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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
Glycomic mapping of polylactosaminoglycans, terminal disialyl and sialyl sulfo N-acetyllactosamine motifs on mammalian cells
No full text以質譜為基礎的醣質體及醣蛋白質體大多著重在鑑定醣鏈末端乙酰基乳糖胺上的唾液酸及岩藻醣化，對於N型醣鏈上是否為直鏈或是帶有支鏈的多乳糖胺聚醣則較少著墨，且大多只是憑藉著質譜所得的數據來推算其存在和可能的組成為何，因此，本篇論文主要是利用人類內皮細胞、老鼠及人類的B淋巴球為樣品，鑑定並挑戰分析多乳糖胺聚醣的結構特徵及其末端的唾液酸化和硫酸化修飾。
首先，以人類內皮細胞：EA.hy926和HUVEC為起始原料，利用介質輔助雷射脫附法和電噴灑離子化方法在MS及MS/MS的階段來仔細地探討多乳糖胺聚醣結構，同時並搭配endo-β-galactosidase酵素及Smith降解反應來鑑定其是否為分支醣鏈及長鏈延伸的起始位置。和HUVEC相比，EA.hy926細胞的N型醣鏈帶有較少的唾液酸化和岩藻醣化，但多乳糖胺聚醣的長度較長且具有分支醣鏈，其延伸點並不侷限在目前已被證實具有相當重要生物意義的甘露醣6號碳上。拓展至醣質體方面的研究上，則利用Lycopersicon esculentum凝集素分別在醣、醣蛋白及醣胜肽的階段做純化，較為專一的兩步驟純化方法讓我們得知了至少有40個以上的醣蛋白候補者可能帶有乳糖胺聚醣。
小鼠B細胞株—BCL1上N型醣鏈的修飾主要為核心岩藻醣化，末端α鏈結半乳糖及唾液酸(Neu5Gc)化，且為非分支的多乳糖胺聚醣；相反的是，其O型醣鏈主要為簡單的core 1結構，帶有單唾液酸或雙唾液酸修飾。利用唾液酸酶、 endo-β-galactosidase、MS/MS及化學分析方法可知，雙唾液酸主要靠α2-8鏈結，並同時存在於具有多乳糖胺聚醣延伸或非延伸的N型醣鏈上。以螢光標記唾液酸並搭配高效液相層析儀顯示雙唾液酸結構的含量在N型醣鏈和O型醣鏈是相當的，且CD45為其攜帶者之ㄧ。透過小鼠α2,8-sialyltransferase VI(ST8sia VI)基因抑制實驗可知，此酵素同時參與N型醣鏈和O型醣鏈上雙唾液酸的生合成，且ST8Sia VI和雙唾液酸結構的表現量皆會隨著B細胞分化而增加。
有趣的是，儘管其生理功能目前還不是很清楚，BCL1的N型醣鏈末端的單唾液酸、雙唾液酸化乙酰基乳糖胺，及N型醣鏈核心結構皆可被硫酸化修飾。另外，在人類活化的B淋巴球上也鑑定到了α2,6-sialyated 6-sulfo-LacNAc結構，單和α2-6唾液酸化乙酰基乳糖胺相比，其為目前已知CD22更好的配體，這些B細胞上多乳糖胺聚醣鏈附加修飾的鑑定，使得Galectin和Siglec對B細胞分化的調控可以更為複雜精緻。總而言之，質譜分析技術的發展和進步，對於我們詳細地鑑定多乳糖胺聚醣結構來講，為一個相當重要的基礎，有助於我們對醣生物學及其它生理功能更近一步的了解。Most mass spectrometry (MS)-based glycomic and glycoproteomic analyses focus on identifying changes in terminal glyco-epitopes represented by sialylation and fucosylation at specific positions of the terminal N-acetyllactosamine units. Much less attention was accorded to the underlying linear or branched poly-N-acetyllactosamine (polyLacNAc) extension from the N-glycan trimannosyl core other than a simple inference of its presence due to mass data and hence glycosyl compositional assignment. To advance the frontiers of glycomics, this thesis work aims primarily to address the analytical challenges in structural characterization of polylactosaminoglycans and associated terminal modifications such as sialylation and sulfation decorating the human endothelial cells, mouse and human B cells.
Using the human endothelial cells, EA.hy926 and HUVEC, as starting materials, we have systematically investigated the MALDI- and ESI-MS-based methodologies for probing the structural details of polyLacNAc at both MS and MS/MS levels in conjunction with the use of endo-β-galactosidase and Smith degradation to identify branching motifs and initiation sites. N-glycans in EA.hy926 were found to be less sialylated and fucosylated but more extended and branched than those of HUVEC, thus demonstrating a fundamental glycomic difference. For EA.hy926, its polyLacNAc chains were shown to be not restricted to extending from a specific antenna including the biologically important 6-arm position. Extending to glycoproteomics, the Lycopersicon esculentum lectin based enrichment strategy was optimized at glycan, glycoprotein, and glycopeptide levels, leading to identification of over 40 protein carriers utilizing a two-step enrichment workflow.
