scholarly journals Mitochondrial introgression suggests extensive ancestral hybridization events amongSaccharomycesspecies

2015 ◽  
Author(s):  
David Peris ◽  
Armando Arias ◽  
Sandi Orlić ◽  
Carmela Belloch ◽  
Laura Pérez-Través ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Homing Endonuclease ◽  
Complex Model ◽  
Geographic Origins ◽  
Mitochondrial Region ◽  
Gc Clusters ◽  
Different Types ◽  
Genome Annotations ◽  
Different Sources

1.AbstractHorizontal Gene Transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested betweenS. cerevisiaeandS. paradoxus. However, few strains have been explored due to the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur and their role in cytonuclear incompatibilities and fitness. In fact, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. In this study, we have explored the mitochondrial inheritance of several worldwide distributedSaccharomycesspecies isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in the mitochondrial regionCOX2-ORF1, likely mediated by the transfer of two different types ofORF1(F-SceIII), encoding a freestanding homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur at intra- as well as at interspecific levels. This suggest a complex model ofSaccharomycesevolution which involve several ancestral hybridization events in wild environments.

scholarly journals How to measure uncertainty in uncertainty sampling for active learning

2021 ◽  
Author(s):  
Vu-Linh Nguyen ◽  
Mohammad Hossein Shaker ◽  
Eyke Hüllermeier
Keyword(s):  
Machine Learning ◽  
Active Learning ◽  
Sampling Strategies ◽  
Total Uncertainty ◽  
Uncertainty Sampling ◽  
Different Types ◽  
Alternative Approaches ◽  
Active Learner ◽  
Probabilistic Nature ◽  
Different Sources

AbstractVarious strategies for active learning have been proposed in the machine learning literature. In uncertainty sampling, which is among the most popular approaches, the active learner sequentially queries the label of those instances for which its current prediction is maximally uncertain. The predictions as well as the measures used to quantify the degree of uncertainty, such as entropy, are traditionally of a probabilistic nature. Yet, alternative approaches to capturing uncertainty in machine learning, alongside with corresponding uncertainty measures, have been proposed in recent years. In particular, some of these measures seek to distinguish different sources and to separate different types of uncertainty, such as the reducible (epistemic) and the irreducible (aleatoric) part of the total uncertainty in a prediction. The goal of this paper is to elaborate on the usefulness of such measures for uncertainty sampling, and to compare their performance in active learning. To this end, we instantiate uncertainty sampling with different measures, analyze the properties of the sampling strategies thus obtained, and compare them in an experimental study.

scholarly journals Model-Based Probabilistic Inversion Using Magnetic Data: A Case Study on the Kevitsa Deposit

Geosciences ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 150
Author(s):  
Nilgün Güdük ◽  
Miguel de la Varga ◽  
Janne Kaukolinna ◽  
Florian Wellmann
Keyword(s):  
Structural Parameters ◽  
Rock Properties ◽  
Magnetic Data ◽  
Geological Model ◽  
Borehole Data ◽  
Likelihood Functions ◽  
Different Types ◽  
Geophysical Information ◽  
Different Sources

Structural geological models are widely used to represent relevant geological interfaces and property distributions in the subsurface. Considering the inherent uncertainty of these models, the non-uniqueness of geophysical inverse problems, and the growing availability of data, there is a need for methods that integrate different types of data consistently and consider the uncertainties quantitatively. Probabilistic inference provides a suitable tool for this purpose. Using a Bayesian framework, geological modeling can be considered as an integral part of the inversion and thereby naturally constrain geophysical inversion procedures. This integration prevents geologically unrealistic results and provides the opportunity to include geological and geophysical information in the inversion. This information can be from different sources and is added to the framework through likelihood functions. We applied this methodology to the structurally complex Kevitsa deposit in Finland. We started with an interpretation-based 3D geological model and defined the uncertainties in our geological model through probability density functions. Airborne magnetic data and geological interpretations of borehole data were used to define geophysical and geological likelihoods, respectively. The geophysical data were linked to the uncertain structural parameters through the rock properties. The result of the inverse problem was an ensemble of realized models. These structural models and their uncertainties are visualized using information entropy, which allows for quantitative analysis. Our results show that with our methodology, we can use well-defined likelihood functions to add meaningful information to our initial model without requiring a computationally-heavy full grid inversion, discrepancies between model and data are spotted more easily, and the complementary strength of different types of data can be integrated into one framework.

scholarly journals Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wen-Ge Dong ◽  
Yalun Dong ◽  
Xian-Guo Guo ◽  
Renfu Shao
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Organization ◽  
Trna Gene ◽  
Trna Genes ◽  
Single Chromosome ◽  
Gene Translocation ◽  
Sucking Lice ◽  
Different Types ◽  
Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

