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Burrell, J.

Publications and source records attributed to Burrell, J..

3 recordsLinked to original sources

Nanopore sequencing undergoes catastrophic sequence failure at inverted duplicated DNA sequences

Inverted duplicated sequences are a common feature of structural variants (SVs) and copy number variants (CNVs). Analysis of CNVs containing inverted duplicated sequences using nanopore sequencing identified recurrent aberrant behavior characterized by incorrect and low confidence base calls that result from a systematic elevation in the current recorded by the sequencing pore. The coincidence of inverted duplicated sequences with catastrophic sequence failure suggests that secondary DNA structures may impair transit through the nanopore.

genomics↗

Real brains in virtual worlds: Validating a novel oddball paradigm in virtual reality

Electroencephalography (EEG) research is typically conducted in controlled laboratory settings. This limits the generalizability to real-world situations. Virtual reality (VR) sits as a transitional tool that provides tight experimental control with more realistic stimuli. To test the validity of using VR for event-related potential (ERP) research we used a well-established paradigm, the oddball task. For our first study, we compared VR to traditional, monitor-based stimulus presentation using visual and auditory oddball tasks while EEG data was recorded. We were able to measure ERP waveforms typically associated with such oddball tasks, namely the P3 and earlier N2 components, in both conditions. Our results suggest that ERPs collected using VR head mounted displays and typical monitors were comparable on measures of latency, amplitude, and spectral composition. In a second study, we implemented a novel depth-based oddball task and we were able to measure the typical oddball-related ERPs elicited by the presentation of near and far stimuli. Interestingly, we observed significant differences in early ERPs components between near and far stimuli, even after controlling for the effects of the oddball task. Current results suggest that VR can serve as a valid means of stimulus presentation in novel or otherwise inaccessible environments for EEG experimentation. We demonstrated the capability of a depth-based oddball in reliably eliciting a P3 waveform. We also found an interaction between the depth at which objects are presented and early ERP responses. Further research is warranted to better explain this influence of depth on the EEG and ERP activity.

neuroscience↗

Investigating low-velocity fluid flow in tumours using convection-MRI

Several distinct fluid flow phenemena occur in solid tumours, including intravascular blood flow and interstitial convection. To probe low-velocity flow in tumors resulting from raised interstitial fluid pressure, we have developed a novel magnetic resonance imaging (MRI) technique named convection-MRI. It uses a phase-contrast acquisition with a dual-inversion vascular nulling preparation to separate intra- and extra-vascular flow. Here, we report the results of experiments in flow phantoms, numerical simulations and tumor xenograft models to investigate the technical feasibility of convection-MRI. We report a good correlation between estimates of effective fluid pressure from convection-MRI with gold-standard, invasive measurements of interstitial fluid pressure in mouse models of human colorectal carcinoma and show that convection-MRI can provide insights into the growth and response to vascular-targeting therapy in colorectal cancers.

biophysics↗