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  • 1
    Publication Date: 2017-08-12
    Description: High-throughput sectioning and optical imaging of tissue samples using traditional immunohistochemical techniques can be costly and inaccessible in resource-limited areas. We demonstrate three-dimensional (3D) imaging and phenotyping in optically transparent tissue using lens-free holographic on-chip microscopy as a low-cost, simple, and high-throughput alternative to conventional approaches. The tissue sample is passively cleared using a simplified CLARITY method and stained using 3,3'-diaminobenzidine to target cells of interest, enabling bright-field optical imaging and 3D sectioning of thick samples. The lens-free computational microscope uses pixel super-resolution and multi-height phase recovery algorithms to digitally refocus throughout the cleared tissue and obtain a 3D stack of complex-valued images of the sample, containing both phase and amplitude information. We optimized the tissue-clearing and imaging system by finding the optimal illumination wavelength, tissue thickness, sample preparation parameters, and the number of heights of the lens-free image acquisition and implemented a sparsity-based denoising algorithm to maximize the imaging volume and minimize the amount of the acquired data while also preserving the contrast-to-noise ratio of the reconstructed images. As a proof of concept, we achieved 3D imaging of neurons in a 200-μm-thick cleared mouse brain tissue over a wide field of view of 20.5 mm 2 . The lens-free microscope also achieved more than an order-of-magnitude reduction in raw data compared to a conventional scanning optical microscope imaging the same sample volume. Being low cost, simple, high-throughput, and data-efficient, we believe that this CLARITY-enabled computational tissue imaging technique could find numerous applications in biomedical diagnosis and research in low-resource settings.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 2
    Publication Date: 2014-10-17
    Description: MiR-29b controls fetal mouse neurogenesis by regulating ICAT-mediated Wnt/β-catenin signaling Cell Death and Disease 5, e1473 (October 2014). doi:10.1038/cddis.2014.439 Authors: J Shin, Y Shin, S-M Oh, H Yang, W-J Yu, J-P Lee, S-O Huh, S H Lee, Y-H Suh, S Chung & H-S Kim
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 3
    Publication Date: 2012-04-11
    Description: Low-cost, high-yield production of graphene nanosheets (GNs) is essential for practical applications. We have achieved high yield of edge-selectively carboxylated graphite (ECG) by a simple ball milling of pristine graphite in the presence of dry ice. The resultant ECG is highly dispersable in various solvents to self-exfoliate into single- and few-layer (≤ 5 layers) GNs. These stable ECG (or GN) dispersions have been used for solution processing, coupled with thermal decarboxylation, to produce large-area GN films for many potential applications ranging from electronic materials to chemical catalysts. The electrical conductivity of a thermally decarboxylated ECG film was found to be as high as 1214 S/cm, which is superior to its GO counterparts. Ball milling can thus provide simple, but efficient and versatile, and eco-friendly (CO2-capturing) approaches to low-cost mass production of high-quality GNs for applications where GOs have been exploited and beyond.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 4
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    Soc. Explorat. Geophys.
    In:  47th Annual Meeting of SEG, Kiel, Soc. Explorat. Geophys., vol. 30, no. DS 1980:17, pp. 4-29, (ISBN 3-933346-037)
    Publication Date: 1977
    Keywords: Seismics (controlled source seismology) ; Wave equation ; seismic Migration
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  • 5
    Publication Date: 2016-05-07
    Description: Author(s): Sang Won Seo, Woo Jin Kwon, Seji Kang, and Y. Shin We present an experimental study on the interaction and dynamics of half-quantum vortices (HQVs) in an antiferromagnetic spinor Bose-Einstein condensate. By exploiting the orbit motion of a vortex dipole in a trapped condensate, we perform a collision experiment of two HQV pairs, and observe that th… [Phys. Rev. Lett. 116, 185301] Published Fri May 06, 2016
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
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  • 6
    Publication Date: 2016-10-12
    Description: Author(s): Min-Seok Kim, Jeongwon Lee, Jae Hoon Lee, Y. Shin, and Jongchul Mun We present measurements of the optical Feshbach resonances (OFRs) of Yb 174 atoms for the intercombination transition. We measure the photoassociation (PA) spectra of a pure Yb 174 Bose-Einstein condensate (BEC) and determine the dependence of OFRs on PA laser intensities and frequencies for four leas… [Phys. Rev. A 94, 042703] Published Mon Oct 10, 2016
    Keywords: Atomic and molecular collisions and interactions
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
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  • 7
    Publication Date: 2014-12-17
    Description: Pluripotency is defined by the ability of a cell to differentiate to the derivatives of all the three embryonic germ layers: ectoderm, mesoderm and endoderm. Pluripotent cells can be captured via the archetypal derivation of embryonic stem cells or via somatic cell reprogramming. Somatic cells are induced to acquire a pluripotent stem cell (iPSC) state through the forced expression of key transcription factors, and in the mouse these cells can fulfil the strictest of all developmental assays for pluripotent cells by generating completely iPSC-derived embryos and mice. However, it is not known whether there are additional classes of pluripotent cells, or what the spectrum of reprogrammed phenotypes encompasses. Here we explore alternative outcomes of somatic reprogramming by fully characterizing reprogrammed cells independent of preconceived definitions of iPSC states. We demonstrate that by maintaining elevated reprogramming factor expression levels, mouse embryonic fibroblasts go through unique epigenetic modifications to arrive at a stable, Nanog-positive, alternative pluripotent state. In doing so, we prove that the pluripotent spectrum can encompass multiple, unique cell states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tonge, Peter D -- Corso, Andrew J -- Monetti, Claudio -- Hussein, Samer M I -- Puri, Mira C -- Michael, Iacovos P -- Li, Mira -- Lee, Dong-Sung -- Mar, Jessica C -- Cloonan, Nicole -- Wood, David L -- Gauthier, Maely E -- Korn, Othmar -- Clancy, Jennifer L -- Preiss, Thomas -- Grimmond, Sean M -- Shin, Jong-Yeon -- Seo, Jeong-Sun -- Wells, Christine A -- Rogers, Ian M -- Nagy, Andras -- MOP102575/Canadian Institutes of Health Research/Canada -- England -- Nature. 2014 Dec 11;516(7530):192-7. doi: 10.1038/nature14047.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. ; 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 3H7, Canada. ; 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5T 3H7, Canada. ; 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5T 3H7, Canada. ; 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, South Korea [2] Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea [3] Department of Biochemistry, Seoul National University College of Medicine, Seoul 110-799, South Korea. ; Department of Systems &Computational Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA. ; Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia. ; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia. ; Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), Australian Capital Territory 2601, Australia. ; 1] Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), Australian Capital Territory 2601, Australia [2] Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia. ; 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, South Korea [2] Life Science Institute, Macrogen Inc., Seoul 153-781, South Korea. ; 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 110-799, South Korea [2] Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, South Korea [3] Department of Biochemistry, Seoul National University College of Medicine, Seoul 110-799, South Korea [4] Life Science Institute, Macrogen Inc., Seoul 153-781, South Korea. ; 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Department of Physiology, University of Toronto, Toronto, Ontario M5T 3H7, Canada [3] Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario M5T 3H7, Canada. ; 1] Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada [2] Institute of Medical Science, University of Toronto, Toronto, Ontario M5T 3H7, Canada [3] Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario M5T 3H7, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25503232" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cellular