Visual Tracking of Instruments in Minimally Invasive Surgery

Reducing access trauma has been a focal point for modern surgery and tackling the challenges that arise from new operating techniques and instruments is an exciting and open area of research. Lack of awareness and control from indirect manipulation and visualization has created a need to augment the surgeon's understanding and perception of how their instruments interact with the patient's anatomy but current methods of achieving this are inaccurate and difficult to integrate into the surgical workflow. Visual methods have the potential to recover the position and orientation of the instruments directly in the reference frame of the observing camera without the need to introduce additional hardware to the operating room and perform complex calibration steps. This thesis explores how this problem can be solved with the fusion of coarse region and fine scale point features to enable the recovery of both the rigid and articulated degrees of freedom of laparoscopic and robotic instruments using only images provided by the surgical camera. Extensive experiments on different image features are used to determine suitable representations for reliable and robust pose estimation. Using this information a novel framework is presented which estimates 3D pose with a region matching scheme while using frame-to-frame optical flow to account for challenges due to symmetry in the instrument design. The kinematic structure of articulated robotic instruments is also used to track the movement of the head and claspers. The robustness of this method was evaluated on calibrated ex-vivo images and in-vivo sequences and comparative studies are performed with state-of-the-art kinematic assisted tracking methods

Light attenuation characteristics of glacially-fed lakes

Transparency is a fundamental characteristic of aquatic ecosystems and is highly responsive to changes in climate and land use. The transparency of glacially-fed lakes may be a particularly sensitive sentinel characteristic of these changes. However, little is known about the relative contributions of glacial flour versus other factors affecting light attenuation in these lakes. We sampled 18 glacially-fed lakes in Chile, New Zealand, and the U.S. and Canadian Rocky Mountains to characterize how dissolved absorption, algal biomass (approximated by chlorophyll a), water, and glacial flour contributed to attenuation of ultraviolet radiation (UVR) and photosynthetically active radiation (PAR, 400–700 nm). Variation in attenuation across lakes was related to turbidity, which we used as a proxy for the concentration of glacial flour. Turbidity-specific diffuse attenuation coefficients increased with decreasing wavelength and distance from glaciers. Regional differences in turbidity-specific diffuse attenuation coefficients were observed in short UVR wavelengths (305 and 320 nm) but not at longer UVR wavelengths (380 nm) or PAR. Dissolved absorption coefficients, which are closely correlated with diffuse attenuation coefficients in most non-glacially-fed lakes, represented only about one quarter of diffuse attenuation coefficients in study lakes here, whereas glacial flour contributed about two thirds across UVR and PAR. Understanding the optical characteristics of substances that regulate light attenuation in glacially-fed lakes will help elucidate the signals that these systems provide of broader environmental changes and forecast the effects of climate change on these aquatic ecosystems

“An ethnographic seduction”: how qualitative research and Agent-based models can benefit each other

We provide a general analytical framework for empirically informed agent-based simulations. This methodology provides present-day agent-based models with a sound and proper insight as to the behavior of social agents — an insight that statistical data often fall short of providing at least at a micro level and for hidden and sensitive populations. In the other direction, simulations can provide qualitative researchers in sociology, anthropology and other fields with valuable tools for: (a) testing the consistency and pushing the boundaries, of specific theoretical frameworks; (b) replicating and generalizing results; (c) providing a platform for cross-disciplinary validation of results

Soluble Cytokine Receptors (sIL-2Rα, sIL-2Rβ) Induce Subunit-Specific Behavioral Responses and Accumulate in the Cerebral Cortex and Basal Forebrain

