Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the Biodiversity of Understudied Benthic Taxa at Mesophotic and Deeper Depths: Examples From the Order Zoantharia (Anthozoa: Hexacorallia)

Research on so-called ‘minor taxa’ at mesophotic depths has lagged behind that of more commonly researched groups such as fish or hard corals. Exemplar taxa include species of the order Zoantharia, benthic colonial anemones that are cosmopolitan in distribution but understudied in many ecoregion and ecosystems. In this study, we examine the results of rare mesophotic to deep sea surveys (one rebreather, one remotely operated submersible (ROV) + nets, two ROV surveys) from Japan and Israel. We examined the collected images and video data to provide a first estimate of Zoantharia diversity at mesophotic depths. Zoantharians were observed in all surveys, indicating their ubiquitous presence in mesophotic and deeper ecosystems. Additionally, specimens (n=12) acquired via these surveys were phylogenetically analyzed with three DNA markers. Phylogenetic results showed the presence of undescribed species based on the uniqueness of acquired DNA sequences, including one specimen belonging to the family Abyssoanthidae, previously only reported from depths below 2000 m. Other specimens belong to groups that inhabit shallower and deeper depths (Antipathozoanthus, Epizoanthus and Parazoanthidae). These results depart from surveys of mesophotic coral ecosystem fishes and crustaceans, which indicate affiliations almost exclusively with shallow genera and families. We hypothesize that mesophotic depths are an ecotone for zoantharian diversity, with links to both deeper and shallower ecosystem diversity. Future surveys in mesophotic depths should incorporate phylogenetic methods to better catalogue so-called ‘minor taxa’ (not only including Zoantharia) and enhance the scientific foundation for conserving the biodiversity of these threatened ecosystems.
Bedside Measurement of Volatile Organic Compounds in the Atmosphere of Neonatal Incubators Using Ion Mobility Spectrometry

Background: Early and non-invasive diagnosis of common diseases is of great importance in the care of preterm infants. We hypothesized that volatile organic compounds (VOC) can be successfully measured in the neonatal incubator atmosphere. Methods: This is a feasibility study to investigate whether the discrimination of occupied and unoccupied neonatal incubators is possible by bedside measurement of volatile organic compounds (VOCs) on the neonatal intensive care unit. VOC profiles were measured in the incubator air using ion mobility spectrometry coupled to multi-capillary columns (BreathDiscovery B&S Analytik GmbH, Dortmund, Germany). Results: Seventeen incubators occupied by preterm infants (50 measurements) and nine unoccupied neonatal incubators were sampled, using 37 room air measurements as controls. Three VOC signals that allow the discrimination between occupied and unoccupied incubators were identified. The best discrimination was reached by peak P20 exhibiting a sensitivity, specificity, positive predictive value and negative predictive value of 94.0, 88.9, 97.3, and 72.3%, respectively. Use of a decision tree improved these values to 100.0, 88.9, 98.0, and 100.0%, respectively. Discussion: A bedside method that allows the characterization of VOC profiles in the neonatal incubator atmosphere using ion mobility spectrometry was established. Occupied and unoccupied incubators could be discriminated by characterizing VOC profiles. This technique has the potential to yield results within minutes. Thus, future studies are recommended to test the hypothesis that VOCs within neonatal incubators are useful biomarkers for non-invasive diagnostics in preterm neonates.
The EtnaPlumeLab (EPL) research cluster: advance the understanding of Mt. Etna plume, from source characterisation to downwind impact

In 2013, a multidisciplinary research cluster named EtnaPlumeLab (EPL) was established, gathering experts from volcanology and atmospheric science communities. Target of EPL is to advance the understanding of Mt. Etna's gas and aerosol emissions and the related processes, from source to its regional climatic impact in the Mediterranean area. Here, we present the cluster and its three interacting modules: EPL-RADIO (Radioactive Aerosols and other source parameters for better atmospheric Dispersion and Impact estimatiOns), SMED (Sulfur MEditerranean Dispersion) and Med-SuV (MEDiterranean SUpersite Volcanoes) Work Package 5. Preliminary results have for the first time highlighted the relevance of Mt. Etna's plume impact at the Mediterranean regional scale. These results underline that further efforts need to be made to get insight into a synoptic volcanogenic-atmospheric chemistry/climatic understanding of volcanic plumes impact.
Escalation and Morphological Constraints of Antagonistic Armaments in Water Striders

