The nuclear pore complex (NPC) is a proteinaceous gateway embedded in the nuclear envelope (NE) that regulates nucleocytoplasmic transport of molecules in eukaryotes. The NPC is formed by hundreds of proteins that are classified into approximately thirty different types of proteins called nucleoporin (Nup), each presents in multiples of eight copies. These nucleoporins are divided into two categories: the scaffold Nups forming the main structure of the NPC and the phenylalanine-glycine (FG) Nups that contain multiple repeats of intrinsically disordered and hydrophobic FG domains. These FG-Nups constitute the selective permeability barrier in the central channel of the NPC, which mediates the nuclear import of proteins into the nucleus, and the nuclear export of mRNA and pre-ribosomal subunits out of the nucleus. However, the precise copies of these Nups and their specific roles in the nucleocytoplasmic transport mechanism remain largely unknown. Moreover, the dysfunctional nuclear transport and the mutations of Nups have been closely associated with numerous human diseases, such as cancer, tumor and liver cirrhosis. We have developed and employed live-cell high-speed single-molecule microscopy to elucidate these critical questions remained in the nuclear transport and provide the fundamental knowledge for developing therapies. In this dissertation, I will present my major findings for the following three research projects: 1) determine the dynamic components of FG-Nups in native NPCs; 2) track the nucleocytoplasmic transport of transcription factor Smad proteins under ligand-activated conditions; and 3) elucidate the relationship between the nuclear export of mRNA and the presence and absence of specific Nups in live cells.Determination of the dynamic components for FG-Nups in native NPCs. Scaffold Nups have been intensively studied with electron microscopy to reveal their spatial positions and architecture in the past decades. However, the spatial organization of FG-Nups remains obscure due to the challenge of probing these disordered and dynamic polypeptides in live NPCs. By employing high-speed single-molecule microscopy and a live cell HaloTag labeling technique, I have mapped the spatial distribution for all eleven known mammalian FG-Nups within individual NPCs. Results show that all FG-Nups within NPCs are distinct in conformations and organized to form a ~300nm long hourglass shaped toroidal channel through the nuclear envelope. Exceptionally, the two remaining Nups (Nup98 and hCG1) almost extend through the entire NPC and largely overlap with all other FG-Nups in their spatial distributions. These results provide a complete map of FG-Nup organization within the NPC and also offer structural and functional insights into nucleocytoplasmic transport models. Tracking of the nucleocytoplasmic transport of Smad proteins under ligand-activated conditions. The inducement of transforming growth factor β1 (TGF-β1) was reported to cause the nuclear accumulation of Smad2/Smad4 heterocomplexes. However, the relationship between nuclear accumulation and the nucleocytoplasmic transport kinetics of Smad proteins in the presence of TGF-β1 remains obscure. By combining a high-speed single-molecule tracking microscopy technique (FRET), I tracked the entire TGF-β1-induced process of Smad2/Smad4 heterocomplex formation, as well as their transport through nuclear pore complex in live cells. The FRET results have revealed that in TGF-β1-treated cells, Smad2/Smad4 heterocomplexes formed in the cytoplasm, imported through the nuclear pore complexes as entireties, and finally dissociated in the nucleus. Moreover, it was found that basal-state Smad2 or Smad4 cannot accumulate in the nucleus without the presence of TGF-β1, mainly because both of them have an approximately twofold higher nuclear export efficiency compared to their nuclear import. Remarkably and reversely, heterocomplexes of Smad2/Smad4 induced by TGF-β1 can rapidly concentrate in the nucleus because of their almost fourfold higher nuclear import rate in comparison with their nuclear export rate. Thus, these single-molecule tracking data elucidate the basic molecular mechanism to understand nuclear transport and accumulation of Smad protein. Elucidation of the relationship between the nuclear export of mRNA and the presence and absence of specific Nups in live cells. In addition to explore the dynamic organization of NPC, in vivo characterization of the exact copy number and the specific function of each nucleoporin in the nuclear pore complex (NPC) remains desirable and challenging. Using live-cell high-speed super-resolution single-molecule microscopy, we first quantify the native copies of nuclear basket FG-Nups (Nup153, Nup50 and Tpr). Second, with same imaging technique and the auxin-inducible degradation strategies, I track the nuclear export of mRNA through native NPCs in absence of these FG-Nups. I found that these FG-Nups proteins possess the stoichiometric ratio of 1:1:1 and play distinct roles in the nuclear export of mRNAs in live cells. Tpr’s absence in the NPC dominantly reduces nuclear mRNA’s probability of entering the NPC for export. Complete depletion of Nup153 causes mRNA’s successful nuclear export efficiency dropped approximately four folds. Remarkably, the relationship between mRNA’s successful export efficiency and the copy number of Nup153 is not linear but instead follows a sigmoid function, in which mRNA can gain its maximum successful export efficiency as Nup153 increased from zero to around half of their full copies in the NPC. Lastly, the absence of Tpr or Nup153 also alters mRNA’s export routes through the NPC, but the removal of only Nup50 has almost no impact upon mRNA export route and kinetics. / Biology

