VictorJuiz/thesis huggingface dataset:
Design of Force-Sensing Sleeve for Minimal Access Surgical Instruments
Keywords: Force
Instrument
Minmal Access Surgery
Surgery

Due to the nature of Minimal Access Surgery (MAS), surgeons are faced with multiple challenges including: (1) lack of direct hand-eye coordination, (2) loss of depth perception, (3) fixed access points, (4) long surgical instruments, and (5) reduced access to the surgical site. These challenges ultimately affect the surgeon's ability to sense the forces between the laparoscopic instrument and tissue. Improper force control can lead to poor clinical outcomes such as tissue necrosis, infection, and scarring. Currently, minimal literature exists on the benefit of force metrics in training and clinical environments. Moreover, existing MAS force-sensing technologies prevent researchers and surgeons from conducting extensive MAS force studies due to their limited applications in MAS training or the operating room, and/or complex manufacturing processes. This thesis work describes the design of a novel force sensor for a broad range of standard MAS instruments and procedures. The proposed Force-Sensing Sleeve (FSS) design utilizes a flexible printed circuit and multiple strain gauges to determine distal instrument forces from mechanical deformations measured in the MAS tool's exterior shaft. The FSS acts as a minimally disruptive add-on and can be applied to standard MAS instruments in a simple and low-cost assembly process. A supporting-system for the FSS was also developed to provide the full force-sensing solution capable of wirelessly measuring, logging, and displaying force data in real-time. A standard MAS needle holder was equipped with the FSS system and tested in a realistic surgical training environment of the most complex Fundamentals of Laparoscopic Surgery (FLS) task (Intracorporeal Suture Knot Task (ISKT)); this proof of concept study's preliminary findings demonstrated the potential use of ISKT mean force measurements as a first approximation of surgical expertise, however more sophisticated dynamic force metrics are likely required for the further classification of surgeon expertise. The FSS system's ability to leverage existing operating room instruments and potential to be used in both standardized MAS training programs and surgical environments creates the opportunity for extensive force investigations in standard MAS tasks to determine how force metrics can benefit the surgical community and enhance patient safety and care.
The Composer-Performer Interrelationship in the Bayan and Accordion Compositions of Sofia Gubaidulina
Keywords: accordion
bayan
collaboration
contemporary music
performance
Sofia Gubaidulina

This dissertation explores creative collaborations between Sofia Gubaidulina, a contemporary Russian composer, and four internationally prominent bayanists and accordionists: Elsbeth Moser, Friedrich Lips, Geir Draugsvoll, and Alberdi Iñaki. I analyze their dialogues about both the composition and performance of some of Gubaidulina’s most significant pieces for bayan and accordion. My consideration not only provides a deeper understanding of this music, but it also provides insight into Gubaidulina’s compositional process. By examining how she addresses issues of collaboration, her authorial voice, changing intentions, and interpretation in performance, I implicitly provide a framework through which musicians might approach some of the Gubaidulina’s music in future performances. Various unique features of the bayan and accordion necessitate approaches to composition that differ from those used for more “standard” keyboard instruments, such as piano or organ. For these reasons, a number of composers have collaborated closely with performers who provide insight into the limitations and possibilities of the accordion and bayan in a general sense—that is, as a bellows driven free reed aerophone—and also in relation to the specifics of their personal instruments, which can vary in terms of keyboard layout and range. Through ongoing dialogues, Gubaidulina and the four elite performers mentioned above formed creative collectives characterized by mutual interdependence, akin to what sociologist Howard S. Becker (1982) describes as an “art world.” By considering these relationships, I explain how Gubaidulina and her collaborating musicians crafted her De Profundis, Silenzio, Fachwerk, and Cadenza—music that, on one hand, would not exist without her as the composer, but that, on the other hand, would sound vastly different if created with a different network of contributing artists. Moving beyond the compositional processes, I discuss the implications of the artists’ dialogues in preparing Gubaidulina’s In Croce by examining four notable recorded performances in relation to the scores and transcriptions used and the discussions between performer and composer that preceded the recording sessions. What emerges is a sense of how Gubaidulina’s musical voice is the product of her personal musical vision, her openness to input from other artists, and perhaps most importantly a willingness and ability to adapt according to that input over the course of time.
Antisociality in Men Who Perpetrate Domestic Violence: Heterogeneity, Psychophysiological and Neurocognitive Factors
Keywords: antisociality
batterer typology
Domestic violence
HRV
psychophysiology
response reversal

