scholarly journals Challenges in Identifying and Interpreting Organizational Modules in Morphology

2017 ◽  
Author(s):  
Borja Esteve-Altava
Keyword(s):  
Complete Analysis ◽  
Mathematical Framework ◽  
Body Parts ◽  
Organizational Modularity ◽  
Generative Processes ◽  
Variational Modularity ◽  
Possible Cause ◽  
Potential Use ◽  
New Framework ◽  
Anatomical Network Analysis

AbstractForm is a rich concept that agglutinates information about the proportions and topological arrangement of body parts. Modularity is readily observable in both the variation of proportions (variational modules) and the organization of topology (organizational modules). The study of variational modularity and of organizational modularity faces similar challenges regarding the identification of meaningful modules and the validation of generative processes; however, most studies in morphology focus solely on variational modularity, while organizational modularity is much less understood. A possible cause for this bias is the successful development in the last twenty years of morphometrics, and specially geometric morphometrics, to study patters of variation. This contrasts with the lack of a similar mathematical framework to deal with patterns of organization. Recently, a new mathematical framework has been proposed to study the organization of anatomical parts using tools from Network Theory, so-called anatomical network analysis. This essay explores the potential use of this new framework – and the challenges it faces in identifying and validating biologically meaningful modules in morphological systems –, by providing an example of a complete analysis of modularity of the human skull and upper limb. Finally, we suggest further directions of research that may bridge the gap between variational and organizational modularity studies.

scholarly journals Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits

2019 ◽  
Vol 68 (5) ◽  
pp. 698-716 ◽  
Author(s):  
Sergei Tarasov
Keyword(s):  
Regulatory Networks ◽  
Markov Models ◽  
Phylogenetic Inference ◽  
Phenotypic Traits ◽  
Character State ◽  
Body Parts ◽  
Ancestral Character State ◽  
State Models ◽  
Hidden States ◽  
New Framework

Abstract Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes—hierarchical and hidden—which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks (GRNs) underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models (SMM) equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of SMM with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of GRNs and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing “tail color problem,” in which the trait is scored for species with tails of different colors or no tails. It also presents a previously unknown issue called the “two-scientist paradox,” in which the nature of coding the trait and the hidden processes driving the trait’s evolution are confounded; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This article gives practical examples of using the new framework for phylogenetic inference and comparative analysis.

Investigating Predictive Metamodeling for Additive Manufacturing

2016 ◽  
Author(s):  
Zhuo Yang ◽  
Douglas Eddy ◽  
Sundar Krishnamurty ◽  
Ian Grosse ◽  
Peter Denno ◽  
...  
Keyword(s):  
Additive Manufacturing ◽  
Welding Process ◽  
Disruptive Technology ◽  
Mathematical Framework ◽  
Future Directions ◽  
Process Plans ◽  
Complex Relationships ◽  
Physical Phenomena ◽  
Potential Use

Additive manufacturing (AM) is a new and disruptive technology that comes with a set of unique challenges. One of them is the lack of understanding of the complex relationships between the numerous physical phenomena occurring in these processes. Metamodels can be used to provide a simplified mathematical framework for capturing the behavior of such complex systems. At the same time, they offer a reusable and composable paradigm to study, analyze, diagnose, forecast, and design AM parts and process plans. Training a metamodel requires a large number of experiments and even more so in AM due to the various process parameters involved. To address this challenge, this work analyzes and prescribes metamodeling techniques to select optimal sample points, construct and update metamodels, and test them for specific and isolated physical phenomena. A simplified case study of two different laser welding process experiments is presented to illustrate the potential use of these concepts. We conclude with a discussion on potential future directions, such as data and model integration while also accounting for sources of uncertainty.

scholarly journals LOW-COST 3D DEVICES AND LASER SCANNERS COMPARISON FOR THE APPLICATION IN ORTHOPEDIC CENTRES

2018 ◽  
Vol XLII-2 ◽  
pp. 953-960 ◽  
Author(s):  
D. F. Redaelli ◽  
S. Gonizzi Barsanti ◽  
P. Fraschini ◽  
E. Biffi ◽  
G. Colombo
Keyword(s):  
Human Body ◽  
Low Cost ◽  
Complete Analysis ◽  
Body Parts ◽  
3D Data ◽  
Starting Point ◽  
Laser Scanners ◽  
Good Starting Point ◽  
Structure Sensor ◽  
Test Objects

Low-cost 3D sensors are nowadays widely diffused and many different solutions are available on the market. Some of these devices were developed for entertaining purposes, but are used also for acquisition and processing of different 3D data with the aim of documentation, research and study. Given the fact that these sensors were not developed for this purpose, it is necessary to evaluate their use in the capturing process. This paper shows a preliminary research comparing the Kinect 1 and 2 by Microsoft, the Structure Sensor by Occipital and the O&P Scan by Rodin4D in a medical scenario (i.e. human body scans). In particular, these sensors were compared to Minolta Vivid 9i, chosen as reference because of its higher accuracy. Different test objects were analysed: a calibrated flat plane, for the evaluation of the systematic distance error for each device, and three different parts of a mannequin, used as samples of human body parts. The results showed that the use of a certified flat plane is a good starting point in characterizing the sensors, but a complete analysis with objects similar to the ones of the real context of application is required. For example, the Kinect 2 presented the best results among the low-cost sensors on the flat plane, while the Structure Sensor was more reliable on the mannequin parts.

Retooling our anti-corruption arsenals: exploring the potential use of CAQDAS in corruption investigation

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Hendi Yogi Prabowo
Keyword(s):  
Computer Assisted ◽  
Content Type ◽  
New Perspective ◽  
Qualitative Data Analysis Software ◽  
Analytical Tools ◽  
Investigation Process ◽  
Practical Implications ◽  
Potential Use ◽  
New Framework

Purpose This paper aims to explore the potential of computer-assisted qualitative data analysis software (CAQDAS) to be used as a corruption investigation tool to help investigators in carrying out their investigative works. Design/methodology/approach By reviewing the literature on qualitative research and fraud investigation, this exploratory study identifies similarities between the two types of inquiries and thus proposing the use of CAQDAS as an innovation in the field of corruption investigation. To demonstrate how a QDA application can support corruption investigators, NVivo is used as a case study from which various key analytical tools are discussed to highlight their potential in supporting a corruption investigation. Findings As a fundamental part of anti-corruption practice in a country, corruption investigation must be planned and executed professionally and adequately. This paper highlights various stages in fraud investigation to identify areas that can be improved with the use of a CAQDAS. Based on the discussion in this paper, the author concludes that the capability of a CAQDAS to assist users in data reduction and data display has the potential to increase the effectiveness and efficiency in various stages of a corruption investigation. Research limitations/implications Based on a self-funded study, this paper only uses a simulation case with a fictitious company to illustrate how a CAQDAS application can be used to support a corruption investigation process. Future studies may benefit from using actual corruption cases in illustrating how such an application can support the investigation process. Practical implications This paper contributes to the innovation in anti-corruption practice by proposing a new framework and tool to develop corruption investigation capacity. Originality/value This paper brings a new perspective into the field of anti-corruption to stimulate innovation in the area of corruption investigation.

scholarly journals Integration of anatomy ontologies and evo-devo using structured Markov models suggests a new framework for modeling discrete phenotypic traits

2017 ◽  
Author(s):  
Sergei Tarasov
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Markov Models ◽  
Phylogenetic Inference ◽  
Phenotypic Traits ◽  
Character State ◽  
Body Parts ◽  
Gene Regulatory ◽  
Hidden States ◽  
New Framework

AbstractModeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes – hierarchical and hidden – which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of structured Markov models with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of gene regulatory networks and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing tail color problem (that aims at coding tail when it is absent) and presents a previously unknown issue called the “two-scientist paradox”. The latter issue refers to the confounding nature of the coding of a trait and the hidden processes driving the trait’s evolution; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This paper gives practical examples of using the new framework for phylogenetic inference and comparative analysis.

scholarly journals Probiotic Characterization and Population Diversity Analysis of Gut-Associated Pediococcus acidilactici for Its Potential Use in the Dairy Industry

2021 ◽  
Vol 11 (20) ◽  
pp. 9586
Author(s):  
Hafsa Kanwal ◽  
Alessandro Di Cerbo ◽  
Freeha Zulfiqar ◽  
Carla Sabia ◽  
Amara Nawaz ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Starter Culture ◽  
Dairy Industry ◽  
Population Diversity ◽  
Complete Analysis ◽  
Diffusion Method ◽  
Optimal Dosage ◽  
Diversity Analysis ◽  
Pediococcus Acidilactici ◽  
Potential Use

In recent years, gut-tailored probiotics have been proven to be beneficial for host health. Probiotic strains such as lactic acid bacteria (LAB) are known to exhibit antimicrobial activity, acting as natural substitutes for the regulation of foodborne pathogens. In the present study, a complete analysis, isolation, biochemical characterization, and molecular identification of Pediococcus acidilactici (NMCC-11) from Nili Ravi water buffalo (Bubalis bubalis) gut was carried out. NMCC-11 showed the best enzymatic potential, antimicrobial activity against known pathogenic strains, and survivability at a wide pH range (pH 4–pH 6) out of all isolates. The isolates were screened for their antimicrobial activity against the five most infectious microbes such as Escherichia coli (ATCC 8739), Pseudomonas aeruginosa (ATCC9027), Staphylococcus aureus (ATCC6538), Listeria monocytogenes (ATCC13932), and Bacillus cereus (ATCC 11778) using the agar-well diffusion method. Moreover, after NMCC-11 isolation, a comparative diversity analysis against a variety of other randomly selected strains from around the world was carried out using R software. This study showed relatively low genetic diversity, which also contributed to the claim of the stability of this probiotic strain and its potential use as a starter culture and feed probiotic in the dairy industry. However, further studies are certainly warranted to determine its optimal dosage, time frame, and intake frequency.

