scholarly journals Intra- and Interspecies Variability of Single-Cell Innate Fluorescence Signature of Microbial Cell

2019 ◽  
Vol 85 (18) ◽  
Author(s):  
Yutaka Yawata ◽  
Tatsunori Kiyokawa ◽  
Yuhki Kawamura ◽  
Tomohiro Hirayama ◽  
Kyosuke Takabe ◽  
...  
Keyword(s):  
Single Cell ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Population Level ◽  
Microbial Cell ◽  
Physiological Status ◽  
Growth Phases ◽  
Content Type ◽  
A Cell ◽  
Three Dimensional Space

ABSTRACT Here we analyzed the innate fluorescence signature of the single microbial cell, within both clonal and mixed populations of microorganisms. We found that even very similarly shaped cells differ noticeably in their autofluorescence features and that the innate fluorescence signatures change dynamically with growth phases. We demonstrated that machine learning models can be trained with a data set of single-cell innate fluorescence signatures to annotate cells according to their phenotypes and physiological status, for example, distinguishing a wild-type Aspergillus nidulans cell from its nitrogen metabolism mutant counterpart and log-phase cells from stationary-phase cells of Pseudomonas putida. We developed a minimally invasive method (confocal reflection microscopy-assisted single-cell innate fluorescence [CRIF] analysis) to optically extract and catalog the innate cellular fluorescence signatures of each of the individual live microbial cells in a three-dimensional space. This technique represents a step forward from traditional techniques which analyze the innate fluorescence signatures at the population level and necessitate a clonal culture. Since the fluorescence signature is an innate property of a cell, our technique allows the prediction of the types or physiological status of intact and tag-free single cells, within a cell population distributed in a three-dimensional space. Our study presents a blueprint for a streamlined cell analysis where one can directly assess the potential phenotype of each single cell in a heterogenous population by its autofluorescence signature under a microscope, without cell tagging. IMPORTANCE A cell’s innate fluorescence signature is an assemblage of fluorescence signals emitted by diverse biomolecules within a cell. It is known that the innate fluoresce signature reflects various cellular properties and physiological statuses; thus, they can serve as a rich source of information in cell characterization as well as cell identification. However, conventional techniques focus on the analysis of the innate fluorescence signatures at the population level but not at the single-cell level and thus necessitate a clonal culture. In the present study, we developed a technique to analyze the innate fluorescence signature of a single microbial cell. Using this novel method, we found that even very similarly shaped cells differ noticeably in their autofluorescence features, and the innate fluorescence signature changes dynamically with growth phases. We also demonstrated that the different cell types can be classified accurately within a mixed population under a microscope at the resolution of a single cell, depending solely on the innate fluorescence signature information. We suggest that single-cell autofluoresce signature analysis is a promising tool to directly assess the taxonomic or physiological heterogeneity within a microbial population, without cell tagging.

Collision avoidance for mobile robots based on artificial potential field and obstacle envelope modelling

2016 ◽  
Vol 36 (3) ◽  
pp. 318-332 ◽  
Author(s):  
Zhenyu Wu ◽  
Guang Hu ◽  
Lin Feng ◽  
Jiping Wu ◽  
Shenglan Liu
Keyword(s):  
Mobile Robot ◽  
Collision Avoidance ◽  
Potential Field ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Artificial Potential Field ◽  
Content Type ◽  
Negative Pole ◽  
Avoidance Problem ◽  
Three Dimensional Space

Purpose This paper aims to investigate the collision avoidance problem for a mobile robot by constructing an artificial potential field (APF) based on geometrically modelling the obstacles with a new method named the obstacle envelope modelling (OEM). Design/methodology/approach The obstacles of arbitrary shapes are enveloped in OEM using the primitive, which is an ellipse in a two-dimensional plane or an ellipsoid in a three-dimensional space. As the surface details of obstacles are neglected elegantly in OEM, the workspace of a mobile robot is made simpler so as to increase the capability of APF in a clustered environment. Findings Further, a dipole is applied to the construction of APF produced by each obstacle, among which the positive pole pushes the robot away and the negative pole pulls the robot close. Originality/value As a whole, the dipole leads the robot to make a derivation around the obstacle smoothly, which greatly reduces the local minima and trajectory oscillations. Computer simulations are conducted to demonstrate the effectiveness of the proposed approach.

