scholarly journals Improving the gnomonic approach with the gnomonicM R-package to estimate natural mortality throughout different life stages

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11229
Author(s):  
Josymar Torrejón-Magallanes ◽  
Enrique Morales-Bojórquez ◽  
Francisco Arreguín-Sánchez
Keyword(s):  
Developmental Stages ◽  
Auxiliary Information ◽  
Stochastic Approach ◽  
R Package ◽  
Biological Information ◽  
Fish Stock ◽  
Natural Mortality ◽  
Life Stages ◽  
And Performance ◽  
Stochastic Functions

Natural mortality (M) is defined as the rate of loss that occurs in a fish stock due to natural (non-fishing) causes and can be influenced by density-dependent or density-independent factors. Different methods have been used to estimate M, one of these is the gnomonic approach. This method estimates M rates by dividing the life cycle of a species into subunits of time that increase as a constant proportion of the time elapsed from birth up to the initiation of each subdivision. In this study, an improved gnomonic approach is proposed to estimate natural mortality throughout different life stages in marine stocks using the gnomonicM package written in R software. This package was built to require data about (i) the number of gnomonic intervals, (ii) egg stage duration, (iii) longevity, and (iv) fecundity. With this information, it is possible to estimate the duration and natural mortality (Mi) of each gnomonic interval. The gnomonicM package uses a deterministic or stochastic approach, the latter of which assesses variability in M by assuming that the mean lifetime fecundity (MLF) is the main source of uncertainty. Additionally, the gnomonicM package allows the incorporation of auxiliary information related to the observed temporal durations of specific gnomonic intervals, which is useful for calibrating estimates of M vectors. The gnomonicM package, tested via deterministic and stochastic functions, was supported by the reproducibility and verification of the results obtained from different reports, thus guaranteeing its functionality, applicability, and performance in estimating M for different ontogenetic developmental stages. Based on the biological information of Pacific chub mackerel (Scomber japonicus), we presented a new case study to provide a comprehensive guide to data collection to obtain results and explain the details of the application of the gnomonicM package and avoid its misuse. This package could provide an alternative approach for estimating M and provide basic input data for ecological models, allowing the option of using estimates of variable natural mortality across different ages, mainly for life stages affected by fishing. The inputs for the gnomonicM packages are composed of numbers, vectors, or characters depending on whether the deterministic or stochastic approach is used, making the package quick, flexible, and easy to use; this allows users to focus on obtaining and interpreting results rather than the calculation process.

scholarly journals ramr: an R package for detection of rare aberrantly methylated regions

2020 ◽  
Author(s):  
Oleksii Nikolaienko ◽  
Per Eystein Lønning ◽  
Stian Knappskog
Keyword(s):  
Performance Metrics ◽  
Developmental Stages ◽  
R Package ◽  
Data Sets ◽  
Bioinformatic Tools ◽  
Public Data ◽  
Risk Of Disease ◽  
Low Incidence ◽  
And Performance ◽  
Risk Of Cancer

AbstractMotivationWith recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyse such events.ResultsWe have developed a method (ramr) to identify aberrantly methylated DNA regions (AMRs). ramr can be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics of ramr and confirmed its applicability for analysis of large public data sets. Using ramr we identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages.Availability and implementationThe R package is freely available at https://github.com/BBCG/ramr

scholarly journals Temporal Dynamics of ‘Ca. Phytoplasma mali’ Load in the Insect Vector Cacopsylla melanoneura

Insects ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 592
Author(s):  
Valentina Candian ◽  
Monia Monti ◽  
Rosemarie Tedeschi
Keyword(s):  
Host Plants ◽  
Developmental Stages ◽  
Temporal Dynamics ◽  
Control Strategies ◽  
Vector Competence ◽  
Insect Vector ◽  
Life Stages ◽  
Candidatus Phytoplasma Mali ◽  
High Infection ◽  
Cacopsylla Melanoneura

The transmission of phytoplasmas is the result of an intricate interplay involving pathogens, insect vectors and host plants. Knowledge of the vector’s competence during its lifespan allows us to define more sustainable well-timed control strategies targeted towards the most worrisome life stages. We investigated the temporal dynamics of ‘Candidatus Phytoplasma mali’ load in Cacopsylla melanoneura in the different developmental stages in Northwest Italy. The phytoplasma load in the vector was evaluated in overwintering adults, nymphs and newly emerged adults after different acquisition access periods. Moreover, we followed the multiplication of the phytoplasma during the aestivation and the overwintering period on conifers. Our results confirmed the ability of remigrants to retain the phytoplasma until the end of winter. We also highlighted the high acquisition efficiency and vector competence, based on phytoplasma load, of nymphs and newly emerged adults. Therefore, particular attention should be paid to the management of overwintered C. melanoneura as soon as they return to the orchards, but also to newly emerged adults, particularly in orchards with a high infection rate and when the migration to conifers is delayed.

