scholarly journals EvoSeg: Automated Electron Microscopy Segmentation through Random Forests and Evolutionary Optimization

Biomimetics ◽  
2021 ◽  
Vol 6 (2) ◽  
pp. 37
Author(s):  
Manuel Zumbado-Corrales ◽  
Juan Esquivel-Rodríguez
Keyword(s):  
Electron Microscopy ◽  
Structural Information ◽  
Evolutionary Optimization ◽  
Molecular Structures ◽  
Segmentation Algorithm ◽  
Additional Information ◽  
Initial Segmentation ◽  
Classic Approach ◽  
Specific Proteins ◽  
The Cost

Electron Microscopy Maps are key in the study of bio-molecular structures, ranging from borderline atomic level to the sub-cellular range. These maps describe the envelopes that cover possibly a very large number of proteins that form molecular machines within the cell. Within those envelopes, we are interested to find what regions correspond to specific proteins so that we can understand how they function, and design drugs that can enhance or suppress a process that they are involved in, along with other experimental purposes. A classic approach by which we can begin the exploration of map regions is to apply a segmentation algorithm. This yields a mask where each voxel in 3D space is assigned an identifier that maps it to a segment; an ideal segmentation would map each segment to one protein unit, which is rarely the case. In this work, we present a method that uses bio-inspired optimization, through an Evolutionary-Optimized Segmentation algorithm, to iteratively improve upon baseline segments obtained from a classical approach, called watershed segmentation. The cost function used by the evolutionary optimization is based on an ideal segmentation classifier trained as part of this development, which uses basic structural information available to scientists, such as the number of expected units, volume and topology. We show that a basic initial segmentation with the additional information allows our evolutionary method to find better segmentation results, compared to the baseline generated by the watershed.

Electron Microscopy in Molecular Biology

1967 ◽  
Vol 25 ◽  
pp. 2-3
Author(s):  
Cecil E. Hall
Keyword(s):  
Electron Microscopy ◽  
Molecular Biology ◽  
Noise Level ◽  
Molecular Structures ◽  
Material Structure ◽  
The Arts ◽  
Shadow Casting ◽  
Electron Image ◽  
High Degree ◽  
Very High

The visualization of organic macromolecules such as proteins, nucleic acids, viruses and virus components has reached its high degree of effectiveness owing to refinements and reliability of instruments and to the invention of methods for enhancing the structure of these materials within the electron image. The latter techniques have been most important because what can be seen depends upon the molecular and atomic character of the object as modified which is rarely evident in the pristine material. Structure may thus be displayed by the arts of positive and negative staining, shadow casting, replication and other techniques. Enhancement of contrast, which delineates bounds of isolated macromolecules has been effected progressively over the years as illustrated in Figs. 1, 2, 3 and 4 by these methods. We now look to the future wondering what other visions are waiting to be seen. The instrument designers will need to exact from the arts of fabrication the performance that theory has prescribed as well as methods for phase and interference contrast with explorations of the potentialities of very high and very low voltages. Chemistry must play an increasingly important part in future progress by providing specific stain molecules of high visibility, substrates of vanishing “noise” level and means for preservation of molecular structures that usually exist in a solvated condition.

Microtubule nucleation sequence studied by time-resolved x-ray scattering and electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 766-767
Author(s):  
Eva-Maria Mandelkow ◽  
Eckhard Mandelkow ◽  
Joan Bordas
Keyword(s):  
Electron Microscopy ◽  
Dynamic Equilibrium ◽  
Time Resolved ◽  
X Ray ◽  
Additional Information ◽  
X Ray Scattering ◽  
Low Concentrations ◽  
Microtubule Growth ◽  
Ray Patterns ◽  
Ray Scattering

When a solution of microtubule protein is changed from non-polymerising to polymerising conditions (e.g. by temperature jump or mixing with GTP) there is a series of structural transitions preceding microtubule growth. These have been detected by time-resolved X-ray scattering using synchrotron radiation, and they may be classified into pre-nucleation and nucleation events. X-ray patterns are good indicators for the average behavior of the particles in solution, but they are difficult to interpret unless additional information on their structure is available. We therefore studied the assembly process by electron microscopy under conditions approaching those of the X-ray experiment. There are two difficulties in the EM approach: One is that the particles important for assembly are usually small and not very regular and therefore tend to be overlooked. Secondly EM specimens require low concentrations which favor disassembly of the particles one wants to observe since there is a dynamic equilibrium between polymers and subunits.

Ultimate resolution and information in electron microscopy

1991 ◽  
Vol 49 ◽  
pp. 496-497
Author(s):  
D. Van Dyck
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Transfer Function ◽  
Information Transfer ◽  
Communication Channel ◽  
Structural Information ◽  
Information Rate ◽  
Noise Power ◽  
Signal Power ◽  
Imaging Device

An (electron) microscope can be considered as a communication channel that transfers structural information between an object and an observer. In electron microscopy this information is carried by electrons. According to the theory of Shannon the maximal information rate (or capacity) of a communication channel is given by C = B log2 (1 + S/N) bits/sec., where B is the band width, and S and N the average signal power, respectively noise power at the output. We will now apply to study the information transfer in an electron microscope. For simplicity we will assume the object and the image to be onedimensional (the results can straightforwardly be generalized). An imaging device can be characterized by its transfer function, which describes the magnitude with which a spatial frequency g is transferred through the device, n is the noise. Usually, the resolution of the instrument ᑭ is defined from the cut-off 1/ᑭ beyond which no spadal information is transferred.

Two-Dimensional Crystallization of Tetanus Toxin

1985 ◽  
Vol 43 ◽  
pp. 528-529
Author(s):  
Jeffry A. Reidler ◽  
John P. Robinson
Keyword(s):  
Electron Microscopy ◽  
Tetanus Toxin ◽  
Structural Information ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Membrane Interface ◽  
3D Reconstructions ◽  
Cellular Receptors ◽  
Computer Reconstruction ◽  
2D Crystals

We have prepared two-dimensional (2D) crystals of tetanus toxin using procedures developed by Uzgiris and Kornberg for the directed production of 2D crystals of monoclonal antibodies at an antigen-phospholipid monolayer interface. The tetanus toxin crystals were formed using a small mole fraction of the natural receptor, GT1, incorporated into phosphatidyl choline monolayers. The crystals formed at low concentration overnight. Two dimensional crystals of this type are particularly useful for structure determination using electron microscopy and computer image refinement. Three dimensional (3D) structural information can be derived from these crystals by computer reconstruction of photographs of toxin crystals taken at different tilt angles. Such 3D reconstructions may help elucidate the mechanism of entry of the enzymatic subunit of toxins into cells, particularly since these crystals form directly on a membrane interface at similar concentrations of ganglioside GT1 to the natural cellular receptors.

Progress in high-resolution CRYO-SEM imaging of viral particles

1996 ◽  
Vol 54 ◽  
pp. 818-819
Author(s):  
Ya Chen ◽  
Geoffrey Letchworth ◽  
John White
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
High Resolution ◽  
Structural Information ◽  
Signal To Noise Ratio ◽  
Flexible Structures ◽  
Simian Virus ◽  
Topographic Features ◽  
Viral Particles ◽  
Scanning Electron

Low-temperature high-resolution scanning electron microscopy (cryo-HRSEM) has been successfully utilized to image biological macromolecular complexes at nanometer resolution. Recently, imaging of individual viral particles such as reovirus using cryo-HRSEM or simian virus (SIV) using HRSEM, HV-STEM and AFM have been reported. Although conventional electron microscopy (e.g., negative staining, replica, embedding and section), or cryo-TEM technique are widely used in studying of the architectures of viral particles, scanning electron microscopy presents two major advantages. First, secondary electron signal of SEM represents mostly surface topographic features. The topographic details of a biological assembly can be viewed directly and will not be obscured by signals from the opposite surface or from internal structures. Second, SEM may produce high contrast and signal-to-noise ratio images. As a result of this important feature, it is capable of visualizing not only individual virus particles, but also asymmetric or flexible structures. The 2-3 nm resolution obtained using high resolution cryo-SEM made it possible to provide useful surface structural information of macromolecule complexes within cells and tissues. In this study, cryo-HRSEM is utilized to visualize the distribution of glycoproteins of a herpesvirus.

Atomic chemistry by HREM and image simulations?

1986 ◽  
Vol 44 ◽  
pp. 828-829
Author(s):  
J.M. Howe ◽  
R. Gronsky
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Structural Information ◽  
High Resolution Electron Microscopy ◽  
Resolution Electron ◽  
Image Simulations

The technique of high-resolution electron microscopy (HREM) is invaluable to the materials scientist because it allows examination of microstructural features at levels of resolution that are unobtainable by most other methods. Although the structural information which can be determined by HREM and accompanying image simulations has been well documented in the literature, there have only been a few cases where this technique has been used to reveal the chemistry of individual columns or planes of atoms, as occur in segregated and ordered materials.

Electron microscopy and diffraction of crystalline dendrimers and macrocycles

1993 ◽  
Vol 51 ◽  
pp. 1218-1219
Author(s):  
C. J. Buchko ◽  
P. M. Wilson ◽  
Z. Xu ◽  
J. Zhang ◽  
S. Lee ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Liquid Crystalline ◽  
Structural Information ◽  
High Resolution Electron Microscopy ◽  
Scanning Calorimetry ◽  
Tertiary Butyl ◽  
Phenyl Acetylene ◽  
Selected Area Electron Diffraction ◽  
Liquid Crystalline Phases ◽  
Resolution Electron

The synthesis of well-defined organic molecules with unique geometries opens new opportunities for understanding and controlling the organization of condensed matter. Here, we study dendrimers and macrocycles which are synthesized from rigid phenyl-acetylene spacer units, Both units are solubilized by the presence of tertiary butyl groups located at the periphery of the molecule. These hydrocarbon materials form crystalline and liquid crystalline phases which have been studied by differential scanning calorimetry, hot stage optical microscopy, and wide-angle x-ray scattering (WAXS).The precisely defined architecture of these molecules makes it possible to investigate systematic variations in chemical architecture on the nature of microstructural organization. Here we report on the transmission electron microscopy (TEM), selected area electron diffraction (SAED), and high resolution electron microscopy (HREM) studies of crystalline thin films formed by deposition of these materials onto carbon substrates from dilute solution. Electron microscopy is very attractive for gaining structural information on new molecules due to the scarcity of material to grow single crystals suitable for conventional crystallography.

scholarly journals ALPINE: Active Link Prediction Using Network Embedding

2021 ◽  
Vol 11 (11) ◽  
pp. 5043
Author(s):  
Xi Chen ◽  
Bo Kang ◽  
Jefrey Lijffijt ◽  
Tijl De Bie
Keyword(s):  
Active Learning ◽  
Protein Interactions ◽  
Link Prediction ◽  
Prediction Accuracy ◽  
Real Data ◽  
Network Embedding ◽  
Protein Protein Interactions ◽  
Additional Information ◽  
The Cost ◽  
Active Link

Many real-world problems can be formalized as predicting links in a partially observed network. Examples include Facebook friendship suggestions, the prediction of protein–protein interactions, and the identification of hidden relationships in a crime network. Several link prediction algorithms, notably those recently introduced using network embedding, are capable of doing this by just relying on the observed part of the network. Often, whether two nodes are linked can be queried, albeit at a substantial cost (e.g., by questionnaires, wet lab experiments, or undercover work). Such additional information can improve the link prediction accuracy, but owing to the cost, the queries must be made with due consideration. Thus, we argue that an active learning approach is of great potential interest and developed ALPINE (Active Link Prediction usIng Network Embedding), a framework that identifies the most useful link status by estimating the improvement in link prediction accuracy to be gained by querying it. We proposed several query strategies for use in combination with ALPINE, inspired by the optimal experimental design and active learning literature. Experimental results on real data not only showed that ALPINE was scalable and boosted link prediction accuracy with far fewer queries, but also shed light on the relative merits of the strategies, providing actionable guidance for practitioners.

scholarly journals Nanostructured and Modulated Low-Dimensional Systems

2013 ◽  
Vol 203-204 ◽  
pp. 42-47
Author(s):  
Albert Prodan ◽  
Herman J.P. van Midden ◽  
Erik Zupanič ◽  
Rok Žitko
Keyword(s):  
Charge Density ◽  
Structural Information ◽  
Density Wave ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Additional Information ◽  
Related Pair ◽  
Good Accord ◽  
Long Range Ordering ◽  
Low Dimensional

Charge density wave (CDW) ordering in NbSe3 and the structurally related quasi one-dimensional compounds is reconsidered. Since the modulated ground state is characterized by unstable nano-domains, the structural information obtained from diffraction experiments is to be supplemented by some additional information from a method, able to reveal details on a unit cell level. Low-temperature (LT) scanning tunneling microscopy (STM) can resolve both, the local atomic structure and the superimposed charge density modulation. It is shown that the established model for NbSe3 with two incommensurate (IC) modes, q1 = (0,0.241,0) and q2 = (0.5,0.260,0.5), locked in at T1=144K and T2=59K and separately confined to two of the three available types of bi-capped trigonal prismatic (BCTP) columns, must be modified. The alternative explanation is based on the existence of modulated layered nano-domains and is in good accord with the available LT STM results. These confirm i.a. the presence of both IC modes above the lower CDW transition temperature. Two BCTP columns, belonging to a symmetry-related pair, are as a rule alternatively modulated by the two modes. Such pairs of columns are ordered into unstable layered nano-domains, whose q1 and q2 sub-layers are easily interchanged. The mutually interchangeable sections of the two unstable IC modes keep a temperature dependent long-range ordering. Both modes can formally be replaced by a single highly inharmonic long-period commensurate CDW.

scholarly journals FSBu 25/2018 “Accounting for Leases”   and IFRS 16 “Leases”: A comparative Analysis of Key Provisions

2020 ◽  
Vol 6 (6) ◽  
pp. 42-51
Author(s):  
V. S. Plotnikov ◽  
O. V. Plotnikova
Keyword(s):  
Structural Information ◽  
Balance Sheet ◽  
Financial Statements ◽  
Practical Significance ◽  
Accounting System ◽  
The Subject ◽  
The Cost ◽  
Lease Accounting ◽  
Comparative Description

The article is devoted to the problem of accounting reflection of rental relations, which has been the subject of discussion by professional accountants for more than 100 years. At present, more standards are devoted to this problem in world practice than to other accounting objects. Nevertheless, a number of issues remain unresolved. The methodological framework of the study is based on a comparative description of the provisions of IFRS 16 “Leases” and FSBU 25/2018 “Accounting for Leases” and includes a new institutional theory, Conceptual framework for the presentation of financial statements. The research methodology provides for the reclassification of balance sheet items, which allows for significant structural information regarding the reflection of rental objects. The analysis revealed the following differences in standards: the Russian FSBU 25/2018 unreasonably introduces accounting for leasing transactions into the financial lease accounting system; insufficiently convincingly and without proper evidence the issues of identification of financial lease accounting objects are covered. The prospective direction of accounting for financial leases is the possibility of reflecting the property transferred by the lessee as an element of the cost of financial capital, at the same time, the tenant’s long-term obligations should be recognized as existing obligations. The practical significance of the study is determined by the possibility of reducing the level of debt in the balance of the parties to the lease transaction.

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