Despite the overlap between generally antisocial and criminal populations and those involved in domestic violence, the fields of domestic violence and criminology have historically been separated from each other. While the field of domestic violence has made considerable advances in the understanding of heterogeneity, internalizing psychopathology and the general antisociality of men who perpetrate such violence, less is known about the neurobiological and neurocognitive factors that underlie the development of antisocial behaviour in this population. This dissertation combines domestic violence and criminological approaches to understanding of antisociality in men who perpetrate domestic violence. The dissertation is comprised of two papers. The first examined variables related to history of maltreatment and antisocial behaviours, internalizing psychopathology and neurocognitive and psychophysiological variables in three groups of male participants: men with a history of domestic violence perpetration and criminal behaviours (n=56), men who only perpetrated domestic violence (n=56) and a comparison group with no history of violence perpetration (n=82). The two domestic violence groups were distinguishable on most measures, with the domestically violent and criminal men scoring highest on measures of childhood antisociality, internalizing psychopathology and maltreatment history. Furthermore, the domestically violent and criminal group was unique with respect to some psychophysiological and cognitive variables. The domestic violence only group resembled the comparison group in most domains. The second paper examined the relationship of autonomic and neurocognitive functioning with antisociality in men who perpetrate domestic violence by comparing the low arousal and the neurovisceral integration theories. The sample (n=185) included men with varying history of domestic violence and criminal behaviour as well as those with no such history. Consistent with the neurovisceral integration theory, heart rate variability change to task and reversal learning impairments were predictive of antisociality. Contrary to the low arousal theory, autonomic reactivity and response inhibition impairments did not predict antisociality. Theoretical and practical implications of these findings were discussed.
Non-Equilibrium Dynamics of Strongly Interacting Fermions
Keywords: Degenerate Fermi gases
Quantum optics
Ultracold gases

This thesis summarizes experimental work investigating strongly interacting Fermi gases in two and three dimensions. Radio-frequency spin manipulation is used to initialize and probe strongly interacting Fermi gases dynamically to measure relaxation to a steady-state. Time-resolved spectroscopy is used to discover the p-wave contacts by observing how correlations in the system develop after quenching the atoms into an interacting state. By combining quasi-steady state measurements with new contact relations, an attractive p-wave interaction energy as large as half the Fermi energy is inferred. Spin echo measurements of the magnetization dynamics are used to observe spin transport in two and three dimensions in the presence of strong interactions. The bare spin diffusivity is distinguished from the Leggett-Rice effect, in which demagnetization is slowed by precession of a spin current around the local magnetization. Observations of the demagnetization dynamics support the conjecture that a general quantum bound on spin transport is obeyed where the diffusivity D greater than or similar to ħ/m, where m is the particle mass.
Flow mediated dilatation (FMD) assessment via an MRI integrated signal intensity (IntSI) approach: A comparison with ultrasound
Keywords: Endothelial dysfunction
Flow Mediated Dilatation
Magnetic Resonance Imaging
Popliteal artery
Ultrasound
Vascular function

Endothelial dysfunction is a precursor of atherosclerosis. Flow mediated dilatation (FMD) is a measure of endothelial function. Ultrasound (US) is often used during FMD studies, but US- FMD is technically challenging. MRI methods for FMD rely on high spatial resolution but this entails a trade off involving temporal resolution and SNR. An adequate temporal sampling frequency is however required to detect the peak dilatation. In this thesis, concepts in hemodynamics and MRI physics were explored in order to develop a reliable MRI-FMD technique that is comparable with US-FMD. The approach was to measure the luminal area as a function of the integrated signal intensity (IntSI) of the lumen, since signal intensity increases with area. An equation was derived to account for concurrent velocity based increases in signal intensity. Phantom studies showed the IntSI technique as a reliable means of measuring the luminal area, provided that certain assumptions are not violated. Next, the IntSI technique was adapted for in vivo application. The popliteal artery was the artery of choice based on its anatomical advantages. The velocity profile and time averaged velocities of the popliteal artery were determined from spectral Doppler analysis, in order to design an in vivo technique that is compatible with the assumptions on which the IntSI technique is based. When applied in vivo, the IntSI technique overestimated luminal area measurements compared to a conventional MRI approach. Numerical optimization was used to obtain a correction factor to account for the bias. Subsequently, the IntSI technique was applied for measuring the luminal area during MRI-FMD and compared with US-FMD. The IntSI technique provided repeatable FMD measurements. Although the thesis did not demonstrate that the popliteal MRI-FMD using the IntSI technique was superior to US-FMD, it was non-inferior to US-FMD.
Laboratory Spectroscopy of Fluorinated Molecules for Atmospheric Physics
Keywords: Density Functional Theory
Global Warming Potential
Radiative efficiency
Spectroscopy

