Solutions for providing web-accessible, semi-standardised ecosystem research site information

2020 ◽  
Author(s):  
Christoph Wohner ◽  
Johannes Peterseil ◽  
Tomáš Kliment ◽  
Doron Goldfarb
Keyword(s):  
Information Management System ◽  
Third Party ◽  
Data Format ◽  
Ecosystem Research ◽  
Data Formats ◽  
Research Infrastructures ◽  
Low Threshold ◽  
Rest Api ◽  
Research Domains

<p>There are a number of systems dedicated to the storage of information about ecosystem research sites, often used for the management of such facilities within research networks or research infrastructures. If such systems provide interfaces for querying this information, these interfaces and especially their data formats may vary greatly with no established data format standard to follow.</p><p>DEIMS-SDR (Dynamic Ecological Information Management System - Site and Dataset Registry; https://deims.org) is one such service that allows registering and discovering long-term ecosystem research sites, along with the data gathered at those sites and networks associated with them. We present our approach to make the hosted information openly available via a REST-API. While this allows flexibility in the way information is structured, it also follows interoperability standards and specifications that provide clear rules on how to parse this information.</p><p>The REST-API follows the OpenAPI 3.0 specification, including the usage of JSON schemas for describing the exact structure of available records. In addition, DEIMS-SDR also issues persistent, unique and resolvable identifiers for sites independent of the affiliation with research infrastructures or networks.</p><p>The flexible design of the DEIMS-SDR data model and the underlying REST-API based approach provide a low threshold for incorporating information from other research domains within the platform itself as well as integrating its exposed metadata with third party information through external means.</p>

scholarly journals Data sharing and interoperability from multi-source long term observations: challenges and opportunities in marine biology

2018 ◽  
Author(s):  
Mara Sangiovanni ◽  
Roberta Piredda ◽  
Marco Miralto ◽  
Michael Tangherlini ◽  
Maria Luisa Chiusano
Keyword(s):  
Marine Biology ◽  
Data Access ◽  
Data Retrieval ◽  
Ecosystem Research ◽  
Data Formats ◽  
Challenges And Opportunities ◽  
Different Sources ◽  
Anton Dohrn ◽  
Stazione Zoologica

Long-term observatories are widely used in marine sciences to monitor marine ecosystems and investigate their evolution. Recently, data from innovative technologies as well as ‘omics-based' approaches is being collected alongside physical, biogeochemical and taxonomic information. Their integration represents a challenging opportunity, pushing for suitable computational approaches to for data retrieval, storage, interoperability, reusability and sharing. Several initiatives are addressing these issues, suggesting the most appropriate and sensitive strategies and protocols. Ensuring interoperability among different sources and providing seamless data access is essential when designing tools to store and share the collected information.Here we present our effort in the development of web-accessible resources for Long-Term Ecosystem Research (LTER), taking into account available protocols and approaching appropriate software solutions for: i) collecting and integrating real-time environmental and biological observations with -omics data; ii) exploiting international established data formats and protocols to expose through RESTful APIs the collected data; iii) accessing the collections through an interactive, web-accessible resource to permit aggregated views.The aim of this effort is to reinforce the leadership of the Stazione Zoologica “Anton Dohrn” as a Mediterranean Sea marine observatory, and to be ready for the next era challenges in marine biology.

scholarly journals Data sharing and interoperability from multi-source long term observations: challenges and opportunities in marine biology

2018 ◽  
Author(s):  
Mara Sangiovanni ◽  
Roberta Piredda ◽  
Marco Miralto ◽  
Michael Tangherlini ◽  
Maria Luisa Chiusano
Keyword(s):  
Marine Biology ◽  
Data Access ◽  
Data Retrieval ◽  
Ecosystem Research ◽  
Data Formats ◽  
Challenges And Opportunities ◽  
Different Sources ◽  
Anton Dohrn ◽  
Stazione Zoologica

Long-term observatories are widely used in marine sciences to monitor marine ecosystems and investigate their evolution. Recently, data from innovative technologies as well as ‘omics-based' approaches is being collected alongside physical, biogeochemical and taxonomic information. Their integration represents a challenging opportunity, pushing for suitable computational approaches to for data retrieval, storage, interoperability, reusability and sharing. Several initiatives are addressing these issues, suggesting the most appropriate and sensitive strategies and protocols. Ensuring interoperability among different sources and providing seamless data access is essential when designing tools to store and share the collected information.Here we present our effort in the development of web-accessible resources for Long-Term Ecosystem Research (LTER), taking into account available protocols and approaching appropriate software solutions for: i) collecting and integrating real-time environmental and biological observations with -omics data; ii) exploiting international established data formats and protocols to expose through RESTful APIs the collected data; iii) accessing the collections through an interactive, web-accessible resource to permit aggregated views.The aim of this effort is to reinforce the leadership of the Stazione Zoologica “Anton Dohrn” as a Mediterranean Sea marine observatory, and to be ready for the next era challenges in marine biology.