For mouse B cells, the N-glycans of a B lymphoma cell line, BCL1, were found to be mostly core-fucosylated, capped with α-Gal or Neu5Gc sialic acid, and carry non-branched polyLacNAcs. In contrast, its O-glycans were based on simple core 1 structures, mono- or disialylated on both arms. Sialidase digestion, in conjunction with further MS/MS and chemical analyses, established the identity of the terminal disialyl motif as Neu5Gcα2-8Neu5Gc-, which was shown by endo-β-galatosidase digestion to be additionally present on both polyLacNAc extended and non-extended N-glycans. Fluorescent-labeling of released sialic acids coupled with fluorometric high performance liquid chromatography analysis revealed that the amount of the disialyl motif was comparable for both N- and O-glycans, and CD45 is one of the protein carriers. Gene knockdown studies provided positive correlation indicative of mouse α2,8-sialyltransferase VI (ST8sia VI) being involved in the biosynthesis of disialic acid on both N- and O-glycans. Importantly, both the expression level of ST8sia VI and the total amount of disialic acids increase during B cell differentiation.
Interestingly, sulfation was additionally found on the terminal mono- and disialylated LacNAc of the polyLAcNAc chains, as well as on the LacNAc proximal to the trimannosyl core in BCL1 although its biological relevance is at present unclear. On the other hand, similar analysis led to identification of α2,6-sialylated 6-sulfo-LacNAc epitope on both the N- and O-glycans of activated human B cells, which is known to constitute a better ligand than the non-sulfated α2,6-sialylated LacNAc for human CD22. These additional modifications of polyLacNAcs apparently complicate the simplistic interpretation of the modulating roles of galectins and Siglecs in the B cell differentiation model. The development of enabling analytical techniques sensitive enough to identify and characterize the fine structural details of the underlying polyLAcNAc is an important step towards a better understanding of the glycobiology of this and many other physiological processes
Isolation of Potential Pathogenic TCR ?chain Genes in Myasthenia Gravis Patients
No full text肌無力症是一種自體免疫疾病，主要的致病原因是由於病人體內產生一種乙醯膽鹼受體（acetylcholine receptor）的抗體，因而阻礙神經的傳導，並造成乙醯膽鹼受體的減少。本論文主旨在分析肌無力病人的T細胞接受器?鴗WVδ5及V?的基因使用，以及這些T細胞接受器CDR3 區域的核酸序列，希望藉由這些實驗能分析出與肌無力症相關的致病的T細胞，以期望可以藉由知道這些T細胞接受器的基因序列發展出專一的治療方式，而能更有效的治療肌無力症。
本論文中，我們取得四位肌無力病人（MG-D, MG-Y, MG-Ⅳ, MG-L）和三位正常人（HC-W, HC-R, HC-A）的周邊血液，及MG-L的胸腺內T淋巴細胞及甲狀腺的組織侵入性淋巴球(tissue infiltrating lymphocyte)來作分析，利用RT-PCR的技術，分析Vδ5-Cㄓ垝?-Cㄢo兩種基因組合在肌無力病人和正常人的表現情形，並進一步做T細胞接受器上CDR3區域的DNA定序分析。
首先，我們觀察到在Vδ5-Cㄟ穧]的使用上，肌無力病人的T細胞接受器CDR3區域的第六個或第七個（junction區域）帶有Arginine（R）正電荷氨基酸的比例比正常人高出很多，這樣的結果和EAMG老鼠所得到的結果有原先未料到的高符合性，因此，我們推斷此類的T細胞應該就是所謂的致病的T細胞。
在V?-Cㄟ穧]的使用上，除了MG-Ⅳ以外，其餘肌無力病人和正常人間T細胞接受器CDR3區域的氨基酸分子並沒有什麼差別，但在V?-Cㄟ穧]的使用上，我們找到了新的，可說是人類第三條的invariant TCR，也就是V?-J?2-Cㄢo條T細胞接受器?魽A而這類T細胞接受器顯然被病人的CD4+CD8+DP T cell所使用，且有expansion的現象。
我們相信目前所得到的結果，已帶領我們走向正確的了解致病的TCR，下一步將走向老鼠的實驗系統，製造出帶有此類TCR的transgenic mice，以確定此些TCR對導致肌無力所扮演的角色，並進而發展出對此類自體免疫疾病的專一療法。Myasthenia gravis (MG) is an autoimmune disease mediated by autoantibody against acetylcholine receptor (AchR). These antibodies blocked the signal transduction between neuromuscular junctions and resulted in muscle weakness. In this study, we analyzed the Vδ5- and V?-containing T cell receptor (TCR) ?chain gene usages, and the nucleotide sequences of the CDR3 region in MG patients and healthy controls. The aim is to find potential pathogenic T cells to aid the development of specific therapy for the disease of myasthenia gravis.
