1,721,107 research outputs found
공간 오믹스를 위한 자동 세포 분리 분석
Full text link학위논문(박사) -- 서울대학교대학원 : 공과대학 전기·정보공학부, 2023. 2. 권성훈.Spatial omics profiling technologies have been recognized recently for its ability to decipher the genetic molecules that are structurally relevant in pathology. Especially, in tumor biology, tumor is not the group of malignant tumor cells, but rather group of various cells such as tumor cells, immune cells, fibroblasts, etc. gathers together, constructing the tumor microenvironments. Technologies to analyze such microstructures have evolved from bulk sequencing, single cell sequencing to spatial omics profiling technologies. Spatial omics profiling technologies have highly influenced in decoding cancerous mechanisms by questioning the tumor heterogeneity, tumor microenvironment and spatial biomarkers.
Most of the spatial omics technologies focus on mapping the spatial omics landscape in a large scale. They rather introduces the spatially-barcoded capture probes or fluorescence labeled target probes to spatially locate the genetic molecules. The information depth and the scalability of the techniques varies according to the purpose of the spatial assay techniques. Such technologies are capable of discovering the spatial heterogeneity and the spatial landscape of the consisting cell types due to relatively low depth of the omics information. To effectively address the target molecules for therapeutics or diagnostics, higher depth of the omics information are required. To meet the needs, region of interest (ROI)-based spatial technologies isolated the target regions and applies chemistries for higher coverage omics data.
Conventional cell sorters utilizes microfluidic channels to sort cells of interest which requires cell dissociation in a solution phase. For instance, Fluorescence activated cell sorter (FACS) or Magnetic-activated cell sorting (MACS) uses fluorescence or magnetic particles, respectively, to designate the cells of interest in dissociated cell solutions. Spatially isolating techniques such as laser capture microdissection (LCM) is able to sort out the ROIs while preserving the spatial context, but it approximately takes an hour for isolating the targets. Also, it uses rather UV laser to dissect out cells or IR-activated melting of polymers to stick out cells which might cause damage to cells.
Here, I developed the automated spatially resolved laser activated cell sorter that isolates the cells in target per second while preserving the spatial context of the cells. Specific region of indium tin oxide (ITO) coated slide glass evaporates when illuminated by IR laser pulse, plunging the cells into the desired reservoir. The applicability of the suggested cell sorter are demonstrated in omics profiling chemistries such as DNA sequencing, RNA sequencing, mass spectrometry, etc.종양은 종양세포만이 원인이 되는 질병이 아닌, 면역세포와 혈관 구조, 표피 세포 등 다양한 세포들이 공동체를 이뤄 질병을 발전시키는 복합적인 질병이다. 이를 분석하기 위하여 차세대 시퀀싱 (NGS), 단일 세포 분석, 유세포 분석 등 다양한 기술이 활용되어 왔다. 특히 RNA sequencing 을 포함한 단일 세포 분석은 종양 내에서 성장, 전이, 진화, 약물의 내성과 관련된 타겟을 발굴하고 이를 조절할 수 있는 인자들을 개발하는 등 종양 연구의 혁신을 이끌었다. 그러나 이러한 접근 방법은 종양 미세 환경 내에서 세포가 존재하고 있는 위치 정보가 손실 되기 때문에 종양의 온전한 그림을 제공하지 못한다. 최근에는 종양 내 이형적으로 분포하고 있는 유전 물질들을 이해하면 종양의 이형성과 종양 미세환경의 탐구와 암의 진화 및 발전 메커니즘을 이해하여 이전에는 발견하지 못한 새로운 제약, 진단 타겟을 발굴 할 수 있을 것이라는 관점들이 제시되고 있다.
다중의 형광 프로브를 활용한 방식으로 DNA, RNA, 단백질 등의 위치를 표적하여 종양의 전체적인 그림을 파악하는 기술들이 최근 폭발적으로 개발되고 있고, 현장 바코딩 방식으로 위치 별로 발현하고 있는 유전 물질을 표적하여 정량화 할 수 있는 방법도 상용화 되어 종양 에서 새로운 발견을 이끌어내고 있다. 그러나 위의 제시된 기술들 모두 De novo로 새로운 제약 진단 타겟을 발굴하는 데에는 한계가 존재한다.
