scholarly journals Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies

2021 ◽  
Author(s):  
Qiqing Tao ◽  
Jose Barba-Montoya ◽  
Sudhir Kumar
Keyword(s):  
Data Driven ◽  
Species Divergence ◽  
Simple Method ◽  
Empirical Bayesian ◽  
Practical Applications ◽  
Accuracy And Precision ◽  
Fossil Records ◽  
Age Estimates ◽  
Birth Death

AbstractMotivationPrecise time calibrations needed to estimate ages of species divergence are not always available due to fossil records’ incompleteness. Consequently, clock calibrations available for Bayesian dating analyses can be few and diffused, i.e., phylogenies are calibration-poor, impeding reliable inference of the timetree of life. We examined the role of speciation birth-death tree prior on Bayesian node age estimates in calibration-poor phylogenies and tested the usefulness of an informative, data-driven tree prior to enhancing the accuracy and precision of estimated times.ResultsWe present a simple method to estimate parameters of the birth-death tree prior from the molecular phylogeny for use in Bayesian dating analyses. The use of a data-driven birth-death (ddBD) tree prior leads to improvement in Bayesian node age estimates for calibration-poor phylogenies. We show that the ddBD tree prior, along with only a few well-constrained calibrations, can produce excellent node ages and credibility intervals, whereas the use of an uninformative, uniform (flat) tree prior may require more calibrations. Relaxed clock dating with ddBD tree prior also produced better results than a flat tree prior when using diffused node calibrations. We also suggest using ddBD tree priors to improve the detection of outliers and influential calibrations in cross-validation analyses.ConclusionEmpirical Bayesian dating analyses with ddBD tree priors enable more accurate and precise node age estimates for calibration-poor phylogenies. Our results have practical applications because the ddBD tree prior reduces the number of well-constrained calibrations necessary to obtain reliable node age estimates. This would help address key impediments in building the grand timetree of life, revealing the process of speciation, and elucidating the dynamics of biological diversification.AvailabilityAn R module for computing the ddBD tree prior, simulated datasets, and empirical datasets are available at https://github.com/cathyqqtao/ddBD-tree-prior.

scholarly journals A Simple Method to Reduce Interpretation Error of Ages Estimated from Otoliths

2016 ◽  
Vol 9 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Bradley J. Smith ◽  
Daniel J. Dembkowski ◽  
Daniel A. James ◽  
Melissa R. Wuellner
Keyword(s):  
Age Estimation ◽  
Smallmouth Bass ◽  
Alternative Methods ◽  
Micropterus Dolomieu ◽  
Viable Option ◽  
Simple Method ◽  
Alternative Method ◽  
Accuracy And Precision ◽  
Coefficients Of Variation ◽  
Age Estimates

We designed and tested a novel otolith viewing apparatus termed the otolith illumination device (OID) to ascertain if its use would result in a reduction of interpretation error as determined by increased precision of age estimates obtained from otoliths of walleye Sander vitreus and smallmouth bass Micropterus dolomieu. Clarity of annuli on otolith sections viewed with the OID was generally greater than clarity of annuli on sections viewed with an alternative method. OID-based age estimates were equally as, and in some instance more precise than ages estimated using the alternative method. Additionally, no systematic differences in coefficients of variation across ages were detected between the OID and alternative methods of fish age estimation. Results suggest that the OID may be useful for inexperienced readers and is a viable option for reducing interpretation error, which may improve reader efficiency and accuracy and precision in estimating fish ages.

scholarly journals Out of the loop? On the radical and the routine in urban big data

Urban Studies ◽  
2021 ◽  
pp. 004209802110140
Author(s):  
Sarah Barns
Keyword(s):  
Artificial Intelligence ◽  
Big Data ◽  
Computational Models ◽  
Data Driven ◽  
Urban Systems ◽  
Out Of The Loop ◽  
Urban Futures ◽  
Urban Behaviour ◽  
The City

This commentary interrogates what it means for routine urban behaviours to now be replicating themselves computationally. The emergence of autonomous or artificial intelligence points to the powerful role of big data in the city, as increasingly powerful computational models are now capable of replicating and reproducing existing spatial patterns and activities. I discuss these emergent urban systems of learned or trained intelligence as being at once radical and routine. Just as the material and behavioural conditions that give rise to urban big data demand attention, so do the generative design principles of data-driven models of urban behaviour, as they are increasingly put to use in the production of replicable, autonomous urban futures.

