Observation of Nuclei Reassembled from Demembranated Xenopus Sperm Nuclei and Analysis of Their Lamina Com- Ponents
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Landscape Analysis of Overcomplete Tensor and Neural Collapse
Landscape Analysis of Overcomplete Tensor and Neural Collapse Qing Qu Dept. of EECS, University of Michigan May 17, 2021 Outline of this Talk • Introduction • Overcomplete Tensor Decomposition (Representation Learning) • Neural Collapse in Deep Network Training Outline of this Talk • Introduction • Overcomplete Tensor Decomposition (Representation Learning) • Neural Collapse in Deep Network Training Nonconvex Problems in Representation Learning 5/18/21 4 General Nonconvex Problems 5/18/21 5 General Nonconvex Problems 5/18/21 6 General Nonconvex Problems 5/18/21 7 Optimizing Nonconvex Problems Globally 5/18/21 8 Nonconvex Problems with Benign Landscape • Generalized Phase Retrieval [Sun’18] • Low-rank Matrix Recovery [Ma’16, Jin’17, Chi’19] • (Convolutional) Sparse Dictionary Learning [Sun’16, Qu’20] • (Orthogonal) Tensor Decomposition [Ge’15] • Sparse Blind Deconvolution [Zhang’17, Li’18, Kuo’19] • Deep Linear Network [Kawaguchi’16] • ... 5/18/21 9 Outline of this Talk • Introduction • Overcomplete Tensor Decomposition (Representation Learning) • Neural Collapse in Deep Network Training Landscape Analysis of Overcomplete Learning Q. Qu, Y. Zhai, X. Li, Y. Zhang, Z. Zhu, Analysis of optimization landscapes for overcomplete learning, ICLR’20, (oral, top 1.9%) • Provide the global landscape for overcomplete representation learning problems. • Explains why they can be efficiently optimized to global optimality Overcomplete Tensor Decomposition We consider decomposing a 4-th order tensor of rank m in the following form Core problem for several unsupervised representation learning problems (ICA and mixture of Gaussian [Anandkumar’12], dictionary learning [Barak’14,Qu’20]), and even training neural networks [Ge’17]. Overcomplete Tensor Decomposition A natural (nonconvex) objective to find one component Overcomplete Tensor Decomposition Overcomplete Tensor Decomposition • For overcomplete case, most of existing landscape analysis results [Ge’17] are local, or are based on Sum-of-Squares relaxations [Barak’15, Ma’16] which is computationally expensive. -
Revealing the Mechanism of Xist-Mediated Silencing
Revealing the Mechanism of Xist-mediated Silencing Thesis by Chun-Kan Chen In Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy CALIFORNIA INSTITUTE OF TECHNOLOGY Pasadena, California 2018 Defended November 1, 2017 ii 2017 Chun-Kan Chen ORCID: 0000-0002-1194-9137 iii ACKNOWLEDGEMENTS First of all, I’d like to thank my great mentor, Dr. Mitch Guttman (California Institute of Technology, Pasadena, CA), who led me to become an independent researcher and gave me valuable advice that guided me to accomplish this thesis. He has always been supportive of my future plans and career goals. I really enjoyed every discussion we have had. We often generated some interesting ideas for projects during our discussions. I would also like to send my thanks to my lab mates, Amy Chow, Mario Blanco, and Erik Aznauryan, who helped me with many experiments to move the project forward. I’d like to acknowledge Dr. Kathrin Plath (University of California, Los Angeles, Los Angeles, CA) for the collaboration and his critical comments on this project. Also, I want to thank Jesse Engreitz and Patrick McDonel, who provided helpful comments and suggestions to the project. I want to thank my parents, brother, and parents-in-law who provided both instrumental and emotional support to assist me in completing my Ph.D. degree. I also want to thank my friends, Lily Chen, Pei-Ying Lin, Tzu-Yao Wang, and Wei Li, for giving me valuable social support during my years in graduate school. Last but not least, I would like to send my special thanks to my wife, Christine Juang, who has always been supportive. -
Upon Microbial Challenge, Human Neutrophils Undergo Rapid Changes in Nuclear Architecture and Chromatin Folding to Orchestrate an Immediate Inflammatory Gene Program
Downloaded from genesdev.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Upon microbial challenge, human neutrophils undergo rapid changes in nuclear architecture and chromatin folding to orchestrate an immediate inflammatory gene program Matthew Denholtz,1,5 Yina Zhu,1,5 Zhaoren He,1 Hanbin Lu,1 Takeshi Isoda,1,4 Simon Döhrmann,2 Victor Nizet,2,3 and Cornelis Murre1 1Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, California 92039, USA; 2Department of Pediatrics, University of California at San Diego School of Medicine, La Jolla, California 92093, USA; 3Skaggs School of Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093, USA Differentiating neutrophils undergo large-scale changes in nuclear morphology. How such alterations in structure are established and modulated upon exposure to microbial agents is largely unknown. Here, we found that prior to encounter with bacteria, an armamentarium of inflammatory genes was positioned in a transcriptionally passive environment suppressing premature transcriptional activation. Upon microbial exposure, however, human neu- trophils rapidly (<3 h) repositioned the ensemble of proinflammatory genes toward the transcriptionally permissive compartment. We show that the repositioning of genes was closely associated with the swift recruitment of cohesin across the inflammatory enhancer landscape, permitting an immediate transcriptional response upon bacterial exposure. We found that activated enhancers, marked by increased deposition of H3K27Ac, were highly enriched for cistromic elements associated with PU.1, CEBPB, TFE3, JUN, and FOSL2 occupancy. These data reveal how upon microbial challenge the cohesin machinery is recruited to an activated enhancer repertoire to instruct changes in chromatin folding, nuclear architecture, and to activate an inflammatory gene program. -
Is Shuma the Chinese Analog of Soma/Haoma? a Study of Early Contacts Between Indo-Iranians and Chinese
SINO-PLATONIC PAPERS Number 216 October, 2011 Is Shuma the Chinese Analog of Soma/Haoma? A Study of Early Contacts between Indo-Iranians and Chinese by ZHANG He Victor H. Mair, Editor Sino-Platonic Papers Department of East Asian Languages and Civilizations University of Pennsylvania Philadelphia, PA 19104-6305 USA [email protected] www.sino-platonic.org SINO-PLATONIC PAPERS FOUNDED 1986 Editor-in-Chief VICTOR H. MAIR Associate Editors PAULA ROBERTS MARK SWOFFORD ISSN 2157-9679 (print) 2157-9687 (online) SINO-PLATONIC PAPERS is an occasional series dedicated to making available to specialists and the interested public the results of research that, because of its unconventional or controversial nature, might otherwise go unpublished. The editor-in-chief actively encourages younger, not yet well established, scholars and independent authors to submit manuscripts for consideration. Contributions in any of the major scholarly languages of the world, including romanized modern standard Mandarin (MSM) and Japanese, are acceptable. In special circumstances, papers written in one of the Sinitic topolects (fangyan) may be considered for publication. Although the chief focus of Sino-Platonic Papers is on the intercultural relations of China with other peoples, challenging and creative studies on a wide variety of philological subjects will be entertained. This series is not the place for safe, sober, and stodgy presentations. Sino- Platonic Papers prefers lively work that, while taking reasonable risks to advance the field, capitalizes on brilliant new insights into the development of civilization. Submissions are regularly sent out to be refereed, and extensive editorial suggestions for revision may be offered. Sino-Platonic Papers emphasizes substance over form. -
Nuclear Domains
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Cold Spring Harbor Laboratory Institutional Repository CELL SCIENCE AT A GLANCE 2891 Nuclear domains dynamic structures and, in addition, nuclear pore complex has been shown to rapid protein exchange occurs between have a remarkable substructure, in which David L. Spector many of the domains and the a basket extends into the nucleoplasm. Cold Spring Harbor Laboratory, One Bungtown nucleoplasm (Misteli, 2001). An The peripheral nuclear lamina lies Road, Cold Spring Harbor, NY 11724, USA extensive effort is currently underway by inside the nuclear envelope and is (e-mail: [email protected]) numerous laboratories to determine the composed of lamins A/C and B and is biological function(s) associated with thought to play a role in regulating Journal of Cell Science 114, 2891-2893 (2001) © The Company of Biologists Ltd each domain. The accompanying poster nuclear envelope structure and presents an overview of commonly anchoring interphase chromatin at the The mammalian cell nucleus is a observed nuclear domains. nuclear periphery. Internal patches of membrane-bound organelle that contains lamin protein are also present in the the machinery essential for gene The nucleus is bounded by a nuclear nucleoplasm (Moir et al., 2000). The expression. Although early studies envelope, a double-membrane structure, cartoon depicts much of the nuclear suggested that little organization exists of which the outer membrane is envelope/peripheral lamina as within this compartment, more contiguous with the rough endoplasmic transparent, so that internal structures contemporary studies have identified an reticulum and is often studded with can be more easily observed. -
Nuclear Envelope Laminopathies: Evidence for Developmentally Inappropriate Nuclear Envelope-Chromatin Associations
Nuclear Envelope Laminopathies: Evidence for Developmentally Inappropriate Nuclear Envelope-Chromatin Associations by Jelena Perovanovic M.S. in Molecular Biology and Physiology, September 2009, University of Belgrade M.Phil. in Molecular Medicine, August 2013, The George Washington University A Dissertation submitted to The Faculty of The Columbian College of Arts and Sciences of The George Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy August 31, 2015 Dissertation directed by Eric P. Hoffman Professor of Integrative Systems Biology The Columbian College of Arts and Sciences of The George Washington University certifies that Jelena Perovanovic has passed the Final Examination for the degree of Doctor of Philosophy as of May 5, 2015. This is the final and approved form of the dissertation. Nuclear Envelope Laminopathies: Evidence for Developmentally Inappropriate Nuclear Envelope-Chromatin Associations Jelena Perovanovic Dissertation Research Committee: Eric P. Hoffman, Professor of Integrative Systems Biology, Dissertation Director Anamaris Colberg-Poley, Professor of Integrative Systems Biology, Committee Member Robert J. Freishtat, Associate Professor of Pediatrics, Committee Member Vittorio Sartorelli, Senior Investigator, National Institutes of Health, Committee Member ii © Copyright 2015 by Jelena Perovanovic All rights reserved iii Acknowledgments I am deeply indebted to countless individuals for their support and encouragement during the past five years of graduate studies. First and foremost, I would like to express my gratitude to my mentor, Dr. Eric P. Hoffman, for his unwavering support and guidance, and keen attention to my professional development. This Dissertation would not have been possible without the critical input he provided and the engaging environment he created. -
Dynamic Force-Induced Direct Dissociation of Protein Complexes in a Nuclear Body in Living Cells
ARTICLE Received 13 Jan 2012 | Accepted 26 Apr 2012 | Published 29 May 2012 DOI: 10.1038/ncomms1873 Dynamic force-induced direct dissociation of protein complexes in a nuclear body in living cells Yeh-Chuin Poh1, Sergey P. Shevtsov2, Farhan Chowdhury1, Douglas C. Wu1, Sungsoo Na3, Miroslav Dundr2 & Ning Wang1 Despite past progress in understanding mechanisms of cellular mechanotransduction, it is unclear whether a local surface force can directly alter nuclear functions without intermediate biochemical cascades. Here we show that a local dynamic force via integrins results in direct displacements of coilin and SMN proteins in Cajal bodies and direct dissociation of coilin-SMN associated complexes. Spontaneous movements of coilin increase more than those of SMN in the same Cajal body after dynamic force application. Fluorescence resonance energy transfer changes of coilin-SMN depend on force magnitude, an intact F-actin, cytoskeletal tension, Lamin A/C, or substrate rigidity. Other protein pairs in Cajal bodies exhibit different magnitudes of fluorescence resonance energy transfer. Dynamic cyclic force induces tiny phase lags between various protein pairs in Cajal bodies, suggesting viscoelastic interactions between them. These findings demonstrate that dynamic force-induced direct structural changes of protein complexes in Cajal bodies may represent a unique mechanism of mechanotransduction that impacts on nuclear functions involved in gene expression. 1 Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Champaign, Illinois 61801, USA. 2 Department of Cell Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois 60064, USA. 3 Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indiana 46202, USA. -
