scholarly journals Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot

2018 ◽  
Author(s):  
Juan Antonio Balbuena ◽  
Óscar Alejandro Pérez-Escobar ◽  
Cristina Llopis-Belenguer ◽  
Isabel Blasco-Costa
Keyword(s):  
Recursive Partitioning ◽  
Computational Time ◽  
Ecological Diversity ◽  
Passerine Birds ◽  
Symbiotic Associations ◽  
The Public ◽  
Novel Approach ◽  
Open Issue ◽  
Key Driver ◽  
Global Fit

AbstractSymbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals and nodes that maximize phylogenetic congruence. By means of simulations, we show that the output value produced is inversely proportional to the number and proportion of cospeciation events employed to build simulated tanglegrams. In addition, with time-calibrated trees, Random TaPas is also efficient at distinguishing cospeciation from pseudocospeciation. Random TaPas can handle large tanglegrams in affordable computational time and incorporates phylogenetic uncertainty in the analyses. We demonstrate its application with two real examples: Passerine birds and their feather mites, and orchids and bee pollinators. In both systems, Random TaPas revealed low cophylogenetic signal, but mapping its variation onto the tanglegram pointed to two different coevolutionary processes. We suggest that the recursive partitioning of the tanglegram buffers the effect of phylogenetic nonindependence occurring in current global-fit methods and therefore Random TaPas is more reliable than regular global-fit methods to identify host-symbiont associations that contribute most to cophylogenetic signal. Random TaPas can be implemented in the public-domain statistical software R with scripts provided herein. A User’s Guide is also available at GitHub.

scholarly journals Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot

2020 ◽  
Vol 69 (6) ◽  
pp. 1212-1230
Author(s):  
Juan Antonio Balbuena ◽  
Óscar Alejandro Pérez-Escobar ◽  
Cristina Llopis-Belenguer ◽  
Isabel Blasco-Costa
Keyword(s):  
Recursive Partitioning ◽  
Computational Time ◽  
Ecological Diversity ◽  
Passerine Birds ◽  
Symbiotic Associations ◽  
The Public ◽  
Novel Approach ◽  
Open Issue ◽  
Key Driver ◽  
Global Fit

Abstract Symbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic congruence. By means of simulations, we show that the output value produced is inversely proportional to the number and proportion of cospeciation events employed to build simulated tanglegrams. In addition, with time-calibrated trees, Random TaPas can also distinguish cospeciation from pseudocospeciation. Random TaPas can handle large tanglegrams in affordable computational time and incorporates phylogenetic uncertainty in the analyses. We demonstrate its application with two real examples: passerine birds and their feather mites, and orchids and bee pollinators. In both systems, Random TaPas revealed low cophylogenetic signal, but mapping its variation onto the tanglegram pointed to two different coevolutionary processes. We suggest that the recursive partitioning of the tanglegram buffers the effect of phylogenetic nonindependence occurring in current global-fit methods and therefore Random TaPas is more reliable than regular global-fit methods to identify host–symbiont associations that contribute most to cophylogenetic signal. Random TaPas can be implemented in the public-domain statistical software R with scripts provided herein. A User’s Guide is also available at GitHub.[Codiversification; coevolution; cophylogenetic signal; Symbiosis.]

Public Involvement in the Design of Public Projects

2019 ◽  
Vol 44 (4) ◽  
pp. 73-79
Author(s):  
Emad S. Mushtaha ◽  
Omar Hassan Omar ◽  
Dua S. Barakat ◽  
Hessa Al-Jarwan ◽  
Dima Abdulrahman ◽  
...  
Keyword(s):  
Decision Making ◽  
Design Process ◽  
Public Involvement ◽  
Decision Making Process ◽  
Quantitative Methodology ◽  
Public Project ◽  
The Public ◽  
Public Projects ◽  
Novel Approach ◽  
Building Program

The involvement of the public in the decision-making process is essential, especially in the early stages of a design process. This study aims to achieve the development of an architectural program for a memorial public project, using the outcomes of the Analytical Hierarchy Process (AHP) based on public opinion. It employs a novel approach that sharply focuses on public involvement in the design process, using a quantitative methodology for the development of a suitable building program and selecting a memorial form that meets the public's needs in a practical way. The study drew on data from various memorial projects to identify possible spaces and their selection criteria. A written questionnaire was distributed to a sample of 105 members of the public, to narrow down the number of spaces according to public response. Then, a hearing (spoken) questionnaire was conducted on a sample of 20 to produce the program for development by generating the most strongly preferred form of memorial. The results contradicted the existing norm for a memorial as a sculpture; it was revealed that most of the public preferred memorial landscapes to buildings and great structures. The study concluded that AHP could be used to further involve the relevant stakeholders in the decision-making process of the design of a public project.

A Novel Approach to Detect Abnormal Chest X-rays of COVID-19 Patients Using Image Processing and Deep Learning

2021 ◽  
pp. 23-41
Author(s):  
Subhagata Chattopadhyay
Keyword(s):  
Mean Squared Error ◽  
Signal To Noise Ratio ◽  
Median Filter ◽  
Hessian Matrix ◽  
Region Of Interest ◽  
Computational Time ◽  
X Rays ◽  
Feed Forward Neural Network ◽  
Novel Approach ◽  
Input Dataset

The study proposes a novel approach to automate classifying Chest X-ray (CXR) images of COVID-19 positive patients. All acquired images have been pre-processed with Simple Median Filter (SMF) and Gaussian Filter (GF) with kernel size (5, 5). The better filter is then identified by comparing Mean Squared Error (MSE) and Peak Signal-to-Noise Ratio (PSNR) of denoised images. Canny's edge detection has been applied to find the Region of Interest (ROI) on denoised images. Eigenvalues [-2, 2] of the Hessian matrix (5 × 5) of the ROIs are then extracted, which constitutes the 'input' dataset to the Feed Forward Neural Network (FFNN) classifier, developed in this study. Eighty percent of the data is used for training the said network after 10-fold cross-validation and the performance of the network is tested with the remaining 20% of the data. Finally, validation has been made on another set of 'raw' normal and abnormal CXRs. Precision, Recall, Accuracy, and Computational time complexity (Big(O)) of the classifier are then estimated to examine its performance.

scholarly journals Joint Pedestrian and Body Part Detection via Semantic Relationship Learning

2019 ◽  
Vol 9 (4) ◽  
pp. 752 ◽  
Author(s):  
Junhua Gu ◽  
Chuanxin Lan ◽  
Wenbai Chen ◽  
Hu Han
Keyword(s):  
Pedestrian Detection ◽  
Body Part ◽  
Upper Body ◽  
Whole Body ◽  
Body Parts ◽  
Semantic Relationship ◽  
The Public ◽  
Novel Approach ◽  
In The Wild ◽  
Person Search

While remarkable progress has been made to pedestrian detection in recent years, robust pedestrian detection in the wild e.g., under surveillance scenarios with occlusions, remains a challenging problem. In this paper, we present a novel approach for joint pedestrian and body part detection via semantic relationship learning under unconstrained scenarios. Specifically, we propose a Body Part Indexed Feature (BPIF) representation to encode the semantic relationship between individual body parts (i.e., head, head-shoulder, upper body, and whole body) and highlight per body part features, providing robustness against partial occlusions to the whole body. We also propose an Adaptive Joint Non-Maximum Suppression (AJ-NMS) to replace the original NMS algorithm widely used in object detection, leading to higher precision and recall for detecting overlapped pedestrians. Experimental results on the public-domain CUHK-SYSU Person Search Dataset show that the proposed approach outperforms the state-of-the-art methods for joint pedestrian and body part detection in the wild.

Religion in the EU: Using Modified Public Reason to Define European Human Rights

2009 ◽  
Vol 10 (11) ◽  
pp. 1439-1468 ◽  
Author(s):  
Brian M. Awe
Keyword(s):  
Human Rights ◽  
John Rawls ◽  
Public Reason ◽  
The European Union ◽  
The Public ◽  
Common Value ◽  
Novel Approach ◽  
Dialectical Process ◽  
Comprehensive Doctrines ◽  
The Eu

At the current stage of its evolution, the European Union (“Union” or “EU”) has reached a juncture where many leaders and scholars believe that greater integration is both desirable and necessary. Presumably, a primary method by which greater solidarity and integration can be achieved within the EU is through the public inclusion of common value-laden concepts – as defined through a dialectical process – present within comprehensive doctrines such as religion. To date, however, an effective and inclusive means for utilizing religion in this manner has yet to be formulated. In response, this article takes two prominent paradigms – Jurgen Habermas' intersubjective discourse theory and John Rawls' liberalism – to approach the problem and draws from them a new solution that, while tied to their theoretical underpinnings, is nonetheless a novel approach to achieving greater integration within the Union. Under this new framework, the process of legislatively defining human rights allows the morality common to European comprehensive doctrines – including official and unofficial religions – to bolster the Union's solidarity, legitimacy, and democracy both procedurally and substantively.

