Background: In treatment planning for intensity-modulated proton therapy (IMPT), we aim to deliver the prescribed dose to the target yet minimize the dose to adjacent healthy tissue. Mixed-integer programming (MIP) has been applied in radiation therapy to generate treatment plans. However, MIP has not been used effectively for IMPT treatment planning with dose-volume constraints. In this study, we incorporated dose-volume constraints in an MIP model to generate treatment plans for IMPT. Methods: We created a new MIP model for IMPT with dose volume constraints. Two groups of IMPT treatment plans were generated for each of three patients by using MIP models for a total of six plans: one plan was derived with the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) method while the other plan was derived with our MIP model with dose-volume constraints. We then compared these two plans by dose-volume histogram (DVH) indices to evaluate the performance of the new MIP model with dose-volume constraints. In addition, we developed a model to more efficiently find the best balance between tumor coverage and normal tissue protection. Results: The MIP model with dose-volume constraints generates IMPT treatment plans with comparable target dose coverage, target dose homogeneity, and the maximum dose to organs at risk (OARs) compared to treatment plans from the conventional quadratic programming method without any tedious trial-and-error process. Some notable reduction in the mean doses of OARs is observed. Conclusions: The treatment plans from our MIP model with dose-volume constraints can meetall dose-volume constraints for OARs and targets without any tedious trial-and-error process. This model has the potential to automatically generate IMPT plans with consistent plan quality among different treatment planners and across institutions and better protection for important parallel OARs in an effective way.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22038号 / 医博第4523号 / 新制||医||1038(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 大森 孝一, 教授 松村 由美, 教授 富樫 かおり / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

The ability to generate a range of concentrations of various solutions rapidly and conveniently is an ongoing need in biotechnology. In this thesis we demonstrate how we took advantage of the full process control afforded by our recent custom high resolution 3D printer and resin advances to realize highly integrated and miniaturized microfluidic components for simultaneous on-chip serial dilution for dose-response assays. With judicious selection of mixed layer thicknesses and pixel-by-pixel dose control, we show that the diameter of 3D printed membrane valves can be reduced from 300 µm to 46 µm. We further introduce an entirely new kind of 3D printed valve, termed a squeeze valve, in which the active area is reduced still further to 15 µm x 15 µm. We demonstrate and characterize pumps based on each type of valve and introduce a short (<1 mm long) high aspect ratio channel that enables rapid diffusion-based mixing. We show that combining two pumps with this diffusion mixing channel results in a highly compact 1:1 mixer component. Connecting 10 of these components in series yields a miniature 10 stage 2-fold microfluidic serial dilution module that from two solution inputs simultaneously generates 10 output concentrations that cover three orders of magnitude. We show the efficacy of our serial dilution approach by demonstrating an assay for dose-dependent permeabilization of A549 cells in different concentrations of digitonin integrated into a single device. Our demonstration of component miniaturization in conjunction with a high degree of integration illustrates the promise of 3D printing to enable highly functional and compact microfluidic devices for a variety of biomolecular applications.

Athlete preparation and performance continue to increase in complexity and costs. Modern coaches are shifting from reliance on personal memory, experience, and opinion to evidence from collected training-load data. Training-load monitoring may hold vital information for developing systems of monitoring that follow the training process with such precision that both performance prediction and day-to-day management of training become adjuncts to preparation and performance. Time-series data collection and analyses in sport are still in their infancy, with considerable efforts being applied in "big data" analytics, models of the appropriate variables to monitor, and methods for doing so. Training monitoring has already garnered important applications but lacks a theoretical framework from which to develop further. As such, we propose a framework involving the following: analyses of individuals, trend analyses, rules-based analysis, and statistical process control.

Seventy percent of stroke survivors experience loss of upper limb function after stroke and rehabilitative therapy is the only option to reduce impairments. However, uncertainty remains as to the optimal dose of therapy that should be prescribed. It has been suggested to report multiple parameters of dose, to increase standardization within the field, and to gain a better understanding of the dose-response relationship. This study investigated the automatic quantification of multiple dose parameters in a rat model of ischemic stroke, with rehabilitation paradigms whereby rats repeatedly grasp for food pellets to train their forelimb function. Starting 7 days post-stroke, groups of rats received 4, 8, or 12 rehabilitative training sessions for 10 days, practicing either high-quality (precision practice) or less skilled (mass practice) reaching movements. Pellet consumption was measured after each session and various metrics were analyzed using deep learning-based software (DeepLabCut, DLC) to represent parameters of dose intensity (number of reaches, paw path length) and session density (time on task). Functional outcome was assessed with the Montoya staircase task. Computer algorithms were validated against human analysis, demonstrating reach detection accuracy and reliability >80%. Interestingly, the number of training sessions did not alter the accumulated movement practice across rehabilitation, in either task. However, the number of sessions inversely affected training intensity, resulting in more forelimb use per session in rats with 4 sessions compared to 12 sessions. We found strong positive correlations between the number of reaches, time on task, paw path length, and pellets consumed in the precision practice, but only between reaches and pellets consumed in mass practice. This work demonstrates the quantification of multiple dose parameters using deep learning software and shows subtle differences between the two commonly used forelimb training tasks. Moreover, our data suggest that rehabilitative training at a frequency that is too high may negatively impact performance per session.

