Abstract:
:The goal of this study is to evaluate the performance of software for automated particle-boxing, and in particular the performance of a new tool (TextonSVM) that recognizes the characteristic texture of particles of interest. As part of a high-throughput protocol, we use human editing that is based solely on class-average images to create final data sets that are enriched in what the investigator considers to be true-positive particles. The Fourier shell correlation (FSC) function is then used to characterize the homogeneity of different single-particle data sets that are derived from the same micrographs by two or more alternative methods. We find that the homogeneity is generally quite similar for class-edited data sets obtained by the texture-based method and by SIGNATURE, a cross-correlation-based method. The precision-recall characteristics of the texture-based method are, on the other hand, significantly better than those of the cross-correlation based method; that is to say, the texture-based approach produces a smaller fraction of false positives in the initial set of candidate particles. The computational efficiency of the two approaches is generally within a factor of two of one another. In situations when it is helpful to use a larger number of templates (exemplars), however, TextonSVM scales in a much more efficient way than do boxing programs that are based on localized cross-correlation.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Arbeláez P,Han BG,Typke D,Lim J,Glaeser RM,Malik Jdoi
10.1016/j.jsb.2011.05.017subject
Has Abstractpub_date
2011-09-01 00:00:00pages
319-28issue
3eissn
1047-8477issn
1095-8657pii
S1047-8477(11)00165-1journal_volume
175pub_type
杂志文章abstract::Interdoublet sliding rates were assessed in bull sperm, utilizing a freeze-thaw procedure to allow axonemal disintegration. The sliding rate of 23 degrees C increased with increasing MgATP concentrations up to 1 mM ATP, to plateau at 8 microns/sec. The analyzed interdoublet shear in both live and demembranated (Triton...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1996.0059
更新日期:1996-05-01 00:00:00
abstract::Lichens are symbiotic associations of fungi and algae (or cyanobacteria). Fungal cells produce large amounts of lipid, assisted by algae, and secrete them out of the cells. Some of the secreted lipids crystallize in the thallus of the lichen. The crystalline materials sometimes occupy 30% of total dry weight of the th...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2004.01.015
更新日期:2004-06-01 00:00:00
abstract::The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accompli...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107447
更新日期:2020-03-01 00:00:00
abstract::The mature dentinoenamel junction (DEJ) is viewed by some investigators and the current authors, not as a fossilized, sharp transition between enamel and dentin, but as a relatively broad structural transition zone including the mantle dentin and the inner aprismatic enamel. In this study, the DEJ structure in bovine ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.10.006
更新日期:2008-02-01 00:00:00
abstract::Accurate image alignment is needed for computing three-dimensional reconstructions from transmission electron microscope tilt series. So far, the best results have been obtained by using colloidal gold beads as fiducial markers. If their use has not been possible for some reason, the only option has been the automatic...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2001.4443
更新日期:2001-12-01 00:00:00
abstract::Understanding skeletal aging and predicting fracture risk is increasingly important with a growing elderly population. We hypothesized that when categorized by external bone size, the male femoral diaphysis would show different strength-age trajectories which can be explained by changes in morphology, composition and ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107650
更新日期:2020-12-01 00:00:00
abstract::Nearly a third of all eukaryotic proteins are transported from the ER to the Golgi apparatus through the secretory pathway using COPII coated vesicles. Evidence suggests that this transport occurs via 500-900 Å vesicles that bud from the ER membrane. It has been shown that procollagen molecules utilize the COPII prote...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.09.002
更新日期:2011-02-01 00:00:00
abstract::Antifreeze proteins have the ability to bind to ice with high affinity and inhibit further crystal growth. The insect antifreeze protein from spruce budworm exhibits very high thermal hysteresis activity and is implicated in the protection of overwintering larvae from freezing. This protein has been crystallized in 20...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1999.4087
更新日期:1999-06-01 00:00:00
abstract::The concept of presenting antigens in a repetitive array to obtain high titers of specific antibodies is increasingly applied by using surface-engineered viruses or bacterial envelopes as novel vaccines. A case for this concept was made 25 years ago, when producing high-titer antisera against ordered arrays of gp23, t...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2003.08.004
更新日期:2003-09-01 00:00:00
abstract::The crystallographic structures of the adducts of salicylate 1,2-dioxygenase (SDO) with substrates salicylate, gentisate and 1-hydroxy-2-naphthoate, obtained under anaerobic conditions, have been solved and analyzed. This ring fission dioxygenase from the naphthalenesulfonate-degrading bacterium Pseudaminobacter salic...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.11.026
更新日期:2012-02-01 00:00:00
abstract::We analyzed a tertiary structure of systemin, the first identified polypeptide plant hormone, using two-dimensional NMR spectroscopy. From these data and molecular dynamics calculations we concluded that the peptide can adopt a Z-like-beta-sheet structure, which has previously been found in many specific DNA-binding p...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1995.1026
更新日期:1995-07-01 00:00:00
abstract::In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs fr...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2017.03.006
更新日期:2017-05-01 00:00:00
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
更新日期:2005-09-01 00:00:00
abstract::Structures of highly ordered biological bundles have unique features which call for special experimental and computational methods in electron cryomicroscopy. They can be considered as three-dimensional quasi-crystals and reconstructed using a crystallographic approach. However, they are neither "infinitely" large wit...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1997.3916
更新日期:1997-12-01 00:00:00
abstract::DciA is a newly discovered bacterial protein involved in loading the replicative helicase DnaB onto DNA at the initiation step of chromosome replication. Its three-dimensional structure is composed of a folded N-terminal domain (residues 1-111) resembling K Homology domains and a long disordered C-terminal tail (resid...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107573
更新日期:2020-10-01 00:00:00
abstract::The human vertebral body and intervertebral disc interface forms the region where the cartilaginous endplate, annulus fibrosis and bone of the vertebral body are connected through an intermediate calcified cartilage layer. While properties of both the vertebral body and components of the disc have been extensively stu...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.08.011
更新日期:2013-11-01 00:00:00
abstract::The recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114 (SmelDhp) has been characterised and its crystal structure elucidated at 1.85A. The global architecture of the protein is reminiscent of that of the amidohydrolase superfamily, consisting of two domains; an (alpha/beta)(8) TIM-like barrel domain,...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2009.10.013
更新日期:2010-02-01 00:00:00
abstract::The nuclear arrangement of the ABL, c-MYC, and RB1 genes was quantitatively investigated in human undifferentiated HL-60 cells and in a terminally differentiated population of human granulocytes. The ABL gene was expressed in both cell types, the c-MYC gene was active in HL-60 cells and down-regulated in granulocytes,...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00560-9
更新日期:2002-08-01 00:00:00
abstract::The Membrane Attack Complex-Perforin (MACPF) family is ubiquitously found in all kingdoms. They have diverse cellular roles, however MACPFs with pore-forming toxic function in venoms and poisons are very rare in animals. Here we present the structure of PmPV2, a MACPF toxin from the poisonous apple snail eggs, that ca...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107531
更新日期:2020-08-01 00:00:00
abstract::Single particle electron cryomicroscopy (cryo-EM) allows for structures of proteins and protein complexes to be determined from images of non-crystalline specimens. Cryo-EM data analysis requires electron microscope images of randomly oriented ice-embedded protein particles to be rotated and translated to allow for co...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2015.06.014
更新日期:2015-11-01 00:00:00
abstract::Single crystals of UDP-N-acetylglucosamine enolpyruvyltransferase of Enterobacter cloacae have been grown by vapor diffusion using phosphate buffer as the precipitant. The crystals belong to the monoclinic space group C2 with a = 86.9 A, b = 155.9 A, c = 83.8 A, beta = 91.6 degrees. Assuming two monomers per asymmetri...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1996.0071
更新日期:1996-07-01 00:00:00
abstract::TheL-A virus (LAV) particle is a specialized compartment for the transcription and replication of double-stranded RNA. It is 390 A in diameter and infects yeast. The particle is formed by a capsid containing 120 copies of a 680-residue gene product arranged with T = 1 icosahedral symmetry, approximately two copies of ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2001.4371
更新日期:2001-07-01 00:00:00
abstract::The graphics processing unit (GPU), which originally was used exclusively for visualization purposes, has evolved into an extremely powerful co-processor. In the meanwhile, through the development of elaborate interfaces, the GPU can be used to process data and deal with computationally intensive applications. The spe...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2008.07.006
更新日期:2008-10-01 00:00:00
abstract::Hypercalcified sponges, endowed with a calcium carbonate basal skeleton in addition to their spicules, form one of the most basal metazoan group engaged in extensive biomineralization. The Mediterranean species Petrobiona massiliana was used to investigate biological controls exerted on the biomineralization of its ba...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.04.004
更新日期:2012-06-01 00:00:00
abstract::Mononuclear macrophages are important immune cells in the organisms. The complicated membrane structure underlying the diverse functions of mononuclear-macrophage has been largely unresolved. As a representative of monocyte-derived macrophages, the membrane structure of PMA differentiated THP-1 cells was comprehensive...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2019.04.002
更新日期:2019-06-01 00:00:00
abstract::The exoskeleton of the American lobster Homarus americanus is a hierarchically organized nano-composite material consisting of organic chitin-protein fibers associated with inorganic calcium carbonate. The presence of a well-developed and periodically arranged pore canal system leads to a honeycomb-like structure. The...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.09.022
更新日期:2008-02-01 00:00:00
abstract::Tomo3D is a program for fast tomographic reconstruction on multicore computers. Its high speed stems from code optimization, vectorization with Streaming SIMD Extensions (SSE), multithreading and optimization of disk access. Recently, Advanced Vector eXtensions (AVX) have been introduced in the x86 processor architect...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2014.11.009
更新日期:2015-02-01 00:00:00
abstract::To construct calcium carbonate skeletons of sophisticated architecture, scleractinian corals secrete an extracellular skeletal organic matrix (SOM) from aboral ectodermal cells. The SOM, which is composed of proteins, saccharides, and lipids, performs functions critical for skeleton formation. Even though polysacchari...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.05.011
更新日期:2018-09-01 00:00:00
abstract::Electron cryo-tomography (cryoET) is currently the only technique that allows the direct observation of proteins in their native cellular environment. Sub-volume averaging of electron tomograms offers a route to increase the signal-to-noise of repetitive biological structures, such improving the information content an...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2016.06.024
更新日期:2017-02-01 00:00:00
abstract::Polyketides such as the clinically-valuable antibacterial agent mupirocin are constructed by architecturally-sophisticated assembly lines known as trans-acyltransferase polyketide synthases. Organelle-sized megacomplexes composed of several copies of trans-acyltransferase polyketide synthase assembly lines have been o...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2015.12.011
更新日期:2016-03-01 00:00:00