Nucleolus: a Central Hub for Nuclear Functions Olga Iarovaia, Elizaveta Minina, Eugene Sheval, Daria Onichtchouk, Svetlana Dokudovskaya, Sergey Razin, Yegor Vassetzky
Nucleolus: A Central Hub for Nuclear Functions Olga Iarovaia, Elizaveta Minina, Eugene Sheval, Daria Onichtchouk, Svetlana Dokudovskaya, Sergey Razin, Yegor Vassetzky To cite this version: Olga Iarovaia, Elizaveta Minina, Eugene Sheval, Daria Onichtchouk, Svetlana Dokudovskaya, et al.. Nucleolus: A Central Hub for Nuclear Functions. Trends in Cell Biology, Elsevier, 2019, 29 (8), pp.647-659. 10.1016/j.tcb.2019.04.003. hal-02322927 HAL Id: hal-02322927 https://hal.archives-ouvertes.fr/hal-02322927 Submitted on 18 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Nucleolus: A Central Hub for Nuclear Functions Olga Iarovaia, Elizaveta Minina, Eugene Sheval, Daria Onichtchouk, Svetlana Dokudovskaya, Sergey Razin, Yegor Vassetzky To cite this version: Olga Iarovaia, Elizaveta Minina, Eugene Sheval, Daria Onichtchouk, Svetlana Dokudovskaya, et al.. Nucleolus: A Central Hub for Nuclear Functions. Trends in Cell Biology, Elsevier, 2019, 29 (8), pp.647-659. 10.1016/j.tcb.2019.04.003. hal-02322927 HAL Id: hal-02322927 https://hal.archives-ouvertes.fr/hal-02322927 Submitted on 18 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. -
Ideophones in Middle Chinese
KU LEUVEN FACULTY OF ARTS BLIJDE INKOMSTSTRAAT 21 BOX 3301 3000 LEUVEN, BELGIË ! Ideophones in Middle Chinese: A Typological Study of a Tang Dynasty Poetic Corpus Thomas'Van'Hoey' ' Presented(in(fulfilment(of(the(requirements(for(the(degree(of(( Master(of(Arts(in(Linguistics( ( Supervisor:(prof.(dr.(Jean=Christophe(Verstraete((promotor)( ( ( Academic(year(2014=2015 149(431(characters Abstract (English) Ideophones in Middle Chinese: A Typological Study of a Tang Dynasty Poetic Corpus Thomas Van Hoey This M.A. thesis investigates ideophones in Tang dynasty (618-907 AD) Middle Chinese (Sinitic, Sino- Tibetan) from a typological perspective. Ideophones are defined as a set of words that are phonologically and morphologically marked and depict some form of sensory image (Dingemanse 2011b). Middle Chinese has a large body of ideophones, whose domains range from the depiction of sound, movement, visual and other external senses to the depiction of internal senses (cf. Dingemanse 2012a). There is some work on modern variants of Sinitic languages (cf. Mok 2001; Bodomo 2006; de Sousa 2008; de Sousa 2011; Meng 2012; Wu 2014), but so far, there is no encompassing study of ideophones of a stage in the historical development of Sinitic languages. The purpose of this study is to develop a descriptive model for ideophones in Middle Chinese, which is compatible with what we know about them cross-linguistically. The main research question of this study is “what are the phonological, morphological, semantic and syntactic features of ideophones in Middle Chinese?” This question is studied in terms of three parameters, viz. the parameters of form, of meaning and of use. -
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On A Snowy Night: Yishan Yining (1247-1317) and the Development of Zen Calligraphy in Medieval Japan Xiaohan Du Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2021 © 2021 Xiaohan Du All Rights Reserved Abstract On A Snowy Night: Yishan Yining (1247-1317) and the Development of Zen Calligraphy in Medieval Japan Xiaohan Du This dissertation is the first monographic study of the monk-calligrapher Yishan Yining (1247- 1317), who was sent to Japan in 1299 as an imperial envoy by Emperor Chengzong (Temur, 1265-1307. r. 1294-1307), and achieved unprecedented success there. Through careful visual analysis of his extant oeuvre, this study situates Yishan’s calligraphy synchronically in the context of Chinese and Japanese calligraphy at the turn of the 14th century and