scholarly journals SyncUp

2021 ◽  
Vol 5 (3) ◽  
pp. 1-25
Author(s):  
Zhongyi Zhou ◽  
Anran Xu ◽  
Koji Yatani
Keyword(s):  
User Evaluation ◽  
Body Parts ◽  
Body Movements ◽  
Temporal Alignment ◽  
Similarity Estimation ◽  
Manual Inspection ◽  
Interactive Visualizations ◽  
Practice Standard ◽  
Potential Use

The beauty of synchronized dancing lies in the synchronization of body movements among multiple dancers. While dancers utilize camera recordings for their practice, standard video interfaces do not efficiently support their activities of identifying segments where they are not well synchronized. This thus fails to close a tight loop of an iterative practice process (i.e., capturing a practice, reviewing the video, and practicing again). We present SyncUp, a system that provides multiple interactive visualizations to support the practice of synchronized dancing and liberate users from manual inspection of recorded practice videos. By analyzing videos uploaded by users, SyncUp quantifies two aspects of synchronization in dancing: pose similarity among multiple dancers and temporal alignment of their movements. The system then highlights which body parts and which portions of the dance routine require further practice to achieve better synchronization. The results of our system evaluations show that our pose similarity estimation and temporal alignment predictions were correlated well with human ratings. Participants in our qualitative user evaluation expressed the benefits and its potential use of SyncUp, confirming that it would enable quick iterative practice.

LPCD framework: Analytical tool or psychological model?

2018 ◽  
Vol 41 ◽  
Author(s):  
David Danks
Keyword(s):  
Decision Making ◽  
Analytical Tool ◽  
Mathematical Framework ◽  
Bayesian Decision ◽  
Perceptual Decision Making ◽  
Psychological Model ◽  
Psychological Reality ◽  
Psychological Theories ◽  
Target Article ◽  
Bayesian Decision Making

AbstractThe target article uses a mathematical framework derived from Bayesian decision making to demonstrate suboptimal decision making but then attributes psychological reality to the framework components. Rahnev & Denison's (R&D) positive proposal thus risks ignoring plausible psychological theories that could implement complex perceptual decision making. We must be careful not to slide from success with an analytical tool to the reality of the tool components.

The growth of mica polytypes as studied by conventional and high-resolution TEM

1983 ◽  
Vol 41 ◽  
pp. 174-177
Author(s):  
A. Baronnet ◽  
M. Amouric
Keyword(s):  
Water Pressure ◽  
Point Of View ◽  
Temperature Fields ◽  
Natural Occurrence ◽  
Growth Mechanisms ◽  
Long Period ◽  
High Resolution Tem ◽  
Layer Stacking ◽  
Experimental Works ◽  
Potential Use

The origin of mica polytypes has long been a challenging problem for crystal- lographers, mineralogists and petrologists. From the petrological point of view, interest in this field arose from the potential use of layer stacking data to furnish further informations about equilibrium and/or kinetic conditions prevailing during the crystallization of the widespread mica-bearing rocks. From the compilation of previous experimental works dealing with the occurrence domains of the various mica "polymorphs" (1Mr, 1M, 2M1, 2M2 and 3T) within water-pressure vs temperature fields, it became clear that most of these modifications should be considered as metastable for a fixed mica species. Furthermore, the natural occurrence of long-period (or complex) polytypes could not be accounted for by phase considerations. This highlighted the need of a more detailed kinetic approach of the problem and, in particular, of the role growth mechanisms of basal faces could play in this crystallographic phenomenon.

An atomic-resolution microscope study of Al contracts on GaAs

1986 ◽  
Vol 44 ◽  
pp. 726-727
Author(s):  
Z. Liliental-Weber ◽  
C. Nelson ◽  
R. Ludeke ◽  
R. Gronsky ◽  
J. Washburn
Keyword(s):  
High Speed ◽  
Schottky Contacts ◽  
Detailed Knowledge ◽  
The Past ◽  
Semiconductor Interfaces ◽  
Deposited Metal ◽  
Microwave Applications ◽  
Free Interfaces ◽  
Potential Use

The properties of metal/semiconductor interfaces have received considerable attention over the past few years, and the Al/GaAs system is of special interest because of its potential use in high-speed logic integrated optics, and microwave applications. For such materials a detailed knowledge of the geometric and electronic structure of the interface is fundamental to an understanding of the electrical properties of the contact. It is well known that the properties of Schottky contacts are established within a few atomic layers of the deposited metal. Therefore surface contamination can play a significant role. A method for fabricating contamination-free interfaces is absolutely necessary for reproducible properties, and molecularbeam epitaxy (MBE) offers such advantages for in-situ metal deposition under UHV conditions

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