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  • 1
    Publication Date: 2015-01-16
    Description: We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database ( http://ngs.ym.edu.tw/ym500/ ), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as C ross- L inked I mmuno P recipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function ‘Meta-analysis’ is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2015-04-08
    Description: Tissue homeostasis is achieved through a balance of cell production (growth) and elimination (regression). In contrast to tissue growth, the cells and molecular signals required for tissue regression remain unknown. To investigate physiological tissue regression, we use the mouse hair follicle, which cycles stereotypically between phases of growth and regression while maintaining a pool of stem cells to perpetuate tissue regeneration. Here we show by intravital microscopy in live mice that the regression phase eliminates the majority of the epithelial cells by two distinct mechanisms: terminal differentiation of suprabasal cells and a spatial gradient of apoptosis of basal cells. Furthermore, we demonstrate that basal epithelial cells collectively act as phagocytes to clear dying epithelial neighbours. Through cellular and genetic ablation we show that epithelial cell death is extrinsically induced through transforming growth factor (TGF)-beta activation and mesenchymal crosstalk. Strikingly, our data show that regression acts to reduce the stem cell pool, as inhibition of regression results in excess basal epithelial cells with regenerative abilities. This study identifies the cellular behaviours and molecular mechanisms of regression that counterbalance growth to maintain tissue homeostasis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457634/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457634/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mesa, Kailin R -- Rompolas, Panteleimon -- Zito, Giovanni -- Myung, Peggy -- Sun, Thomas Y -- Brown, Samara -- Gonzalez, David G -- Blagoev, Krastan B -- Haberman, Ann M -- Greco, Valentina -- 1R01AR063663-01/AR/NIAMS NIH HHS/ -- 2P50CA121974/CA/NCI NIH HHS/ -- 5 P30 AR053495-07/AR/NIAMS NIH HHS/ -- 5T32 GM007223/GM/NIGMS NIH HHS/ -- K08 AR066790/AR/NIAMS NIH HHS/ -- P30 AR053495/AR/NIAMS NIH HHS/ -- R01 AR063663/AR/NIAMS NIH HHS/ -- T32 GM007223/GM/NIGMS NIH HHS/ -- England -- Nature. 2015 Jun 4;522(7554):94-7. doi: 10.1038/nature14306. Epub 2015 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA. ; Department of Biopathology and Medical Biotechnology, University of Palermo, via Divisi 83, 90100 Palermo, Italy. ; 1] Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA [2] Department of Dermatology, Yale School of Medicine, New Haven, Connecticut 06510, USA. ; Department of Laboratory Medicine, Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut 06510, USA. ; 1] National Science Foundation, Arlington, Virginia 22230, USA [2] AA Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA. ; 1] Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA [2] Department of Dermatology, Yale School of Medicine, New Haven, Connecticut 06510, USA [3] Yale Stem Cell Center, Yale School of Medicine, New Haven, Connecticut 06510, USA [4] Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25849774" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; *Cell Death ; Dermis/cytology/metabolism ; Epithelial Cells/*cytology/metabolism ; Hair Follicle/*cytology/metabolism ; Homeostasis ; Mice ; Phagocytes/cytology ; *Phagocytosis ; Regeneration ; Signal Transduction ; Stem Cell Niche/*physiology ; Stem Cells/*cytology/metabolism ; Transforming Growth Factor beta/metabolism ; beta Catenin/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-03-22
    Description: Wnt/beta-catenin signaling is critical for tissue regeneration. However, it is unclear how beta-catenin controls stem cell behaviors to coordinate organized growth. Using live imaging, we show that activation of beta-catenin specifically within mouse hair follicle stem cells generates new hair growth through oriented cell divisions and cellular displacement. beta-Catenin activation is sufficient to induce hair growth independently of mesenchymal dermal papilla niche signals normally required for hair regeneration. Wild-type cells are co-opted into new hair growths by beta-catenin mutant cells, which non-cell autonomously activate Wnt signaling within the neighboring wild-type cells via Wnt ligands. This study demonstrates a mechanism by which Wnt/beta-catenin signaling controls stem cell-dependent tissue growth non-cell autonomously and advances our understanding of the mechanisms that drive coordinated regeneration.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096864/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096864/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Deschene, Elizabeth R -- Myung, Peggy -- Rompolas, Panteleimon -- Zito, Giovanni -- Sun, Thomas Yang -- Taketo, Makoto M -- Saotome, Ichiko -- Greco, Valentina -- 1R01AR063663-01/AR/NIAMS NIH HHS/ -- 2P50CA121974/CA/NCI NIH HHS/ -- 5P30 AR053495-07/AR/NIAMS NIH HHS/ -- K08 AR066790/AR/NIAMS NIH HHS/ -- P30 CA016359/CA/NCI NIH HHS/ -- P50 CA121974/CA/NCI NIH HHS/ -- R01 AR063663/AR/NIAMS NIH HHS/ -- T32 GM007223/GM/NIGMS NIH HHS/ -- TG32 GM007223/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2014 Mar 21;343(6177):1353-6. doi: 10.1126/science.1248373.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Yale Stem Cell Center, Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24653033" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Division ; Hair/*growth & development ; Hair Follicle/*cytology/*metabolism ; Ligands ; Mice ; Models, Biological ; Mutation ; Stem Cell Niche ; Stem Cells/cytology/*metabolism ; Tamoxifen/pharmacology ; Up-Regulation ; Wnt Proteins/genetics/metabolism ; *Wnt Signaling Pathway ; beta Catenin/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 1 (1948), S. 135-137 