Sexual conflict may result in the escalating coevolution of sexually antagonistic traits. However, our understanding of the evolutionary dynamics of antagonistic traits and their role in association with sex-specific escalation remains limited. Here we study sexually antagonistic coevolution in a genus of water striders called Rhagovelia. We identified a set of male grasping traits and female anti-grasping traits used during pre-mating struggles and show that natural variation of these traits is associated with variation in mating performance in the direction expected for antagonistic coevolution. Phylogenetic mapping detected signal of escalation of these sexually antagonistic traits suggesting an ongoing arms race. Moreover, their escalation appears to be influenced by a trade-off with dispersal through flight in both sexes. Altogether our results highlight how sexual interactions and natural selection may have shaped sex-specific antagonistic trait coevolution.
A Test in a High Altitude Lake of a Multi-Parametric Rapid Methodology for Assessing Life in Liquid Environments on Planetary Bodies: A Potential New Freshwater Polychaete Tubeworm Community

On our planet, aqueous environments such as deep sea or high-altitude aphotic lakes, subject to present or past volcanic activity and active deglaciation, may provide analogues to the aqueous environments found on such planetary bodies as Europa, Titan or Enceladus. We report here methodologies and technologies tested in Laguna Negra, a high altitude lake in the Central Andes, Chile, for exploring and assessing the presence of life within planetary lakes or interior oceans. We adopted a multi-parametric Rapid Ecological Assessment (REA) approach centered around collecting video imagery (by an Underwater Imaging System) and sampling benthic sediments (for sedimentological, biological and geochemical analysis) to depths of 272 m, to complement physico-chemical sampling of the water column and collection of shallow sediments for microbiological analysis (reported in separate publications). This enabled us to classify and assess the apparent status of benthic habitats, based on substrata and environmental characteristics, together with floral and faunal community characteristics and bioturbation artifacts. Videos imagery showed that the lower water column was characterized by a variably intense sestonic flux of particles and debris among which were planktonic organisms such as ostracods, copepods and possibly cladocerans. Sediment analysis revealed at all depths abundant diatom frustules, mainly of an acidophile pennade diatom Pinnularia acidicola, amid vegetal debris likely originating from littoral macrophytes. Video imagery showed that the lakebed was partly covered by microbial mats and depositional matter and harboured an unexpectedly rich assortment of macrofauna, including sponges, tubificid worms, flatworms, bivalves and crustaceans. Various forms of bioturbation were also encountered, some with the animals in the tracks. Most notably, at the deepest site, a previously undescribed faunal feature was evident, apparently formed by a mat-like community of several layers of what appeared to be polychaete tubeworms, possibly of the family Siboglinidae. It is hypothesized that the hydrothermal activity observed in the region may supply the compounds able to support the deep-water microrganisms from which such tubeworms typically gain sustenance. Such processes could be present on other deep and aphotic liquid-water-bearing planetary bodies.
Theoretical Insights Into the Depolymerization Mechanism of Lignin to Methyl p-hydroxycinnamate by [Bmim][FeCl4] Ionic Liquid

Depolymerization of lignin into valuable aromatic compounds is an important starting point for its valorization strategies, which requires the cleavage of C-O and C-C bonds between lignin monomer units. The catalytic cleavage of these bonds is still difficult and challenging. Our previous experimental investigation (Green Chem., 2018, 20: 3743) has shown that methyl p-hydroxycinnamate (MPC) can be produced from molecular tailoring of H unit in lignin by the cleavage of the γ-O ester bond. In this study, the mechanism of [Bmim][FeCl4]-catalyzed depolymerization of lignin was investigated by using the density functional theory (DFT) method. The results reveal that [FeCl4]− anion of the catalyst plays a decisive role in the whole catalytic process, where two possible activation modes including three different potential reaction pathways can realize the depolymerization of lignin model compound. The calculated overall barriers of the catalytic conversion along these potential routes show that the third potential pathway, i.e., methanol firstly activated by [Bmim][FeCl4], has the most probability with the lowest energy barrier, while the second pathway is excluded because the energy barrier is too high. Also, the results illustrate that the solvent effect is beneficial to the reduction of the relative energy for the reaction to form the transition states. Hence, the obtained molecular level information can identify the favorable conversion process catalyzed by metallic ionic liquids to a certain extent, and it is desirable to enhance the utilization of biomass as a ubiquitous feedstock.
“Beige” Cross Talk Between the Immune System and Metabolism