Reprogramming/*genetics/*physiology ; Embryonic Stem Cells/cytology/metabolism ; *Epigenesis, Genetic ; Female ; Fibroblasts/classification/cytology/metabolism ; Histone Deacetylases/metabolism ; Induced Pluripotent Stem Cells/classification/*cytology/*metabolism ; Mice ; Mice, Nude ; Transcription Factors/genetics/metabolism ; Transgenes/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2015-06-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tonge, Peter D -- Corso, Andrew J -- Monetti, Claudio -- Hussein, Samer M I -- Puri, Mira C -- Michael, Iacovos P -- Li, Mira -- Lee, Dong-Sung -- Mar, Jessica C -- Cloonan, Nicole -- Wood, David L -- Gauthier, Maely E -- Korn, Othmar -- Clancy, Jennifer L -- Preiss, Thomas -- Grimmond, Sean M -- Shin, Jong-Yeon -- Seo, Jeong-Sun -- Wells, Christine A -- Rogers, Ian M -- Nagy, Andras -- England -- Nature. 2015 Jul 30;523(7562):626. doi: 10.1038/nature14607. Epub 2015 Jun 17.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26083751" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2011-10-28
    Description: Brain development and function depend on the precise regulation of gene expression. However, our understanding of the complexity and dynamics of the transcriptome of the human brain is incomplete. Here we report the generation and analysis of exon-level transcriptome and associated genotyping data, representing males and females of different ethnicities, from multiple brain regions and neocortical areas of developing and adult post-mortem human brains. We found that 86 per cent of the genes analysed were expressed, and that 90 per cent of these were differentially regulated at the whole-transcript or exon level across brain regions and/or time. The majority of these spatio-temporal differences were detected before birth, with subsequent increases in the similarity among regional transcriptomes. The transcriptome is organized into distinct co-expression networks, and shows sex-biased gene expression and exon usage. We also profiled trajectories of genes associated with neurobiological categories and diseases, and identified associations between single nucleotide polymorphisms and gene expression. This study provides a comprehensive data set on the human brain transcriptome and insights into the transcriptional foundations of human neurodevelopment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566780/" 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/PMC3566780/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Hyo Jung -- Kawasawa, Yuka Imamura -- Cheng, Feng -- Zhu, Ying -- Xu, Xuming -- Li, Mingfeng -- Sousa, Andre M M -- Pletikos, Mihovil -- Meyer, Kyle A -- Sedmak, Goran -- Guennel, Tobias -- Shin, Yurae -- Johnson, Matthew B -- Krsnik, Zeljka -- Mayer, Simone -- Fertuzinhos, Sofia -- Umlauf, Sheila -- Lisgo, Steven N -- Vortmeyer, Alexander -- Weinberger, Daniel R -- Mane, Shrikant -- Hyde, Thomas M -- Huttner, Anita -- Reimers, Mark -- Kleinman, Joel E -- Sestan, Nenad -- DA026119/DA/NIDA NIH HHS/ -- G0700089/Medical Research Council/United Kingdom -- G9900837/Medical Research Council/United Kingdom -- GR082557/Wellcome Trust/United Kingdom -- HD000836/HD/NICHD NIH HHS/ -- MH081896/MH/NIMH NIH HHS/ -- MH089929/MH/NIMH NIH HHS/ -- NS054273/NS/NINDS NIH HHS/ -- R01 NS054273/NS/NINDS NIH HHS/ -- R01 NS054273-07/NS/NINDS NIH HHS/ -- RC2 MH089929/MH/NIMH NIH HHS/ -- RC2 MH089929-02/MH/NIMH NIH HHS/ -- U01 MH081896/MH/NIMH NIH HHS/ -- U01 MH081896-03/MH/NIMH NIH HHS/ -- England -- Nature. 2011 Oct 26;478(7370):483-9. doi: 10.1038/nature10523.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology and Kavli Institute for Neuroscience, Yale University 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/22031440" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Aged ; Aged, 80 and over ; Aging/*genetics ; Brain/embryology/*growth & development/*metabolism ; Child ; Child, Preschool ; Exons/genetics ; Female ; Fetus/metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental/*genetics ; Gene Regulatory Networks/genetics ; Humans ; Infant ; Male ; Middle Aged ; Quality Control ; Quantitative Trait Loci/genetics ; Sex Characteristics ; Time Factors ; Transcriptome/*genetics ; Young Adult
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2005-03-26
    Description: We demonstrated an experimental technique based on stimulated light scattering to continuously sample the relative phase of two spatially separated Bose-Einstein condensates of atoms. The phase measurement process created a relative phase between two condensates with no initial phase relation, read out the phase, and monitored the phase evolution. This technique was used to realize interferometry between two trapped Bose-Einstein condensates without need for splitting or recombining the atom cloud.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saba, M -- Pasquini, T A -- Sanner, C -- Shin, Y -- Ketterle, W -- Pritchard, D E -- New York, N.Y. -- Science. 2005 Mar 25;307(5717):1945-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, MIT-Harvard Center for Ultracold Atoms, and Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. msaba@mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15790851" target="_blank"〉PubMed〈/a〉
    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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