scholarly journals Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

2019 ◽  
Vol 7 ◽  
Author(s):  
Brian Stucky ◽  
James Balhoff ◽  
Narayani Barve ◽  
Vijay Barve ◽  
Laura Brenskelle ◽  
...  
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Use Cases ◽  
Data Systems ◽  
Multiple Sources ◽  
History Data ◽  
Insect Ecology ◽  
Many Sources ◽  
Multicellular Organisms ◽  
Initial Results

Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.

scholarly journals Accessible Routes Integrating Data from Multiple Sources

2020 ◽  
Vol 10 (1) ◽  
pp. 7
Author(s):  
Miguel R. Luaces ◽  
Jesús A. Fisteus ◽  
Luis Sánchez-Fernández ◽  
Mario Munoz-Organero ◽  
Jesús Balado ◽  
...  
Keyword(s):  
Information System ◽  
Data Model ◽  
Large Scale ◽  
Heterogeneous Data ◽  
Multiple Sources ◽  
Heterogeneous Data Sources ◽  
Different Types ◽  
Software Sensors ◽  
The City

Providing citizens with the ability to move around in an accessible way is a requirement for all cities today. However, modeling city infrastructures so that accessible routes can be computed is a challenge because it involves collecting information from multiple, large-scale and heterogeneous data sources. In this paper, we propose and validate the architecture of an information system that creates an accessibility data model for cities by ingesting data from different types of sources and provides an application that can be used by people with different abilities to compute accessible routes. The article describes the processes that allow building a network of pedestrian infrastructures from the OpenStreetMap information (i.e., sidewalks and pedestrian crossings), improving the network with information extracted obtained from mobile-sensed LiDAR data (i.e., ramps, steps, and pedestrian crossings), detecting obstacles using volunteered information collected from the hardware sensors of the mobile devices of the citizens (i.e., ramps and steps), and detecting accessibility problems with software sensors in social networks (i.e., Twitter). The information system is validated through its application in a case study in the city of Vigo (Spain).

scholarly journals PEDRERA. Positive Energy District Renovation Model for Large Scale Actions

Energies ◽  
2021 ◽  
Vol 14 (10) ◽  
pp. 2833
Author(s):  
Paolo Civiero ◽  
Jordi Pascual ◽  
Joaquim Arcas Abella ◽  
Ander Bilbao Figuero ◽  
Jaume Salom
Keyword(s):  
Simulation Model ◽  
Performance Indicators ◽  
Large Scale ◽  
Key Performance Indicators ◽  
Positive Energy ◽  
Design Phase ◽  
Multiple Sources ◽  
Reliable Prediction ◽  
Sensitive Analysis ◽  
Web Platform

In this paper, we provide a view of the ongoing PEDRERA project, whose main scope is to design a district simulation model able to set and analyze a reliable prediction of potential business scenarios on large scale retrofitting actions, and to evaluate the overall co-benefits resulting from the renovation process of a cluster of buildings. According to this purpose and to a Positive Energy Districts (PEDs) approach, the model combines systemized data—at both building and district scale—from multiple sources and domains. A sensitive analysis of 200 scenarios provided a quick perception on how results will change once inputs are defined, and how attended results will answer to stakeholders’ requirements. In order to enable a clever input analysis and to appraise wide-ranging ranks of Key Performance Indicators (KPIs) suited to each stakeholder and design phase targets, the model is currently under the implementation in the urbanZEB tool’s web platform.

scholarly journals The Use of External Controls in FDA Regulatory Decision Making

2021 ◽  
Author(s):  
Mahta Jahanshahi ◽  
Keith Gregg ◽  
Gillian Davis ◽  
Adora Ndu ◽  
Veronica Miller ◽  
...  
Keyword(s):  
Decision Making ◽  
Natural History ◽  
Product Development ◽  
Rare Diseases ◽  
The United States ◽  
External Control ◽  
Common Source ◽  
Published Data ◽  
History Data ◽  
Benefit Risk Assessment