Soluble cytokine receptors are normal constituents of body fluids that regulate peripheral cytokine and lymphoid activity. Levels of soluble IL-2 receptors (sIL-2R) are elevated in psychiatric disorders linked with autoimmune processes, including ones in which repetitive stereotypic behaviors and motor disturbances are present. However, there is no evidence that sIL-2Rs (or any peripheral soluble receptor) induce such behavioral changes, or that they localize in relevant brain regions. Here, we determined in male Balb/c mice the effects of single peripheral injections of sIL-2Rα or sIL-2Rβ (0–2 µg/male Balb/c mouse; s.c.) on novelty-induced ambulatory activity and stereotypic motor behaviors. We discovered that sIL-2Rα increased the incidence of in-place stereotypic motor behaviors, including head up head bobbing, rearing/sniffing, turning, and grooming behavior. A wider spectrum of behavioral changes was evident in sIL-2Rβ-treated mice, including increases in vertical and horizontal ambulatory activity and stereotypic motor movements. To our knowledge, this is the first demonstration that soluble receptors induce such behavioral disturbances. In contrast, soluble IL-1 Type-1 receptors (0–4 µg, s.c.) didn't appreciably affect these behaviors. We further demonstrated that sIL-2Rα and sIL-2Rβ induced marked increases in c-Fos in caudate-putamen, nucleus accumbens and prefrontal cortex. Anatomical specificity was supported by the presence of increased activity in lateral caudate in sIL-2Rα treated mice, while sIL-2Rβ treated mice induced greater c-Fos activity in prepyriform cortex. Moreover, injected sIL-2Rs were widely distributed in regions that showed increased c-Fos expression. Thus, sIL-2Rα and sIL-2Rβ induce marked subunit- and soluble cytokine receptor-specific behavioral disturbances, which included increases in the expression of ambulatory activity and stereotypic motor behaviors, while inducing increased neuronal activity localized to cortex and striatum. These findings suggest that sIL-2Rs act as novel immune-to- brain messengers and raise the possibility that they contribute to the disease process in psychiatric disorders in which marked increases in these receptors have been reported

IL-4-secreting CD4+ T cells are crucial to the development of CD8+ T-cell responses against malaria liver stages.

CD4+ T cells are crucial to the development of CD8+ T cell responses against hepatocytes infected with malaria parasites. In the absence of CD4+ T cells, CD8+ T cells initiate a seemingly normal differentiation and proliferation during the first few days after immunization. However, this response fails to develop further and is reduced by more than 90%, compared to that observed in the presence of CD4+ T cells. We report here that interleukin-4 (IL-4) secreted by CD4+ T cells is essential to the full development of this CD8+ T cell response. This is the first demonstration that IL-4 is a mediator of CD4/CD8 cross-talk leading to the development of immunity against an infectious pathogen

Formation of heavy d-electron quasiparticles in Sr₃Ru₂O₇

The phase diagram of Sr3Ru2O7 shows hallmarks of strong electron correlations despite the modest Coulomb interaction in the Ru 4d shell. We use angle-resolved photoelectron spectroscopy measurements to provide microscopic insight into the formation of the strongly renormalized heavy d-electron liquid that controls the physics of Sr3Ru2O7. Our data reveal itinerant Ru 4d-states confined over large parts of the Brillouin zone to an energy range of <6 meV, nearly three orders of magnitude lower than the bare band width. We show that this energy scale agrees quantitatively with a characteristic thermodynamic energy scale associated with quantum criticality and illustrate how it arises from a combination of back-folding due to a structural distortion and the hybridization of light and strongly renormalized, heavy quasiparticle bands. The resulting heavy Fermi liquid has a marked k-dependence of the renormalization which we relate to orbital mixing along individual Fermi surface sheets

Using a disciplinary discourse lens to explore how representations afford meaning making in a typical wave physics course

We carried out a case study in a wave physics course at a Swedish university in order to investigate the relations between the representations used in the lessons and the experience of meaning making in interview–discussions. The grounding of these interview–discussions also included obtaining a rich description of the lesson environment in terms of the communicative approaches used and the students’ preferences for modes of representations that best enable meaning making. The background for this grounding was the first two lessons of a 5-week course on wave physics (70 students). The data collection for both the grounding and the principal research questions consisted of video recordings from the first two lessons: a student questionnaire of student preferences for representations (given before and after the course) and video-recorded interview–discussions with students (seven pairs and one on their own). The results characterize the use of communicative approaches, what modes of representation were used in the lectures, and the trend in what representations students’ preferred for meaning making, all in order to illustrate how students engage with these representations with respect to their experienced meaning making. Interesting aspects that emerged from the study are discussed in terms of how representations do not, in themselves, necessarily enable a range of meaning making; that meaning making from representations is critically related to how the representations get situated in the learning environment; and how constellations of modes of disciplinary discourse may be necessary but not always sufficient. Finally, pedagogical comments and further research possibilities are presented.Web of Scienc

