Autonomous Soft Tissue Retraction Using Demonstration-Guided Reinforcement Learning

In the context of surgery, robots can provide substantial assistance by performing small, repetitive tasks such as suturing, needle exchange, and tissue retraction, thereby enabling surgeons to concentrate on more complex aspects of the procedure. However, existing surgical task learning mainly pertains to rigid body interactions, whereas the advancement towards more sophisticated surgical robots necessitates the manipulation of soft bodies. Previous work focused on tissue phantoms for soft tissue task learning, which can be expensive and can be an entry barrier to research. Simulation environments present a safe and efficient way to learn surgical tasks before their application to actual tissue. In this study, we create a Robot Operating System (ROS)-compatible physics simulation environment with support for both rigid and soft body interactions within surgical tasks. Furthermore, we investigate the soft tissue interactions facilitated by the patient-side manipulator of the DaVinci surgical robot. Leveraging the pybullet physics engine, we simulate kinematics and establish anchor points to guide the robotic arm when manipulating soft tissue. Using demonstration-guided reinforcement learning (RL) algorithms, we investigate their performance in comparison to traditional reinforcement learning algorithms. Our in silico trials demonstrate a proof-of-concept for autonomous surgical soft tissue retraction. The results corroborate the feasibility of learning soft body manipulation through the application of reinforcement learning agents. This work lays the foundation for future research into the development and refinement of surgical robots capable of managing both rigid and soft tissue interactions. Code is available at https://github.com/amritpal-001/tissue_retract.Comment: 10 Pages, 5 figures, MICCAI 2023 conference (AECAI workshop

Landau-Zener Tunnelling in a Nonlinear Three-level System

We present a comprehensive analysis of the Landau-Zener tunnelling of a nonlinear three-level system in a linearly sweeping external field. We find the presence of nonzero tunnelling probability in the adiabatic limit (i.e., very slowly sweeping field) even for the situation that the nonlinear term is very small and the energy levels keep the same topological structure as that of linear case. In particular, the tunnelling is irregular with showing an unresolved sensitivity on the sweeping rate. For the case of fast-sweeping fields, we derive an analytic expression for the tunnelling probability with stationary phase approximation and show that the nonlinearity can dramatically influence the tunnelling probability when the nonlinear "internal field" resonate with the external field. We also discuss the asymmetry of the tunnelling probability induced by the nonlinearity. Physics behind the above phenomena is revealed and possible application of our model to triple-well trapped Bose-Einstein condensate is discussed.Comment: 8 pages, 8 figure

Ultrafast heterogeneous electron transfer reactions Comparative theoretical studies on time and frequency domain data

Recent theoretical studies on linear absorption spectra of dye semiconductor systems perylene attached to nanostructured TiO2, L. Wang et al., J. Phys. Chem. B 109, 9589 2005 are extended here in different respects. Since the systems show ultrafast photoinduced heterogeneous electron transfer the time dependent formulation used to compute the absorbance is also applied to calculate the temporal evolution of the sub 100 fs charge injection dynamics after a 10 fs laser pulse excitation. These studies complement our recent absorption spectra fit for two perylene bridge anchor group TiO2 systems. Moreover, the time dependent formulation of the absorbance is confronted with a frequency domain description. The latter underlines the central importance of the self energy caused by the coupling of the dye levels to the semiconductor band continuum. The used model is further applied to study the effect of different parameters such as 1 the dependence on the reorganization energies of the involved intramolecular transitions, 2 the effect of changing the transfer integral which couples the excited dye state with the band continuum, and 3 the effect of the concrete form of the semiconductor band density of states. Emphasis is also put on the case where the charge injection level of the dye is near or somewhat below the band edge. This nicely demonstrates the change from a structureless absorption to a well resolved vibrational progression including characteristic shifts of the absorption lines which are a direct measure for the dye semiconductor couplin

ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses

© 2008 Stokes et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.DOI: 10.1186/1471-2105-9-S6-S18Background. A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the "curse-of-dimension" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create "intelligent" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. Results. To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers (Semantic Agents) such as Google to further enhance data discovery. Conclusions. Microarray data and meta information in ArrayWiki are distributed and visualized using a novel and compact data storage format, BioPNG. Also, they are open to the research community for curation, modification, and contribution. By making a small investment of time to learn the syntax and structure common to all sites running MediaWiki software, domain scientists and practioners can all contribute to make better use of microarray technologies in research and medical practices. ArrayWiki is available at http://www.bio-miblab.org/arraywiki

The neighborhood food environment: sources of historical data on retail food stores

With the rapidly increasing prevalence of obesity in the United States, and the minimal success of education-based interventions, there is growing interest in understanding the role of the neighborhood food environment in determining dietary behavior. This study, as part of a larger study, identifies historical data on retail food stores, evaluates strengths and limitations of the data for research, and assesses the comparability of historical retail food store data from a government and a commercial source. Five government and commercial listings of retail food stores were identified. The California State Board of Equalization (SBOE) database was selected and then compared to telephone business directory listings. The Spearman's correlation coefficient was used to assess the congruency of food store counts per census tract between the SBOE and telephone business directory databases. The setting was four cities in Northern California, 1979–1990. The SBOE and telephone business directory databases listed 127 and 351 retail food stores, respectively. The SBOE listed 36 stores not listed by the telephone business directories, while the telephone business directories listed 260 stores not listed by the SBOE. Spearman's correlation coefficients between estimates of stores per census tract made from the SBOE listings and those made from the telephone business directory listings were approximately 0.5 (p < .0001) for the types of stores studied (chain supermarkets, small grocery stores, and chain convenience markets). We conclude that, depending on the specific aims of the study, caution and considerable effort must be exercised in using and applying historical data on retail food stores