In the study, cDNA of peripheral blood lymphocytes (PBLs) were made from four MG patients & three healthy controls (HCs). Additionally, the thymus and thyroid surgically removed and obtained from one of the MG patients were also included in this study. TCR genes carrying Vδ5 or V? were specifically amplified from cDNA by C?specific primer paired with Vδ5- and V?- specific primers, respectively. The PCR products were then subcloned and sequenced to analyze the nucleotide sequences of the CDR3 region.
First of all, in the Vδ5-C?gene usage, we observed a significant differential usage on TCRs with charged amino acids on the sixth or seventh position of the CDR3 region between patients and healthy controls. This result unexpectedly correlates well with the data obtained from experimental autoimmune myasthenia gravis (EAMG) and strongly indicates these TCRs are related to the development of the MG.
Second of all, in the V?-C?gene usage, there were no significant sequence differences in the CDR3 region between MG patients and the HC, except MG-Ⅳ, which did not use invariant TCR bearing V? sequences in our data. In addition, we also found a new third invariant TCR ?chain in human—V?-J?2-C? This type of TCR was detected as an expanded population in CD4+CD8+ DP T cells from one of the MG patients.
We believe that our data do shed light on understanding the TCR usage in MG patients and the potential pathogenic TCRs. Generating mice carrying our TCR ?chain sequences is the next step in order to confirm the role of the T cells bearing our TCRs. To help developing the specific therapy to medicate myasthenia gravis will be our final goal.目錄……………………………………………………………………Ⅰ
中文摘要………………………………………………………………Ⅳ
英文摘要………………………………………………………………Ⅴ
縮寫表…………………………………………………………………Ⅵ
一、前言…………………………………………………………………1
1.1免疫系統……………………………………………………………1
1.2 T細胞和B細胞………………………………………………………1
1.2.1 T細胞……………………………………………………………1
1.2.2 B細胞……………………………………………………………3
1.3 T細胞抗原接受器(T Cell Recepter, TCR)與抗原(Antigen)以及主要組織相容性複合體(Major Histocompatibility Complex, MHC)………………………………………………………………………4
1.3.1 T細胞抗原接受器………………………………………………4
1.3.2 不變的T細胞接受器（Invariant TCR）………………………5
1.3.3 T細胞抗原接受器的基因座 (TCR loci)………………………6
1.3.4 T細胞接受器的V（D）J基因重組………………………………6
1.3.5 T細胞接受器與抗原以及主要組織相容性複合體(MHC)之間的作用………………………………………………………………………8
1.4 T細胞與自體免疫疾病……………………………………………8
1.5 肌無力症(Myasthenia Gravis)…………………………………10
1.5.1 神經末稍傳導途徑—乙醯膽鹼及其受器……………………10
1.5.2 EAMG（Experimental Autoimmune Myasthenia Gravis）…11
1.5.3 胸腺與肌無力症………………………………………………11
1.5.4 重症肌無力與T細胞抗原接受器………………………………12
1.5.5 目前治療肌無力症的主要方法………………………………13
1.6本論文所探討的主要問題…………………………………………13
二、實驗材料與方法…………………………………………………15
2.1實驗材料……………………………………………………………15
2.2實驗方法……………………………………………………………15
2.2.1分離出周邊淋巴球………………………………………………15
2.2.2引子(primer)的合成……………………………………………15
2.2.3 訊息核醣核酸（mRNA）與單股互補去氧核醣核酸（first strand cDNA）的製備…………………………………………………16
2.2.4訊息核醣核酸（mRNA）與單股互補去氧核醣核酸（first strand cDNA）的製備…………………………………………………16
2.2.5低熔點洋菜膠電泳分析（Low-melting Point Agarose Gel Electrophoresis）……………………………………………………17
2.2.6選植(Cloning)…………………………………………………17
2.2.6.1去氧核醣核酸的接合反應(DNA ligation)…………………17
2.2.6.2勝任細胞 (competent cell) 的製備………………………17
2.2.6.3轉型作用（Transformation）………………………………18
2.2.6.4 質體DNA的抽取………………………………………………………………………18
2.2.6.5核酸限制酶切割反應 (Digestion of Restriction Enzyme)…………………………………………………………………………19
2.2.6.6菌落聚合酶鍊鎖反應（colony-PCR）………………………19