scholarly journals Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Richard R. Rodrigues ◽  
Manoj Gurung ◽  
Zhipeng Li ◽  
Manuel García-Jaramillo ◽  
Renee Greer ◽  
...  
Keyword(s):  
Functional Role ◽  
Reduced Glutathione ◽  
Western Diet ◽  
Data Driven ◽  
Data Driven Approach ◽  
Probiotic Strains ◽  
Host Metabolism ◽  
Harmful Effects

AbstractWestern diet (WD) is one of the major culprits of metabolic disease including type 2 diabetes (T2D) with gut microbiota playing an important role in modulating effects of the diet. Herein, we use a data-driven approach (Transkingdom Network analysis) to model host-microbiome interactions under WD to infer which members of microbiota contribute to the altered host metabolism. Interrogation of this network pointed to taxa with potential beneficial or harmful effects on host’s metabolism. We then validate the functional role of the predicted bacteria in regulating metabolism and show that they act via different host pathways. Our gene expression and electron microscopy studies show that two species from Lactobacillus genus act upon mitochondria in the liver leading to the improvement of lipid metabolism. Metabolomics analyses revealed that reduced glutathione may mediate these effects. Our study identifies potential probiotic strains for T2D and provides important insights into mechanisms of their action.

The role of the Big Five personality factors in vigilance performance and workload

2002 ◽  
Vol 16 (3) ◽  
pp. 185-200 ◽  
Author(s):  
Cynthia Laurie Rose ◽  
Laura Bennett Murphy ◽  
Lynn Byard ◽  
Katherina Nikzad
Keyword(s):  
Reaction Times ◽  
Personality Factors ◽  
False Alarms ◽  
Big Five Personality ◽  
Perceptual Sensitivity ◽  
Practical Applications ◽  
Perceived Workload ◽  
Big Five Personality Factors ◽  
Task Parameters

Using the five‐factor personality model, the present study explored the influence of personality factors on sustained attention and perceived workload. Ninety‐six college‐aged participants were administered a 12 minute vigilance fast event rate task. Following the vigil, participants were asked to first, rate their perceived workload of the task using the NASA‐TLX, and then second, complete the NEO‐PI‐R personality inventory. Traditional measures of hits, false alarms, and reaction times were examined as well as the signal detection indices of perceptual sensitivity and response bias. Extraversion correlated with false alarms (r = 0.181; eta2 = 0.055) and conscientiousness correlated with both false alarms (r = −0.275, eta2 = 0.097) and perceptual sensitivity (r = 0.227, eta2 = 0.052). With regard to perceived workload, neuroticism was related to perceived frustration (r = 0.238, eta2 = 0.057). The findings are discussed in terms of theoretical implications, impact of task parameters, and practical applications. Copyright © 2002 John Wiley & Sons, Ltd.

Managing uncertainty in a general insurance company

1990 ◽  
Vol 117 (2) ◽  
pp. 173-277 ◽  
Author(s):  
C. D. Daykin ◽  
G. B. Hey
Keyword(s):  
Computer Model ◽  
Flow Model ◽  
Insurance Companies ◽  
Simulation Methods ◽  
Insurance Company ◽  
Practical Applications ◽  
General Insurance ◽  
Alternative Approaches ◽  
The Impact

AbstractA cash flow model is proposed as a way of analysing uncertainty in the future development of a general insurance company. The company is modelled alongside the market in aggregate so that the impact of changes in premium rates relative to the market can be assessed. An extensive computer model is developed along these lines, intended for use in practical applications by actuaries advising the management of genera1 insurance companies. Simulation methods are used to explore the consequences of uncertainty, particularly in regard to inflation and investments. Some comments are made on the role of actuaries in general insurance. Alternative approaches to describing the behaviour of an insurance firm in the market are considered.

