scholarly journals A General Framework for Representing and Annotating Multifaceted Cell Heterogeneity in Human Cell Atlas

2021 ◽  
Author(s):  
Haoxiang Gao ◽  
Kui Hua ◽  
Sijie Chen ◽  
Qijin Yin ◽  
Rui Jiang ◽  
...  
Keyword(s):  
Coordinate System ◽  
Human Cell ◽  
Dimensional Space ◽  
Hierarchical Structures ◽  
The Body ◽  
External Information ◽  
Cell Heterogeneity ◽  
Gene Expressions ◽  
Healthy Human ◽  
Molecular Features

AbstractThe goal of big projects like Human Cell Atlas (HCA) and Human BioMedical Atlas Program (HuBMAP) is to build maps that comprehensively define and describe all cell types and their molecular features in a healthy human being. Just like geographical maps must have coordinates, a key task in building cell maps is to provide coordinate systems for cells. A well-designed coordinate system helps better understand the highly orchestrated function and organization of different cells. Cells could be depicted by external information like their spatial locations in the body and organ, the sex and race of the donor, and multiple endogenous attributes of cells such as their types, states, functions, developing trajectory, etc. These heterogeneities are encoded in or can be predicted with transcriptomics and other omics data. Cell heterogeneities are multifaceted, including three major types: continuous values or scores, categorical groups and structured annotations. Here we propose to a unified multidimensional coordinate system UniCoord to represent the multifaceted heterogeneities of cells. It is based on a general deep learning framework, with a supervised VAE structure to learn the mapping relationship between gene expressions and the generated coordinates in a low-dimensional space that encode multiple cell attributes of the three types. Experiment results on several datasets showed that UniCoord was able to represent a variety of cell heterogeneous properties that are discrete, continuous or of hierarchical structures. The trained UniCoord model can be used to automatically label attributes of cells and generate the corresponding expression data. Experiments showed that UniCoord is a feasible coordinates framework for representing multifaceted cell heterogeneity in comprehensive cell atlases.

Flight performance and visual control of flight of the free-flying housefly ( Musca domestica L.) I. Organization of the flight motor

1986 ◽  
Vol 312 (1158) ◽  
pp. 527-551 ◽  
Keyword(s):  
Coordinate System ◽  
Degrees Of Freedom ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Rigid Bodies ◽  
The Body ◽  
Midsagittal Plane ◽  
Torque Vector ◽  
Translation Velocity ◽  
Flight Motor

Free-flying houseflies have been filmed simultaneously from two sides. The orientation of the flies’ body axes in three-dimensional space can be seen on the films. A method is presented for the reconstruction of the flies’ movements in a fly-centred coordinate system, relative to an external coordinate system and relative to the airstream. The flies are regarded as three-dimensionally rigid bodies. They move with respect to the six degrees of freedom they thus possess. The analysis of the organization of the flight motor from the kinematic data leads to the following conclusions: the sideways movements can, at least qualitatively, be explained by taking into account the sideways forces resulting from rolling the body about the long axis and the influence of inertia. Thus, the force vector generated by the flight motor is most probably located in the fly’s midsagittal plane. The direction of this vector can be varied by the fly in a restricted range only. In contrast, the direction of the torque vector can be freely adjusted by the fly. No coupling between the motor force and the torques is indicated. Changes of flight direction may be explained by changes in the orientation of the body axes: straight flight at an angle of sideslip differing from zero is due to rolling. Sideways motion during the banked turns as well as the decrease of translation velocity observed in curves are a consequence of the inertial forces and rolling. The results are discussed with reference to studies about the aerodynamic performance of insects and the constraints for aerial pursuit.

scholarly journals Zur exakten Behandlung von kollektiven Rotationen Teil A: Theorie / On the Exact Treatment of Collective Rotations Part A: Theory

1973 ◽  
Vol 28 (2) ◽  
pp. 206-215
Author(s):  
Hanns Ruder
Keyword(s):  
Coordinate System ◽  
Perturbation Expansion ◽  
Rotational Energy ◽  
The Body ◽  
System A ◽  
N Body Problem ◽  
Definition Of ◽  
Fixed System ◽  
Body Fixed Coordinate System ◽  
Groundstate Energy

Basic in the treatment of collective rotations is the definition of a body-fixed coordinate system. A kinematical method is derived to obtain the Hamiltonian of a n-body problem for a given definition of the body-fixed system. From this exact Hamiltonian, a consequent perturbation expansion in terms of the total angular momentum leads to two exact expressions: one for the collective rotational energy which has to be added to the groundstate energy in this order of perturbation and a second one for the effective inertia tensor in the groundstate. The discussion of these results leads to two criteria how to define the best body-fixed coordinate system, namely a differential equation and a variational principle. The equivalence of both is shown.

Medicine: Experimentation, Politics, Emergent Bodies

2012 ◽  
Vol 18 (3-4) ◽  
pp. 1-17 ◽  
Author(s):  
Mike Michael ◽  
Marsha Rosengarten
Keyword(s):  
Public Health Policy ◽  
Science And Technology Studies ◽  
Controlled Trial ◽  
Judith Butler ◽  
The Body ◽  
The Political ◽  
Medical Evidence ◽  
Special Issue ◽  
Healthy Human ◽  
Randomized Controlled

In this introduction, we address some of the complexities associated with the emergence of medicine’s bodies, not least as a means to ‘working with the body’ rather than simply producing a critique of medicine. We provide a brief review of some of the recent discussions on how to conceive of medicine and its bodies, noting the increasing attention now given to medicine as a technology or series of technologies active in constituting a multiplicity of entities – bodies, diseases, experimental objects, the individualization of responsibility for health and even the precarity of life. We contrast what feminist theorists in the tradition of Judith Butler have referred to as the question of matter, and Science and Technology Studies with its focus on practice and the nature of emergence. As such we address tensions that exist in analyses of the ontological status of ‘the body’ – human and non-human – as it is enacted in the work of the laboratory, the randomized controlled trial, public health policy and, indeed, the market that is so frequently entangled with these spaces. In keeping with the recent turns toward ontology and affect, we suggest that we can regard medicine as concerned with the contraction and reconfiguration of the body’s capacities to affect and be affected, in order to allow for the subsequent proliferation of affects that, according to Bruno Latour, marks corporeal life. Treating both contraction and proliferation circumspectly, we focus on the patterns of affects wrought in particular by the abstractions of medicine that are described in the contributions to this special issue. Drawing on the work of A.N. Whitehead, we note how abstractions such as ‘medical evidence’, the ‘healthy human body’ or the ‘animal model’ are at once realized and undercut, mediated and resisted through the situated practices that eventuate medicine’s bodies. Along the way, we touch on the implications of this sort of perspective for addressing the distribution of agency and formulations of the ethical and the political in the medical eventuations of bodies.

scholarly journals Computation of electrostatic fields in anisotropic human tissues using the Finite Integration Technique (FIT)

2005 ◽  
Vol 2 ◽  
pp. 309-313 ◽  
Author(s):  
V. C. Motresc ◽  
U. van Rienen
Keyword(s):  
Coordinate System ◽  
Electromagnetic Fields ◽  
Human Body ◽  
Local Coordinate System ◽  
Anisotropic Materials ◽  
The Body ◽  
Integration Technique ◽  
Data Set ◽  
Computer Data ◽  
Finite Integration Technique

Abstract. The exposure of human body to electromagnetic fields has in the recent years become a matter of great interest for scientists working in the area of biology and biomedicine. Due to the difficulty of performing measurements, accurate models of the human body, in the form of a computer data set, are used for computations of the fields inside the body by employing numerical methods such as the method used for our calculations, namely the Finite Integration Technique (FIT). A fact that has to be taken into account when computing electromagnetic fields in the human body is that some tissue classes, i.e. cardiac and skeletal muscles, have higher electrical conductivity and permittivity along fibers rather than across them. This property leads to diagonal conductivity and permittivity tensors only when expressing them in a local coordinate system while in a global coordinate system they become full tensors. The Finite Integration Technique (FIT) in its classical form can handle diagonally anisotropic materials quite effectively but it needed an extension for handling fully anisotropic materials. New electric voltages were placed on the grid and a new averaging method of conductivity and permittivity on the grid was found. In this paper, we present results from electrostatic computations performed with the extended version of FIT for fully anisotropic materials.

