Creating Detailed Metadata for an R Shiny Analysis of Rodent Behavior Sequence Data Detected Along One Light-Dark Cycle

Automated mouse phenotyping through the high-throughput analysis of home cage behavior has brought hope of a more effective and efficient method for testing rodent models of diseases. Advanced video analysis software is able to derive behavioral sequence data sets from multiple-day recordings. However, no dedicated mechanisms exist for sharing or analyzing these types of data. In this article, we present a free, open-source software actionable through a web browser (an R Shiny application), which performs an analysis of home cage behavioral sequence data, which is designed to spot differences in circadian activity while preventing p-hacking. The software aligns time-series data to the light/dark cycle, and then uses different time windows to produce up to 162 behavior variables per animal. A principal component analysis strategy detected differences between groups. The behavior activity is represented graphically for further explorative analysis. A machine-learning approach was implemented, but it proved ineffective at separating the experimental groups. The software requires spreadsheets that provide information about the experiment (i.e., metadata), thus promoting a data management strategy that leads to FAIR data production. This encourages the publication of some metadata even when the data are kept private. We tested our software by comparing the behavior of female mice in videos recorded twice at 3 and 7 months in a home cage monitoring system. This study demonstrated that combining data management with data analysis leads to a more efficient and effective research process

Complex behavioural changes after odour exposure in Drosophila larvae

A variety of odorants attract Drosophila larvae, although this behaviour can be modulated by experience. For instance, larvae pre-exposed to an attractive odorant may subsequently display less attraction towards the same compound. In previous reports, this phenomenon has been interpreted as a drop in olfactory sensitivity, caused by sensory adaptation. We tried to elucidate the basis of this behavioural modification by pre-exposing larvae to various odours. After multiple pre-exposure cycles larvae were repulsed by initially attractive odours, and pre-exposure did not change the threshold concentration driving a behavioural response. We therefore believe that sensitivity to the odorant was only slightly affected in our protocol. Our results thus do not support the previous interpretation and rather suggest that olfactory pre-exposure induces a change in the hedonic value of the odour. Although we did not succeed in elucidating the exact nature of the underlying mechanism, we can reject an association of the odour with the absence of food as an interpretation of the observed behavioural changes; this is because addition of food did not abolish the repulsion to the pre-exposed odour. In addition to ruling out previous interpretations of odour pre-exposure effects, this study stresses the complexity of Drosophila larval behaviour

A decision underlies phototaxis in an insecticide

Like a moth into the flame-phototaxis is an iconic example for innate preferences. Such preferences probably reflect evolutionary adaptations to predictable situations and have traditionally been conceptualized as hard-wired stimulus-response links. Perhaps for that reason, the century-old discovery of flexibility in Drosophila phototaxis has received little attention. Here, we report that across several different behavioural tests, light/dark preference tested in walking is dependent on various aspects of flight. If we temporarily compromise flying ability, walking photopreference reverses concomitantly. Neuronal activity in circuits expressing dopamine and octopamine, respectively, plays a differential role in photopreference, suggesting a potential involvement of these biogenic amines in this case of behavioural flexibility. We conclude that flies monitor their ability to fly, and that flying ability exerts a fundamental effect on action selection in Drosophila. This work suggests that even behaviours which appear simple and hard-wired comprise a value-driven decision-making stage, negotiating the external situation with the animal's internal state, before an action is selected

Is authorship sufficient for today’s collaborative research? A call for contributor roles

Assigning authorship and recognizing contributions to scholarly works is challenging on many levels. Here we discuss ethical, social, and technical challenges to the concept of authorship that may impede the recognition of contributions to a scholarly work. Recent work in the field of authorship shows that shifting to a more inclusive contributorship approach may address these challenges. Recent efforts to enable better recognition of contributions to scholarship include the development of the Contributor Role Ontology (CRO), which extends the CRediT taxonomy and can be used in information systems for structuring contributions. We also introduce the Contributor Attribution Model (CAM), which provides a simple data model that relates the contributor to research objects via the role that they played, as well as the provenance of the information. Finally, requirements for the adoption of a contributorship-based approach are discussed

Anthropogenic VOCs in Abidjan, southern West Africa : From source quantification to atmospheric impacts