With thymic senescence the epithelial network shrinks to be replaced by adipose tissue. Transcription factor TBX-1 controls thymus organogenesis, however, the same TBX-1 has also been reported to orchestrate beige adipose tissue development. Given these different roles of TBX-1, we have assessed if thymic TBX-1 expression persists and demonstrates this dualism during adulthood. We have also checked whether thymic adipose involution could yield beige adipose tissue. We have used adult mouse and human thymus tissue from various ages to evaluate the kinetics of TBX-1 expression, as well as mouse (TEP1) and human (1889c) thymic epithelial cells (TECs) for our studies. Electron micrographs show multi-locular lipid deposits typical of beige adipose cells. Histology staining shows the accumulation of neutral lipid deposits. qPCR measurements show persistent and/or elevating levels of beige-specific and beige-indicative markers (TBX-1, EAR-2, UCP-1, PPAR-gamma). We have performed miRNome profiling using qPCR-based QuantStudio platform and amplification-free NanoString platform. We have observed characteristic alterations, including increased miR21 level (promoting adipose tissue development) and decreased miR34a level (bias toward beige adipose tissue differentiation). Finally, using the Seahorse metabolic platform we have recorded a metabolic profile (OCR/ECAR ratio) indicative of beige adipose tissue. In summary, our results support that thymic adipose tissue emerging with senescence is bona fide beige adipose tissue. Our data show how the borders blur between a key immune tissue (the thymus) and a key metabolic tissue (beige adipose tissue) with senescence. Our work contributes to the understanding of cross talk between the immune system and metabolism.
Empathy in Females With Autism Spectrum Disorder

Objective: Despite the fact that autism spectrum disorder (ASD) is a common psychiatric diagnosis, knowledge about the special behavioral and neurobiological female phenotype is still scarce. The present study aimed to investigate neural correlates of empathy for physical and social pain and to assess the impact of egocentric perspective taking on social pain empathy in complex social situations in women and girls with ASD. Methods: Nine female individuals with high functioning ASD were compared to nine matched peers without ASD during two functional magnetic resonance imaging (fMRI) experiments, examining empathy for physical and social pain using well-established paradigms. Participants viewed multiple pictorial stimuli depicting a social target in either physically painful or socially unpleasant situations. In the social situations, the participant either shared the social target’s knowledge about the inappropriateness of the situation (observed social target is aware about the embarrassment of the situation; e.g., tripping in public) or not (observed social target is unaware about the embarrassment of the situation; e.g., open zipper). Results: Females with ASD did not rate the physical pain stimuli differently from non-clinical controls. Social pain situations, however, posed a greater challenge to females with ASD: For non-shared knowledge situations, females with ASD rated the social target’s embarrassment as more intense. Thus, compared to non-clinical controls, females with ASD had a stronger egocentric perspective of the situation rather than sharing the social target’s perspective. On the neural systems level, both groups showed activation of areas of the so-called empathy network that was attenuated in females with ASD during empathy for physical and social pain with a particular reduction in insula activation. Conclusion: Females with high functioning ASD are able to share another person’s physical or social pain on the neural systems level. However, hypoactivation of the anterior insula in contrast to individuals without ASD suggests that they are less able to rely on their shared representations of emotions along with difficulties to take over a person’s perspective and to make a clear distinction between their own and someone else’s experience of embarrassment.
LbDSF, the Lysobacter brunescens Quorum-Sensing System Diffusible Signaling Factor, Regulates Anti- Xanthomonas XSAC Biosynthesis, Colony Morphology, and Surface Motility