Environmental regulations and their effect on innovation and competitiveness in tourism in Barbados, Guyana and Jamaica

2019 ◽  
Vol 11 (2) ◽  
pp. 147-154
Author(s):  
Eritha Olinda Huntley Lewis
Keyword(s):  
Environmental Regulations ◽  
Self Regulation ◽  
Tourism Industry ◽  
Content Type ◽  
Novel Approach ◽  
Key Issues ◽  
Key Driver ◽  
The Caribbean ◽  
Caribbean Tourism ◽  
Effective Use

Purpose This paper aims to explore the need for innovation in Caribbean tourism with stringent (mandatory) environmental regulations as the key driver of the process. It draws examples from three destinations, Barbados, Guyana and Jamaica. Design/methodology/approach This assessment entailed a review of the literature on the key issues. Theories on innovation, regulations and competitiveness were examined in brief. The paper also presents an overview of Caribbean tourism to provide context. Of note is the dearth of information on the drivers of innovation and its effect on the Caribbean tourism industry which was a major limitation of this assessment. Findings The main implication of this review is that it attempts to highlight the need for discourse on the effective use of environmental regulations to influence the behaviour of industry operatives towards achieving sustainable tourism. Within the context of climate change and the threat that this poses to Caribbean tourism, there is the critical need for this discourse. Consideration is also given to the value stringency of regulation since it is theorised that, if applied correctly, this may be the impetus to drive businesses to innovate to be competitive. Originality/value This is a novel approach to the management of the tourism industry which has shown a preference for self-regulation. Given the proposed outcome, the paper advocates mandatory, stringent regulations since self-regulation is a choice left solely to the industry operatives.

scholarly journals Translucent players: Explaining cooperative behavior in social dilemmas

2019 ◽  
Vol 31 (4) ◽  
pp. 371-408
Author(s):  
Valerio Capraro ◽  
Joseph Y Halpern
Keyword(s):  
Prisoner's Dilemma ◽  
Cooperative Behavior ◽  
Prisoner’S Dilemma ◽  
Dominant Strategy ◽  
The Other ◽  
Public Goods Game ◽  
The Public ◽  
Conflict Situations ◽  
Novel Approach ◽  
Equity And Efficiency

In the past few decades, numerous experiments have shown that humans do not always behave so as to maximize their material payoff. Cooperative behavior when noncooperation is a dominant strategy (with respect to the material payoffs) is particularly puzzling. Here we propose a novel approach to explain cooperation, assuming what Halpern and Pass call translucent players. Typically, players are assumed to be opaque, in the sense that a deviation by one player in a normal-form game does not affect the strategies used by other players. However, a player may believe that if he switches from one strategy to another, the fact that he chooses to switch may be visible to the other players. For example, if he chooses to defect in Prisoner’s Dilemma, the other player may sense his guilt. We show that by assuming translucent players, we can recover many of the regularities observed in human behavior in well-studied games such as Prisoner’s Dilemma, Traveler’s Dilemma, Bertrand Competition, and the Public Goods game. The approach can also be extended to take into account a player’s concerns that his social group (or God) may observe his actions. This extension helps explain prosocial behavior in situations in which previous models of social behavior fail to make correct predictions (e.g. conflict situations and situations where there is a trade-off between equity and efficiency).

scholarly journals Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms

2019 ◽  
Vol 35 (24) ◽  
pp. 5146-5154 ◽  
Author(s):  
Joanna Zyla ◽  
Michal Marczyk ◽  
Teresa Domaszewska ◽  
Stefan H E Kaufmann ◽  
Joanna Polanska ◽  
...  
Keyword(s):  
False Positive Rate ◽  
R Package ◽  
Supplementary Information ◽  
Computational Time ◽  
P Value ◽  
Gene Set ◽  
Related Data ◽  
Novel Approach ◽  
Positive Rate ◽  
Real World Datasets

