scholarly journals incR: a new R package to analyse incubation behaviour

2017 ◽  
Author(s):  
Pablo Capilla-Lasheras
Keyword(s):  
Incubation Temperature ◽  
Life Stage ◽  
R Package ◽  
Practical Implementation ◽  
Crucial Importance ◽  
New Approach ◽  
Avian Embryos ◽  
Incubation Behaviour ◽  
Avian Incubation ◽  
Environmental Temperatures

AbstractIncubation represents a life stage of crucial importance for the optimal development of avian embryos. For most birds, incubation poses a trade-off between investing in self-maintenance and offspring care. Furthermore, incubation is affected by environmental temperatures and, therefore, will be likely impacted by climate change. Despite its relevance and readily available temperature logging methods, avian incubation research is hindered by recognised limitations in available software. In this paper, a new quantitative approach to analyse incubation behaviour is presented. This new approach is embedded in a free R package, incR. The flexibility of the R environment eases the analysis, validation and visualisation of incubation temperature data. The core algorithm in incR is validated here and it is shown that the method extracts accurate metrics of incubation behaviour (e.g. number and duration of incubation bouts). This paper also presents a suggested workflow along with detailed R code to aid the practical implementation of incR.

scholarly journals Reproductive strategy, egg characteristics and embryonic development of Greenland halibut (Reinhardtius hippoglossoides)

2012 ◽  
Vol 70 (2) ◽  
pp. 342-351 ◽  
Author(s):  
Rosario Domínguez-Petit ◽  
Patrick Ouellet ◽  
Yvan Lambert
Keyword(s):  
Embryonic Development ◽  
Reproductive Strategy ◽  
Biochemical Composition ◽  
Incubation Temperature ◽  
Life Stage ◽  
Early Life Stage ◽  
Greenland Halibut ◽  
Hatching Time ◽  
Greenland Halibut Reinhardtius Hippoglossoides ◽  
Reinhardtius Hippoglossoides

Abstract Domínguez-Petit, R., Ouellet, P., and Lambert, Y. 2013. Reproductive strategy, egg characteristics and embryonic development of Greenland halibut (Reinhardtius hippoglossoides). – ICES Journal of Marine Science, 70: 342–351. Despite the commercial importance of Greenland halibut (GH), important gaps exist in our knowledge of the reproductive and early life stage biology for this species. The present study examined through laboratory experiments the spawning strategy, realized fecundity, egg characteristics, biochemical composition, and embryonic development of GH. The results confirmed the hypothesis that GH is a single-batch spawner producing large eggs, resulting in low realized fecundity. Embryonic development and hatching time are highly dependent on incubation temperature; 50% hatching occurred after 46, 30, and 24 days at 2, 4, and 6°C, respectively. Few changes in the biochemical composition of the eggs are observed during embryonic development. Newly hatched larvae are not well developed, having a large yolk sac, no pigmentation and incomplete development of the jaws. Egg specific density confirmed the mesopelagic distribution of the eggs at sea. However, important buoyancy changes occurring in the last 3–4 days before hatching indicate that larvae hatch higher in the water column. These results are important for understanding advection and dispersion processes of GH eggs and larvae and the connectivity between spawning grounds and nursery areas.

scholarly journals ‘Green incubation': avian offspring benefit from aromatic nest herbs through improved parental incubation behaviour

2018 ◽  
Vol 285 (1880) ◽  
pp. 20180376 ◽  
Author(s):  
Helga Gwinner ◽  
Pablo Capilla-Lasheras ◽  
Caren Cooper ◽  
Barbara Helm
Keyword(s):  
Strong Support ◽  
Nest Attendance ◽  
Artificial Nests ◽  
Avian Embryos ◽  
Critical Thresholds ◽  
Offspring Fitness ◽  
Incubation Behaviour ◽  
Thermal Changes ◽  
Aromatic Herbs ◽  
Study Species

Development of avian embryos requires thermal energy, usually from parents. Parents may, however, trade off catering for embryonic requirements against their own need to forage through intermittent incubation. This dynamically adjusted behaviour can be affected by properties of the nest. Here, we experimentally show a novel mechanism by which parents, through incorporation of aromatic herbs into nests, effectively modify their incubation behaviour to the benefit of their offspring. Our study species, the European starling, includes in its nest aromatic herbs which promote offspring fitness. We provided wild starlings with artificial nests including or excluding the typically selected fresh herbs and found strong support for our prediction of facilitated incubation. Herb effects were not explained by thermal changes of the nests per se , but by modified parental behaviours. Egg temperatures and nest attendance were higher in herb than herbless nests, egg temperatures dropped less frequently below critical thresholds and parents started their active day earlier. These effects were dynamic over time and particularly strong during early incubation. Incubation period was shorter in herb nests, and nestlings were heavier one week after hatching. Aromatic herbs hence influenced incubation in beneficial ways for offspring, possibly through pharmacological effects on incubating parents.