Pacific origin of the abrupt increase in Indian Ocean heat content during the warming hiatus

Global mean surface warming has stalled since the end of the twentieth century1, 2, but the net radiation imbalance at the top of the atmosphere continues to suggest an increasingly warming planet. This apparent contradiction has been reconciled by an anomalous heat flux into the ocean3, 4, 5, 6, 7, 8, induced by a shift towards a La Niña-like state with cold sea surface temperatures in the eastern tropical Pacific over the past decade or so. A significant portion of the heat missing from the atmosphere is therefore expected to be stored in the Pacific Ocean. However, in situ hydrographic records indicate that Pacific Ocean heat content has been decreasing9. Here, we analyse observations along with simulations from a global ocean–sea ice model to track the pathway of heat. We find that the enhanced heat uptake by the Pacific Ocean has been compensated by an increased heat transport from the Pacific Ocean to the Indian Ocean, carried by the Indonesian throughflow. As a result, Indian Ocean heat content has increased abruptly, which accounts for more than 70% of the global ocean heat gain in the upper 700 m during the past decade. We conclude that the Indian Ocean has become increasingly important in modulating global climate variability

Identification and characterization of a novel non-structural protein of bluetongue virus

Bluetongue virus (BTV) is the causative agent of a major disease of livestock (bluetongue). For over two decades, it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins. The non-structural proteins (NS1, NS2, NS3/NS3a) play different key roles during the viral replication cycle. In this study we show that BTV expresses a fourth non-structural protein (that we designated NS4) encoded by an open reading frame in segment 9 overlapping the open reading frame encoding VP6. NS4 is 77–79 amino acid residues in length and highly conserved among several BTV serotypes/strains. NS4 was expressed early post-infection and localized in the nucleoli of BTV infected cells. By reverse genetics, we showed that NS4 is dispensable for BTV replication in vitro, both in mammalian and insect cells, and does not affect viral virulence in murine models of bluetongue infection. Interestingly, NS4 conferred a replication advantage to BTV-8, but not to BTV-1, in cells in an interferon (IFN)-induced antiviral state. However, the BTV-1 NS4 conferred a replication advantage both to a BTV-8 reassortant containing the entire segment 9 of BTV-1 and to a BTV-8 mutant with the NS4 identical to the homologous BTV-1 protein. Collectively, this study suggests that NS4 plays an important role in virus-host interaction and is one of the mechanisms played, at least by BTV-8, to counteract the antiviral response of the host. In addition, the distinct nucleolar localization of NS4, being expressed by a virus that replicates exclusively in the cytoplasm, offers new avenues to investigate the multiple roles played by the nucleolus in the biology of the cell

To respond or not to respond - a personal perspective of intestinal tolerance

For many years, the intestine was one of the poor relations of the immunology world, being a realm inhabited mostly by specialists and those interested in unusual phenomena. However, this has changed dramatically in recent years with the realization of how important the microbiota is in shaping immune function throughout the body, and almost every major immunology institution now includes the intestine as an area of interest. One of the most important aspects of the intestinal immune system is how it discriminates carefully between harmless and harmful antigens, in particular, its ability to generate active tolerance to materials such as commensal bacteria and food proteins. This phenomenon has been recognized for more than 100 years, and it is essential for preventing inflammatory disease in the intestine, but its basis remains enigmatic. Here, I discuss the progress that has been made in understanding oral tolerance during my 40 years in the field and highlight the topics that will be the focus of future research