scholarly journals COLUMN TESSELLATIONS

2015 ◽  
Vol 34 (2) ◽  
pp. 87 ◽  
Author(s):  
Linh Ngoc Nguyen ◽  
Viola Weiss ◽  
Richard Cowan
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Mean Values ◽  
New Class ◽  
A Cell ◽  
Spatial Tessellation ◽  
Spatial Construction ◽  
Base Facet ◽  
Stationary Planar ◽  
Three Dimensional Space

A new class of non facet-to-facet random tessellations in three-dimensional space is introduced -- the so-called column tessellations. The spatial construction is based on a stationary planar tessellation; each cell of the spatial tessellation is a prism whose base facet is  congruent to a cell of the planar tessellation. Thus intensities, topological and metric mean values of the spatial tessellation can be calculated from suitably chosen parameters of the planar tessellation.

Computational fluid dynamics and laminar heat transfer of water/Cu nanofluid in ribbed microchannel with a two-phase approach

2019 ◽  
Vol 29 (5) ◽  
pp. 1563-1589 ◽  
Author(s):  
Navid Ahmadi Cheloii ◽  
Omid Ali Akbari ◽  
Davood Toghraie
Keyword(s):  
Heat Transfer ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Phase ◽  
Rectangular Microchannel ◽  
Content Type ◽  
Performance Evaluation Criterion ◽  
Phase Mixture ◽  
Three Dimensional Space

Purpose This study aims to numerically investigate the heat transfer and laminar forced and two-phase flow of Water/Cu nanofluid in a rectangular microchannel with oblique ribs with angle of attacks equal to 0-45°. This simulation was conducted in the range of Reynolds numbers of 5-120 in volume fractions of 0, 2 and 4 per cent of solid nanoparticles in three-dimensional space. Design/methodology/approach This study investigates the effect of the changes of angle of attack of rectangular rib on heat transfer and hydrodynamics of two-phase flow. This study was done in three-dimensional space and simulation was done with finite volume method. SIMPLEC algorithm and second-order discretization of equations were used to increase the accuracy of results. The usage of nanofluid, application of rips with different angles of attacks and using the two-phase mixture method is the distinction of this paper compared with other studies. Findings The results of this research revealed that the changing angle of attack of ribs is an effective factor in heat transfer enhancement. On the other hand, the existence of rib on the internal surfaces of a microchannel increases friction coefficient. By increasing the volume fraction of nanoparticles, due to the augmentation of fluid density and viscosity, the pressure drop increases significantly. For all of the angle of attacks studied in this paper, the maximum rate of performance evaluation criterion has been obtained in Reynolds number of 30 and the minimum amount of performance evaluation criterion was been obtained in Reynolds numbers of 5 and 120. Originality/value Many studies have been done in the field of heat transfer in ribbed microchannel. In this paper, the laminar flow in the ribbed microchannel Water/Cu nanofluid in a rectangular microchannel by using two-phase mixture method is numerically investigated with different volume fractions (0-4 per cent), Reynolds numbers (5-120) and angle of attacks of rectangular rib in the indented microchannel (0-45°).

scholarly journals CellexalVR: A virtual reality platform to visualise and analyse single-cell data

2018 ◽  
Author(s):  
Oscar Legetth ◽  
Johan Rodhe ◽  
Stefan Lang ◽  
Parashar Dhapola ◽  
Joel Pålsson ◽  
...  
Keyword(s):  
Virtual Reality ◽  
Single Cell ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Cell Populations ◽  
Virtual Reality Environment ◽  
Reduction Methods ◽  
Cell Data ◽  
Three Dimensional Space

AbstractSingle-cell RNAseq is a routinely used technique to explore the composition of cell populations, and they are often visualised using dimension reduction methods where the cells are represented in two or three dimensional space. Many tools are available to do this but visualising and cross-comparing these representations can be challenging, especially when cells are projected onto three dimensions which can be more informative for complex datasets. Here we present CellexalVR (www.cellexalvr.med.lu.se), a feature-rich, fully interactive virtual reality environment for the visualisation and analysis of single-cell experiments that allows researchers to intuitively and collaboratively gain an understanding of their data.