Westerse filosofie en de koorddans tussen geloof en weten

2021 ◽  
Vol 113 (2) ◽  
pp. 221-234
Author(s):  
Pieter Pekelharing
Keyword(s):  
Collective Learning ◽  
Learning Processes ◽  
Western Philosophy ◽  
Crucial Importance ◽  
The West ◽  
New Approach ◽  
Axial Age ◽  
Modern Thought ◽  
History Of ◽  
Nature And Society

Abstract Western philosophy and the tightrope between faith and knowledge In Auch eine Geschichte der Philosophie (2019), Habermas develops a new view of the history of philosophy. Dating philosophy back to the axial age, he presents its history as the result of a collective learning process, spanning a period of three millennia. In this new approach he highlights the crucial importance of faith and religion which resulted in a specific constellation of belief and knowledge that, though unique to the West, has universal import, and led to greater ‘reasonable freedom (Vernüftige Freiheit). In Habermas’ view The West’s Judeo-Christian heritage was not a passing phase in the emergence of modern thought and politics, but contributed its essential core. Though sympathetic to the idea of learning processes spanning many centuries, one may ask whether reasoning and learning processes always tend to lead, as Habermas claims, in the direction of greater freedom instead of its opposite. In this respect Habermas could have learnt more from the sceptical tradition in philosophy and its persistent interest in the various ways in which reasoning processes are non-cognitively embedded in human nature and society and influence the direction these processes take.

scholarly journals AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions

2019 ◽  
Author(s):  
Deepank R Korandla ◽  
Jacob M Wozniak ◽  
Anaamika Campeau ◽  
David J Gonzalez ◽  
Erik S Wright
Keyword(s):  
R Package ◽  
Evolutionary Conservation ◽  
Supplementary Information ◽  
Bioconductor Package ◽  
Gene Finding ◽  
Proteomics Data ◽  
Protein Coding ◽  
New Approach ◽  
Protein Coding Genes ◽  
Clear Winner

Abstract Motivation A core task of genomics is to identify the boundaries of protein coding genes, which may cover over 90% of a prokaryote's genome. Several programs are available for gene finding, yet it is currently unclear how well these programs perform and whether any offers superior accuracy. This is in part because there is no universal benchmark for gene finding and, therefore, most developers select their own benchmarking strategy. Results Here, we introduce AssessORF, a new approach for benchmarking prokaryotic gene predictions based on evidence from proteomics data and the evolutionary conservation of start and stop codons. We applied AssessORF to compare gene predictions offered by GenBank, GeneMarkS-2, Glimmer and Prodigal on genomes spanning the prokaryotic tree of life. Gene predictions were 88–95% in agreement with the available evidence, with Glimmer performing the worst but no clear winner. All programs were biased towards selecting start codons that were upstream of the actual start. Given these findings, there remains considerable room for improvement, especially in the detection of correct start sites. Availability and implementation AssessORF is available as an R package via the Bioconductor package repository. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A New Approach to Testing Mediation of the Microbiome using the LDM

2021 ◽  
Author(s):  
Ye Yue ◽  
Yi-Juan Hu
Keyword(s):  
Relative Abundance ◽  
Type I Error ◽  
R Package ◽  
New Method ◽  
Type I ◽  
Inverse Regression ◽  
Global Test ◽  
New Approach ◽  
Mediation Analyses ◽  
Mediating Role

Background: Understanding whether and which microbes played a mediating role between an exposure and a disease outcome are essential for researchers to develop clinical interventions to treat the disease by modulating the microbes. Existing methods for mediation analysis of the microbiome are often limited to a global test of community-level mediation or selection of mediating microbes without control of the false discovery rate (FDR). Further, while the null hypothesis of no mediation at each microbe is a composite null that consists of three types of null (no exposure-microbe association, no microbe-outcome association given the exposure, or neither), most existing methods for the global test such as MedTest and MODIMA treat the microbes as if they are all under the same type of null. Methods: We propose a new approach based on inverse regression that regresses the (possibly transformed) relative abundance of each taxon on the exposure and the exposure-adjusted outcome to assess the exposure-taxon and taxon-outcome associations simultaneously. Then the association p-values are used to test mediation at both the community and individual taxon levels. This approach fits nicely into our Linear Decomposition Model (LDM) framework, so our new method is implemented in the LDM and enjoys all the features of the LDM, i.e., allowing an arbitrary number of taxa to be tested, supporting continuous, discrete, or multivariate exposures and outcomes as well as adjustment of confounding covariates, accommodating clustered data, and offering analysis at the relative abundance or presence-absence scale. We refer to this new method as LDM-med. Results: Using extensive simulations, we showed that LDM-med always controlled the type I error of the global test and had compelling power over existing methods; LDM-med always preserved the FDR of testing individual taxa and had much better sensitivity than alternative approaches. In contrast, MedTest and MODIMA had severely inflated type I error when different taxa were under different types of null. The flexibility of LDM-med for a variety of mediation analyses is illustrated by the application to a murine microbiome dataset. Availability and Implementation: Our new method has been added to our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.

scholarly journals BaTiO3 films for multilayer devices by tape casting

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
S. Ivanchenko ◽  
S. Umerova ◽  
D. Baranovskyi ◽  
O. Kovalenko ◽  
A. Ragulya
Keyword(s):  
Surface Roughness ◽  
Printed Electronics ◽  
Tape Casting ◽  
Practical Implementation ◽  
Nanosized Powders ◽  
New Approach ◽  
Temperature Changes ◽  
Nanostructured Ceramic ◽  
Polymer Ratio