Temperature-dependent absorption cross-sections are presented for five fluorinated molecules considered to be greenhouse gases due to being radiatively active in the mid-infrared. The molecules studied are perfluorotributylamine (PFTBA), 2,2,3,3,3- pentafluoropropanol (PFPO), 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), perfluorodecalin (PFDC), and 2H,3H-perfluoropentane (HFC-43-10mee). HFIP is a fluorinated liquid commonly used as a specialty solvent for some polar polymers and in organic synthesis. PFTBA, PFPO, and HFC-43-10mee are commonly used in electronic and industrial applications. PFDC is capable of dissolving large quantities of gases, making it useful for a variety of medical applications. Experimental absorption cross-sections were derived from Fourier transform infrared spectra recorded from 530 to 3400 cm â 1 with a resolution of 0.1 cm â 1 over a temperature range of 298 to 360 K. These results were compared to theoretical density functional theory (DFT) calculations and previously published experimental measurements made at room temperature. Theoretical DFT calculations were performed using the B3LYP method and a minimum basis set of 6-311+G(d,p). The calculations have determined the optimized geometrical configuration, infrared intensities, and wavenumbers of the harmonic frequencies for different ground-state configurations due to the presence of internal rotors. As the population of each configuration changes with temperature, changes in the experimental spectra were used to make accurate band assignments. From these band assignments, the DFT spectra were calibrated to match the experimental spectra, increasing the accuracy of the DFT prediction outside of the experimental range. Using the adjusted DFT-calculated spectra, the wavenumber range was extended beyond the experimental range to calculate radiative efficiencies and global warming potentials. When using only the experimental range, the new values agreed with previously published values. However, when the range was extended using the DFT spectra, the radiative efficiency and global warming potential were increased, suggesting that the current values are underestimating the climate impacts of these species. Additionally, work done on building a multipass White cell is presented. This new system can be used in the future to resolve weak lines to extract line parameters needed for atmospheric trace gas retrievals.
Resting Network Synchronization in Atypical Development
Keywords: autism
brain development
functional connectivity
magnetoencephalopgrahy
resting state
very preterm birth

The development of the human brain, which extends well beyond adolescence, is characterized by maturational processes underlying significant improvements in cognition and perception. Neural synchronization represents a versatile mechanism for flexible communication within and between cortical areas, and is thought to be disrupted in atypical brain development. To date, most of our knowledge concerning human brain maturation has come from studies using functional or structural magnetic resonance imaging. While these techniques have been crucial to our understanding of typical and atypical brain development, work investigating synchronized spontaneous brain activity using magnetoencephalography (MEG) may provide additional insight into the spatiotemporal organization of brain networks relevant to cognition. The present work examines the synchronization of spontaneous MEG activity in atypical neurodevelopment, specifically, in autism spectrum disorder (ASD) and following very premature birth. In both these populations, neural synchronization was disrupted across a range of frequencies. These changes in neural communication affected functional integration and segregation within large-scale brain networks related to executive function in very preterm children and social cognition in ASD. Children born very preterm showed global reductions in neural synchronization, resulting in disconnected networks implicating executive function abilities. In ASD, a different pattern of disruption was detected, such that the brain was hypo-connected in posterior regions but over-connected in frontal and subcortical areas. With increasing age, over-connectivity was observed at faster frequencies, implicating intrinsic segregation and integration of large-scale functional connectivity in the brain. These disruptions in functional connectivity vary by frequency throughout childhood to adulthood, and affect different brain regions in addition to large-scale resting state networks (RSNs). These findings highlight the importance of understanding functional connectivity using a neurophysiological perspective, as the interplay of oscillatory activity throughout the brain changes over development and implicates functional network organization within the connectome. This work opens dialogue between cellular and cognitive neuroscience which is critical to the development of detection and therapeutic interventions in populations with atypical development, where altered neuromagnetic connectivity in multiple frequencies may be linked to mechanistic models of pathology and injury affecting brain development and behavioural outcomes.
GERMLINE & SOMATIC VARIATION IN GASTROINTESTINAL MALIGNANCIES
Keywords: Bioinformatics
Cancer Genomics
Colorectal cancer
Computational biology
Molecular biology
Pancreatic cancer