Development of ground experiment system for space end-effector capturing the floating target in 3-dimensional space

2015 ◽  
Vol 42 (4) ◽  
pp. 347-358 ◽  
Author(s):  
Haitao Yang ◽  
Zongwu Xie ◽  
Kui Sun ◽  
Xiaoyu Zhao ◽  
Minghe Jin ◽  
...  
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Admittance Control ◽  
End Effector ◽  
Content Type ◽  
Experiment System ◽  
Ground Experiment ◽  
Motion State ◽  
Basic Functions ◽  
Three Dimensional Space

Purpose – The purpose of this paper is to develop a set of ground experiment system to verify the basic functions of space effector and the capturing reliability of space end-effector for the free-floating target payload in the three-dimensional space. The development of ground experiment system for space end-effector is essential and significant, because it costs too much to launch a space robot or other spacecraft and carry out operation tasks in space. Owing to the negligible gravity in space, which is different from that in the ground environment, ground experiment system for space end-effector should have the capability of verifying the basic functions of space effector and the reliability of space end-effector in capturing the free-floating target payload in space. Design/methodology/approach – The ground experiment system for space end-effector mainly adopts the hybrid simulation method, which includes the real hardware experiment and software simulation. To emulate the micro-gravity environment, the contact dynamics simulator is applied to emulating the motion state of the free-floating target payload, while the admittance control is used to realize the “soft” capturing of space end-effector to simulate the real situation in space. Findings – With the gravity compensation, the influence of gravity is almost eliminated and the results meet the requirements of the experiment. In the ground experiment, the admittance control is effective and the actual motion state of space end-effector capturing the target in space can be simulated. The experiment results show that space end-effector can capture the free-floating target payload successfully and hopefully have the ability to capture a free-floating target in space. Originality/value – The system can verify space end-effector capturing the free-floating target payload in three-dimensional space and imitate the motion of space end-effector capturing the free-floating target in space. The system can also be modified and improved for application in the verification of space robot capturing and docking the target, which is valuable for the ground verification of space applications.

Introducing data analytics to the robotic drilling process

2018 ◽  
Vol 45 (3) ◽  
pp. 371-378 ◽  
Author(s):  
Toufik Al Khawli ◽  
Hamza Bendemra ◽  
Muddasar Anwar ◽  
Dewald Swart ◽  
Jorge Dias
Keyword(s):  
Point Cloud ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Data Sets ◽  
Drilling Process ◽  
Data Set ◽  
Content Type ◽  
Robotic Drilling ◽  
Geometric Primitives ◽  
Three Dimensional Space

PurposeThis paper presents a method for extracting the geometric primitives of a circle in a three-dimensional space from a discrete point cloud data set obtained by a laser stripe sensor. This paper aims to first establish a reference frame for the robotic drilling process by detecting the position and orientation of a reference hole on structural parts in a pre-drilling step, and second, to perform quality inspection of the hole in a post-drilling step.Design/methodology/approachThe method is divided into the following steps: a plane is initially fitted on the data by evaluating the principle component analysis using singular value decomposition; the data points or measurements are then rotated around an arbitrary axis using the Rodrigues’ rotation formula such that the normal direction of the estimated plane and thez-axis direction is parallel; the Delaunay triangulation is constructed on the point cloud and the confidence interval is estimated for segmenting the data set located at the circular boundary; and finally, a circular profile is fitted on the extracted set and transformed back to the original position.FindingsThe geometric estimation of the circle in three-dimensional space constitutes of the position of the center, the diameter and the orientation, which is represented by the normal vector of the plane that the circle lives in. The method is applied on both simulated data set with the addition of several noise levels and experimental data sets. The main purpose of both the tests is to quantify the accuracy of the estimated diameter. The results show good accuracy (mean relative error < 1 per cent) and high robustness to noise.Research limitations/implicationsThe proposed method is applied here to estimate the geometric primitives of only one circle (the reference hole). If multiple circles are needed, an addition clustering procedure is required to cluster the segmented data into multiple data sets. Each data set represents a circle. Also, the method does not operate efficiently on a sparse data sets. Dense data are required to cover the hole (at least ten scans to cover the hole diameter).Practical implicationsResearchers and practitioners can integrate this method with several robotic manufacturing applications where high accuracy is required. The extracted position and orientation of the hole are used to minimize the positioning and alignment errors between the mounted tool tip and the workpiece.Originality/valueThe method introduces data analytics for estimating the geometric primitives in the robotic drilling application. The main advantage of the proposed method is to register the top surface of the workpiece with respect to robot base frame with a high accuracy. An accurate workpiece registration is extremely necessary in the lateral direction (identifying where to drill), as well as in the vertical direction (identifying how far to drill).

