当前位置： SCI文献检索 > JOURNAL OF STRUCTURAL BIOLOGY期刊下所有文献 > Unsupervised mitochondria segmentation using recursive spectral clustering and adaptive similarity models.

Unsupervised mitochondria segmentation using recursive spectral clustering and adaptive similarity models.

Abstract：

:The unsupervised segmentation method proposed in the current study follows the evolutional ability of human vision to extrapolate significant structures in an image. In this work we adopt the perceptual grouping strategy by selecting the spectral clustering framework, which is known to capture perceptual organization features, as well as by developing similarity models according to Gestaltic laws of visual segregation. Our proposed framework applies but is not limited to the detection of cells and organelles in microscopic images and attempts to provide an effective alternative to presently dominating manual segmentation and tissue classification practice. The main theoretical contribution of our work resides in the formulation of robust similarity models which automatically adapt to the statistical structure of the biological domain and return optimal performance in pixel classification tasks under the wide variety of distributional assumptions.

journal_name

J Struct Biol

journal_title

Journal of structural biology

authors

Dietlmeier J,Ghita O,Duessmann H,Prehn JH,Whelan PF

doi

10.1016/j.jsb.2013.10.013

subject

Has Abstract

pub_date

2013-12-01 00:00:00

pages

401-8

issue

3

eissn

1047-8477

issn

1095-8657

pii

S1047-8477(13)00278-5

journal_volume

184

pub_type

杂志文章

相关文献

JOURNAL OF STRUCTURAL BIOLOGY文献大全
  • Silicon uptake and metabolism of the marine diatom Thalassiosira pseudonana: Solid-state 29Si NMR and fluorescence microscopic studies.

    abstract：:Uptake and metabolism of silicon by diatoms are studied by the combined use of solid-state 29Si NMR spectroscopy and confocal laser fluorescence microscopy especially with respect to the presence and nature of an intracellular silicon-storage pool. Cells of the marine diatom Thalassiosira pseudonana were synchronized ...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2007.09.010

    authors： Gröger C,Sumper M,Brunner E

    更新日期：2008-01-01 00:00:00

  • CTFFIND4: Fast and accurate defocus estimation from electron micrographs.

    abstract：:CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm whi...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2015.08.008

    authors： Rohou A,Grigorieff N

    更新日期：2015-11-01 00:00:00

  • Three-dimensional network of Drosophila brain hemisphere.

    abstract：:The first step to understanding brain function is to determine the brain's network structure. We report a three-dimensional analysis of the brain network of the fruit fly Drosophila melanogaster by synchrotron-radiation tomographic microscopy. A skeletonized wire model of the left half of the brain network was built b...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2013.08.012

    authors： Mizutani R,Saiga R,Takeuchi A,Uesugi K,Suzuki Y

    更新日期：2013-11-01 00:00:00

  • The crystal structure of a lysozyme c from housefly Musca domestica, the first structure of a digestive lysozyme.

    abstract：:Lysozymes from family 22 of glycoside hydrolases are usually part of the defense system against bacteria. However in ruminant artiodactyls and saprophagous insects, lysozymes are involved in the digestion of bacteria. Here, we report the first crystallographic structure of a digestive lysozyme in its native and comple...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2007.07.008

    authors： Cançado FC,Valério AA,Marana SR,Barbosa JA

    更新日期：2007-10-01 00:00:00

  • From colloidal nanoparticles to a single crystal: new insights into the formation of nacre's aragonite tablets.

    abstract：:Nacre has long served as a model for understanding the biomineralization mechanism and designing bio-inspired materials. However, its basic building blocks, the aragonite tablets, are still under debate in terms of their fine structure at the nanoscale and corresponding formation mechanism. Here, using a field emissio...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2013.01.010

    authors： Zhang G,Xu J

    更新日期：2013-04-01 00:00:00

  • Almost pure I(alpha) cellulose in the cell wall of Glaucocystis.

    abstract：:Crystalline features of cellulose microfibrils in the cell walls of Glaucocystis (Glaucophyta) were studied by combined spectroscopy and diffraction techniques, and the results were compared with those of Oocystis (Chlorophyta). Although these algae are grouped into two different classes, by the composition of their c...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1006/jsbi.1999.4160

    authors： Imai T,Sugiyama J,Itoh T,Horii F

    更新日期：1999-10-01 00:00:00

  • Discontinuous membrane helices in transport proteins and their correlation with function.

    abstract：:Alpha-helical bundles and beta-barrel proteins represent the two basic types of architecture known for integral membrane proteins. Irregular structural motifs have been revealed with the growing number of structures determined. "Discontinuous" helices are present in membrane proteins that actively transport ions. In t...

    journal_title：Journal of structural biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jsb.2007.01.011

    authors： Screpanti E,Hunte C

    更新日期：2007-08-01 00:00:00

  • Crystallization and preliminary X-ray crystallographic study of the ribosomal protein S7 from Bacillus stearothermophilus.

    abstract：:Overproduction and crystallization of Bacillus stearothermophilus ribosomal protein S7 (BstS7), a primary 16S rRNA binding protein and also a translational repressor protein, have been performed to analyze its three-dimensional structure by X-ray crystallography. Ribosomal protein BstS7 was expressed in the cytoplasmi...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1006/jsbi.1997.3907

    authors： Harada N,Sano K,Kimura M,Hosaka H,Nakagawa A,Tanaka I

    更新日期：1997-10-01 00:00:00

  • Crystallographic Characterization of the DNA-Binding Domain of Interferon Regulatory Factor-2 Complexed with DNA.

    abstract：:Interferon regulatory factors (IRFs) are transcription factors for interferon-related genes, which manifest both antiviral and tumor-suppressor activities and regulate cell growth in response to DNA damage. For the transcription initiation of the interferon-beta gene, IRFs form a macromolecular assembly bound to the p...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1006/jsbi.1998.3970

    authors： Kusumoto M,Fujii Y,Tsukuda Y,Ohira T,Kyougoku Y,Taniguchi T,Hakoshima T

    更新日期：1998-01-01 00:00:00

  • Collagen matrix remodeling in 3-dimensional cellular space resolved using second harmonic generation and multiphoton excitation fluorescence.

    abstract：:The structural remodeling of collagen is important in biological processes such as fibrosis, developmental morphogenesis and wound repair. Highly ordered collagen macromolecules produce second harmonic generation signals without the need for any exogenous label. Conversely, the cellular components stained with exogeno...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2009.07.023

    authors： Abraham T,Carthy J,McManus B

    更新日期：2010-01-01 00:00:00

  • Actin filament tracking in electron tomograms of negatively stained lamellipodia using the localized radon transform.

    abstract：:The aim of this work was to develop a protocol for automated tracking of actin filaments in electron tomograms of lamellipodia embedded in negative stain. We show that a localized version of the Radon transform for the detection of filament directions enables three-dimensional visualizations of filament network archit...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2012.02.011

    authors： Winkler C,Vinzenz M,Small JV,Schmeiser C

    更新日期：2012-04-01 00:00:00

  • High-throughput screening of cellular features using high-resolution light-microscopy; application for profiling drug effects on cell adhesion.

    abstract：:High-resolution light-microscopy and high-throughput screening are two essential methodologies for characterizing cellular phenotypes. Optimally combining these methodologies in cell-based screening to test detailed molecular and cellular responses to multiple perturbations constitutes a major challenge. Here we descr...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2006.12.013

    authors： Paran Y,Ilan M,Kashman Y,Goldstein S,Liron Y,Geiger B,Kam Z

    更新日期：2007-05-01 00:00:00

  • The structure of ibuprofen bound to cyclooxygenase-2.

    abstract：:The cyclooxygenases (COX-1 and COX-2) catalyze the rate-limiting step in the biosynthesis of prostaglandins, and are the pharmacological targets of non-steroidal anti-inflammatory drugs (NSAIDs) and COX-2 selective inhibitors (coxibs). Ibuprofen (IBP) is one of the most commonly available over-the-counter pharmaceutic...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2014.11.005

    authors： Orlando BJ,Lucido MJ,Malkowski MG

    更新日期：2015-01-01 00:00:00

  • Modeling membrane proteins: The importance of cysteine amino-acids.

    abstract：:Computational modeling of membrane proteins is critical to understand biochemical systems and to support chemical biology. In this work, we use a dataset of 448 non-redundant membrane protein chains to expose a "rule" that governs membrane protein structure: free cysteine thiols are not found accessible to oxidative c...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2019.10.002

    authors： Grazhdankin E,Stepniewski M,Xhaard H

    更新日期：2020-01-01 00:00:00

  • Utility of Butvar support film and methylamine tungstate stain in three-dimensional electron microscopy: agreement between stain and frozen-hydrated reconstructions.

    abstract：:A random conical tilt reconstruction of negatively stained Saccharomyces cerevisiae fatty acid synthase was used as a model to compute a three-dimensional reconstruction from untilted stain specimens of the molecules in multiple orientations using a three-dimensional projection alignment method. The resulting structur...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1006/jsbi.1997.3911

    authors： Kolodziej SJ,Penczek PA,Stoops JK

    更新日期：1997-11-01 00:00:00

  • Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation.

    abstract：:The configuration of the active site of E2 ligases, central enzymes in the ubiquitin/ubiquitin-like protein (Ub/Ubl) conjugation systems, has long puzzled researchers. Taking advantage of the wealth of newly available structures and sequences of E2s from diverse organisms, we performed a large-scale comparative analys...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2007.12.006

    authors： Burroughs AM,Jaffee M,Iyer LM,Aravind L

    更新日期：2008-05-01 00:00:00

  • Visualization of poly(A)-binding protein complex formation with poly(A) RNA using atomic force microscopy.

    abstract：:Poly(A)-binding protein (PABP) is an RNA-binding protein that binds specifically to the poly(A) tail of messenger RNAs in eukaryotes. The PABP/poly(A) tail complex has been implicated as being important in promoting the efficient initiation of translation as well as in maintaining the integrity of the mRNA. PABP binds...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1006/jsbi.1997.3864

    authors： Smith BL,Gallie DR,Le H,Hansma PK

    更新日期：1997-07-01 00:00:00

  • The 17A structure of the 420 kDa lobster clottable protein by single particle reconstruction from cryoelectron micrographs.

    abstract：:Crustaceans form clots by the rapid crosslinking of a hemolymph clottable protein (CP) to form long, branched polymers. Clotting limits hemolymph loss from wounds as well as playing a part in the innate immune response. CP is a 420 kDa homodimer with a large quantity of associated lipid, primarily the carotenoid pigme...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2005.06.008

    authors： Kollman JM,Quispe J

    更新日期：2005-09-01 00:00:00

  • The two-step mode of growth in the scleractinian coral skeletons from the micrometre to the overall scale.

    abstract：:It has been known since the 19th century that coral skeletons are built of aragonite crystals with taxonomy-linked arrangements, but the way by which each coral species controls this crystallization process remains an unsolved question. The problem became still more intriguing when it was shown that isotopic compositi...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2005.03.004

    authors： Cuif JP,Dauphin Y

    更新日期：2005-06-01 00:00:00

  • Axially aligned organic fibers and amorphous calcium phosphate form the claws of a terrestrial isopod (Crustacea).

    abstract：:Skeletal elements that are exposed to heavy mechanical loads may provide important insights into the evolutionary solutions to mechanical challenges. We analyzed the microscopic architecture of dactylus claws in the woodlice Porcellio scaber and correlated these observations with analyses of the claws' mineral composi...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2016.06.008

    authors： Vittori M,Srot V,Žagar K,Bussmann B,van Aken PA,Čeh M,Štrus J

    更新日期：2016-08-01 00:00:00

  • Structural and biochemical characterization of bacterial YpgQ protein reveals a metal-dependent nucleotide pyrophosphohydrolase.

    abstract：:The optimal balance of cellular nucleotides and the efficient elimination of non-canonical nucleotides are critical to avoiding erroneous mutation during DNA replication. One such mechanism involves the degradation of excessive or abnormal nucleotides by nucleotide-hydrolyzing enzymes. YpgQ contains the histidine-aspa...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2016.04.002

    authors： Jeon YJ,Park SC,Song WS,Kim OH,Oh BC,Yoon SI

    更新日期：2016-07-01 00:00:00

  • Sequence analyses of Type I and Type II chains in human hair and epithelial keratin intermediate filaments: promiscuous obligate heterodimers, Type II template for molecule formation and a rationale for heterodimer formation.

    abstract：:Sequence comparisons have been undertaken for all hair and epithelial keratin IF chains from a single species--human. The results lead to several new proposals. First, it is clear that not only is the chain structure of the molecule an obligate heterodimer but promiscuous association of Type I and Type II chains must ...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2006.12.002

    authors： Smith TA,Parry DA

    更新日期：2007-06-01 00:00:00

  • Strategies for the crystallization of viruses: using phase diagrams and gels to produce 3D crystals of Grapevine fanleaf virus.

    abstract：:The small icosahedral plant RNA nepovirus Grapevine fanleaf virus (GFLV) is specifically transmitted by a nematode and causes major damage to vineyards worldwide. To elucidate the molecular mechanisms underlying the recognition between the surface of its protein capsid and cellular components of its vector, host and v...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2011.02.007

    authors： Schellenberger P,Demangeat G,Lemaire O,Ritzenthaler C,Bergdoll M,Oliéric V,Sauter C,Lorber B

    更新日期：2011-05-01 00:00:00

  • Three-dimensional structure of an invertebrate intercellular communicating junction.

    abstract：:Gap junctions containing extensive, highly ordered crystalline arrays of hexagonally packed connexons have been isolated from the hepatopancreas of the arthropod, Homarus americanus (American lobster). The structure of such junctions has been studied to a resolution of approximately 25 A in three dimensions by electro...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/1047-8477(91)90075-8

    authors： Sikerwar SS,Downing KH,Glaeser RM

    更新日期：1991-06-01 00:00:00

  • Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding.

    abstract：:Gly missense mutations in type I collagen, which replace a conserved Gly in the repeating (Gly-Xaa-Yaa)n sequence with a larger residue, are known to cause Osteogenesis Imperfecta (OI). The clinical consequences of such mutations range from mild to lethal, with more serious clinical severity associated with larger Gly...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2018.05.003

    authors： Qiu Y,Mekkat A,Yu H,Yigit S,Hamaia S,Farndale RW,Kaplan DL,Lin YS,Brodsky B

    更新日期：2018-09-01 00:00:00

  • Spectroscopy on the wing: Investigating possible differences in protein secondary structures in feather shafts of birds using Raman spectroscopy.

    abstract：:The central shaft of a bird's flight feather bears most of the aerodynamic load during flight and exhibits some remarkable mechanical properties. The shaft comprises two parts, the calamus and the rachis. The calamus is at the base of the shaft, while the rachis is the longer upper part which supports the vanes. The s...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2020.107529

    authors： Laurent CM,Dyke JM,Cook RB,Dyke G,de Kat R

    更新日期：2020-07-01 00:00:00

  • The unusual extended C-terminal helix of the peroxisomal α/β-hydrolase Lpx1 is involved in dimer contacts but dispensable for dimerization.

    abstract：:The yeast peroxisomal hydrolase Lpx1 belongs to the α/β-hydrolase superfamily. In the absence of Lpx1, yeast peroxisomes show an aberrant vacuolated morphology similar to what is found in peroxisomal disorder patients. Here, we present the crystal structure of Lpx1 determined at a resolution of 1.9 Å. The structure re...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2011.06.008

    authors： Thoms S,Hofhuis J,Thöing C,Gärtner J,Niemann HH

    更新日期：2011-09-01 00:00:00

  • Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps.

    abstract：:We present RIBFIND, a method for detecting flexibility in protein structures via the clustering of secondary structural elements (SSEs) into rigid bodies. To test the usefulness of the method in refining atomic structures within cryoEM density we incorporated it into our flexible fitting protocol (Flex-EM). Our benchm...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2011.10.011

    authors： Pandurangan AP,Topf M

    更新日期：2012-02-01 00:00:00

  • Quantitative analysis of spin exchange interactions to identify β strand and turn regions in Ure2 prion domain fibrils with site-directed spin labeling.

    abstract：:Amyloid formation is associated with a range of debilitating human disorders including Alzheimer's and prion diseases. The amyloid structure is essential for understanding the role of amyloids in these diseases. Amyloid formation of Ure2 protein underlies the yeast prion [URE3]. Here we use site-directed spin labeling...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2012.08.008

    authors： Ngo S,Chiang V,Guo Z

    更新日期：2012-11-01 00:00:00

  • Structural insights into serine protease inhibition by a marine invertebrate BPTI Kunitz-type inhibitor.

    abstract：:Proteins isolated from marine invertebrates are frequently characterized by exceptional structural and functional properties. ShPI-1, a BPTI Kunitz-type inhibitor from the Caribbean Sea anemone Stichodactyla helianthus, displays activity not only against serine-, but also against cysteine-, and aspartate proteases. As...

    journal_title：Journal of structural biology

    pub_type： 杂志文章

    doi：10.1016/j.jsb.2012.08.009

    authors： García-Fernández R,Pons T,Perbandt M,Valiente PA,Talavera A,González-González Y,Rehders D,Chávez MA,Betzel C,Redecke L

    更新日期：2012-11-01 00:00:00