Automorphisms of monomial groups

Dissertation (Ph. D.)--University of Kansas, Mathematics, 1955

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Disturbance legacies and climate jointly drive tree growth and mortality in an intensively studied boreal forest.

Most North American forests are at some stage of post-disturbance regrowth, subject to a changing climate, and exhibit growth and mortality patterns that may not be closely coupled to annual environmental conditions. Distinguishing the possibly interacting effects of these processes is necessary to put short-term studies in a longer term context, and particularly important for the carbon-dense, fire-prone boreal forest. The goals of this study were to combine dendrochronological sampling, inventory records, and machine-learning algorithms to understand how tree growth and death have changed at one highly studied site (Northern Old Black Spruce, NOBS) in the central Canadian boreal forest. Over the 1999-2012 inventory period, mean tree diameter increased even as stand density and basal area declined significantly. Tree mortality averaged 1.4 ± 0.6% yr-(1), with most mortality occurring in medium-sized trees; new recruitment was minimal. There have been at least two, and probably three, significant influxes of new trees since stand initiation, but none in recent decades. A combined tree ring chronology constructed from sampling in 2001, 2004, and 2012 showed several periods of extreme growth depression, with increased mortality lagging depressed growth by ~5 years. Higher minimum and maximum air temperatures exerted a negative influence on tree growth, while precipitation and climate moisture index had a positive effect; both current- and previous-year data exerted significant effects. Models based on these variables explained 23-44% of the ring-width variability. We suggest that past climate extremes led to significant mortality still visible in the current forest structure, with decadal dynamics superimposed on slower patterns of fire and succession. These results have significant implications for our understanding of previous work at NOBS, the carbon sequestration capability of old-growth stands in a disturbance-prone landscape, and the sustainable management of regional forests in a changing climate

Differential Contributions of Vision, Touch and Muscle Proprioception to the Coding of Hand Movements

To further elucidate the mechanisms underlying multisensory integration, this study examines the controversial issue of whether congruent inputs from three different sensory sources can enhance the perception of hand movement. Illusory sensations of clockwise rotations of the right hand were induced by either separately or simultaneously stimulating visual, tactile and muscle proprioceptive channels at various intensity levels. For this purpose, mechanical vibrations were applied to the pollicis longus muscle group in the subjects’ wrists, and a textured disk was rotated under the palmar skin of the subjects’ right hands while a background visual scene was projected onto the rotating disk. The elicited kinaesthetic illusions were copied by the subjects in real time and the EMG activity in the adductor and abductor wrist muscles was recorded. The results show that the velocity of the perceived movements and the amplitude of the corresponding motor responses were modulated by the nature and intensity of the stimulation. Combining two sensory modalities resulted in faster movement illusions, except for the case of visuo-tactile co-stimulation. When a third sensory input was added to the bimodal combinations, the perceptual responses increased only when a muscle proprioceptive stimulation was added to a visuo-tactile combination. Otherwise, trisensory stimulation did not override bimodal conditions that already included a muscle proprioceptive stimulation. We confirmed that vision or touch alone can encode the kinematic parameters of hand movement, as is known for muscle proprioception. When these three sensory modalities are available, they contribute unequally to kinaesthesia. In addition to muscle proprioception, the complementary kinaesthetic content of visual or tactile inputs may optimize the velocity estimation of an on-going movement, whereas the redundant kinaesthetic content of the visual and tactile inputs may rather enhance the latency of the perception