A Stochastic Approach to Risk Management and Decision Making in Defined Benefit Pension Schemes

2003 ◽  
Vol 9 (3) ◽  
pp. 493-586 ◽  
Author(s):  
S. Haberman ◽  
C. Day ◽  
D. Fogarty ◽  
M. Z. Khorasanee ◽  
M. McWhirter ◽  
...  
Keyword(s):  
Decision Making ◽  
Performance Measures ◽  
Asset Allocation ◽  
Stochastic Approach ◽  
Free Variable ◽  
Defined Benefit ◽  
Contribution Rate ◽  
And Performance ◽  
Allocation Decisions ◽  
Made In

ABSTRACTThe trustees and sponsors of defined benefit schemes rely on the advice of the Scheme Actuary to make important decisions concerning the funding of the scheme, the investment of its assets, and the use of surplus assets to improve benefits. These decisions have to be made in the face of considerable uncertainty about financial and demographic factors that will affect the future experience of the scheme and its success in meeting various objectives.The traditional actuarial valuation combined with actuarial judgement has played an important role in guiding decision making; but we argue that stochastic methods can add value in certain crucial areas, in particular the financial risk management of defined benefit schemes. Rather than dealing with risk by incorporating margins in the valuation basis, a stochastic approach allows the actuary to evaluate specific and quantifiable risk and performance measures for alternative funding and investment strategies.This paper recommends a framework that, when combined with a suitable stochastic model, measures the risks inherent in contribution rate and asset allocation decisions, allowing better decisions to be made. In doing this, we suggest and apply various risk and performance measures that may be thought appropriate, although our intention is to illustrate their use rather than prescribe them as objective standards. The framework provides the means to explore the trade-offs involved in possible contribution and asset allocation decisions, and points to decision strategies expected to give improved outcomes for the same level of risk. A feature of the approach that marks it out from current asset/liability techniques is that it examines the funding and investment decisions together. It does not derive a contribution rate in the traditional way, but leaves this as free variable, in the same way that the investment decision is taken to be a free variable. Another distinctive feature of our framework is that it is based on projection rather than on valuation, involving stochastic simulation of the experience of the scheme over a time horizon reflecting the concerns of the trustees and the sponsoring employer.The paper provides a case study (based on a model final salary pension scheme) showing the advantages of the framework, and goes on to explain how the results may practically be communicated to trustees and scheme sponsors.

scholarly journals Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa

2018 ◽  
Vol 19 (7) ◽  
pp. 2064 ◽  
Author(s):  
Mingliang Jiang ◽  
Xiangshu Dong ◽  
Hong Lang ◽  
Wenxing Pang ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Developmental Stages ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Gc Content ◽  
Biological Information ◽  
Lower Percentage ◽  
Orphan Genes ◽  
Conserved Genes

Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.

scholarly journals Cnidome and Morphological Features of Pelagia noctiluca (Cnidaria: Scyphozoa) Throughout the Different Life Cycle Stages

2021 ◽  
Vol 8 ◽  
Author(s):  
Ainara Ballesteros ◽  
Carina Östman ◽  
Andreu Santín ◽  
Macarena Marambio ◽  
Mridvika Narda ◽  
...  
Keyword(s):  
Life Cycle ◽  
Developmental Stages ◽  
Later Life ◽  
Life Stages ◽  
Accurate Identification ◽  
Early Stages ◽  
Pelagia Noctiluca ◽  
Life Cycle Stages ◽  
Advanced Stages ◽  
Stage 1