scholarly journals Cost-effectiveness of a hybrid emergency room system for severe trauma: a health technology assessment from the perspective of the third-party payer in Japan

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Takahiro Kinoshita ◽  
Kensuke Moriwaki ◽  
Nao Hanaki ◽  
Tetsuhisa Kitamura ◽  
Kazuma Yamakawa ◽  
...  
Keyword(s):  
Cost Effectiveness ◽  
Emergency Room ◽  
Healthcare Costs ◽  
Cost Effective ◽  
Severe Trauma ◽  
Third Party ◽  
Trauma Patients ◽  
Short Term ◽  
The Third

Abstract Background Hybrid emergency room (ER) systems, consisting of an angiography-computed tomography (CT) machine in a trauma resuscitation room, are reported to be effective for reducing death from exsanguination in trauma patients. We aimed to investigate the cost-effectiveness of a hybrid ER system in severe trauma patients without severe traumatic brain injury (TBI). Methods We conducted a cost-utility analysis comparing the hybrid ER system to the conventional ER system from the perspective of the third-party healthcare payer in Japan. A short-term decision tree and a long-term Markov model using a lifetime time horizon were constructed to estimate quality-adjusted life years (QALYs) and associated lifetime healthcare costs. Short-term mortality and healthcare costs were derived from medical records and claims data in a tertiary care hospital with a hybrid ER. Long-term mortality and utilities were extrapolated from the literature. The willingness-to-pay threshold was set at $47,619 per QALY gained and the discount rate was 2%. Deterministic and probabilistic sensitivity analyses were conducted. Results The hybrid ER system was associated with a gain of 1.03 QALYs and an increment of $33,591 lifetime costs compared to the conventional ER system, resulting in an ICER of $32,522 per QALY gained. The ICER was lower than the willingness-to-pay threshold if the odds ratio of 28-day mortality was < 0.66. Probabilistic sensitivity analysis indicated that the hybrid ER system was cost-effective with a 79.3% probability. Conclusion The present study suggested that the hybrid ER system is a likely cost-effective strategy for treating severe trauma patients without severe TBI.

scholarly journals Methods to Prevent Future Severe Animal Welfare Problems Caused by COVID-19 in the Pork Industry

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 830
Author(s):  
Temple Grandin
Keyword(s):  
Animal Welfare ◽  
Detrimental Effect ◽  
Third Party ◽  
Electrical Parameters ◽  
Short Term ◽  
Pork Industry ◽  
Third Party Auditing ◽  
The Cost ◽  
High Welfare

In the U.S., the most severe animal welfare problems caused by COViD-19 were in the pork industry. Thousands of pigs had to be destroyed on the farm due to reduced slaughter capacity caused by ill workers. In the future, both short-term and long-term remedies will be needed. In the short-term, a portable electrocution unit that uses scientifically validated electrical parameters for inducing instantaneous unconsciousness, would be preferable to some of the poor killing methods. A second alternative would be converting the slaughter houses to carcass production. This would require fewer people to process the same number of pigs. The pandemic revealed the fragility of large centralized supply chains. A more distributed supply chain with smaller abattoirs would be more robust and less prone to disruption, but the cost of pork would be greater. Small abattoirs can coexist with large slaughter facilities if they process pigs for specialized premium markets such as high welfare pork. The pandemic also had a detrimental effect on animal welfare inspection and third party auditing programs run by large meat buyers. Most in-person audits in the slaughter plants were cancelled and audits were done by video. Video audits should never completely replace in-person audits.

scholarly journals Consistency in mutualism relies on local, rather than wider community biodiversity

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Katie Dunkley ◽  
Jo Cable ◽  
Sarah E. Perkins
Keyword(s):  
Biodiversity Loss ◽  
Context Dependency ◽  
Third Party ◽  
Interaction Patterns ◽  
Specific Time ◽  
Specific Time Point ◽  
Service Resource ◽  
Resource Mutualism ◽  
Time Point

AbstractMutualistic interactions play a major role in shaping the Earth’s biodiversity, yet the consistent drivers governing these beneficial interactions are unknown. Using a long-term (8 year, including > 256 h behavioural observations) dataset of the interaction patterns of a service-resource mutualism (the cleaner-client interaction), we identified consistent and dynamic predictors of mutualistic outcomes. We showed that cleaning was consistently more frequent when the presence of third-party species and client partner abundance locally increased (creating choice options), whilst partner identity regulated client behaviours. Eight of our 12 predictors of cleaner and client behaviour played a dynamic role in predicting both the quality (duration) and quantity (frequency) of interactions, and we suggest that the environmental context acting on these predictors at a specific time point will indirectly regulate their role in cleaner-client interaction patterns: context-dependency can hence regulate mutualisms both directly and indirectly. Together our study highlights that consistency in cleaner-client mutualisms relies strongly on the local, rather than wider community—with biodiversity loss threatening all environments this presents a worrying future for the pervasiveness of mutualisms.