본 논문에서는 공간 오믹스를 가능하게 하는 세포 분리 분석기를 개발하여 관심영역의 세포를 분리하고 이후 DNA, RNA, 단백질 등을 분석하는 어세이들과 연결하여 위치정보를 포함하면서도 높은 정보량으로 세포를 분석하고, 이전까지 발굴하지 못하였던 새로운 진단 제약 타겟을 탐색할 수 있는 기술에 대하여 설명한다. 레이저를 조사하면 희생층이 승화되며 조사 영역에 위치한 세포들을 회수할 수 있고, 현존하는 생화학 어세이를 수행 할 수 있다. 자동으로 이미지 프로세싱을 통하여 원하는 세포들을 특정할 수 있는 프로그램을 개발하였고, 이를 세포주와 임상 샘플에 적용하고 이후 생화학 어세이 적용을 입증하였다. 항원 항체 반응을 이용한 염색 방법 이외에도 높은 정보량으로 유전체 지도를 그리는 염색법 등 다양한 염색 이미지에 적용했으며 본 기술을 활용하여 향후 응용할 수 있는 연구를 제안하였다.CHAPTER 1. INTRODUCTION １
1.1. The Need for Spatial Profiling in Cancer Biology ２
1.1.1. Historical Review of Technologies to Address Cancer Research ２
1.2. Spatial Landscape Profiling Technologies ６
1.2.1. Spatial transcriptomics profiling technologies ６
1.2.2. Spatial Omics Technologies ９
1.3. Spatial ROI-profiling technology １５
1.3.1. Previous sorting systems for spatial omics １５
1.3.2. The need for the development of automated spatially-resolved cell sorter １８
1.4. Outline of the dissertation ２１
1.4.1. Previous work from our group ２１
1.4.2. Main concept: Automated cell sorting system for multi omics ２４
1.4.3. Outline of the dissertation ２４
CHAPTER 2. DEVELOPMENT OF THE SPATIALLY RESOLVED LASER-ACTIVATED CELL SORTING PLATFORM ２６
2.1. Development of the SLACS system ２７
2.1.1. Advantage of the SLACS system compared to other cell sorting technologies ２７
2.1.2. Workflow and design of the SLACS system ２９
2.2. The quality of the spatial omics assays after cell isolation via SLACS ３６
CHAPTER 3. AUTOMATED IMAGE-BASED CELL SORTING PLATFORM ４０
3.1. Validation of the automated targeting and transferring using the encoded microparticles ４１
3.1.1. Design of the encoded microparticles for the validation ４１
3.1.2. Neural net-based pattern recognition for decoding the encoded microparticles ４４
3.2. Automated cell sorting for targeting the rare cells ４９
3.2.1. The need for automated cell sorting in isolating the circulating tumor cells (CTCs) ４９
3.2.2. Development of the cell sorting algorithm ５２
3.2.3. The quality of the biomolecules from the isolated cells ５８
3.2.4. Application to isolating the circulating tumor cells (CTCs) ６０
3.3. Automated cell sorting for targeting the clinical tissue samples ６３
3.3.1. Need for sorting the tumor regions for specific markers ６３
3.3.2. Cell sorting of the target markers in clinical samples ６５
CHAPTER 4. INTEGRATED SPATIAL PROFILING TECHNOLOGIES ６７
4.1. Integration with the other spatial landscape profiling technologies ６８
4.1.1. In situ sequencing for profiling the spatial landscape ６８
4.1.2. Gene annotation and analysis of In situ sequencing data ７１
4.2. Multi-omics analysis in integrated spatial profiling ７２
4.2.1. In situ sequencing in two different groups ７２
4.2.2. Multi-omics profiling by integrating in situ sequencing to its genomic aberrations ７４
4.2.3. Combination with other spatial profiling technologies ７６
CHAPTER 5.CONCLUSION AND DISCUSSION ７７
5.1.1. Summary of the dissertation ７８
5.1.2. Limitation of the technology ７９
5.1.3. The impact of the suggesting technology ８０
BIBLIOGRAPHY ８２
국문 초록 ９７박
Sumin Lee, violin
No full textProgram for recital offered in partial fulfillment of the requirements for the degree of Master of Music. With Hsiao-Ying Lin, piano
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Jacob Plaisted, voice
No full textProgram for recital offered in partial fulfillment of the requirements for the Gradute Performance Diploma. With Kim Zhang, piano; Sumin Lee, violin; Isabel Rushall, violin; Sarah Cummings, viola; Deborah Okhotina, cello
- …