diachronically in the history of the relationship between calligraphy and Buddhism. This study also examines Yishan’s prolific inscriptional practice, in particular the relationship between text and image, and its connection to the rise of ink monochrome landscape painting genre in 14th century Japan. This study fills a gap in the history of Chinese calligraphy, from which monk- calligraphers and their practices have received little attention. It also contributes to existing Japanese scholarship on bokuseki by relating Zen calligraphy to religious and political currents in Kamakura Japan. Furthermore, this study questions the validity of the “China influences Japan” model in the history of calligraphy and proposes a more fluid and nuanced model of synthesis between the wa and the kan (Japanese and Chinese) in examining cultural practices in East Asian culture. -
The “Masters” in the Shiji
T’OUNG PAO T’oungThe “Masters” Pao 101-4-5 in (2015) the Shiji 335-362 www.brill.com/tpao 335 The “Masters” in the Shiji Martin Kern (Princeton University) Abstract The intellectual history of the ancient philosophical “Masters” depends to a large extent on accounts in early historiography, most importantly Sima Qian’s Shiji which provides a range of longer and shorter biographies of Warring States thinkers. Yet the ways in which personal life experiences, ideas, and the creation of texts are interwoven in these accounts are diverse and uneven and do not add up to a reliable guide to early Chinese thought and its protagonists. In its selective approach to different thinkers, the Shiji under-represents significant parts of the textual heritage while developing several distinctive models of authorship, from anonymous compilations of textual repertoires to the experience of personal hardship and political frustration as the precondition for turning into a writer. Résumé L’histoire intellectuelle des “maîtres” de la philosophie chinoise ancienne dépend pour une large part de ce qui est dit d’eux dans l’historiographie ancienne, tout particulièrement le Shiji de Sima Qian, qui offre une série de biographies plus ou moins étendues de penseurs de l’époque des Royaumes Combattants. Cependant leur vie, leurs idées et les conditions de création de leurs textes se combinent dans ces biographies de façon très inégale, si bien que l’ensemble ne saurait être considéré comme l’équivalent d’un guide de la pensée chinoise ancienne et de ses auteurs sur lequel on pourrait s’appuyer en toute confiance. -
Chinese Language and Characters
Chinese Language and Characters Pronunciation of Chinese Words Consonants Pinyin WadeGiles Pronunciation Example: Pinyin(WadeGiles) Aspirated: p p’ pin Pao (P’ao) t t’ tip Tao (T’ao) k k’ kilt Kuan (K’uan) ch ch’ ch in, ch urch Chi (Ch’i) q ch’ ch eek Qi (Ch’i) c ts’ bi ts Cang (Ts’ang) Un- b p bin Bao (Pao) aspirated: d t dip Dao (Tao) g k gilt Guan (Kuan) r j wr en Ren (Jen) sh sh sh ore Shang (Shang) si szu Si (Szu) x hs or sh sh oe Xu (Hsu) z ts or tz bi ds Zang (Tsang) zh ch gin Zhong (Chong) zh j jeep Zhong (Jong) zi tzu Zi (Tzu) Vowels - a a father usually Italian e e ei ght values eh eh broth er yi i mach ine, p in Yi (I) i ih sh ir t Zhi (Chih) o soap u goo se ü über Dipthongs ai light ao lou d ei wei ght ia Will ia m ieh Kor ea ou gr ou p ua swa n ueh do er ui sway Hui (Hui) uo Whoah ! Combinations ian ien Tian (Tien) ui wei Wei gh Shui (Shwei) an and ang bun and b ung en and eng wood en and am ong in and ing sin and s ing ong un and ung u as in l oo k Tong (T’ung) you yu Watts, Alan; Tao The Watercourse Way, Pelican Books, 1976 http://acc6.its.brooklyn.cuny.edu/~phalsall/texts/chinlng1.html Tones 1 2 3 4 ā á ă à ē é ĕ È è Ī ī í ĭ ì ō ó ŏ ò ū ú ŭ ù Pinyin (Wade Giles) Meaning Ai Bā (Pa) Eight, see Numbers Bái (Pai) White, plain, unadorned Băi (Pai) One hundred, see Numbers Bāo Envelop Bāo (Pao) Uterus, afterbirth Bēi Sad, Sorrow, melancholy Bĕn Root, origin (Biao and Ben) see Biao Bi Bi (bei) Bian Bi āo Tip, dart, javelin, (Biao and Ben) see Ben Bin Bin Bing Bu Bu Can Cang Cáng (Ts’ang) Hidden, concealed (see Zang) Cháng Intestine Ch ōng (Ch’ung) Surging Ch ōng (Ch’ung) Rushing Chóu Worry Cóng Follow, accord with Dăn (Tan) Niche or shrine Dăn (Tan) Gall Bladder Dān (Tan) Red Cinnabar Dào (Tao) The Way Dì (Ti) The Earth, i.e.