Oscillations and Long-Lasting Correlations in a Model of the Lateral Geniculate Nucleus and Visual Cortex

2000 ◽  
Vol 84 (4) ◽  
pp. 1863-1868 ◽  
Author(s):  
Kyle L. Kirkland ◽  
Adam M. Sillito ◽  
Helen E. Jones ◽  
David C. West ◽  
George L. Gerstein
Keyword(s):  
Experimental Data ◽  
Visual Cortex ◽  
Cell Membrane ◽  
Lateral Geniculate Nucleus ◽  
Feedback Inhibition ◽  
Frequency Range ◽  
Lateral Geniculate ◽  
Low Threshold ◽  
Thalamocortical System

We have previously developed a model of the corticogeniculate system to explore cortically induced synchronization of lateral geniculate nucleus (LGN) neurons. Our model was based on the experiments of Sillito et al. Recently Brody discovered that the LGN events found by Sillito et al. correlate over a much longer period of time than expected from the stimulus-driven responses and proposed a cortically induced slow covariation in LGN cell membrane potentials to account for this phenomenon. We have examined the data from our model, and we found, to our surprise, that the model shows the same long-term correlation. The model's behavior was the result of a previously unsuspected oscillatory effect, not a slow covariation. The oscillations were in the same frequency range as the well-known spindle oscillations of the thalamocortical system. In the model, the strength of feedback inhibition from the cortex and the presence of low-threshold calcium channels in LGN cells were important. We also found that by making the oscillations more pronounced, we could get a better fit to the experimental data.

scholarly journals Bio::DB::NextProt: A Perl Module for neXtProt Database Information Retrieval

2014 ◽  
Author(s):  
Felipe V Leprevost
Keyword(s):  
Object Oriented ◽  
Third Party ◽  
Reference Database ◽  
Perl Module ◽  
Comprehensive Knowledge ◽  
Knowledge Platform ◽  
Structured Information ◽  
Rest Api ◽  
Human Proteome Project ◽  
Fast Dynamic

The neXtProt database is a comprehensive knowledge platform recently adopted by the Chromosome-centric Human Proteome Project as the main reference database. The primary goal of the project is to identify and catalog every human protein encoded in the human genome. For such, computational approaches have an important role as data analysis and dedicated software are indispensable. Here we describe Bio::DB::NextProt, a Perl module that provides an object-oriented access to the neXtProt REST Web services, enabling the programatically retrieval of structured information. The Bio::DB::NextProt module presents a new way to interact and download information from the neXtProt database. Every parameter available through REST API is covered by the module allowing a fast, dynamic and ready-to-use alternative for those who need to access neXtProt data. Bio::DB::NextProt is an easy-to-use module that provides automatically retrieval of data, ready to be integrated into third-party software or to be used by other programmers on the fly. The module is freely available from from CPAN (metacpan.org/release/Bio-DB-NextProt) and GitHub (github.com/Leprevost/Bio-DB-NextProt) and is released under the perl\_5 license.

scholarly journals The dyad is not enough

2021 ◽  
Vol 58 (3) ◽  
Author(s):  
Torbjörn Bildtgård ◽  
Marianne Winqvist ◽  
Peter Öberg
Keyword(s):  
Life Course ◽  
Exploratory Study ◽  
Social Dynamics ◽  
Intimate Partner ◽  
Life Course Perspective ◽  
Third Party ◽  
Older Parents ◽  
Biological Children ◽  
Over Time

The increasing prevalence of ageing stepfamilies and the potential of stepchildren to act as a source of support for older parents have increased the interest in long-term intergenerational step relationships. Applying a life-course perspective combined with Simmel’s theorizing on social dynamics, this exploratory study aims to investigate the preconditions for cohesion in long-term intergenerational step relationships. The study is based on interviews with 13 older parents, aged 66–79, who have raised both biological children and stepchildren. Retrospective life-course interviews were used to capture the development of step relationships over time. Interviews were analysed following the principles of analytical induction. The results reveal four central third-party relationships that are important for cohesion in intergenerational step relationships over time, involving: (1) the intimate partner; (2) the non-residential parent; (3) the bridge child; and (4) the stepchild-in-law. The findings have led to the conclusion that if we are to understand the unique conditions for cohesion in long-term intergenerational step relationships, we cannot simply compare biological parent–child dyads with step dyads, because the step relationship is essentially a mediated relationship.

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