The diversity of the applicational scope of modern printed electronics relentlessly requires the improvement of operational properties simultaneously with reducing the overall dimensions of devices. One of the most effective ways to overcome this major obstacle is the reduction of functional layers thickness in respect to the size of the device. In the present article, we are discussing a simple way of practical implementation of miniaturization concept through the application of a well-known high-productive industrial method of tape casting for obtaining thin nanostructured ceramic layers based on BaTiO3 nanopowders for MLCC. Using of nanosized powders per se imply a new approach of developing suspensions with suitable rheology for tape casting. We demonstrate, that a length of polymer molecule defines the size of floccules and therefore influences the thickness and surface quality of tape casted films. A certain nanopowder/polymer ratio contributes to the formation of the tapes with the surface roughness comparable with the size of one nanoparticle (20-25 nm). Moreover, it was established that developed suspensions are extremely sensitive to temperature changes. Lowering the temperature significantly affects the flow character of suspension and thus the thickness of casted tapes. Considering this fact, we propose an effective self-developed pre-cooling method of nanopowder suspension casting, which allows obtaining extremely thin and smooth tapes with a thickness of less than 1 µm and surface roughness of 20–25 nm by tape casting method.

scholarly journals Breaking the measurement and evaluation deadlock: a new approach and model

2015 ◽  
Vol 19 (4) ◽  
pp. 371-387 ◽  
Author(s):  
Jim Macnamara
Keyword(s):  
Public Relations ◽  
Delphi Study ◽  
Critical Analysis ◽  
Large Body ◽  
Corporate Communication ◽  
Theory And Practice ◽  
Practical Implementation ◽  
New Approach ◽  
Content Type ◽  
Measurement And Evaluation

Purpose – Noting findings by Michaelson and Stacks in the USA and Zerfass and colleagues in Europe that research-based measurement and evaluation (M & E) of public relations and corporate communication are still not widely applied despite more than a century of discussion and intense focus since the 1970s, the purpose of this paper is to explore the causes of this deadlock and presents an alternative approach and model to overcome identified obstacles and provide new insights to advance this important area of theory and practice. Design/methodology/approach – This paper is informed by critical analysis of the large body of literature on M & E, analysis of M & E reports, and ethnographic research among senior management. Findings – This analysis reveals that, along with long-cited barriers such as lack of budget, lack of knowledge and lack of standards, three other obstacles prevent demonstration of the value of PR and corporate communication. Based on critical analysis of literature and M & E reports and ethnography, this paper presents a new approach and model for M & E to help practitioners overcome these obstacles. Research limitations/implications – This analysis and the approach and model presented address an area of concern identified in research globally, such as a 2008 Delphi study by Watson and the European Communication Monitor in 2011 and 2012. The findings provide theoretical and practical contributions to address the deadlock between normative theories of M & E and practical implementation. Originality/value – The approach and M & E model presented make a significant original contribution to theory and practice.

The Influence of Incubation Temperature on Bacterial Counts in a Meat Production System

1990 ◽  
Vol 53 (5) ◽  
pp. 418-422 ◽  
Author(s):  
G. L. NORTJÉ ◽  
L. NEL ◽  
E. JORDAAN ◽  
K. BADENHORST ◽  
G. GOEDHART ◽  
...  
Keyword(s):  
Total Population ◽  
Incubation Temperature ◽  
Plate Count ◽  
Meat Production ◽  
Time Saving ◽  
Cold Tolerant ◽  
Retail Display ◽  
Aerobic Plate Count ◽  
Minced Meat ◽  
Environmental Temperatures

Samples for microbial evaluation were taken from various surfaces including those on carcasses, and equipment at an abattoir, a wholesaler, and 10 different supermarkets. Samples were also taken of minced meat in retail display cabinets. These surfaces were monitored by means of a modified agar sausage technique. A total aerobic plate count (30°C for 24 – 48 h), a psychrotrophic count (5°C for 7 d), and a total aerobic plate count (25°C for 2 to 3 d) were investigated. Counts obtained at 30°C, yielded higher numbers than those acquired at 25°C. The accuracy of predicting the psychrotrophic population by means of a 25°C count, depends on the habitat and environmental conditions. To predict the spoilage population, a count at 25°C for 2 to 3 d can be a time saving and fairly accurate tool, provided that some equation is used to account for inherent differences. The conditions regarding habitat, environmental temperatures, and vectors should also be accounted for in the interpretation of results. The present work proved that to study a specific population, the quantitative study should be conducted at the revelant temperature (30°C for the total population, 7°C for a psychrotrophic population, and 37°C for a mesophilic population). Hence, to study the cold tolerant spoilage population encountered in a certain habitat (e. g. meat), it is advisable to do the quantitative survey at 7°C and further studies on the isolates made at this incubation temperature, could be done at 20 to 25°C.

Sign in / Sign up

Export Citation Format

Share Document