Several field campaigns were conducted in the framework of the Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa (DACCIWA) project to measure a broad range of atmospheric constituents. Here we present the analysis of an unprecedented and comprehensive dataset integrating up to 56 volatile organic compounds (VOCs) from ambient sites and emission sources. VOCs were collected on multi-sorbent tubes in the coastal city of Abidjan, Côte d'Ivoire, in winter and summer 2016 and later analysed by gas chromatography coupled with flame ionization and mass spectrometer detectors (GC-FID and GC-MS) at the laboratory. The comparison between VOC emission source profiles and ambient profiles suggests the substantial impact of two-stroke motorized two-wheel vehicles and domestic fires on the composition of Abidjan's atmosphere. However, despite high VOC concentrations near-source, moderate ambient levels were observed (by factors of 10 to 4000 lower), similar to the concentrations observed in northern mid-latitude urban areas. Besides photochemistry, the reported high wind speeds seem to be an essential factor that regulates air pollution levels in Abidjan. Emission ratios (ΔVOC/CO) were established based on real-world measurements achieved for a selected number of representative combustion sources. Maximum measured molar mass emissions were observed from two-wheel vehicles, surpassing other regional sources by 2 orders of magnitude. Local practices like waste burning also make a significant contribution to VOC emissions, higher than those from light-duty vehicles by 1.5 to 8 orders of magnitude. These sources also largely govern the VOC's atmospheric impacts in terms of OH reactivity, secondary organic aerosol formation (SOAP), and photochemical ozone creation potential (POCP). While the contribution of aromatics dominates the atmospheric impact, our measurements reveal the systematic presence of anthropogenic terpenoids in all residential combustion sectors. Finally, emission factors were used to retrieve and quantify VOC emissions from the main anthropogenic source sectors at the national level. Our detailed estimation of VOC emissions suggests that the road transport sector is the dominant source in Côte d'Ivoire, emitting around 1200Gg yr-1 of gas-phase VOCs. These new estimates are 100 and 160 times larger than global inventory estimations from MACCity or EDGAR (v4.3.2), respectively. Additionally, the residential sector is largely underestimated in the global emission inventories, by factors of 13 to 43. Considering only Côte d'Ivoire, these new estimates for VOCs are 3 to 6 times higher than the whole of Europe. Given the significant underestimation of VOC emissions from the transport and residential sectors in Côte d'Ivoire, there is an urgent need to build more realistic and region-specific emission inventories for the entire West African region. This might be true not only for VOCs, but also for all atmospheric pollutants. The lack of waste burning, wood fuel burning and charcoal burning, and fabrication representation in regional inventories also needs to be addressed, particularly in low-income areas where these types of activities are ubiquitous sources of VOC emissions

Is Authorship Sufficient for Today’s Collaborative Research? A Call for Contributor Roles

Assigning authorship and recognizing contributions to scholarly works is challenging on many levels. Here we discuss ethical, social, and technical challenges to the concept of authorship that may impede the recognition of contributions to a scholarly work. Recent work in the field of authorship shows that shifting to a more inclusive contributorship approach may address these challenges. Recent efforts to enable better recognition of contributions to scholarship include the development of the Contributor Role Ontology (CRO), which extends the CRediT taxonomy and can be used in information systems for structuring contributions. We also introduce the Contributor Attribution Model (CAM), which provides a simple data model that relates the contributor to research objects via the role that they played, as well as the provenance of the information. Finally, requirements for the adoption of a contributorship-based approach are discussed

Particle and VOC emission factor measurements for anthropogenic sources in West Africa

A number of campaigns have been carried out to establish the emission factors of pollutants from fuel combustion in West Africa, as part of work package 2 ("Air Pollution and Health") of the DACCIWA (Dynamics-Aerosol-Chemistry-Cloud Interactions in West Africa) FP7 program. Emission sources considered here include wood (hevea and iroko) and charcoal burning, charcoal making, open trash burning, and vehicle emissions, including trucks, cars, buses and two-wheeled vehicles. Emission factors of total particulate matter (TPM), elemental carbon (EC), primary organic carbon (OC) and volatile organic compounds (VOCs) have been established. In addition, emission factor measurements were performed in combustion chambers in order to reproduce field burning conditions for a tropical hardwood (hevea), and obtain particulate emission factors by size (PM0.25, PM1, PM2.5 and PM10). Particle samples were collected on quartz fiber filters and analyzed using gravimetric method for TPM and thermal methods for EC and OC. The emission factors of 58 VOC species were determined using offline sampling on a sorbent tube. Emission factor results for two species of tropical hardwood burning of EC, OC and TPM are 0.98 ± 0.46 g kg-1 of fuel burned (g kg-1), 11.05 ± 4.55 and 41.12 ± 24.62 g kg-1, respectively. For traffic sources, the highest emission factors among particulate species are found for the two-wheeled vehicles with two-stroke engines (2.74 g kg-1 fuel for EC, 65.11 g kg-1 fuel for OC and 496 g kg-1 fuel for TPM). The largest VOC emissions are observed for two-stroke two-wheeled vehicles, which are up to 3 times higher than emissions from light-duty and heavy-duty vehicles. Isoprene and monoterpenes, which are usually associated with biogenic emissions, are present in almost all anthropogenic sources investigated during this work and could be as significant as aromatic emissions in wood burning (1 g kg-1 fuel). EC is primarily emitted in the ultrafine fraction, with 77 % of the total mass being emitted as particles smaller than 0.25 μm. The particles and VOC emission factors obtained in this study are generally higher than those in the literature whose values are discussed in this paper. This study underlines the important role of in situ measurements in deriving realistic and representative emission factors