Big data-driven supply chain and performance: a resource-based view

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Shampy Kamboj ◽  
Shruti Rana
Keyword(s):  
Big Data ◽  
Supply Chain ◽  
Small And Medium Enterprises ◽  
Data Driven ◽  
Equation Modeling ◽  
Firm Age ◽  
Content Type ◽  
Sustainable Performance ◽  
Medium Enterprises

PurposeThe main objective of this paper is to study the role of supply chain performance (SCP) as a mediator between big data-driven supply chain (BDDSC) and firm sustainable performance. In addition, the role of firm age as a moderator between BDDSC and SCP as well as between SCP and firm sustainable performance has also been explored.Design/methodology/approachThe 200 managers of medium or senior level positions in micro, small and medium enterprises (MSMEs) located at Delhi-NCR have been contacted. Further, collected data have been confirmed with confirmatory factor analysis (CFA). In this paper, structure equation modeling (SEM) has been employed to empirically check the proposed hypotheses and their relationships.FindingsThe findings confirmed that SCP mediates the link between BDDSC and firm sustainable performance. Additionally, firm age moderates the association between BDDSC and SCP as well as between SCP and firm sustainable performance.Research limitations/implicationsThe role of SCP and firm age between BDDSC and sustainable performance have been examined in the context of MSMEs in Delhi-NCR and thereby limit the generalization of results to other industries and country contexts.Originality/valueThe present study adds to the existing literature via recognizing the blackbox using SCP and firm age to comprehend BDDSC and firm sustainable performance relationship.

A data-driven model of the role of energy in sepsis

2021 ◽  
pp. 110948
Author(s):  
Ivan Ramirez-Zuniga ◽  
Jonathan. E. Rubin ◽  
David Swigon ◽  
Heinz Redl ◽  
Gilles Clermont
Keyword(s):  
Data Driven

Sentiment Analysis with Text Mining in Contexts of Big Data

2017 ◽  
Vol 13 (3) ◽  
pp. 47-67 ◽  
Author(s):  
Carina Sofia Andrade ◽  
Maribel Yasmina Santos
Keyword(s):  
Big Data ◽  
Text Mining ◽  
Sentiment Analysis ◽  
Decision Making Process ◽  
Practical Applications ◽  
Information Models ◽  
Evolution Of Technology ◽  
The Common ◽  
Analyse Data

The evolution of technology, along with the common use of different devices connected to the Internet, provides a vast growth in the volume and variety of data that are daily generated at high velocity, phenomenon commonly denominated as Big Data. Related with this, several Text Mining techniques make possible the extraction of useful insights from that data, benefiting the decision-making process across multiple areas, using the information, models, patterns or tendencies that these techniques are able to identify. With Sentiment Analysis, it is possible to understand which sentiments and opinions are implicit in this data. This paper proposes an architecture for Sentiment Analysis that uses data from the Twitter, which is able to collect, store, process and analyse data on a real-time fashion. To demonstrate its utility, practical applications are developed using real world examples where Sentiment Analysis brings benefits when applied. With the presented demonstration case, it is possible to verify the role of each used technology and the techniques adopted for Sentiment Analysis.

Total Productive Maintenance: Competing or Complementary to other Initiatives?

2013 ◽  
Vol 315 ◽  
pp. 472-476
Author(s):  
Adnan Hj. Bakri ◽  
Abdul Rahman Abdul Rahim ◽  
Noordin Mohd Yusof
Keyword(s):  
Large Scale ◽  
Manufacturing Industry ◽  
Short Review ◽  
The Other ◽  
Total Quality ◽  
Total Productive Maintenance ◽  
Quality Initiatives ◽  
Practical Applications ◽  
Manufacturing Organization

The objective of this short review paper is to examine the practical applications of Total Productive Maintenance (TPM) in the manufacturing industry. In this short review, an attempt was made to critically discuss the previous literatures related to TPM with the other established quality initiatives in the manufacturing, such as Total Quality Management (TQM) and Just-In-Time practice (JIT). This literature review-based research revealed an important research gaps related to TPM. The significance role of TPM as an important complementary to either TQM or JIT initiative is observed not been well addressed in the available literatures. Most of the researches available investigate these initiatives separately, focuses on the other element rather than addressing on the significant role of TPM as one of the main thrust. The separate implementation of such quality initiatives in the manufacturing organization means the requirement of large scale human, financial and technical resources as well the associated problems of running competing project in the company. The outcomes from this review justify the needs of further research in the area of TPM integration with other available initiatives, to further enhance its methodology aimed at solidifying its philosophy towards more realistic practical applications.

Sign in / Sign up

Export Citation Format

Share Document