A process for the use of multihypothesis prediction in the reconstruction of images is proposed for use in both compressed-sensing reconstruction as well as single-image super-resolution. Specifically, for compressed-sensing reconstruction of a single still image, multiple predictions for an image block are drawn from spatially surrounding blocks within an initial non-predicted reconstruction. The predictions are used to generate a residual in the domain of the compressed-sensing random projections. This residual being typically more compressible than the original signal leads to improved compressed-sensing reconstruction quality. To appropriately weight the hypothesis predictions, a Tikhonov regularization to an ill-posed least-squares optimization is proposed. An extension of this framework is applied to the compressed-sensing reconstruction of hyperspectral imagery is also studied. Finally, the multihypothesis paradigm is employed for single-image superresolution wherein each patch of a low-resolution image is represented as a linear combination of spatially surrounding hypothesis patches.

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Game engines such as Unreal Engine 5 are widely used to create photo-realistic renderings. To run these renderings at high quality without experiencing any performance issues,high-performance hardware is often required. In situations where the hardware is lacking,users may be forced to lower the quality and resolution of renderings to maintain goodperformance. While this may be acceptable in some situations, it limits the benefit that apowerful tool like Unreal Engine 5 can provide. This thesis aims to explore the possibilityof using a Real-ESRGAN, fine-tuned on a custom data set, to increase both the resolutionand quality of screenshots taken in Unreal Engine 5. By doing this, users can lower theresolution and quality of their Unreal Engine 5 rendering while still being able to generatehigh quality screenshots similar to those produced when running the rendering at higherresolution and higher quality. To accomplish this, a custom data set was created by randomizing camera positionsand capturing screenshots in an Unreal Engine 5 rendering. This data set was used to finetune a pre-trained Real-ESRGAN model. The fine-tuned model could then generate imagesfrom low resolution and low quality screenshots taken in Unreal Engine 5. The resultingimages were analyzed and evaluated using both quantitative and qualitative methods.The conclusions drawn from this thesis indicate that images generated using the finetuned weights are of high quality. This conclusion is supported by quantitative measurements, demonstrating that the generated images and the ground truth images are similar.Furthermore, visual inspection conducted by the authors confirms that the generated images are similar to the reference images, despite occasional artifacts.

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No description available.

Video from aerial surveillance can provide a rich source of data for analysts. From the time-critical perspective of wilderness search and rescue operations, information extracted from aerial videos can mean the difference between a successful search and an unsuccessful search. When using low-cost, payload-limited mini-UAVs, as opposed to more expensive platforms, several challenges arise, including jittery video, narrow fields of view, low resolution, and limited time on screen for key features. These challenges make it difficult for analysts to extract key information in a timely manner. Traditional approaches may address some of these issues, but no existing system effectively addresses all of them in a unified and efficient manner. Building upon a hierarchical dense image correspondence technique, we create a unifying framework for reducing jitter, enhancing resolution, and expanding the field of view while lengthening the time that features remain on screen. It also provides for easy extraction of moving objects in the scene. Our method incorporates locally adaptive warps which allows for robust image alignment even in the presence of parallax and without the aid of internal or external camera parameters. We accelerate the image registration process using commodity Graphics Processing Units (GPUs) to accomplish all of these tasks in near real-time with no external telemetry data.

