<div><div><div><p>Determining the locations of nuclei in Zebrafish embryos is crucial for the study of the spatio-temporal behavior of these cells during the development process. With image seg- mentations, not only the location of the cell can be known, but also determine if each pixels is background or part of a nucleus. Traditional image processing techniques have been thor- oughly applied to this problem. These techniques suffer from bad generalization, many times relying on heuristic that apply to a specific type of image to reach a high accuracy when doing pixel by pixel segmentation. In previous work from our research lab, wavelet image segmentation was applied, but heuristics relied on expected nuclei size .</p><p>Machine learning techniques, and more specifically convolutional neural networks, have recently revolutionized image processing and computer vision in general. By relying on vast amounts of data and deep networks, problems in computer vision such as classification or semantic segmentation have reached new state of the art performance, and these techniques are continuously improving and pushing the boundaries of state of the art.</p><p>The lack of labeled data to as input to a machine learning model was the main bottleneck. To overcome this, this work utilized Amazon Turk platform. This platform allows users to create a task and give instructions to ‘Workers‘ , which agree to a price to complete each task. The data was preprocessed before being presented to the workers, and revised to make sure it was properly labeled.</p><p>Once labeled data was ready, the images and its corresponding segmented labels were used to train a U-Net model. In a nutshell, this models takes the input image, and at different scales, maps the image to a smaller vector. From this smaller vector, the model , again at different scales, constructs an image from this vector. During model training, the weights of the model are updated so that the image that is reconstructed minimizes the difference between the label image and the pixel segmentation.</p><p>We show that this method not only fits better the labeled ground truth image by the workers, but also generalizes well to other images of Zebrafish embryos. Once the model is trained, inference to obtain the segmented image is also orders of magnitude faster than previous techniques, including our previous wavelet segmentation method.</p></div></div></div>

Microscopic polyangiitis (MPA) is a rare condition characterized by nonspecific symptoms of fatigue, fever, or loss of appetite and additional symptoms related to areas of involvement. The rarity of the disease and its variable presentation can delay its diagnosis in the acute setting, potentially leading to delay in effective treatment and poor outcomes. This is a case report of a 68-year-old man, who presented to the hospital after being found poorly responsive at home. He was sedated and intubated in the field and brought to the ER. He was found to be hypotensive. History revealed abdominal aortic aneurysm, but no known history of GI bleed or use of blood-thinners. Physical exam revealed rhonchi throughout both lung fields, a soft, nondistended abdomen with normoactive bowel sounds, and cool extremities with weak palpable pulses. CBC was suggestive of anemia. BUN and creatinine were elevated indicating kidney injury. CT abdomen showed no acute pathology and an intact abdominal aortic aneurysm. CT chest revealed left lower lobe atelectasis and bilateral pulmonary edema. CT head was consistent with watershed infarction. Numerous blood transfusions were given. However, slow decline in hemoglobin continued to occur. Colonoscopy was considered for possible identification of the source of bleeding, however was not performed due to the family’s wish for conservative management. Bronchoscopy was performed, revealing extensive mucus plugging and bloody plugs. He was eventually weaned off sedation but remained largely unresponsive, occasionally opening his eyes to stimuli. On hospital day 7, necrotic lesions were noted on the patient’s ear and fingers. These findings prompted serologic studies for vasculitis that resulted in positive p-ANCA and myeloperoxidase antibodies, consistent with MPA. He was started on pulse dose IV steroids resulting in modest improvement in renal parameters and hemoglobin, but no discernible change in neurological status. The patient was transitioned to comfort care and palliative extubation was performed. Four days later, the patient expired. This case illustrates the potential for hypovolemic shock as a consequence of undiagnosed vasculitis. In this case, a definite diagnosis was not made, due to inability to perform a lung biopsy because of patient being on comfort measures. However, given that he was p-ANCA and myeloperoxidase positive, along with visualized blood on bronchoscopy, a presumptive diagnosis of MPA can be made. Although this patient may not have recovered even with early immunosuppressive treatment, vasculitis should be considered as a differential diagnosis in patients presenting in hypovolemic shock, especially if history, exam and noninvasive testing are unrevealing.

Fire is a primary driver of environmental change that can originate from natural or human ignition. Macroscopic charcoal (>125 "m) deposited into lake sediment is a record of a local fire event, whereas microscopic charcoal indicates fire activity on a broad landscape scale. Patterns of charcoal deposition may shed light on both human activities and climate history over long-time scales. Whether lowland Caribbean forests have experienced natural fire regimes over the long-term is unknown. Laguna Limón is a little-studied, large, freshwater lake on the northeastern coast of the Dominican Republic. We extracted four overlapping sediment cores totaling 315 cm in depth, and conducted analysis of macroscopic charcoal (2-cm), microscopic charcoal (16-cm), and loss-on-ignition (1-cm) to examine the long-term fire and environmental history of the area. Loss-on-ignition data established that the lake has only recently become organic rich, and was likely open to the sea as a low energy bay until 1400 Cal. Yr BP. The lake existed briefly as a wetland before transitioning to the modern freshwater lake 1200 Cal. Yr BP. Macroscopic charcoal was most abundant in the freshwater section of the core while microscopic charcoal peaked near the bottom of the core, and aligns well with other regional microscopic charcoal records. Overall the charcoal record reflects a combination of climatic and anthropogenic related charcoal deposition suggesting that fire has played an active role in the environmental history Laguna Limón. / Master of Science

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20757号 / 医博第4287号 / 新制||医||1024(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 生田 宏一, 教授 濵﨑 洋子, 教授 髙折 晃史 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

The dislocation etch pits formed on the cleavage surfaces of lithium fluoride in an aqueous solution containing varying concentrations of ferric ions are investigated by electron microscopy. The results obtained reveal the powerful influence of the inhibitor in the stabilisation of kinks and macroledges. There is some evidence for the nucleation of disso­lution at imperfections other than the dislocations. Dissolution spirals are observed in some cases suggesting the presence of helical dislocations in lithium fluoride. / Thesis / Master of Science (MS)

Background and study aims: It has been suggested that smoking may be associated with microscopic colitis (MC) in some studies; however, there are conflicting results in the current literature with many of these studies having significant limitations. Our study aims to offer a meta-analysis evaluating the association between MC, including both its subtypes, and smoking. Patients and methods: A systemic review was conducted in PUBMED, Embase, PubMed Central, and ScienceDirect databases from inception through December 2019. Effect estimates from the individual studies were extracted and combined using the random effect, generic inverse variance method of DerSimonian and Laird and a pooled odds ratio (OR) was calculated. Forest plots were generated, and publication bias was assessed for using conventional techniques. Results: Eight observation studies with a total of 1461 patients with MC were included in this study, 383 of whom were active smokers (26.2%). Current smoking was significantly associated with MC (OR 3.58, 95% CI, 2.51–5.11), lymphocytic colitis (LC) (OR 3.64, 95% CI, 2.46–5.38), and collagenous colitis (CC) (OR 4.43, 95% CI, 2.68–7.32). Gender-specific subgroup analysis showed a significant association with smoking was found for CC in men (OR 4.53, 95% CI, 1.59–12.85), CC in women (OR 3.27, 95% CI, 2.35–4.54), LC in women (OR 2.27, 95% CI, 1.27–4.06) and MC in women (OR 2.93, 95% CI, 2.09–4.10). We found no publication bias as assessed by the funnel plots and Egger's regression asymmetry test. Conclusion: Our meta-analysis found a statistically significant association between smoking and both subtypes of MC.

Though comparisons of simulation models have been conducted, few investigations have examined in detail the logical differences between models. If the output measures of effectiveness are to be interpreted correctly, it is important that the analyst understand some of the underlying logic and assumptions upon which the results are based. An understanding of model logic and its inherent effect on the results will aid the transportation analyst in the application and calibration of a simulation model. In this thesis, the car-following behavior of the CORSIM and INTEGRATION simulation models are examined in significant detail, and its impact on output results explained. In addition, the thesis presents a calibration procedure for the CORSIM sub-model, FRESIM. Currently, FRESIM is calibrated by ad hoc trial-and-error, or by utilizing empirically developed cross-referencing tables. The literature reveals that the relationship between the microscopic input parameters of the CORSIM model, and the macroscopic parameters of capacity is not understood. The thesis addresses this concern. Finally, the thesis compares the INTEGRATION and CORSIM models in freeway and urban environments. The comparison is unique in that the simulated networks were configured such that differences in results could be identified, isolated, and explained. Additionally, the simplified nature of the test networks allowed for the formulation of analytical solutions. The thesis begins by relating steady-state car-following behavior to macroscopic traffic stream models. This is done so that a calibration procedure for the FRESIM (Pipes) car-following model could be developed. The proposed calibration procedure offers an avenue to calibrate microscopic car-following behavior using macroscopic field measurements that can be easily obtained from loop detectors. The calibration procedure, while it does not overcome the inherent shortcomings of the Pipes model, does provide an opportunity to better calibrate the network FRESIM car-following sensitivity factor to existing roadway conditions. The thesis then reports an observed inconsistency in the link-specific car-following sensitivity factor of the FRESIM model. Because calibration of a network on a link-specific basis is key to an accurate network representation, a correction factor was developed that should be applied to the analytically calculated link-specific car-following sensitivity factor. The application of the correction factor resulted in observed saturation flow rates that were within 5% of the desired saturation flow rates. The thesis concludes with a comparison of the CORSIM and INTEGRATION models for transient conditions. As a result of the various intricacies and subtleties that are involved in transient behavior, the comparisons were conducted by running the models on simple networks where analytical solutions to the problem could be formulated. In urban environments, it was observed that the models are consistent in estimates of delay and travel time, and inconsistent in estimates of vehicle stops, stopped delay, fuel consumption, and emissions. Specifically, it was observed that the NETSIM model underestimates the number of vehicle stops in comparison with INTEGRATION and the analytical formulation. It was also observed that the NETSIM vehicles speed and acceleration profiles are characterized by abrupt accelerations and decelerations. These abrupt movements significantly impact stopped time delay and vehicle emissions estimates. Inconsistencies in emissions estimates can also be attributed to differences in the embedded rate tables of each model. In freeway environments for under-saturated conditions, INTEGRATION returned higher values of travel time and delay, and lower values of average speed than the FRESIM model. These results are consistent with the analytical solution, and can be attributed to the speed-flow relationship of each model. In saturated conditions, when the capacity of the bottleneck is equal to the demand volume, the emergent vehicle behavior of the FRESIM model was observed to be inconsistent with the analytical solution. The FRESIM vehicles were observed to dramatically decelerate upon entering a lower-capacity link. This deceleration behavior led to higher travel time and delay time estimates in FRESIM than in INTEGRATION. In over-saturated conditions, longer queue lengths were observed in FRESIM than in INTEGRATION, resulting in slightly higher travel and delay estimates in the FRESIM model. The reason for the discrepancy in queue lengths is unclear, as the network jam density in each model was equivalent. / Master of Science

Carbon dioxide electroreduction (CO2R) is a promising and sustainable route to generate valuable feedstocks through the electrochemical conversion from CO2 with electricity generated by renewable energy resources, to reduce greenhouse gas emissions, thereby protecting the global environment. One of the critical challenges for developing practical CO2R developments is understanding the structures and chemistry of CO2R electrocatalysts, and then generating fundamental insights to guide the design and optimization of high-performance electrocatalysts. During my Ph.D. studies, synchrotron-based X-ray spectro-microscopy techniques, scanning transmission X-ray microscopy (STXM) and X-ray spectro-ptychography, were used to study nickel-nitrogen-carbon (Ni-N-C) and electrodeposited Cu-based CO2R electrocatalysts. STXM and ptychography were upgraded to in situ characterizations to provide spectroscopic characterization and quantitative, chemically selective imaging of these catalytic materials under CO2R conditions. To achieve in situ STXM and spectro-ptychography, a micro-fluidic based, liquid-flow electrochemical in situ device was developed, fabricated, and implemented. The in situ device is optimized from previous versions developed by Vinod Prabu, past graduate student of Hitchcock group, and the initial concept was provided by Pablo Ingino and Dr. Martin Obst, collaborators at the University of Bayreuth. In situ STXM and spectro-ptychography provided a detailed chemical and morphological evaluation of catalyst materials at different applied potentials during electrochemical processes. The in situ STXM studies of Cu-based catalysts showed that electrodeposited Cu2O particles are converted to metallic Cu with different reaction rates at applied potentials less negative than that for initiation of CO2R. The in situ STXM results show a degree of heterogeneity in the electrochemical response of discrete nanoparticles and metallic Cu as the active catalyst for CO2 reduction which is structurally relatively stable at CO2R-relevant potentials within the spatial resolution of STXM. In situ spectra-ptychography was used to follow morphological changes of a single Cu-based catalytic particle in the electrochemical regime of CO2R. Our results show that the Cu particle lost the initial cubic structure and formed irregular dendritic-like structures during the CO2R process. To the best of my knowledge, this is the first time in situ STXM has been applied to CO2R electrocatalysts under flow liquid and electrochemical conditions and the first report of in situ spectro-ptychography studies. In summary, my research has successfully achieved the in situ STXM and spectro-ptychography experiments and contributed to an improved understanding of Cu nanoparticle CO2R electrocatalysts. / Dissertation / Doctor of Philosophy (PhD)

No description available.

Variable speed limits (VSL) are dynamic traffic management systems designed to increase the efficiency and safety of highways. While the macroscopic performance of VSL systems is well explored in the existing literature, there is a need to further understand the microscopic behavior of vehicles driving in VSL zones. Specifically, driver compliance to advisory VSL systems is quantified based on a driving-simulation experiment and introduced into a broader microscopic behavior model. Statistical analysis indicates that VSL compliance can be predicted based upon several VSL design parameters. The developed two-state microscopic model is calibrated to driving-simulation trajectory data. A calibrated VSL microscopic model can be utilized for new VSL control and macroscopic performance studies, adding an increased dimension of realism to simulation work. As an example, the microscopic model is implemented within VISSIM (overriding the default car-following model) and utilized for a safety-mobility performance assessment of an incident-responsive VSL control algorithm implemented in a MATLAB COM interface. Examination of the multi-objective optimization frontier reveals an inverse relationship between safety and mobility under different control algorithm parameters. Engineers are thus faced with a decision between performing multi-objective optimization and selecting a dominant VSL control objective (e.g. maximizing safety versus mobility performance). / Master of Science