The exposure to high doses of ionizing radiation (>5Gy) is unequivocally associated with increased cancer risk. However, there is substantial experimental evidence showing that in response to low doses of ionizing radiation (LDR: <100mGy), cells and organisms are benefitted with delayed ageing, improved immunity and reduced cancer growth. These intriguing findings have proposed the “Radiation Hormesis” hypothesis. Herein, I studied the senescence effects of LDR exposure to normal human HFL1 cells and examined transcriptional changes. I found that HFL1 cells exposed to 10 mGy of gamma radiation had delayed senescence measured at 12 weeks post-irradiation compared to unirradiated cells. Through qPCR array analysis, I found that genes involved in human cellular senescence functions are differentially regulated in 10 mGy exposed cells at 12 weeks compared to 1-week post-exposure. A nucleolar protein, SIRT7, that belongs to the family of proteins called Sirtuins with known roles in aging, was found to be upregulated transcriptionally in LDR-exposed HFL1 cells. Knocking out SIRT7 protein significantly accelerated senescence in HFL1 cells suggesting a direct role of SIRT7 in the deceleration of senescence and potentially in mediating radiation hormesis. Furthermore, overexpression of the HRAS oncogene strongly accelerated senescence in HFL1 cells through gene expression of cell cycle regulators and checkpoint proteins. Together, my studies revealed that LDR induces unique transcriptional changes resulting in a potentially radio adaptive protective cellular response. I also discuss the HRAS overexpression system as a time-efficient cellular model that could be used to more rapidly study the effect of LDR on senescence using primary cultures.

Aflatoxin B1 (AFB1), a secondary metabolite of Aspergillus flavus and Aspergillus parasiticus, is known for its potent carcinogenicity and immunosuppressive effects. It is also known that AFB1 toxicity appears in different degrees in different animal species and strains. The present study was performed to reveal the involvement of the hypothalamus-pituitary-adrenal gland (HPA) axis in the immunosuppressive effects of AFB1 on C57B/6 mice. Splenic lymphocy1es were assayed to investigate their phenotyping using flow cy1ometry, proliferative response against mitogen and allogenic lymphocy1es, cy1oly1ic cell activity, and IL-2 production. In addition, antibody-mediated immunocompetence was checked using sheep red blood cell (SRBC)-challenged animals by plaque-forming cell (PFC) assay and enzyme-linked immunosorbent assay (ELISA). Corticotropin releasing factor (CRF) in brain hypothalamus and cerebral cortex, plasma adrenocorticotropic hormone (ACTH), and corticosterone were determined by radioimmunoassay (RIA). Hypothalamic catecholamine and its metabolites were assayed by high-performance liquid chromatography (HPLC). The adrenalectomized animals and their respective control animals were used to evaluate corticosterone involvement in AFB1 immunosuppressive effects. A relatively higher dose was applied in the present study, compared to the previous studies that used different strains of mice. Immunosuppressive effects were observed in blastogenic response, IL-2 production, and primary antibody production of splenic cells. The amount of circulating anti-SRBC antibody was also affected. Decreases were observed in the helper-T cell and B cell percentage in phenotyping splenic lymphocyte. No significant changes were observed in natural killer cell activity, mixed lymphocyte response, brain biogenic amine concentrations, concentration of CRF in the hypothalamus, and those of ACTH and corticosterone in plasma. However, the expected effect of adrenalectomy to compensate for the immunosuppression of AFB1 was not observed. The results indicate that the HPA axis does not appear to have a major role in AFB1-induced immunotoxicity.

Indiana University-Purdue University Indianapolis (IUPUI) / The late-onset outcome issue is common in early phase dose- nding clinical trials. This problem becomes more intractable in phase I/II clinical trials because both toxicity and e cacy responses are subject to the late-onset outcome issue. The existing methods applying for the phase I trials cannot be used directly for the phase I/II trial due to a lack of capability to model the joint toxicity{e cacy distribution. We propose a conditional weighted likelihood (CWL) method to circumvent this issue. The key idea of the CWL method is to decompose the joint probability into the product of marginal and conditional probabilities and then weight each probability based on each patient's actual follow-up time. We further extend the proposed method to handle more complex situations where the late-onset outcomes are competing risks or semicompeting risks outcomes. We treat the late-onset competing risks/semi-competing risks outcomes as missing data and develop a series of Bayesian data-augmentation methods to e ciently impute the missing data and draw the posterior samples of the parameters of interest. We also propose adaptive dose- nding algorithms to allocate patients and identify the optimal biological dose during the trial. Simulation studies show that the proposed methods yield desirable operating characteristics and outperform the existing methods.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第18877号 / 医博第3988号 / 新制||医||1008(附属図書館) / 31828 / 京都大学大学院医学研究科医学専攻 / (主査)教授 武田 俊一, 教授 富樫 かおり, 教授 増永 慎一郎 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

http://dx.doi.org/10.1016/j.jad.2015.03.021 / 京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19618号 / 医博第4125号 / 新制||医||1015(附属図書館) / 32654 / 京都大学大学院医学研究科医学専攻 / (主査)教授 川上 浩司, 教授 清水 章, 教授 村井 俊哉 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM