scholarly journals Long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods, data management, and long-term population trends

2013 ◽  
Vol 3 (11) ◽  
pp. 3713-3737 ◽  
Author(s):  
Sami P. Ojanen ◽  
Marko Nieminen ◽  
Evgeniy Meyke ◽  
Juha Pöyry ◽  
Ilkka Hanski
Keyword(s):  
Data Management ◽  
Survey Methods ◽  
Population Trends ◽  
Melitaea Cinxia ◽  
Glanville Fritillary Butterfly

scholarly journals Improved chromosome level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) based on SMRT Sequencing and linkage map

2020 ◽  
Author(s):  
Daniel Blande ◽  
Olli-Pekka Smolander ◽  
Virpi Ahola ◽  
Pasi Rastas ◽  
Jaakko Tanskanen ◽  
...  
Keyword(s):  
Linkage Map ◽  
Model System ◽  
Metapopulation Dynamics ◽  
Melitaea Cinxia ◽  
Smrt Sequencing ◽  
Final Assembly ◽  
Glanville Fritillary Butterfly ◽  
Gene Models ◽  
Chromosome Level

AbstractThe Glanville fritillary (Melitaea cinxia) butterfly is a long-term model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome level assembly of the butterfly’s genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO, indicates that the genome contains 93 - 95% of the BUSCO genes in complete and single copies. We predicted 14,830 gene models using the MAKER pipeline and manually curated 1,232 of these gene models. The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome and genetics studies on this species.

scholarly journals Acute symptoms of mild to moderate COVID-19 are highly heterogeneous across individuals and over time

2021 ◽  
Author(s):  
Thomas L Rodebaugh ◽  
Madelyn R Frumkin ◽  
Angela M Reiersen ◽  
Eric J Lenze ◽  
Michael S Avidan ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Survey Methods ◽  
Clinical Care ◽  
Clinical Deterioration ◽  
Symptom Profiles ◽  
Fluctuating Course ◽  
The Common ◽  
Symptom Changes ◽  
Over Time

Abstract Background The symptoms of COVID-19 appear to be heterogenous, and the typical course of these symptoms is unknown. Our objectives were to characterize the common trajectories of COVID-19 symptoms and assess how symptom course predicts other symptom changes as well as clinical deterioration. Methods 162 participants with acute COVID-19 responded to surveys up to 31 times for up to 17 days. Several statistical methods were used to characterize the temporal dynamics of these symptoms. Because nine participants showed clinical deterioration, we explored whether these participants showed any differences in symptom profiles. Results Trajectories varied greatly between individuals, with many having persistently severe symptoms or developing new symptoms several days after being diagnosed. A typical trajectory was for a symptom to improve at a decremental rate, with most symptoms still persisting to some degree at the end of the reporting period. The pattern of symptoms over time suggested a fluctuating course for many patients. Participants who showed clinical deterioration were more likely to present with higher reports of severity of cough and diarrhea. Conclusion The course of symptoms during the initial weeks of COVID-19 is highly heterogeneous and is neither predictable nor easily characterized using typical survey methods. This has implications for clinical care and early-treatment clinical trials. Additional research is needed to determine whether the decelerating improvement pattern seen in our data is related to the phenomenon of patients reporting long-term symptoms, and whether higher symptoms of diarrhea in early illness presages deterioration.

scholarly journals The on-premise data sharing infrastructure e!DAL: Foster FAIR data for faster data acquisition

GigaScience ◽  
2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Daniel Arend ◽  
Patrick König ◽  
Astrid Junker ◽  
Uwe Scholz ◽  
Matthias Lange
Keyword(s):  
Data Management ◽  
Data Storage ◽  
Best Practice ◽  
Research Process ◽  
Research Data ◽  
Primary Data ◽  
Data Repository ◽  
Plant Genomics ◽  
Quality Of Data

Abstract Background The FAIR data principle as a commitment to support long-term research data management is widely accepted in the scientific community. Although the ELIXIR Core Data Resources and other established infrastructures provide comprehensive and long-term stable services and platforms for FAIR data management, a large quantity of research data is still hidden or at risk of getting lost. Currently, high-throughput plant genomics and phenomics technologies are producing research data in abundance, the storage of which is not covered by established core databases. This concerns the data volume, e.g., time series of images or high-resolution hyper-spectral data; the quality of data formatting and annotation, e.g., with regard to structure and annotation specifications of core databases; uncovered data domains; or organizational constraints prohibiting primary data storage outside institional boundaries. Results To share these potentially dark data in a FAIR way and master these challenges the ELIXIR Germany/de.NBI service Plant Genomic and Phenomics Research Data Repository (PGP) implements a “bring the infrastructure to the data” approach, which allows research data to be kept in place and wrapped in a FAIR-aware software infrastructure. This article presents new features of the e!DAL infrastructure software and the PGP repository as a best practice on how to easily set up FAIR-compliant and intuitive research data services. Furthermore, the integration of the ELIXIR Authentication and Authorization Infrastructure (AAI) and data discovery services are introduced as means to lower technical barriers and to increase the visibility of research data. Conclusion The e!DAL software matured to a powerful and FAIR-compliant infrastructure, while keeping the focus on flexible setup and integration into existing infrastructures and into the daily research process.

scholarly journals Contrasting long-term population trends of beach-nesting shorebirds under shared environmental pressures

2021 ◽  
Vol 260 ◽  
pp. 109178
Author(s):  
Eunbi Kwon ◽  
Samantha Robinson ◽  
Chelsea E. Weithman ◽  
Daniel H. Catlin ◽  
Sarah M. Karpanty ◽  
...  
Keyword(s):  
Population Trends ◽  
Environmental Pressures

scholarly journals Increasing frequency of low summer precipitation synchronizes dynamics and compromises metapopulation stability in the Glanville fritillary butterfly

2015 ◽  
Vol 282 (1806) ◽  
pp. 20150173 ◽  
Author(s):  
Ayco J. M. Tack ◽  
Tommi Mononen ◽  
Ilkka Hanski
Keyword(s):  
Population Dynamics ◽  
Population Change ◽  
Temporal Dynamics ◽  
Summer Precipitation ◽  
Life History Stage ◽  
General Effect ◽  
Spatial Synchrony ◽  
Glanville Fritillary Butterfly ◽  
Spatio Temporal

Climate change is known to shift species' geographical ranges, phenologies and abundances, but less is known about other population dynamic consequences. Here, we analyse spatio-temporal dynamics of the Glanville fritillary butterfly ( Melitaea cinxia ) in a network of 4000 dry meadows during 21 years. The results demonstrate two strong, related patterns: the amplitude of year-to-year fluctuations in the size of the metapopulation as a whole has increased, though there is no long-term trend in average abundance; and there is a highly significant increase in the level of spatial synchrony in population dynamics. The increased synchrony cannot be explained by increasing within-year spatial correlation in precipitation, the key environmental driver of population change, or in per capita growth rate. On the other hand, the frequency of drought during a critical life-history stage (early larval instars) has increased over the years, which is sufficient to explain the increasing amplitude and the expanding spatial synchrony in metapopulation dynamics. Increased spatial synchrony has the general effect of reducing long-term metapopulation viability even if there is no change in average metapopulation size. This study demonstrates how temporal changes in weather conditions can lead to striking changes in spatio-temporal population dynamics.

Harvest rate of sooty shearwaters (Puffinus griseus) by Rakiura Māori: a potential tool to monitor population trends?

2004 ◽  
Vol 31 (3) ◽  
pp. 319 ◽  
Author(s):  
Jane Catherine Kitson
Keyword(s):  
New Zealand ◽  
Cross Section ◽  
Large Scale ◽  
Population Change ◽  
Population Trends ◽  
Harvest Rate ◽  
General Index ◽  
Careful Screening ◽  
Potential Tool

Sooty shearwaters (tītī, muttonbird, Puffinus griseus) are highly abundant migratory seabirds, which return to breeding colonies in New Zealand. The Rakiura Māori annual chick harvest on islands adjacent to Rakiura (Stewart Island), is one of the last large-scale customary uses of native wildlife in New Zealand. This study aimed to establish whether the rate at which muttonbirders can extract chicks from their breeding burrows indicates population trends of sooty shearwaters. Harvest rates increased slightly with increasing chick densities on Putauhinu Island. Birders' harvest rates vary in their sensitivities to changing chick density. Therefore a monitoring panel requires careful screening to ensure that harvest rates of the birders selected are sensitive to chick density, and represents a cross-section of different islands. Though harvest rates can provide only a general index of population change, it can provide an inexpensive and feasible way to measure population trends. Detecting trends is the first step to assessing the long-term sustainability of the harvest.

