Overview of the ImageCLEF 2021: Multimedia Retrieval in Medical, Nature, Internet and Social Media Applications

This paper presents an overview of the ImageCLEF 2021 lab that was organized as part of the Conference and Labs of the Evaluation Forum – CLEF Labs 2021. ImageCLEF is an ongoing evaluation initiative (first run in 2003) that promotes the evaluation of technologies for annotation, indexing and retrieval of visual data with the aim of providing information access to large collections of images in various usage scenarios and domains. In 2021, the 19th edition of ImageCLEF runs four main tasks: (i) a medical task that groups three previous tasks, i.e., caption analysis, tuberculosis prediction, and medical visual question answering and question generation, (ii) a nature coral task about segmenting and labeling collections of coral reef images, (iii) an Internet task addressing the problems of identifying hand-drawn and digital user interface components, and (iv) a new social media aware task on estimating potential real-life effects of online image sharing. Despite the current pandemic situation, the benchmark campaign received a strong participation with over 38 groups submitting more than 250 runs

Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics

The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small “miniphages” and large “megaphages” infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13–200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis

Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche

Recent advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages have brought compelling evidence in support of the emergence of eukaryotes from within the archaeal domain of life (eocyte hypothesis)1,2. The discovery of Asgardarchaeota and its supposed position at the base of the eukaryotic tree of life3,4 provided cues about the long-awaited identity of the eocytic lineage from which the nucleated cells (Eukaryota) emerged. While it is apparent that Asgardarchaeota encode a plethora of eukaryotic-specific proteins (the highest number identified yet in prokaryotes)5, the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that favoured the emergence of the protoeukaryote ancestor. Here, we use advanced phylogenetic analyses for inferring the deep ancestry of eukaryotes, and genome-scale metabolic reconstructions for shedding light on the metabolic milieu of Asgardarchaeota. In doing so, we: (1) show that Heimdallarchaeia (the closest eocytic lineage to eukaryotes to date) are likely to have a microoxic niche, based on their genomic potential, with aerobic metabolic pathways that are unique among Archaea (that is, the kynurenine pathway); (2) provide evidence of mixotrophy within Asgardarchaeota; and (3) describe a previously unknown family of rhodopsins encoded within the recovered genomes

Niche-directed evolution modulates genome architecture in freshwater Planctomycetes

Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche)

Effect of RF Power on the Physical Properties of Sputtered ZnSe Nanostructured Thin Films for Photovoltaic Applications

Zinc selenide (ZnSe) thin films were deposited by RF magnetron sputtering in specific conditions, onto optical glass substrates, at different RF plasma power. The prepared ZnSe layers were afterwards subjected to a series of structural, morphological, optical and electrical characterizations. The obtained results pointed out the optimal sputtering conditions to obtain ZnSe films of excellent quality, especially in terms of better optical properties, lower superficial roughness, reduced micro-strain and a band gap value closer to the one reported for the ZnSe bulk semiconducting material. Electrical characterization were afterwards carried out by measuring the current–voltage (I-V) characteristics at room temperature, of prepared “sandwich”-like Au/ZnSe/Au structures. The analysis of I-V characteristics have shown that at low injection levels there is an Ohmic conduction, followed at high injection levels, after a well-defined transition voltage, by a Space Charge Limited Current (SCLC) in the presence of an exponential trap distribution in the band gap of the ZnSe thin films. The results obtained from all the characterization techniques presented, demonstrated thus the potential of ZnSe thin films sputtered under optimized RF plasma conditions, to be used as alternative environmentally-friendly Cd-free window layers within photovoltaic cells manufacturing

On the physical and photo-electrical properties of organic photovoltaic cells based on 1,10-Phenanthroline and 5,10,15,20-Tetra(4-pyridyl)-21H,23H-porphine non-fullerene thin films

The active layer of the bulk heterojunction organic photovoltaic cells is typically based on a polymeric blend containing a donor polymer and a fullerene-based polymer electron acceptor. However, in the last decade non-fullerene polymer-based solar cells have seen a rapid progress, due to their extraordinary chemical, thermal and photo stability, and because of their ability to decrease the voltage loss. The conventional Organic Photovoltaic Cells (OPVs), structures based on either P3HT:PCBM bulk heterojunction (BHJ) polymeric blend or P3HT/PCBM bilayer heterojunction, have limited efficiency and stability, in principal due to the fullerene derivatives used as acceptor component. PCBM for example, as many other fullerene derivatives, exhibits some deficiencies, such as: limited chemical and energetic tunability, small range of absorption spectra, morphological instability and relatively high production costs. That is why in the last years, novel non-fullerene materials started to be used in order to overcome the above limits associated with the fullerene acceptors. In this paper two different non-fullerene acceptor materials have been tested as potential candidates for the efficient OPVs based on P3HT donor polymer as main absorber: a new conjugated polymer containing chelating ligands like 1,10-Phenanthroline (Phen), and a small-molecule acceptor like 5,10,15,20-Tetra(4-pyridyl)-21H,23H-porphine (TPyP). For both cell configurations a decrease of the voltage loss was obtained, and it was also observed that the thickness of the P3HT donor layer has an important contribution to the output power (Pmax) and fill factor (FF) of the OPV structures (FF and Pmax increased almost two times by decreasing the thickness of the P3HT donor layer)

Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

Background: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions. Results: Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes. Conclusions: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.</p

Spatial Distribution and Molecular Diversity of Archaeal Communities in the Extreme Hypersaline Meromictic Brâncoveanu Lake (Transylvanian Basin, Romania)

<p>Dating from the Middle Miocene, the massive halite deposits lying beneath the Transylvanian Basin (Central Romania) have been valuable mineral resources quarried for millennia. Among the numerous hypersaline pit lakes that resulted from this mining, Brâncoveanu Lake is unique by its extreme salinity. Assessment of physicochemical variables, water chemistry and trophic status indicated that Brâncoveanu Lake is a permanently stratified, pH-neutral, NaCl-rich and eutrophied system. We investigated the abundance, molecular diversity and vertical distribution of archaeal community by culture-independent approaches. Additionally, the most relevant environmental parameters shaping the archaeal community composition were evaluated by statistical methods. Archaea appeared to largely outnumber Bacteria; altogether the great prevalence of Halobacteriaceae-related sequences could imply a major contribution of this group to the biogeochemical carbon turnover. The fairly distinct composition of archaeal communities reflects the lake's physicochemical stratification. Among the limnological factors, salinity and oxygen showed a significant impact on determining the composition and structure of archaeal assemblages. Furthermore, Brâncoveanu Lake might harbor novel microorganisms such as members of the recently described phylum Nanohaloarchaea. Overall, this study reported the occurrence of halophilic Archaea in a little explored hydrogeochemical system and provided a better insight into geomicrobiology of meromictic hypersaline pit lakes.</p

Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

Background: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions. Results: Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes. Conclusions: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimilation than previously assumed.BT/Environmental Biotechnolog