The kidney is one of the most important and complex organs in the human body, filtering hundreds of litres of blood daily. Kidney disease is one of the fastest growing causes of death in the modern world, and this motivates extensive research for better understanding the function of the kidney in health and disease. Some of the most important cellular structures for blood filtration in the kidney are of very small dimensions (on the sub-200 nm scale), and thus electron microscopy has been the only method of choice to visualize these minute structures. In one study, we show for the first time that by combining optical clearing with STED microscopy, protein localizations in the slit diaphragm of the kidney, a structure around 75 nanometers in width, can now be resolved using light microscopy. In a second study, a novel sample preparation method, expansion microscopy, is utilized to physically expand kidney tissue samples. Expansion improves the effective resolution by a factor of 5, making it possible to resolve podocyte foot processes and the slit diaphragm using confocal microscopy. We also show that by combining expansion microscopy and STED microscopy, the effective resolution can be improved further. In a third study, influences on the development of the kidney were studied. There is substantial knowledge regarding what genes (growth factors, receptors etc.) are important for the normal morphogenesis of the kidney. Less is known regarding the physiology behind how paracrine factors are secreted and delivered in the developing kidney. By depleting calcium transients in explanted rat kidneys, we show that calcium is important for the branching morphogenesis of the ureteric tree. Further, the study shows that the calcium-dependent initiator of exocytosis, synaptotagmin, is expressed in the metanephric mesenchyme of the developing kidney, indicating that it could have a role in the secretion of paracrine growth factors, such as GDNF, to drive the branching. / <p>QC 20170523</p>

京都大学 / 新制・課程博士 / 博士(生命科学) / 甲第24304号 / 生博第487号 / 新制||生||65(附属図書館) / 京都大学大学院生命科学研究科高次生命科学専攻 / (主査)教授 渡邊 直樹, 教授 見学 美根子, 教授 今吉 格 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

The Sun is of fundamental importance to life on earth and is studied by scientists from many disciplines. It exhibits phenomena on a wide range of observable scales, timescales and wavelengths and due to technological developments there is a continuing increase in the rate at which solar data is becoming available for study which presents both opportunities and challenges. Two satellites recently launched to observe the sun are STEREO (Solar TErrestrial RElations Observatory), providing simultaneous views of the SUN from two different viewpoints and SDO (Solar Dynamics Observatory) which aims to study the solar atmosphere on small scales and times and in many wavelengths. The STEREO and SDO missions are providing huge volumes of data at rates of about 15 GB per day (initially it was 30 GB per day) and 1.5 terabytes per day respectively. Accessing these huge data volumes efficiently at both high spatial and high time resolutions is important to support scientific discovery but requires increasingly efficient tools to browse, locate and process specific data sets. This thesis investigates the development of new technologies for processing information contained in multiple and overlapping images of the same scene to produce images of improved quality. This area in general is titled Super Resolution (SR), and offers a technique for reducing artefacts and increasing the spatial resolution. Another challenge is to generate 3D images such as Anaglyphs from uncalibrated pairs of SR images. An automated method to generate SR images is presented here. The SR technique consists of three stages: image registration, interpolation and filtration. Then a method to produce enhanced, near real-time, 3D solar images from uncalibrated pairs of images is introduced. Image registration is an essential enabling step in SR and Anaglyph processing. An accurate point-to-point mapping between views is estimated, with multiple images registered using only information contained within the images themselves. The performances of the proposed methods are evaluated using benchmark evaluation techniques. A software application called the SOLARSTUDIO has been developed to integrate and run all the methods introduced in this thesis. SOLARSTUDIO offers a number of useful image processing tools associated with activities highly focused on solar images including: Active Region (AR) segmentation, anaglyph creation, solar limb extraction, solar events tracking and video creation.