The Behavioral Consequences of Conflict Exposure on Risk Preferences

2021 ◽  
Author(s):  
Enrique Fatas ◽  
Nathaly Jiménez ◽  
Lina Restrepo-Plaza ◽  
Gustavo Rincón
Keyword(s):  
Substantial Effect ◽  
Risk Attitudes ◽  
Behavioral Consequences ◽  
Criminal Violence ◽  
Incentive Compatible ◽  
Attitudinal Factors ◽  
Different Types ◽  
Close Relatives ◽  
Different Sources ◽  
Consequences Of Violence

Violent conflict is a polyhedric phenomenon. Beyond the destruction of physical and human capital and the economic, political, and social costs war generates, there is an additional burden carried by victims: persistent changes in the way they make decisions. Exposure to violence generates changes in how individuals perceive other individuals from their group and other groups, how they discount the future, and how they assess and tolerate risk. The behavioral consequences of violence exposure can be documented using experiments in which participants make decisions in a controlled, incentive-compatible scenario. The external validity of experiments is reinforced when the studies are run in postconflict scenarios, for example, in Colombia, with real victims of conflict. The experimental tasks, therefore, may map risk attitudes among victims and nonvictims of the conflict who share a common background, and distinguish between different types of exposure (direct versus indirect) and different sources of violence (conflict-related versus criminal violence). The experimental evidence collected in Colombia is consistent with a long-lasting and substantial effect of conflict exposure on risk attitudes. Victims are more likely to take risks and less likely to make safe choices than nonvictims, controlling for demographic, socioeconomic, and attitudinal factors. The effect is significant only when the source of violence is conflict (exerted by guerrilla or paramilitary militias) and when violence is experienced directly by individuals. Indirect conflict exposure (suffered by close relatives) and criminal violence leave no significant mark on participants’ risk attitudes in the study.

A Review on Green Synthesis and Applications of Iron Oxide Nanoparticles

2021 ◽  
Vol 21 (12) ◽  
pp. 5812-5834
Author(s):  
Rachana Yadwade ◽  
Saili Kirtiwar ◽  
Balaprasad Ankamwar
Keyword(s):  
Iron Oxide ◽  
Iron Oxide Nanoparticles ◽  
Aqueous System ◽  
Oxide Nanoparticles ◽  
Plant Parts ◽  
Different Types ◽  
Removal Of Heavy Metals ◽  
Biological Sources ◽  
Different Sources

Bio-fabrication of iron oxide nanoparticles by using different sources of plants, plant parts and microbial cells have become a great topic of interest nowadays due to its eco-friendly nature. The stabilizing and capping agents in biological sources are biocompatible, stable and non-toxic which make its use beneficial for various biomedical applications. The bacteria are able to utilize metal ions and convert them into their respective nanoparticles by secreting different biomolecules. The plants and plant parts contain different types of phytochemicals which play a key role in synthesis and bio-fabrication of nanoparticles. Iron oxide nanoparticles are known to have various applications in the fields of medicine, environment etc. This review summarizes the applications of iron oxide nanoparticles as antimicrobial agent, drug delivery agent, material for removal of heavy metals and dyes from aqueous system etc. Due to these wide applications of iron oxide nanoparticles its demand in various fields is increasing considerably. This review describes different approaches which are used for biosynthesis of iron oxide nanoparticles and their applications. The review also summarizes about the surface modification strategies of iron oxide nanoparticles by using different polymers, polyelectrolytes which can be used for in-vivo applications.

Loss of Life and Loss of Bodily Integrity: Two Different Sources of Threat for People who are Ill

1985 ◽  
Vol 15 (3) ◽  
pp. 207-222 ◽  
Author(s):  
Linda L. Viney
Keyword(s):  
Healthy People ◽  
Personal Construct ◽  
Personal Construct Theory ◽  
Bodily Integrity ◽  
Loss Of Life ◽  
Psychological States ◽  
Different Types ◽  
Construct Theory ◽  
Positive Feelings ◽  
Different Sources

Personal construct theory was used to generate some questions about the meanings that different types of threat–loss of life and loss of bodily integrity–hold for people who are severely ill. Content analyses of the responses of ill people and healthy people indicated that ill people expressed more concern with both types of threat than healthy people. Ill people who were suffering from acute rather than chronic illness, who were scheduled for surgery and who were hospitalized rather than being cared for at home expressed more concern about loss of life but not about loss of bodily integrity than other ill people. Each type of threatened loss was found to be associated with a different set of psychological states for people who were ill. Threat of loss of life was associated with indirectly expressed anger and uncertainty but also with the expression of many positive feelings. Threat of loss of bodily integrity was also associated with indirectly expressed anger, but with direct expression of it too, together with hopelessness and helplessness. Patients facing the first threat saw themselves as actively engaged in relationships with others, while those facing the second viewed themselves more often as passive participants. The value of this information about the meanings of threats of loss of life and loss of bodily integrity for the counseling of ill people dealing with these threats was illustrated by two case studies.

scholarly journals TERRESTRIAL LASER SCANNERS SELF-CALIBRATION STUDY: DATUM CONSTRAINTS ANALYSES FOR NETWORK CONFIGURATIONS

2015 ◽  
Vol XL-2/W4 ◽  
pp. 1-9 ◽  
Author(s):  
M. A. Abbas ◽  
H. Setan ◽  
Z. Majid ◽  
A. K. Chong ◽  
L. Chong Luh ◽  
...  
Keyword(s):  
Laser Scanner ◽  
Network Configuration ◽  
Calibration Technique ◽  
Self Calibration ◽  
Laser Scanners ◽  
Different Types ◽  
Minimum Number ◽  
Calibration Study ◽  
Different Sources ◽  
Selection Of

Similar to other electronic instruments, terrestrial laser scanner (TLS) can also inherent with various systematic errors coming from different sources. Self-calibration technique is a method available to investigate these errors for TLS which were adopted from photogrammetry technique. According to the photogrammetry principle, the selection of datum constraints can cause different types of parameter correlations. However, the network configuration applied by TLS and photogrammetry calibrations are quite different, thus, this study has investigated the significant of photogrammetry datum constraints principle in TLS self-calibration. To ensure that the assessment is thorough, the datum constraints analyses were carried out using three variant network configurations: 1) minimum number of scan stations; 2) minimum number of surfaces for targets distribution; and 3) minimum number of point targets. Based on graphical and statistical, the analyses of datum constraints selection indicated that the parameter correlations obtained are significantly similar. In addition, the analysis has demonstrated that network configuration is a very crucial factor to reduce the correlation between the calculated parameters.

scholarly journals Perceptions of Auditor Negligence: The Effects of Big Data Visualisations on Jurors’ Decisions

2021 ◽  
Author(s):  
◽  
Travis Christensen
Keyword(s):  
Social Media ◽  
Big Data ◽  
Data Collection ◽  
Jury Verdicts ◽  
Word Clouds ◽  
Audit Litigation ◽  
Different Types ◽  
Different Sources ◽  
Bar Graphs

<p>This study analyses the effects of Big Data visualisations on jurors’ decisions in audit litigation cases. Specifically, the study investigates the effects of different types of Big Data visualisations (word clouds or bar graphs) and different sources of Big Data (emails or social media posts) on jurors’ perceptions of auditors’ work and the size of the negligence awards that jurors recommend. The study theorises that the emotions elicited and the reliability of the data used to create visualisations such as word clouds will have dramatic effects on jury verdicts in audit negligence trials. There is considerable literature to support this assertion. However, after data collection, it was discovered that jurors are not influenced by the emotions elicited by visualisations. Rather, participants were very sceptical of more novel types of visualisations, such as word clouds, but could be persuaded by the inherent emotions elicited and the reliability of the data if they found the visualisation useful.</p>

scholarly journals Genotyping Mycobacterium ulcerans and Mycobacterium marinum by Using Mycobacterial Interspersed Repetitive Units

2005 ◽  
Vol 187 (5) ◽  
pp. 1639-1647 ◽  
Author(s):  
Pieter Stragier ◽  
Anthony Ablordey ◽  
Wayne M. Meyers ◽  
Françoise Portaels
Keyword(s):  
Tandem Repeats ◽  
Central Africa ◽  
Mycobacterium Ulcerans ◽  
Pathogenic Species ◽  
Missing Link ◽  
Potential Value ◽  
Related Organism ◽  
Geographic Origins ◽  
West And Central Africa ◽  
Unique Genotype

ABSTRACT A novel category of variable tandem repeats (VNTR) called mycobacterial interspersed repetitive units (MIRUs) has been identified for Mycobacterium ulcerans (n = 39), M. marinum (n = 27), and one related organism. Fifteen MIRU loci were identified in the genome of M. marinum and were used to genotype M. ulcerans, M. marinum, and an M. marinum-like organism that is considered a possible missing link between M. marinum and M. ulcerans. Seven MIRU loci were polymorphic, and locus-specific PCRs for four of these loci differentiated seven M. ulcerans genotypes, four M. marinum genotypes, and a unique genotype for the missing link organism. The seven M. ulcerans genotypes were related to six different geographic origins of isolates. All isolates from West and Central Africa, including old and recent isolates, belonged to the same genotype, emphasizing the great spatiotemporal homogeneity among African isolates. Unlike the M. ulcerans genotypes, the four M. marinum genotypes could not be clearly related to the geographic origins of the isolates. According to MIRU-VNTR typing, all M. ulcerans and M. marinum isolates of American origin were closely related, suggesting a common American ancestor for these two pathogenic species on the American continents. MIRU typing has significant potential value for discriminating between reoccurrence and reinfection for M. ulcerans disease.

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