Categories in emergency decision-making: prototype-based classification

Kybernetes ◽  
2019 ◽  
Vol 49 (2) ◽  
pp. 526-553
Author(s):  
Mei Cai ◽  
Guo Wei ◽  
Jie Cao
Keyword(s):  
Decision Making ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Decision Makers ◽  
Mutual Distance ◽  
Content Type ◽  
Emergency Decision Making ◽  
Emergency Events ◽  
Emergency Decision ◽  
Three Dimensional Space

PurposeThis paper aims to demonstrate how to make emergency decision when decision makers face a complex and turbulent environment that needs quite different decision-making processes from conventional ones. Traditional decision techniques cannot meet the demands of today’s social stability and security.Design/methodology/approachThe main work is to develop an instance-driven classifier for the emergency categories based upon three fuzzy measures: features for an instance, solution for the instance and effect evaluation of the outcome. First, the information collected from the past emergency events is encodes into a prototype model. Second, a three-dimensional space that describes the locations and mutual distance relationships of the emergency events in different emergency prototypes is formulated. Third, for any new emergency event to be classified, the nearest emergency prototype is identified in the three-dimensional space and is classified into that category.FindingsAn instance-driven classifier based on prototype theory helps decision makers to describe emergency concept more clearly. The maximizing deviation model is constructed to determine the optimal relative weights of features according to the characteristics of the new instance, such that every customized feature space maximizes the influence of features shared by members of the category. Comparisons and discusses of the proposed method with other existing methods are given.Practical implicationsTo reduce the affection to economic development, more and more countries have recognized the importance of emergency response solutions as an indispensable activity. In a new emergency instance, it is very challengeable for a decision maker to form a rational and feasible humanitarian aids scheme under the time pressure. After selecting a most suitable prototype, decision makers can learn most relevant experience and lessons in the emergency profile database and generate plan for the new instance. The proposed approach is to effectively make full use of inhomogeneous information in different types of resources and optimize resource allocation.Originality/valueThe combination of instances can reflect different aspects of a prototype. This feature solves the problem of insufficient learning data, which is a significant characteristic of emergency decision-making. It can be seen as a customized classification mechanism, while the previous classifiers always assume key features of a category.

Transformation of 3D object into flat ribbon for RPS additive manufacturing technology

2017 ◽  
Vol 23 (2) ◽  
pp. 273-279 ◽  
Author(s):  
Vyacheslav Shulunov
Keyword(s):  
Additive Manufacturing ◽  
Coordinate System ◽  
Conformal Transformation ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Cartesian Coordinates ◽  
Content Type ◽  
3D Object ◽  
Three Dimensional Space

Purpose This study aims to give a description of conformal transformation Cartesian coordinates into spiral coordinates using the example of roll powder sintering (RPS) additive manufacturing (AM) technology. RPS has several advantages over dominant AM processes currently available in the market. RPS allows accomplishing designs, which are impossible, very expensive and difficult to create by other methods. The technology requires slicing a 3D object with spiral scanning. Design/methodology/approach The paper describes the possibility of accurate 3D object transformation into a flat ribbon by spiral coordinate system. Parameters of conformal transformation are calculated according to the equation of equivalence between (x, y, z) and (l, z) coordinates. Findings As numerical examples show, it is possible to convert three-dimensional space to two-dimensional one if you know the thickness of the spatial layer. The proposed methodology can be used for the transformation of 3D computer-aided design models into 2D strip models. Originality/value In this paper, the author proposes a method of converting Cartesian coordinates into spiral coordinates. Conformal transformation of three-dimensional space to two-dimensional one by use of spiral coordinate system is demonstrated by RPS AM technology, which allows to produce objects with high accuracy.

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