Pelagia noctiluca is considered the most important jellyfish in the Mediterranean Sea, due to its abundance and the severity of its stings. Despite its importance in marine ecosystems and the health problems caused by its massive arrival in coastal areas, little is known about its early life stages and its cnidome has never been described. This study of the morphological and anatomical features throughout the life cycle identifies four early stages: two ephyra and two metaephyra stages. Ephyra stage 1, newly developed from a planula, has no velar canals, gastric filaments or nematocyst batteries. Ephyra stage 2, has velar canals, a cruciform-shaped manubrium and gastric filaments. Metaephyra stage 3 has eight tentacle buds and nematocyst clusters for the first time. Lastly, in metaephyra stage 4, the eight primary tentacles grow nearly simultaneously, with no secondary tentacles. Complete nematocyst battery patterns gradually develop throughout the later life stages. Four nematocyst types are identified: a-isorhiza, A-isorhiza, O-isorhiza and eurytele. Of these, a-isorhiza and eurytele are the most important throughout the entire life cycle, while A-isorhiza and O-isorhiza have a more important role in advanced stages. All nematocysts show a positive correlation between increasing capsule volumes and increasing body diameter of the ephyrae, metaephyrae, young medusae and adult medusae. In the early stages, the volumes of euryteles in the gastric filaments are larger than those in the exumbrella, indicating that the capsule volume is critical in the absence of marginal tentacles, specialized for feeding. This study provides updated information, the most extensive description to date, including high-resolution photographs and schematic drawings of all the developmental stages in the life cycle of P. noctiluca. Additionally, the first cnidome characterization is provided for each stage to facilitate accurate identification of this species when collected in the water column, and to raise awareness of the potential for human envenomation.

scholarly journals Comparative Microbiota Composition Across Developmental Stages of Natural and Laboratory-Reared Chironomus circumdatus Populations From India

2021 ◽  
Vol 12 ◽  
Author(s):  
Sivan Laviad-Shitrit ◽  
Rotem Sela ◽  
Yehonatan Sharaby ◽  
Leena Thorat ◽  
Bimalendu B. Nath ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Laboratory Culture ◽  
Sampling Location ◽  
Scaling Analysis ◽  
Life Stages ◽  
Microbiota Composition ◽  
Aquatic Life ◽  
Egg Masses ◽  
Microbial Profile ◽  
Field Environment

Chironomids are aquatic insects that undergo a complete metamorphosis of four life stages. Here we studied, for the first time, the microbiota composition of Chironomus circumdatus, a tropical midge species, both from the Mula and Mutha Rivers in Pune, India and as a laboratory-reared culture. We generated a comparative microbial profile of the eggs, larvae and pupae, the three aquatic life stages of C. circumdatus. Non-metric multidimensional scaling analysis (NMDS) demonstrated that the developmental stage had a more prominent effect on the microbiota composition compared to the sampling location. Notably, the microbiota composition of the egg masses from the different sampling points clustered together and differed from laboratory culture larvae. Proteobacteria was the dominant phylum in all the environmental and laboratory-reared egg masses and pupal samples, and in the laboratory-reared larvae, while Fusobacteria was the dominant phylum in the larvae collected from the field environment. The most abundant genera were Cetobacterium, Aeromonas, Dysgonomonas, Vibrio, and Flavobacterium. The ten amplicon sequence variants (ASVs) that most significantly contributed to differences in microbiota composition between the three sampled locations were: Burkholderiaceae (ASVs 04 and 37), C39 (Rhodocyclaceae, ASV 14), Vibrio (ASV 07), Arcobacter (ASV 21), Sphaerotilus (ASV 22), Bacteroidia (ASVs 12 and 28), Flavobacterium (ASV 29), and Gottschalkia (ASV 10). No significant differences were found in the microbial richness (Chao1) or diversity (Shannon H’) of the three sampled locations. In contrast, significant differences were found between the microbial richness of the three life stages. Studying the microbiota of this Chironomus species may contribute to a better understanding of the association of C. circumdatus and its microbial inhabitants.

scholarly journals Estimation of the parameters of fish stock dynamics from catch-at-age data and indices of abundance: can natural and fishing mortality be separated?

2007 ◽  
Vol 64 (8) ◽  
pp. 1130-1142 ◽  
Author(s):  
Sondre Aanes ◽  
Steinar Engen ◽  
Bernt-Erik Sæther ◽  
Ronny Aanes
Keyword(s):  
Gadus Morhua ◽  
State Space Model ◽  
Population Projections ◽  
Quality Data ◽  
Fish Stock ◽  
Natural Mortality ◽  
Fishing Mortality ◽  
Absolute Size ◽  
Data Set ◽  
Long Time

Models for fluctuations in size of fish stocks must include parameters that describe expected dynamics, as well as stochastic influences. In addition, reliable population projections also require assessments about the uncertainties in estimates of vital parameters. Here we develop an age-structured model of population dynamics based on catch-at-age data and indices of abundance in which the natural and fishing mortality are separated in a Bayesian state–space model. Markov chain Monte Carlo methods are used to fit the model to the data. The model is fitted to a data set of 19 years for Northeast Arctic cod (Gadus morhua). By simulations of the fitted model we show that the model captures the dynamical pattern of natural mortality adequately, whereas the absolute size of natural mortality is difficult to estimate. Access to long time series of high-quality data are necessary for obtaining precise estimates of all the parameters in the model, but some parameters cannot be estimated without including some prior information. Nevertheless, our model demonstrates that temporal variability in natural mortality strongly affects perceived variability in stock sizes. Thus, using estimation procedures that neglect temporal fluctuations in natural mortality may therefore give biased estimates of fluctuations in fish stock sizes.