Lysobacter species are emerging as novel sources of antibiotics, but the regulation of these antibiotics has not been thoroughly elucidated to date. In this work, we identified a small diffusible signaling factor (DSF) molecule (LbDSF) that regulates the biosynthesis of a novel Xanthomonas-specific antibiotic compound (XSAC) in Lysobacter brunescens OH23. LbDSF was isolated from the culture broth of L. brunescens OH23, and the chemical structure of the molecule was determined by NMR and MS. The LbDSF compound induced GUS expression in a reporter strain of Xanthomonas campestris pv. campestris FE58, which contained the gus gene under the control of a DSF-inducible engXCA promoter. LbDSF production was found to be linked to the enoyl-CoA hydratase RpfF and dependent on the two-component regulatory system RpfC (hybrid sensor histidine kinase)/RpfG (response regulator), and LbDSF production was increased 6.72 times in the ΔrpfC compared to wild-type OH23. LbDSF-regulated XSAC production was dramatically decreased in ΔrpfF, ΔrpfC, and ΔrpfG. Additionally, a significant reduction in surface motility and a number of changes in colony morphology was observed in the ΔrpfF, ΔrpfC, and ΔrpfG compared to the wild-type OH23. The exogenous LbDSF significantly increased XSAC production in wild-type OH23 and recovered the XSAC biosynthetic ability in ΔrpfF. Taken together, these results showed that LbDSF is a fatty-acid-derived DSF that positively regulates XSAC biosynthesis, cell morphology, and surface motility. Moreover, the RpfC/RpfG quorum-sensing signal transduction pathway mediates XSAC biosynthesis. These findings may facilitate antibiotic production through genetic engineering in Lysobacter spp.
The Role of Relational Reward Benefits for Developing the Non-Financial Value of a Customer to an Organization: Structural Equation Modeling Approach

Research on the customer value to an organization has been widely explored, yet most studies only determined on the financial value based on the customer’s purchasing behavior. The value of customers beyond their purchasing behavior –defined as the relational worth - has not been commonly captured yet. This non-financial value is one of the drivers in retaining customers, hence it becomes a crucial factor in preserving the profitability of the organization. For this reason, this paper aims to examine the customer non-financial valuations of a loyalty reward program. The scope of the study covered a reward program involving consumer exertions in the context of a Frequent Flyer Program (FFP) offered by an airline in Indonesia. The hypotheses are empirically tested with a sample of FFP members conducted through an online survey (n=475). The data were statistically analyzed using structural equation modeling (SEM) as a first order construct. Results indicate that the perceived social rewards lead to an affective and normative commitment as well as consumers’ satisfaction, while the economic reward did not have an effect on developing affective bonds with members for long-term relationships. The relational benefit offered through the FFP creates affectively and normatively committed members who produce relational behaviors, in terms of WOM, immunity, openness and acquiescence of the members to the airline. Furthermore, the FFP members produced social behaviors toward the airline when they felt satisfied with their relational exchanges.
Lessons Learnt From the 2009 Padang Indonesia, 2011 Tōhoku Japan and 2016 Muisne Ecuador Earthquakes

This paper presents the observations during EEFIT’s post-earthquake reconnaissance missions to the September 20, 2009 Padang (Mw7.6), March 11, 2011 Tōhoku (Mw9.0) and April 16, 2016 Muisne (Mw7.8) earthquakes. The performance of buildings and geotechnical structures within the affected regions were investigated to gain insights on their design and construction deficiencies. Findings on these damage observed are compared along with the characteristics of the earthquake and nature of building codes in these countries. They include building damage caused by resonance, deficiencies in reinforcement detailing, vulnerability to soft storey collapse, ground settlement, soil liquefaction and landslides. It was demonstrated that buildings which were severely damaged had natural building frequencies coinciding with the dominant frequencies of the ground shaking. The locations of damage of several such buildings showed insufficient confining reinforcements and lapping of stirrup links. Soft storey collapses were also observed in the three earthquakes, although many were attributed to old building codes that were less effective. In areas affected by the Muisne earthquake, soft storey collapses were mainly found at mid height of the building rather than at the ground floor as observed in the Padang and Tōhoku earthquakes, likely due to extension of building long after the bottom floors were completed. In the aspect of geotechnical failure, foundations of buildings found on piles performed reasonably well, except for areas affected by soil liquefaction. Landslides occurred following these earthquakes led to large concentration of casualties and property losses, motivating the EEFIT teams to invest efforts in hazard mapping and ground-truthing exercises using satellite images at Padang and Muisne earthquakes respectively. Such geospatial tools applied in these three earthquakes were reviewed and demonstrated to be capable of identifying landslide sites and producing reliable landslide hazard map.
Modulation of Growth Performance and Intestinal Microbiota in Chickens Fed Plant Extracts or Virginiamycin