Germline Somatic Variation in Gastrointestinal Malignancies Ashton Antoine Connor Doctor of Philosophy Institute of Medical Science (IMS) University of Toronto 2017 Abstract Primary gastrointestinal malignancies have among the highest incidence, morbidity and mortality rates. We hypothesized that improved understanding of predisposing germline variation and acquired somatic variation would inform novel prevention and treatment strategies. We generated germline and somatic DNA and RNA sequence data from colorectal and pancreatic cancer patients. For the germline, we identified non-silent variation occurring at allele frequencies of less than 1% in the general population in a gene, FAT1, which co-segregates with colorectal adenocarcinoma by exome sequencing of affecteds in pedigrees that meet Familial Colorectal Cancer Type X criteria obtained from Canadian and Australian databases. This observation was not validated by targeted sequencing of affected probands or by a genetically modified mouse model. For the somatic, we identified genomic signatures that describe mutational processes acting on pancreatic ductal adenocarcinomas and transcriptomic signatures that describe the immune component of the tumour-associated stroma by whole genome and transcriptome sequencing of a retrospective cohort of surgically resected specimens. We integrated the two signature types, demonstrating that pancreatic cancers with deficiencies in DNA repair, namely mismatch repair and homologous recombination, were associated with high expression of transcripts representative of active adaptive immunity and co-regulatory pathways. We also studied three separate pancreatic ductal adenocarcinomas that presented in one patient, two of which arose following resection of the primary cancer. By whole genome sequencing, we demonstrated that these secondary lesions were in fact intra-parenchymal metastases sharing a common ancestor with the primary, rather than distinct metachronous lesions arising from separate tumour lineages. The degrees of genomic concordance between the primary and two secondary samples were characterised to determine the molecular phylogeny of the three lesions. Clinically, this informs patient management, as resection of metastatic pancreas cancer is unlikely to result in meaningful disease control. Scientifically, this allows the study of primaries and metastases in a system independent of external selective pressures. Overall, we have identified novel somatic findings in pancreas cancer that will hopefully inform patient management, and we have created germline and somatic repositories of sequencing data from which future investigations of genetic variation can be performed.
Exploration of Degradative Activities of Enterococcus faecalis and Determinants of Bacterial Biofilm Proliferation within the Sealer-Dentin Interfacial Margins
Keywords: biodegradation
Enterococcus faecalis
root canal sealer
salivary enzymes
sealer-dentin interface

Background: Root canal treatment involves disinfecting and sealing the root canal system. The interface between the root canal sealer and dentin might degrade over time, allowing for interfacial microbial biofilm proliferation and passage to the periradicular tissues and treatment failure. Salivary and bacterial enzymes may accelerate this degradation process. One of the commonly detected bacteria in the failed root canal treated teeth is Enterococcus faecalis. Objectives: 1) To investigate the effect of simulated human salivary esterases (SHSE) on the sealer-dentin interfacial integrity, by measuring the depth of interfacial bacterial biofilm proliferation, 2) To investigate the effect of SHSE on the physical properties of root canal sealers, 3) To assess the esterase-like degradative enzymatic activities of E. faecalis and their effect on methacrylate resins, and 4) To assess the collagenase-like enzymatic activities of E. faecalis and their degradative effect on dentin. Methods: Root canal treated specimens were incubated in SHSE for up to 360 days followed by cultivation of E. faecalis biofilm in constant medium fermenter, mimicking pathogenic intraoral growth conditions. Confocal laser scanning microscopy was used to assess the depth of interfacial bacterial biofilm proliferation. E. faecalis esterase and collagenolytic-like activities were measured and their effect on the methacrylate resins and dentinal collagen matrix was evaluated. Results: SHSE increased the sealer-dentin interfacial degradation as measured by the increased bacterial biofilm proliferation, and had an adverse effect on some of the physical properties of the root canal sealers. E. faecalis showed hydrolase, esterase-like and collagenase-like activities in levels that degraded methacrylate resins and dentinal collagen, respectively. Conclusions: This study demonstrated the potential effect of the salivary and bacterial enzymes on the outcome of root canal treatment; hydrolase activities could increase the sealer-dentin interface degradation, and may facilitate bacterial migration from the root canal into the periapical area, compromising the root canal treatment. Development of esterase resistant, and anti-collagenolytic sealers and/or treatment could be used to mitigate the effect of the salivary and bacterial enzymes.