AbstractThe regulatory standards of the United States Food and Drug Administration (FDA) require substantial evidence of effectiveness from adequate and well-controlled trials that typically use a valid comparison to an internal concurrent control. However, when it is not feasible or ethical to use an internal control, particularly in rare disease populations, relying on external controls may be acceptable. To better understand the use of external controls to support product development and approval, we reviewed FDA regulatory approval decisions between 2000 and 2019 for drug and biologic products to identify pivotal studies that leveraged external controls, with a focus on select therapeutic areas. Forty-five approvals were identified where FDA accepted external control data in their benefit/risk assessment; they did so for many reasons including the rare nature of the disease, ethical concerns regarding use of a placebo or no-treatment arm, the seriousness of the condition, and the high unmet medical need. Retrospective natural history data, including retrospective reviews of patient records, was the most common source of external control (44%). Other types of external control were baseline control (33%); published data (11%); and data from a previous clinical study (11%). To gain further insights, a comprehensive evaluation of selected approvals utilizing different types of external control is provided to highlight the variety of approaches used by sponsors and the challenges encountered in supporting product development and FDA decision making; particularly, the value and use of retrospective natural history in the development of products for rare diseases. Education on the use of external controls based on FDA regulatory precedent will allow for continued use and broader application of innovative approaches to clinical trial design, while avoiding delays in product development for rare diseases. Learnings from this review also highlight the need to update regulatory guidance to acknowledge the utility of external controls, particularly retrospective natural history data.

scholarly journals Genome-wide Analysis of Alternative Pre-mRNA Splicing

2007 ◽  
Vol 283 (3) ◽  
pp. 1229-1233 ◽  
Author(s):  
Claudia Ben-Dov ◽  
Britta Hartmann ◽  
Josefin Lundgren ◽  
Juan Valcárcel
Keyword(s):  
Alternative Splicing ◽  
Large Scale ◽  
Mrna Splicing ◽  
Diagnostic Tools ◽  
Primary Transcript ◽  
Genome Wide ◽  
Human Genes ◽  
Multicellular Organisms ◽  
Eukaryotic Genomes ◽  
Key Questions

Alternative splicing of mRNA precursors allows the synthesis of multiple mRNAs from a single primary transcript, significantly expanding the information content and regulatory possibilities of higher eukaryotic genomes. High-throughput enabling technologies, particularly large-scale sequencing and splicing-sensitive microarrays, are providing unprecedented opportunities to address key questions in this field. The picture emerging from these pioneering studies is that alternative splicing affects most human genes and a significant fraction of the genes in other multicellular organisms, with the potential to greatly influence the evolution of complex genomes. A combinatorial code of regulatory signals and factors can deploy physiologically coherent programs of alternative splicing that are distinct from those regulated at other steps of gene expression. Pre-mRNA splicing and its regulation play important roles in human pathologies, and genome-wide analyses in this area are paving the way for improved diagnostic tools and for the identification of novel and more specific pharmaceutical targets.

Synthetic reflection seismograms in three dimensions by a locked‐mode approximation

Geophysics ◽  
1989 ◽  
Vol 54 (3) ◽  
pp. 350-358 ◽  
Author(s):  
G. Nolet ◽  
R. Sleeman ◽  
V. Nijhof ◽  
B. L. N. Kennett
Keyword(s):  
Finite Difference ◽  
Born Approximation ◽  
Large Scale ◽  
Layered Medium ◽  
Three Dimensional ◽  
Simple Algorithm ◽  
Realistic Model ◽  
Three Dimensions ◽  
Acoustic Response ◽  
Many Sources

We present a simple algorithm for computing the acoustic response of a layered structure containing three‐dimensional (3-D) irregularities, using a locked‐mode approach and the Born approximation. The effects of anelasticity are incorporated by use of Rayleigh’s principle. The method is particularly attractive at somewhat larger offsets, but computations for near‐source offsets are stable as well, due to the introduction of anelastic damping. Calculations can be done on small minicomputers. The algorithm developed in this paper can be used to calculate the response of complicated models in three dimensions. It is more efficient than any other method whenever many sources are involved. The results are useful for modeling, as well as for generating test signals for data processing with realistic, model‐induced “noise.” Also, this approach provides an alternative to 2-D finite‐difference calculations that is efficient enough for application to large‐scale inverse problems. The method is illustrated by application to a simple 3-D structure in a layered medium.

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