In this study, the effects of plant extracts (PEs) and virginiamycin (VIRG) on broiler growth performance, as well as on host intestinal microbiota composition and function were investigated. A total of 288 one-day-old male Cobb broiler chickens were randomly divided into four treatment groups (with six replicates per group). The duodenal, ileal, and cecal content of six broilers per treatment group after 14 and 28 days of treatment were sampled. This material was used for high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene. The results showed that chickens fed 400 mg/kg plant extracts (HPE group) had significantly higher average body weights at day 28 as compared to the control group (CT; P < 0.05), and lower feed-to-meat ratios over days 15–42 (P < 0.01). Within the HPE group at day 14, the relative abundances of two bacterial phyla and 10 bacterial genera increased significantly in the ileal microbiota, and the relative abundance of three bacterial phyla and four bacterial genera decreased. The relative abundance of the genus Lactobacillus in the cecal microbiota decreased from 21.48% (CT group) to 8.41% (fed 200 mg/kg PEs; LPE group), 4.2% (HPE group), and 6.58% (fed 30 mg/kg virginiamycin; VIRG group) after 28 days. In contrast, Faecalibacterium and unclassified Rikenellaceae increased in abundance in the HPE group (from 18 to 28.46% and from 10.83 to 27.63%, respectively), while Bacteroides (36.7%) and Lachnospiraceae increased in abundance in the VIRG group. PICRUSt function analysis showed that the ileal microbiota of the PE treatment groups were more enriched in genes related to the meolism of cofactors and vitamins. In addition, the cecal microbiotas of the LPE and HPE groups were enriched in genes predicted to encode enzymes within 15 and 20 pathways, respectively. These pathways included protein digestion and absorption, amino acid metabolism, lipid biosynthesis, lipopolysaccharide biosynthesis, the citrate cycle (TCA cycle), and lipoic acid metabolism. Similarly, the VIRG group was enriched in 55 metabolic pathways (17 in the duodenum, 18 in the ileum, and 20 in the cecum) on day 28 (P < 0.05). Thus, the results indicated that the observed increase in broiler growth performance after PE or VIRG supplementation might be attributed to an improvement in intestinal microbial composition and metabolic function.
Microbially Enhanced Oil Recovery by Alkylbenzene-Oxidizing Nitrate-Reducing Bacteria

Microbially enhanced oil recovery (MEOR) of heavy oil and bitumen is challenging because light hydrocarbons, which can feed resident microbial communities are present in low concentrations, if at all. We have recently shown that increasing the toluene concentration of heavy oil by aqueous injection followed by injection of nitrate boosts the activity of toluene-oxidizing nitrate-reducing bacteria in heavy oil-containing sand pack columns, giving production of residual oil in place (ROIP). In the current work we found that ethylbenzene is as effective as toluene. Microbial community analyses indicated Thauera and Pseudomonas to be main components of nitrate-containing batch and continuous cultures, regardless whether ethylbenzene or toluene was used as the electron donor. Biomass from batch cultures grown with heavy oil amended with ethylbenzene or toluene and nitrate or biomass from continuous cultures grown on ethylbenzene or toluene and nitrate had similar MEOR activity. Increasing the concentration of injected biomass from continuous cultures increased the fraction of ROIP recovered both in the absence and in the presence of nitrate. Nitrate increased the fraction of ROIP recovered by about 2-fold by increasing the concentration of biomass in the columns. Emulsification of oil by surface-adhering biomass and blocking of aqueous flow channels by oil emulsion droplets are proposed as a possible mechanism of hydrocarbon- and nitrate-mediated MEOR. Pure isolates Thauera sp. NS1 and Pseudomonas sp. NS2, which used both ethylbenzene and toluene, were obtained but did not offer improved MEOR compared to the use of batch and continuous cultures.