Pathways for urea production during early life of an air-breathing teleost, the African catfish Clarias gariepinus Burchell

2001 ◽  
Vol 204 (12) ◽  
pp. 2155-2165 ◽  
Author(s):  
Bendik F. Terjesen ◽  
Terry D. Chadwick ◽  
Johan A. J. Verreth ◽  
Ivar Rønnestad ◽  
Patricia A. Wright
Keyword(s):  
Early Development ◽  
Early Life ◽  
Developmental Stages ◽  
Clarias Gariepinus ◽  
African Catfish ◽  
Life Stages ◽  
Carbamoyl Phosphate ◽  
Experimental Conditions ◽  
Air Breathing ◽  
Urea Production

SUMMARY Embryos and larvae of the African catfish Clarias gariepinus excrete significant quantities of urea. The present study focused on the potential urea-generating pathways during early development of this teleost; uricolysis, argininolysis and the ornithine–urea cycle (OUC). Uricase, allantoinase, allantoicase and ureidoglycollate lyase of the uricolytic pathway were expressed in all early life stages and in adult liver of C. gariepinus. Uricase activity increased in starved larvae compared with yolk-sac larvae. The key regulatory enzyme of the teleost OUC, carbamoyl phosphate synthetase III (CPSase III), was expressed predominantly in muscle of developing C. gariepinus larvae and showed negligible activity in the absence of its allosteric effector N-acetyl-l-glutamate. CPSase III and ornithine carbamoyl transferase activities increased in fed larvae compared with starved larvae. In contrast to the early developmental stages, adult C. gariepinus expressed only low and variable levels of CPSase III, suggesting that, under the experimental conditions employed, OUC expression is influenced by developmental stage in this species. The data indicate that early C. gariepinus life stages express the enzymes necessary for urea production by uricolysis, argininolysis and the OUC, and this may explain why urea tissue levels and urea excretion rates are substantial during the early development of this air-breathing teleost.

scholarly journals Simulation Study on the Integration of Health Traits in Horse Breeding Programs

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1153
Author(s):  
Lisa Büttgen ◽  
Johannes Geibel ◽  
Henner Simianer ◽  
Torsten Pook
Keyword(s):  
Osteochondrosis Dissecans ◽  
Selection Index ◽  
R Package ◽  
Breeding Value ◽  
Index Selection ◽  
Threshold Selection ◽  
Horse Breeding ◽  
Frequency Of Use ◽  
Performance Traits ◽  
And Performance

Osteochondrosis dissecans (OCD) is a degenerative disease of the cartilage leading to osseous fragments in the joints. It is important in horse breeding both from an animal welfare and an economic perspective. To study adequate breeding strategies to reduce OCD prevalence, a lifelike simulation of the breeding program of German Warmblood horses was performed with the R package MoBPS. We simulated complex breeding schemes of riding horses with different selection steps and realistic age structure, mimicking the German situation. As an example, osseous fragments in fetlock and hock joints were considered. Different scenarios, either using threshold selection, index selection or genomic index selection, respectively, were compared regarding their impact on health and performance traits. A rigorous threshold selection as well as the integration of OCD in a selection index at the stage of stallion licensing and chosen frequency of use in breeding cases on a selection index that includes breeding values for OCD traits performed best on a comparable level. Simply integrating OCD in this breeding value was less effective in terms of OCD reduction. Scenarios with a higher reduction of OCD also showed a slightly reduced improvement in the riding horse performance traits.

scholarly journals Age and performance at fledging are a cause and consequence of juvenile mortality between life stages

2018 ◽  
Vol 4 (6) ◽  
pp. eaar1988 ◽  
Author(s):  
Thomas E. Martin ◽  
Bret Tobalske ◽  
Margaret M. Riordan ◽  
Samuel B. Case ◽  
Kenneth P. Dial
Keyword(s):  
Life Stages ◽  
Juvenile Mortality ◽  
And Performance
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