Capturing Emerging Realities in Citizen Engagement in Science in Social Media : A Social Media Analytics Protocol for the Allinteract Study

In the digital era, social media has become a space for the socialization and interaction of citizens, who are using social networks to express themselves and to discuss scientific advances with citizens from all over the world. Researchers are aware of this reality and are increasingly using social media as a source of data to explore citizens' voices. In this context, the methods followed by researchers are mainly based on the content analysis using manual, automated or combined tools. The aim of this article is to share a protocol for Social Media Analytics that includes a Communicative Content Analysis (CCA). This protocol has been designed for the Horizon 2020 project Allinteract, and it includes the social impact in social media methodology. The novel contribution of this protocol is the detailed elaboration of methods and procedures to capture emerging realities in citizen engagement in science in social media using a Communicative Content Analysis (CCA) based on the contributions of Communicative Methodology (CM).Peer reviewe

Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast

Background: Bulk segregant analysis (BSA) coupled to high throughput sequencing is a powerful method to map genomic regions related with phenotypes of interest. It relies on crossing two parents, one inferior and one superior for a trait of interest. Segregants displaying the trait of the superior parent are pooled, the DNA extracted and sequenced. Genomic regions linked to the trait of interest are identified by searching the pool for overrepresented alleles that normally originate from the superior parent. BSA data analysis is non-trivial due to sequencing, alignment and screening errors. Results: To increase the power of the BSA technology and obtain a better distinction between spuriously and truly linked regions, we developed EXPLoRA (EXtraction of over-rePresented aLleles in BSA), an algorithm for BSA data analysis that explicitly models the dependency between neighboring marker sites by exploiting the properties of linkage disequilibrium through a Hidden Markov Model (HMM). Reanalyzing a BSA dataset for high ethanol tolerance in yeast allowed reliably identifying QTLs linked to this phenotype that could not be identified with statistical significance in the original study. Experimental validation of one of the least pronounced linked regions, by identifying its causative gene VPS70, confirmed the potential of our method. Conclusions: EXPLoRA has a performance at least as good as the state-of-the-art and it is robust even at low signal to noise ratio's i.e. when the true linkage signal is diluted by sampling, screening errors or when few segregants are available

Active galactic nuclei synapses: X-ray versus optical classifications using artificial neural networks

(Abridged) Many classes of active galactic nuclei (AGN) have been defined entirely throughout optical wavelengths while the X-ray spectra have been very useful to investigate their inner regions. However, optical and X-ray results show many discrepancies that have not been fully understood yet. The aim of this paper is to study the "synapses" between the X-ray and optical classifications. For the first time, the new EFLUXER task allowed us to analyse broad band X-ray spectra of emission line nuclei (ELN) without any prior spectral fitting using artificial neural networks (ANNs). Our sample comprises 162 XMM-Newton/pn spectra of 90 local ELN in the Palomar sample. It includes starbursts (SB), transition objects (T2), LINERs (L1.8 and L2), and Seyferts (S1, S1.8, and S2). The ANNs are 90% efficient at classifying the trained classes S1, S1.8, and SB. The S1 and S1.8 classes show a wide range of S1- and S1.8-like components. We suggest that this is related to a large degree of obscuration at X-rays. The S1, S1.8, S2, L1.8, L2/T2/SB-AGN (SB with indications of AGN), and SB classes have similar average X-ray spectra within each class, but these average spectra can be distinguished from class to class. The S2 (L1.8) class is linked to the S1.8 (S1) class with larger SB-like component than the S1.8 (S1) class. The L2, T2, and SB-AGN classes conform a class in the X-rays similar to the S2 class albeit with larger fractions of SB-like component. This SB-like component is the contribution of the star-formation in the host galaxy, which is large when the AGN is weak. An AGN-like component seems to be present in the vast majority of the ELN, attending to the non-negligible fraction of S1-like or S1.8-like component. This trained ANN could be used to infer optical properties from X-ray spectra in surveys like eRosita.Comment: 15 pages, 7 figures, accepted for publication in A&A. Appendix B only in the full version of the paper here: https://dl.dropboxusercontent.com/u/3484086/AGNSynapsis_OGM_online.pd

Tomato fruit carotenoid biosynthesis is adjusted to actual ripening progression by a light-dependent mechanism

Carotenoids are isoprenoid compounds that are essential for plants to protect the photosynthetic apparatus against excess light. They also function as health-promoting natural pigments that provide colors to ripe fruit, promoting seed dispersal by animals. Work in Arabidopsis thaliana unveiled that transcription factors of the phytochrome-interacting factor (PIF) family regulate carotenoid gene expression in response to environmental signals (i.e. light and temperature), including those created when sunlight reflects from or passes though nearby vegetation or canopy (referred to as shade). Here we show that PIFs use a virtually identical mechanism to modulate carotenoid biosynthesis during fruit ripening in tomato (Solanum lycopersicum). However, instead of integrating environmental information, PIF-mediated signaling pathways appear to fulfill a completely new function in the fruit. As tomatoes ripen, they turn from green to red due to chlorophyll breakdown and carotenoid accumulation. When sunlight passes through the flesh of green fruit, a self-shading effect within the tissue maintains high levels of PIFs that directly repress the master gene of the fruit carotenoid pathway, preventing undue production of carotenoids. This effect is attenuated as chlorophyll degrades, causing degradation of PIF proteins and boosting carotenoid biosynthesis as ripening progresses. Thus, shade signaling components may have been co-opted in tomato fruit to provide information on the actual stage of ripening (based on the pigment profile of the fruit at each moment) and thus finely coordinate fruit color change. We show how this mechanism may be manipulated to obtain carotenoid-enriched fruits.Peer ReviewedPostprint (published version