    ISSN: 0001-5520
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences
    Type of Medium: Electronic Resource
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  • 5
    Publication Date: 2015-12-19
    Description: Nature Materials 15, 27 (2016). doi:10.1038/nmat4457 Authors: Z. K. Liu, L. X. Yang, Y. Sun, T. Zhang, H. Peng, H. F. Yang, C. Chen, Y. Zhang, Y. F. Guo, D. Prabhakaran, M. Schmidt, Z. Hussain, S.-K. Mo, C. Felser, B. Yan & Y. L. Chen Topological Weyl semimetals (TWSs) represent a novel state of topological quantum matter which not only possesses Weyl fermions (massless chiral particles that can be viewed as magnetic monopoles in momentum space) in the bulk and unique Fermi arcs generated by topological surface states, but also exhibits appealing physical properties such as extremely large magnetoresistance and ultra-high carrier mobility. Here, by performing angle-resolved photoemission spectroscopy (ARPES) on NbP and TaP, we directly observed their band structures with characteristic Fermi arcs of TWSs. Furthermore, by systematically investigating NbP, TaP and TaAs from the same transition metal monopnictide family, we discovered their Fermiology evolution with spin–orbit coupling (SOC) strength. Our experimental findings not only reveal the mechanism to realize and fine-tune the electronic structures of TWSs, but also provide a rich material base for exploring many exotic physical phenomena (for example, chiral magnetic effects, negative magnetoresistance, and the quantum anomalous Hall effect) and novel future applications.
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 6
    Publication Date: 2014-03-19
    Description: Author(s): K. Kaneko, Y. Sun, T. Mizusaki, and S. Tazaki Mirror energy differences (MEDs) and triplet energy differences (TEDs) in the T=1 analogue states are important probes of isospin-symmetry breaking. Inspired by the recent spectroscopic data of 66Se, we investigate these quantities for A=66–78 nuclei with large-scale shell-model calculations. For th... [Phys. Rev. C 89, 031302] Published Tue Mar 18, 2014
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
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  • 7
    Publication Date: 2013-04-27
    Description: Author(s): K. Kaneko, Y. Sun, T. Mizusaki, and S. Tazaki For mirror nuclei with masses A =42–95, the effects of isospin-nonconserving nuclear forces are studied with the nuclear shell model using the Coulomb displacement energy and triplet displacement energy as probes. It is shown that the characteristic behavior of the displacement energies can be well r... [Phys. Rev. Lett. 110, 172505] Published Fri Apr 26, 2013
    Keywords: Nuclear Physics
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 8
    Publication Date: 2018-05-04
    Description: Author(s): V. Grinenko, R. Sarkar, P. Materne, S. Kamusella, A. Yamamshita, Y. Takano, Y. Sun, T. Tamegai, D. V. Efremov, S.-L. Drechsler, J.-C. Orain, T. Goko, R. Scheuermann, H. Luetkens, and H.-H. Klauss A nematic transition preceding a long-range spin density wave antiferromagnetic phase is a common feature of many parent compounds of Fe-based superconductors. However, in the FeSe system with a nematic transition at T s ≈ 90 K, no evidence for long-range static magnetism is found down to very low temp... [Phys. Rev. B 97, 201102(R)] Published Thu May 03, 2018
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 9
    Publication Date: 2018-05-17
    Description: In this paper, the crystalline modification of a rare earth nucleating agent (WBG) for isotactic polypropylene (PP) based on its supramolecular self-assembly was investigated by differential scanning calorimetry, wide-angle X-ray diffraction and polarized optical microscopy. In addition, the relationship between the self-assembly structure of the nucleating agent and the crystalline structure, as well as the possible reason for the self-assembly behaviour, was further studied. The structure evolution of WBG showed that the self-assembly structure changed from a needle-like structure to a dendritic structure with increase in the content of WBG. When the content of WBG exceeded a critical value (0.4 wt%), it self-assembled into a strip structure. This revealed that the structure evolution of WBG contributed to the K β and the crystallization morphology of PP with different content of WBG. In addition, further studies implied that the behaviour of self-assembly was a liquid–solid transformation of WBG, followed by a liquid–liquid phase separation of molten isotactic PP and WBG. The formation of the self-assembly structure was based on the free molecules by hydrogen bond dissociation while being heated, followed by aggregation into another structure by hydrogen bond association while being cooled. Furthermore, self-assembly behaviour depends largely on the interaction between WBG themselves.
    Keywords: materials science, chemical physics
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 10
    Publication Date: 2013-07-14
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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