2.2.6.7瓊酯明膠膠體電泳 (Agarose Gel Electrophoresis)……20
2.2.7核酸序列分析(Sequencing)……………………………………20
2.2.7.1循環反應（Cycle Reaction）………………………………20
2.2.7.2聚丙烯胺凝膠電泳分析（Polyacrylamide Gel Electrophoresis）……………………………………………………20
2.2.7.3自動核酸序列分析（Autosequencing）……………………21
三、結果………………………………………………………………22
3.1 V基因的使用情形…………………………………………………22
3.2 J基因的使用情形…………………………………………………23
3.2.1 Vδ5基因使用Jㄟ穧]的情形……………………………………23
3.2.2 V?基因使用Jㄟ穧]的情形……………………………………25
3.3 CDR3的性質………………………………………………………26
四、討論………………………………………………………………28
4.1 V基因的使用情形…………………………………………………28
4.2 J基因的使用情形…………………………………………………29
4.3 Clonal expansion………………………………………………30
4.4 CDR3……………………………………………………………………31
4.5 未來展望…………………………………………………………32
五、參考文獻…………………………………………………………34
圖表
表1. Table of PCR products studied of MG patients and healthy controls in Vδ5-C?and V?-C?genes………………38
表2.TCRVδ5-JΑNA and amino acid sequences 其CDR3 序列整理………………………………………………………………………39
表3.本實驗室所發現的其它條可能的Invariant TCR………………40
表4.在Vδ5基因的使用上，肌無力病人和正常人CDR3 junction區域帶有正電荷氨基酸的比率……………………………………………41
表5.CDR3序列分析整理—與線上基因庫比對的結果………………42
圖1.比較Vδ5和V?基因其Jㄟ穧]的使用情形………………………43
圖2.病人(MG)和正常人(HC)其Vδ5基因的使用下，其所銜接的Jㄟ穧]的使用情形……………………………………………………………44
圖3. 病人(MG)和正常人(HC)其V?基因的使用下，其所銜接的Jㄟ穧]的使用情……………………………………………………………45
圖4. J?usage of Vδ5 gene of HC-W/R/A & MG-D/Y/L…………46
圖5. J?usage of V? gene of HC-W/A & MG-D/Y/Ⅳ……………47
附錄一 T細胞接受器的V（D）J基因重組…………………………48
附錄二 T細胞與自體免疫疾病之間的關係…………………………49
附錄三 正常人與肌無力病人其神經傳導途徑—乙醯膽鹼受器之異同………………………………………………………………………50
附錄四 人類Jㄟ穧]的氨基酸序列…………………………………51
附錄五 EAMG（experimental autoimmune myasthenal gravis）體內所得的TCR ?錀DR3區域氨基酸分子的使用情形…………………53
附錄六 正常人(HC)和肌無力病人(MG)使用了Vδ5-C?& V?-Cㄓ劫細胞接受器CDR3區域的核酸與氨基酸序列
六之1.TCRVδ5-J DNA and amino acid sequences of clones from HC-2W mixed/CD4+/CD8+/ CD4- CD8- DN populations……………54
六之2 TCRVδ5-J DNA and amino acid sequences of clones from HC-1R mixed population ……………………………………………58
六之3 TCRVδ5-J DNA and amino acid sequences of clones from HC-2A mixed population……………………………………………59
六之4 TCRVδ5-J DNA and amino acid sequences of clones from MG-4D mixed population……………………………………………60
六之5 TCRVδ5-J DNA and amino acid sequences of clones from MG-6D mixed population……………………………………………61
六之6 TCRVδ5-J DNA and amino acid sequences of clones from MG-7D mixed population……………………………………………62
六之7. TCRVδ5-J DNA and amino acid sequences of clones from MG-2Y mixed /CD4+/CD8+/CD4+ CD8+ DP populations……63
六之8. TCRVδ5-J DNA and amino acid sequences of clones from MG-1L mixed/thymus/thyroid T cells………………………67
六之9. TCRV?-J DNA and amino acid sequences of clones from HC-2W mixed population………………………………………70
六之10. TCRV?-J DNA and amino acid sequences of clones from HC-2A CD4+/CD8+/CD4-CD8- DN populations………………71
六之11. TCRV?-J DNA and amino acid sequences of clones from MG-4D CD4+/CD8+/CD4-CD8- DN/CD4+ CD8+ DP populations……………………………………………………………74
六之12. TCRV?-J DNA and amino acid sequences of clones from MG-5D mixed population………………………………………77
六之13.TCRV?-J DNA and amino acid sequences of clones from MG-6D mixed population………………………………………78
六之14. TCRV?-J DNA and amino acid sequences of clones from MG-2Y CD4+/CD8+/CD4-CD8-DN/ CD4+ CD8+ DP populations79
六之15. TCRV?-JDNA and amino acid sequences of clones from MG-1Ⅳ mixed population……………………………………8
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
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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