Welfare of rainbow trout at slaughter: integrating behavioural, physiological, proteomic and quality indicators and testing a novel fast-chill stunning method

A critical point in the life of a captive fish is the final stages of production, not only in welfare terms but also due to effects on meat quality, carcass appearance and derived economic impacts. The most common method to slaughter fish is by asphyxia either in ice-water or in the open air. In humane slaughter procedures, however, a stunning method needs to be implemented to render the fish immediately unconscious (within one second) until death. The objective of this research was to evaluate and compare the effectiveness and welfare effects of four types of stunning methods in rainbow trout (O. mykiss): cold shock by fast-chilling as a novel method, where the fish were immersed in liquid water at −8 °C, asphyxia (as the currently used method), electrical stunning, and anaesthesia with MS-222. We used a total of 176 trout (mean weight 524 ± 138 g), combining behavioural (individual swimming activity, equilibrium, opercular movement and eye-roll), physiological (heart rate and electrocardiogram amplitude) and circulating (plasma cortisol and osmolality) indicators with brain proteomic signatures. We also analysed the effects on fillet shelf-life and quality in each method (rigor mortis, water content, fillet colour, pH and ATP degradation). Anaesthesia effectively induced unconsciousness, with regular and strong heartbeat and low cortisol. Quality indicators were the best among all the methods assessed. Electric shock was found to be an effective and irreversible method for inducing unconsciousness, with strong heartbeat and large variation in cortisol response and quality indicators similar to anaesthesia. On the contrary, asphyxia presented indicators of poor welfare (e.g., long-lasting consciousness throughout the slaughter process, high cortisol levels), with very low flesh quality parameters. Fast-chilling also resulted in extreme signs of stress (intense mucus release, haemorrhage and no loss of consciousness), low ATP content and the worst proteomic signatures, along with an early onset and resolution of rigor mortis (6 and 48 h, respectively). Our results reinforce the idea that electric stunning is a promising humane method to stun farmed trout. In contrast, the fast-chilling method showed very poor results both in welfare and in quality, indicating that it is not a viable humane alternative to asphyxia. Moreover, the proteome analysis provided valuable insights into the brain mechanisms of rainbow trout at slaughter, offering potential fine-scale biomarkers of welfare.Provincia Autonoma di Trento; Fundação para a Ciência e a Tecnologiainfo:eu-repo/semantics/acceptedVersio

The Structure of IR Luminous Galaxies at 100 Microns

We have observed twenty two galaxies at 100 microns with the Kuiper Airborne Observatory in order to determine the size of their FIR emitting regions. Most of these galaxies are luminous far-infrared sources, with L_FIR > 10^11 L_sun. This data constitutes the highest spatial resolution ever achieved on luminous galaxies in the far infrared. Our data includes direct measurements of the spatial structure of the sources, in which we look for departures from point source profiles. Additionally, comparison of our small beam 100 micron fluxes with the large beam IRAS fluxes shows how much flux falls beyond our detectors but within the IRAS beam. Several sources with point- like cores show evidence for such a net flux deficit. We clearly resolved six of these galaxies at 100 microns and have some evidence for extension in seven others. Those galaxies which we have resolved can have little of their 100 micron flux directly emitted by a point-like active galactic nucleus (AGN). Dust heated to ~40 K by recent bursts of non-nuclear star formation provides the best explanation for their extreme FIR luminosity. In a few cases, heating of an extended region by a compact central source is also a plausible option. Assuming the FIR emission we see is from dust, we also use the sizes we derive to find the dust temperatures and optical depths at 100 microns which we translate into an effective visual extinction through the galaxy. Our work shows that studies of the far infrared structure of luminous infrared galaxies is clearly within the capabilities of new generation far infrared instrumentation, such as SOFIA and SIRTF.Comment: 8 tables, 23 figure

Growth and Welfare Status of Giant Freshwater Prawn (Macrobrachium rosenbergii) Post-Larvae Reared in Aquaponic Systems and Fed Diets including Enriched Black Soldier Fly (Hermetia illucens) Prepupae Meal

Due to the limited application of insect meal in giant freshwater prawn (Macrobrachium rosenbergii) culture, the present study aimed to (i) produce spirulina-enriched full-fat black soldier fly (Hermetia illucens) prepupae meal (HM) and (ii) test, for the first time, two experimental diets characterized by 3% or 20% of fish meal and fish oil replacement with full-fat HM (HM3 and HM20, respectively) on M. rosenbergii post-larvae during a 60-day feeding trial conducted in aquaponic systems. The experimental diets did not negatively affect survival rates or growth. The use of spirulina-enriched HM resulted in a progressive increase in α-tocopherol and carotenoids in HM3 and HM20 diets that possibly played a crucial role in preserving prawn muscle-quality traits. The massive presence of lipid droplets in R cells in all the experimental groups reflected a proper nutrient provision and evidenced the necessity to store energy for molting. The increased number of B cells in the HM3 and HM20 groups could be related to the different compositions of the lipid fraction among the experimental diets instead of a nutrient absorption impairment caused by chitin. Finally, the expression of the immune response and stress markers confirmed that the experimental diets did not affect the welfare status of M. rosenbergii post-larvae