r = 0.87). The median MD of GTVPET changed from 5.72cm to 2.67cm as the PET thresholds increased. The correlation coefficient of the GTVPET compared with the pathologic finding ranged from 0.51 to 0.77. The correlation coefficient of GTV50 was the best (r = 0.77). Conclusion: Compared with the MD of GTVPET, the MD of GTVCT had better correlation with the pathologic MD. The GTVCT1 and GTV50 had the best correlation with the pathologic results

Fungal community structure in disease suppressive soils assessed by 28S LSU gene sequencing

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils 'suppressive' or 'non-suppressive' for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of 994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and nonsuppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression