Cell Bioprinting: The 3D-Bioplotter™ Case

The classic cell culture involves the use of support in two dimensions, such as a well plate or a Petri dish, that allows the culture of different types of cells. However, this technique does not mimic the natural microenvironment where the cells are exposed to. To solve that, three-dimensional bioprinting techniques were implemented, which involves the use of biopolymers and/or synthetic materials and cells. Because of a lack of information between data sources, the objective of this review paper is, to sum up, all the available information on the topic of bioprinting and to help researchers with the problematics with 3D bioprinters, such as the 3D-Bioplotter™. The 3D-Bioplotter™ has been used in the pre-clinical field since 2000 and could allow the printing of more than one material at the same time, and therefore to increase the complexity of the 3D structure manufactured. It is also very precise with maximum flexibility and a user-friendly and stable software that allows the optimization of the bioprinting process on the technological point of view. Different applications have resulted from the research on this field, mainly focused on regenerative medicine, but the lack of information and/or the possible misunderstandings between papers makes the reproducibility of the tests difficult. Nowadays, the 3D Bioprinting is evolving into another technology called 4D Bioprinting, which promises to be the next step in the bioprinting field and might promote great applications in the future.

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Formation of corner waves in the wake of a partially submerged bluff body

Journal of Fluid Mechanics ◽

10.1017/jfm.2015.192 ◽

2015 ◽

Vol 771 ◽

pp. 547-563 ◽

Cited By ~ 1

Author(s):

P. Martínez-Legazpi ◽

J. Rodríguez-Rodríguez ◽

A. Korobkin ◽

J. C. Lasheras

Keyword(s):

Bluff Body ◽

Physical Mechanism ◽

Essential Feature ◽

Three Dimensional ◽

Two Dimensions ◽

Point Of View ◽

Paper 30: Review of Surface Texture Measurement and the Associated Metrological Problems

Proceedings of the Institution of Mechanical Engineers Conference Proceedings ◽

10.1243/pime_conf_1967_182_331_02 ◽

1967 ◽

Vol 182 (11) ◽

pp. 330-343

Author(s):

E. Green

Keyword(s):

Surface Texture ◽

Quantitative Assessment ◽

Three Dimensional ◽

Two Dimensions ◽

Texture Measurement ◽

Relative Roughness ◽

Electronic Circuitry ◽

Different Types ◽

The Many ◽

Physical Phenomena

A brief review is presented of the physical phenomena (optical, capacitance, conductance, absorption, pneumatic, and hydraulic) which have been utilized in the various types of instruments developed to express, by means of a single index, the relative roughness of different specimens. The readings taken with such instruments are normally functions of the three-dimensional characteristics of the surface under test but, since they are of an empirical nature, there is little or no correlation between measurements made with the different types of instruments. Instruments measuring in two dimensions and recording in absolute units of length have been universally accepted. The most popular instrument is the stylus tracer type with electronic amplification of the stylus movement. The output of these devices is dependent on factors that have been standardized by the manufacturers (electronic circuitry, the form of stylus, etc.) and other elements, the characteristics of which are not uniform for all instruments (stylus support and mounting, etc.). Reference is made to the basic datum to which the readings of tracer instruments refer, the envelope line and the centre line, and the different parameters currently advocated as presenting an adequate means of describing and forming a quantitative assessment of the surface under test. The use of digital computer techniques for eliminating the many analogue devices necessary for the evaluation of the different parameters is explained.

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FoldRate: A Web-Server for Predicting Protein Folding Rates from Primary Sequence

The Open Bioinformatics Journal ◽

10.2174/1875036200903010031 ◽

2009 ◽

Vol 3 (1) ◽

pp. 31-50 ◽

Cited By ~ 55

Author(s):

Chou Kuo-Chen ◽

Shen Hong-Bin

Keyword(s):

3D Structure ◽

Three Dimensional ◽

Web Server ◽

Query Protein ◽

Sequence Information ◽

Folding Rate ◽

Structure Information ◽

The Public ◽

Folding Rates ◽

User Friendly

With the avalanche of gene products in the postgenomic age, the gap between newly found protein sequences and the knowledge of their 3D (three dimensional) structures is becoming increasingly wide. It is highly desired to develop a method by which one can predict the folding rates of proteins based on their amino acid sequence information alone. To address this problem, an ensemble predictor, called FoldRate, was developed by fusing the folding-correlated features that can be either directly obtained or easily derived from the sequences of proteins. It was demonstrated by the jackknife cross-validation on a benchmark dataset constructed recently that FoldRate is at least comparable with or even better than the existing methods that, however, need both the sequence and 3D structure information for predicting the folding rate. As a user-friendly web-server, FoldRate is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/FoldRate/, by which one can get the desired result for a query protein sequence in around 30 seconds.

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Ultrastructural Investigations of the Contractile Filaments of Amoebae

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100050950 ◽

1974 ◽

Vol 32 ◽

pp. 188-189

Author(s):

P.L. Moore

Keyword(s):

Cytoplasmic Streaming ◽

Three Dimensional ◽

Freeze Fracture ◽

Amoeboid Movement ◽

Different Types ◽

Chemical Conditions ◽

Complete Interpretation

Previous freeze fracture results on the intact giant, amoeba Chaos carolinensis indicated the presence of a fibrillar arrangement of filaments within the cytoplasm. A complete interpretation of the three dimensional ultrastructure of these structures, and their possible role in amoeboid movement was not possible, since comparable results could not be obtained with conventional fixation of intact amoebae. Progress in interpreting the freeze fracture images of amoebae required a more thorough understanding of the different types of filaments present in amoebae, and of the ways in which they could be organized while remaining functional.The recent development of a calcium sensitive, demembranated, amoeboid model of Chaos carolinensis has made it possible to achieve a better understanding of such functional arrangements of amoeboid filaments. In these models the motility of demembranated cytoplasm can be controlled in vitro, and the chemical conditions necessary for contractility, and cytoplasmic streaming can be investigated. It is clear from these studies that “fibrils” exist in amoeboid models, and that they are capable of contracting along their length under conditions similar to those which cause contraction in vertebrate muscles.

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Methods for three-dimensional reconstruction of cellular components within a thick section

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100141871 ◽

1986 ◽

Vol 44 ◽

pp. 18-21

Author(s):

J. Frank ◽

B. F. McEwen ◽

M. Radermacher ◽

C. L. Rieder

Keyword(s):

Tilt Angle ◽

Tomographic Reconstruction ◽

3D Structure ◽

Three Dimensional ◽

Thick Section ◽

Three Dimensional Reconstruction ◽

Axis Ratio ◽

Dimensional Reconstruction ◽

Cellular Components

The tomographic reconstruction from multiple projections of cellular components, within a thick section, offers a way of visualizing and quantifying their three-dimensional (3D) structure. However, asymmetric objects require as many views from the widest tilt range as possible; otherwise the reconstruction may be uninterpretable. Even if not for geometric obstructions, the increasing pathway of electrons, as the tilt angle is increased, poses the ultimate upper limitation to the projection range. With the maximum tilt angle being fixed, the only way to improve the faithfulness of the reconstruction is by changing the mode of the tilting from single-axis to conical; a point within the object projected with a tilt angle of 60° and a full 360° azimuthal range is then reconstructed as a slightly elliptic (axis ratio 1.2 : 1) sphere.

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Cryomicroscopy of crotoxin complex crystals at 400 KV

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100156109 ◽

1989 ◽

Vol 47 ◽

pp. 826-827

Author(s):

Jaap Brink ◽

Wah Chiu

Keyword(s):

Signal To Noise Ratio ◽

3D Structure ◽

Three Dimensional ◽

Carbon Films ◽

Depth Of Field ◽

Basic Subunit ◽

Ewald Sphere ◽

Diffraction Patterns ◽

Complex Crystals ◽

Acidic Subunit

The crotoxin complex is a potent neurotoxin composed of a basic subunit (Mr = 12,000) and an acidic subunit (M = 10,000). The basic subunit possesses phospholipase activity whereas the acidic subunit shows no enzymatic activity at all. The complex's toxocity is expressed both pre- and post-synaptically. The crotoxin complex forms thin crystals suitable for electron crystallography. The crystals diffract up to 0.16 nm in the microscope, whereas images show reflections out to 0.39 nm2. Ultimate goal in this study is to obtain a three-dimensional (3D-) structure map of the protein around 0.3 nm resolution. Use of 100 keV electrons in this is limited; the unit cell's height c of 25.6 nm causes problems associated with multiple scattering, radiation damage, limited depth of field and a more pronounced Ewald sphere curvature. In general, they lead to projections of the unit cell, which at the desired resolution, cannot be interpreted following the weak-phase approximation. Circumventing this problem is possible through the use of 400 keV electrons. Although the overall contrast is lowered due to a smaller scattering cross-section, the signal-to-noise ratio of especially higher order reflections will improve due to a smaller contribution of inelastic scattering. We report here our preliminary results demonstrating the feasability of the data collection procedure at 400 kV.Crystals of crotoxin complex were prepared on carbon-covered holey-carbon films, quench frozen in liquid ethane, inserted into a Gatan 626 holder, transferred into a JEOL 4000EX electron microscope equipped with a pair of anticontaminators operating at −184°C and examined under low-dose conditions. Selected area electron diffraction patterns (EDP's) and images of the crystals were recorded at 400 kV and −167°C with dose levels of 5 and 9.5 electrons/Å, respectively.