Habitat factors related to wild rabbit population trends after the initial impact of rabbit haemorrhagic disease

2006 ◽  
Vol 33 (6) ◽  
pp. 467 ◽  
Author(s):  
Carlos Calvete ◽  
Enrique Pelayo ◽  
Javier Sampietro
Keyword(s):  
Habitat Quality ◽  
Population Trends ◽  
Wild Rabbit ◽  
Pest Species ◽  
Predator Species ◽  
Rabbit Population ◽  
Habitat Factors ◽  
Rabbit Haemorrhagic Disease ◽  
Haemorrhagic Disease

The European wild rabbit (Oryctolagus cuniculus) is an introduced pest species in Australia and New Zealand. Rabbits have a devastating negative impact on agricultural production and biodiversity in these countries, and Rabbit Haemorrhagic Disease (RHD) is currently included in control strategies for rabbit populations. On the other hand, the European wild rabbit is a key native prey species in the Iberian Peninsula. Since the arrival of RHD, however, rabbit populations have undergone dramatic decreases and several predator species at risk of extinction are currently dependent on the rabbit population density. Therefore, from the point of view of biodiversity conservation, evaluating habitat correlates and trends of rabbit populations after the first RHD epizootic is of great interest to improve the long-term control or promotion of wild rabbit populations. We estimated the relationship between habitat factors and long-term population trends as well as the relationships between habitat factors and rabbit abundance 2 and 14 years after the arrival of RHD in several Iberian rabbit populations. We observed that only 26% of surveyed populations seemed to experience an increase in rabbit abundance over the last 12 years and that this increase was higher in the low-rabbit-abundance areas of l992, leading to high rabbit abundance in 2004. Our results suggested that short- and long-term impacts of RHD were related to habitat quality. The initial impact of RHD was higher in more suitable habitats, but increasing long-term population trends were positively related to good habitat quality.

scholarly journals How long can we build it? Ensuring usability of a scientific code base

2021 ◽  
Vol 16 (1) ◽  
pp. 11
Author(s):  
Klaus Rechert ◽  
Jurek Oberhauser ◽  
Rafael Gieschke
Keyword(s):  
Data Management ◽  
Source Code ◽  
Research Data ◽  
Scientific Contribution ◽  
Scientific Publications ◽  
Research Data Management ◽  
Code Base

Software and in particular source code became an important component of scientific publications and henceforth is now subject of research data management.  Maintaining source code such that it remains a usable and a valuable scientific contribution is and remains a huge task. Not all code contributions can be actively maintained forever. Eventually, there will be a significant backlog of legacy source-code. In this article we analyse the requirements for applying the concept of long-term reusability to source code. We use simple case study to identify gaps and provide a technical infrastructure based on emulator to support automated builds of historic software in form of source code.  

scholarly journals FAIR Data Austria - Aligning the Implementation of FAIR Tools and Services

2021 ◽  
Vol 74 (2) ◽  
Author(s):  
Susanne Blumesberger ◽  
Nikos Gänsdorfer ◽  
Raman Ganguly ◽  
Eva Gergely ◽  
Alexander Gruber ◽  
...  
Keyword(s):  
Data Management ◽  
Support Services ◽  
Research Data ◽  
Research Results ◽  
Management Plans ◽  
Project Objectives ◽  
Training And Support

This article gives an overview of the FAIR Data Austria project objectives and current results. In collaboration with our project partners, we work on the development and establishment of tools for managing the lifecycle of research data, including machine-actionable Data Management Plans (maDMPs), repositories for long-term archiving of research results, RDM training and support services, models, and profiles for Data Stewards and FAIR Office Austria.

scholarly journals Developing a Strategy for Imputing Missing Traffic Volume Data

2010 ◽  
Author(s):  
Mei Chen ◽  
Jingxin Xia ◽  
Rongfang (Rachel) Liu
Keyword(s):  
Data Management ◽  
Management System ◽  
Implementation Strategy ◽  
Traffic Volume ◽  
Data Management System ◽  
Volume Data ◽  
Potential Resource ◽  
Transportation Applications ◽  
Archive Data

Archived ITS-generated data can provide a potential resource for many long-term transportation applications. However, missing and suspicious data are inevitable due to detector and communication malfunctions. This paper presents a comparative analysis of various techniques for imputing missing traffic volume data in the archived data management system in Kentucky. The applicability of the techniques, as well as their reliability in terms of data requirement, is also discussed. An implementation strategy for the Kentucky archive data management system is then developed based on the performance and the applicability/reliability analyses.

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