scholarly journals How visual experience and task context modulate the use of internal and external spatial coordinate for perception and action

2018 ◽  
Author(s):  
Virginie Crollen ◽  
Tiffany Spruyt ◽  
Pierre Mahau ◽  
Roberto Bottini ◽  
Olivier Collignon
Keyword(s):  
Coordinate System ◽  
Visual Experience ◽  
Simon Task ◽  
Frame Of Reference ◽  
The Body ◽  
Blind People ◽  
Coordinate Systems ◽  
Task Instructions ◽  
Congenitally Blind ◽  
External Frame

Recent studies proposed that the use of internal and external coordinate systems may be more flexible in congenitally blind when compared to sighted individuals. To investigate this hypothesis further, we asked congenitally blind and sighted people to perform, with the hands uncrossed and crossed over the body midline, a tactile TOJ and an auditory Simon task. Crucially, both tasks were carried out under task instructions either favoring the use of an internal (left vs. right hand) or an external (left vs. right hemispace) frame of reference. In the internal condition of the TOJ task, our results replicated previous findings (Röder et al., 2004) showing that hand crossing only impaired sighted participants’ performance, suggesting that blind people did not activate by default a (conflicting) external frame of reference. However, under external instructions, a decrease of performance was observed in both groups, suggesting that even blind people activated an external coordinate system in this condition. In the Simon task, and in contrast with a previous study (Roder et al., 2007), both groups responded more efficiently when the sound was presented from the same side of the response (‘‘Simon effect’’) independently of the hands position. This was true under the internal and external conditions, therefore suggesting that blind and sighted by default activated an external coordinate system in this task. All together, these data comprehensively demonstrate how visual experience shapes the default weight attributed to internal and external coordinate systems for action and perception depending on task demand.

scholarly journals A microarray gene expressions with classification using extreme learning machine

Genetika ◽  
2015 ◽  
Vol 47 (2) ◽  
pp. 523-534
Author(s):  
M. Yasodha ◽  
P. Ponmuthuramalingam
Keyword(s):  
Extreme Learning Machine ◽  
High Speed ◽  
Dna Microarrays ◽  
Research Work ◽  
The Body ◽  
Cancer Classification ◽  
Medical Sciences ◽  
Gene Expressions ◽  
Learning Machine ◽  
Elm Classifier

In the present scenario, one of the dangerous disease is cancer. It spreads through blood or lymph to other location of the body, it is a set of cells display uncontrolled growth, attack and destroy nearby tissues, and occasionally metastasis. In cancer diagnosis and molecular biology, a utilized effective tool is DNA microarrays. The dominance of this technique is recognized, so several open doubt arise regarding proper examination of microarray data. In the field of medical sciences, multicategory cancer classification plays very important role. The need for cancer classification has become essential because the number of cancer sufferers is increasing. In this research work, to overcome problems of multicategory cancer classification an improved Extreme Learning Machine (ELM) classifier is used. It rectify problems faced by iterative learning methods such as local minima, improper learning rate and over fitting and the training completes with high speed.

Rolling Condition and Gyroscopic Moments in Curve Negotiations

2012 ◽  
Author(s):  
Ahmed A. Shabana ◽  
Martin B. Hamper ◽  
James J. O’Shea
Keyword(s):  
Coordinate System ◽  
Degrees Of Freedom ◽  
The Body ◽  
Contact Forces ◽  
Body Motion ◽  
Global Coordinate System ◽  
Gyroscopic Moment ◽  
Absolute Angular Velocity ◽  
Pure Rolling ◽  
The Stability