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Laser Scanning Confocal Microscopy and Three-Dimesnsional Reconstruction of the Mitotic Spindles of Unequally Dividing Embryonic Cells

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100158376 ◽

1990 ◽

Vol 48 (3) ◽

pp. 166-167

Author(s):

J. Holy ◽

G. Schatten

Keyword(s):

Confocal Microscopy ◽

Mitotic Spindle ◽

Laser Scanning ◽

Three Dimensional ◽

Laser Scanning Confocal Microscopy ◽

Two Dimensions ◽

Embryonic Cells ◽

Mitotic Spindles ◽

Cleavage Division ◽

Scanning Confocal Microscopy

One of the classic limitations of light microscopy has been the fact that three dimensional biological events could only be visualized in two dimensions. Recently, this shortcoming has been overcome by combining the technologies of laser scanning confocal microscopy (LSCM) and computer processing of microscopical data by volume rendering methods. We have employed these techniques to examine morphogenetic events characterizing early development of sea urchin embryos. Specifically, the fourth cleavage division was examined because it is at this point that the first morphological signs of cell differentiation appear, manifested in the production of macromeres and micromeres by unequally dividing vegetal blastomeres.The mitotic spindle within vegetal blastomeres undergoing unequal cleavage are highly polarized and develop specialized, flattened asters toward the micromere pole. In order to reconstruct the three-dimensional features of these spindles, both isolated spindles and intact, extracted embryos were fluorescently labeled with antibodies directed against either centrosomes or tubulin.

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Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100181026 ◽

1990 ◽

Vol 48 (1) ◽

pp. 454-455

Author(s):

Jose-Maria Carazo ◽

I. Benavides ◽

S. Marco ◽

J.L. Carrascosa ◽

E.L. Zapata

Keyword(s):

3D Reconstruction ◽

3D Structure ◽

Three Dimensional ◽

Software Tools ◽

Mapping Method ◽

Computer Architectures ◽

Parallel Computer ◽

Reconstruction Process ◽

Computing Power ◽

Order Of Magnitude

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.

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A Study on Utilization of Three-Dimensional Sensor Lip Image for Developing a Pronunciation Recognition System

Journal of Imaging Science and Technology ◽

10.2352/j.imagingsci.technol.2019.63.5.050402 ◽

2019 ◽

Vol 63 (5) ◽

pp. 50402-1-50402-9 ◽

Cited By ~ 1

Author(s):

Ing-Jr Ding ◽

Chong-Min Ruan

Keyword(s):

Principal Component Analysis ◽

Automatic Speech Recognition ◽

Feature Fusion ◽

Three Dimensional ◽

Principal Component ◽

Recognition System ◽

Geometrical Characteristics ◽

3D Geometry ◽

Different Types ◽

The Disabled

Abstract The acoustic-based automatic speech recognition (ASR) technique has been a matured technique and widely seen to be used in numerous applications. However, acoustic-based ASR will not maintain a standard performance for the disabled group with an abnormal face, that is atypical eye or mouth geometrical characteristics. For governing this problem, this article develops a three-dimensional (3D) sensor lip image based pronunciation recognition system where the 3D sensor is efficiently used to acquire the action variations of the lip shapes of the pronunciation action from a speaker. In this work, two different types of 3D lip features for pronunciation recognition are presented, 3D-(x, y, z) coordinate lip feature and 3D geometry lip feature parameters. For the 3D-(x, y, z) coordinate lip feature design, 18 location points, each of which has 3D-sized coordinates, around the outer and inner lips are properly defined. In the design of 3D geometry lip features, eight types of features considering the geometrical space characteristics of the inner lip are developed. In addition, feature fusion to combine both 3D-(x, y, z) coordinate and 3D geometry lip features is further considered. The presented 3D sensor lip image based feature evaluated the performance and effectiveness using the principal component analysis based classification calculation approach. Experimental results on pronunciation recognition of two different datasets, Mandarin syllables and Mandarin phrases, demonstrate the competitive performance of the presented 3D sensor lip image based pronunciation recognition system.

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Simulating Self-Regeneration and Self-Replication Processes Using Movable Cellular Automata with a Mutual Equilibrium Neighborhood

Complex Systems ◽

10.25088/complexsystems.29.4.741 ◽

2020 ◽

Vol 29 (4) ◽

pp. 741-757

Author(s):

Kateryna Hazdiuk ◽

◽

Volodymyr Zhikharevich ◽

Serhiy Ostapov ◽

◽

...

Keyword(s):

Cellular Automata ◽

Cellular Automaton ◽

Three Dimensional ◽

Computer Models ◽

The Self ◽

Model Construction ◽

Natural Phenomena ◽

Different Types ◽

Movable Cellular Automata ◽

Self Replication

This paper deals with the issue of model construction of the self-regeneration and self-replication processes using movable cellular automata (MCAs). The rules of cellular automaton (CA) interactions are found according to the concept of equilibrium neighborhood. The method is implemented by establishing these rules between different types of cellular automata (CAs). Several models for two- and three-dimensional cases are described, which depict both stable and unstable structures. As a result, computer models imitating such natural phenomena as self-replication and self-regeneration are obtained and graphically presented.

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