Abstract Motivation Analysis of gene set (GS) enrichment is an essential part of functional omics studies. Here, we complement the established evaluation metrics of GS enrichment algorithms with a novel approach to assess the practical reproducibility of scientific results obtained from GS enrichment tests when applied to related data from different studies. Results We evaluated eight established and one novel algorithm for reproducibility, sensitivity, prioritization, false positive rate and computational time. In addition to eight established algorithms, we also included Coincident Extreme Ranks in Numerical Observations (CERNO), a flexible and fast algorithm based on modified Fisher P-value integration. Using real-world datasets, we demonstrate that CERNO is robust to ranking metrics, as well as sample and GS size. CERNO had the highest reproducibility while remaining sensitive, specific and fast. In the overall ranking Pathway Analysis with Down-weighting of Overlapping Genes, CERNO and over-representation analysis performed best, while CERNO and GeneSetTest scored high in terms of reproducibility. Availability and implementation tmod package implementing the CERNO algorithm is available from CRAN (cran.r-project.org/web/packages/tmod/index.html) and an online implementation can be found at http://tmod.online/. The datasets analyzed in this study are widely available in the KEGGdzPathwaysGEO, KEGGandMetacoreDzPathwaysGEO R package and GEO repository. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Online Spatial and Temporal Calibration for Monocular Direct Visual-Inertial Odometry

Sensors ◽  
2019 ◽  
Vol 19 (10) ◽  
pp. 2273
Author(s):  
Zheyu Feng ◽  
Jianwen Li ◽  
Lundong Zhang ◽  
Chen Chen
Keyword(s):  
Inertial Measurement Unit ◽  
Prior Information ◽  
Measurement Unit ◽  
Online Calibration ◽  
The Public ◽  
Temporal Parameters ◽  
Novel Approach ◽  
Aerial Vehicle ◽  
Feature Based ◽  
Temporal Offset

Owing to the nonlinearity in visual-inertial state estimation, sufficiently accurate initial states, especially the spatial and temporal parameters between IMU (Inertial Measurement Unit) and camera, should be provided to avoid divergence. Moreover, these parameters are required to be calibrated online since they are likely to vary once the mechanical configuration slightly changes. Recently, direct approaches have gained popularity for their better performance than feature-based approaches in little-texture or low-illumination environments, taking advantage of tracking pixels directly. Based on these considerations, we perform a direct version of monocular VIO (Visual-inertial Odometry), and propose a novel approach to initialize the spatial-temporal parameters and estimate them with all other variables of interest (IMU pose, point inverse depth, etc.). We highlight that our approach is able to perform robust and accurate initialization and online calibration for the spatial and temporal parameters without utilizing any prior information, and also achieves high-precision estimates even when large temporal offset occurs. The performance of the proposed approach was verified through the public UAV (Unmanned Aerial Vehicle) dataset.

scholarly journals LANDFILL URBANISM: OPPORTUNISTIC ECOLOGIES, WASTED LANDSCAPES

Detritus ◽  
2020 ◽  
pp. 19-34
Author(s):  
Dan Weissman
Keyword(s):  
Urban Space ◽  
Industrial Ecology ◽  
Distribution Networks ◽  
Conveyor Belt ◽  
Scrap Metal ◽  
The Public ◽  
Novel Approach ◽  
Policy Measures ◽  
Increasing Demand ◽  
Interdependent Relationships

"As a child, my father would take my brother and I to the local junkyard. We’d watch, amazed, as the compressor squashed our waste into a dumpster, then scavenge through piles of scrap metal and climb gigantic wheeled Caterpillar earthmovers". For better or worse, this archetypal junkyard has given way to massively controlled spaces of waste disposal. Today, continuously increasing demand for material coupled with a culture of disposability, has coincided with heightened policy measures restricting landfill development. We have a crisis of waste management. Meanwhile, as landfilling has grown from a localized phenomenon into a regional set of distribution networks, neo-industrialization is emerging throughout the Great Lakes megaregion, suggesting new opportunities for re-territorialization of wasted landscapes. This project posits that extraction of existing landfill sites for material and energy is inevitable. Landfill Urbanism suggests that the act of landfill mining, a contentious and stinky proposition, has the capacity to foster a localized, robust industrial ecology, while also recasting the public’s relationship with our waste through tactical deployment of architecture and urban space-making. Directed Robotic Trash Extractors (DRT-E) exhume and cultivate material, as the project’s conveyor-belt infrastructure allows individuals, cooperatives and corporations to safely sort and collect based on their needs: a novel approach to accessing our 21st century resource. By allowing complete engagement with the public, Landfill Urbanism fosters productive interdependent relationships between consumers, as well as offering to its users a series of spectacular didactic, practical, and recreational experiences. Where the public of today consumes, the public of Landfill Urbanism harvests.

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