In vehicle system dynamics, the effect of the gyroscopic moments can be significant during curve negotiations. The absolute angular velocity of the body can be expressed as the sum of two vectors; one vector is due to the curvature of the curve, while the second vector is due to the rate of changes of the angles that define the orientation of the body with respect to a coordinate system that follows the body motion. In this paper, the configuration of the body in the global coordinate system is defined using the trajectory coordinates in order to examine the effect of the gyroscopic moments in the case of curve negotiations. These coordinates consist of arc length, two relative translations and three relative angles. The relative translations and relative angles are defined with respect to a trajectory coordinate system that follows the motion of the body on the curve. It is shown that when the yaw and roll angles relative to the trajectory coordinate system are constrained and the motion is predominantly rolling, the effect of the gyroscopic moment on the motion becomes negligible, and in the case of pure rolling and zero yaw and roll angles, the generalized gyroscopic moment associated with the system degrees of freedom becomes identically zero. The analysis presented in this investigation sheds light on the danger of using derailment criteria that are not obtained using laws of motion, and therefore, such criteria should not be used in judging the stability of railroad vehicle systems. Furthermore, The analysis presented in this paper shows that the roll moment which can have a significant effect on the wheel/rail contact forces depends on the forward velocity in the case of curve negotiations. For this reason, roller rigs that do not allow for the wheelset forward velocity cannot capture these moment components, and therefore, cannot be used in the analysis of curve negotiations. A model of a suspended railroad wheelset is used in this investigation to study the gyroscopic effect during curve negotiations.

Neuromuscular transmission in the jellyfish Aglantha digitale

1985 ◽  
Vol 116 (1) ◽  
pp. 1-25 ◽  
Author(s):  
P. A. Kerfoot ◽  
G. O. Mackie ◽  
R. W. Meech ◽  
A. Roberts ◽  
C. L. Singla
Keyword(s):  
Dimensional Space ◽  
Thin Sheet ◽  
Current Source ◽  
Giant Axon ◽  
The Body ◽  
Two Dimensional ◽  
Bathing Medium ◽  
Giant Axons ◽  
Motor Neurones ◽  
Stimulation Of

In the jellyfish Aglantha digitale escape swimming is mediated by the nearly synchronous activity of eight giant motor axons which make direct synaptic contact with contractile myoepithelial cells on the under-surface of the body wall. The delay in transmission at these synapses was 0.7 +/− 0.1 ms (+/− S.D.;N = 6) at 12 degrees C as measured from intracellular records. Transmission depended on the presence of Ca2+ in the bathing medium. It was not blocked by increasing the level of Mg2+ to 127 mmol l-1. The myoepithelium is a thin sheet of electrically coupled cells and injection of current at one point was found to depolarize the surrounding cells. The potential change declined with distance from the current source as expected for two-dimensional current spread. The two-dimensional space constant (lambda) was 770 micron for current flow in the circular direction and 177 micron for radial flow. The internal resistance of the epithelium (178–201 omega cm) and the membrane time constant (5–10 ms) were direction independent. No propagated epithelial action potentials were observed. Spontaneous miniature synaptic potentials of similar amplitude and rise-time were recorded intracellularly at distances of up to 1 mm from the motor giant axon. Ultrastructural evidence confirms that neuro-myoepithelial synapses also occur away from the giant axons. It is likely that synaptic sites are widespread in the myoepithelium, probably associated with the lateral motor neurones as well as the giant axons. Local stimulation of lateral motor neurones generally produced contraction in distinct fields. We suppose that stimulation of a single motor giant axon excites a whole population of lateral motor neurones and hence a broad area of the myoepithelium.

Soft Subspace Clustering for Cancer Microarray Data Analysis

2014 ◽  
pp. 131-145
Author(s):  
Natthakan Iam-On ◽  
Tossapon Boongoen
Keyword(s):  
Microarray Data ◽  
Dimensional Space ◽  
Subspace Clustering ◽  
Research Direction ◽  
Microarray Data Analysis ◽  
Consensus Clustering ◽  
Gene Expressions ◽  
Tumor Subtypes ◽  
Microarray Gene ◽  
New Research

A need has long been identified for a more effective methodology to understand, prevent, and cure cancer. Microarray technology provides a basis of achieving this goal, with cluster analysis of gene expression data leading to the discrimination of patients, identification of possible tumor subtypes, and individualized treatment. Recently, soft subspace clustering was introduced as an accurate alternative to conventional techniques. This practice has proven effective for high dimensional data, especially for microarray gene expressions. In this review, the basis of weighted dimensional space and different approaches to soft subspace clustering are described. Since most of the models are parameterized, the application of consensus clustering has been identified as a new research direction that is capable of turning the difficulty with parameter selection to an advantage of increasing diversity within an ensemble.

Sign in / Sign up

Export Citation Format

Share Document