ALBERT

Description: Consistently high data quality is essential for the development of novel loss functions and architectures in the field of deep learning. The existence of such data and labels is usually presumed, while acquiring high-quality datasets is still a major issue in many cases. Subjective annotations by annotators often lead to ambiguous labels in real-world datasets. We propose a data-centric approach to relabel such ambiguous labels instead of implementing the handling of this issue in a neural network. A hard classification is by definition not enough to capture the real-world ambiguity of the data. Therefore, we propose our method “Data-Centric Classification & Clustering (DC3)” which combines semi-supervised classification and clustering. It automatically estimates the ambiguity of an image and performs a classification or clustering depending on that ambiguity. DC3 is general in nature so that it can be used in addition to many Semi-Supervised Learning (SSL) algorithms. On average, our approach yields a 7.6% better F1-Score for classifications and a 7.9% lower inner distance of clusters across multiple evaluated SSL algorithms and datasets. Most importantly, we give a proof-of-concept that the classifications and clusterings from DC3 are beneficial as proposals for the manual refinement of such ambiguous labels. Overall, a combination of SSL with our method DC3 can lead to better handling of ambiguous labels during the annotation process. (Source code is available at https://github.com/Emprime/dc3).

Description: Interactive exploration of Earth system simulations may have great potential to improve the scientific modeling process. It will allow monitoring of the state of the simulation via dashboards presenting real-time diagnostics within a digital twin world. We present the state of the art for Earth system modeling in this context. Cross-domain data handling and fusion will make it possible to integrate model and observation data in the context of digital twins of the ocean. Domain-driven modularization of monolithic Earth system models allows one to recover interfaces for such a cross-domain fusion. Reverse engineering with static and dynamic analysis enables modularization of Earth system models. The modularization does not only help with restructuring existing Earth system models, it also makes it possible to integrate additional scientific domains into the interactive simulation environment.

Description: In the Western Baltic Sea, climate change is happening at much faster rate than in most other seas and organisms are additionally exposed to a steep and variable salinity gradient. Climate change has previously been shown to affect parasite transmission in other marine ecosystems, yet little is known about potential effects of warming and desalination on parasite–host interactions. In laboratory experiments, we determined the combined effects of projected seawater warming and freshening on the emergence, activity, survival, and infectivity of cercariae (free-swimming infectious stage) of the trematode Himasthla elongata (Mehlis 1831), shed from its first intermediate host, the periwinkle Littorina littorea (Linnaeus 1758), in the Baltic Sea. We also assessed the susceptibility of the second intermediate host, the mussel Mytilus edulis Linnaeus, 1758, to cercarial infections. Generally, salinity was the main driver, particularly of cercarial activity, infectivity, and mussel susceptibility to infection. At the lowest salinity (13), cercariae were 50% less active compared to the highest salinity (19). Infection success and host susceptibility followed a similar pattern, with 47% and 43% less metacercariae (encysted stage) present at salinity 13 than at salinity 19, respectively. In contrast, effects of simulated warming were found only for cercarial survival, with cercarial longevity being higher at 19 than at 23 °C. No significant interactions between temperature and salinity were found. In contrast to the literature, the results suggest that a climate change-driven freshening (partly also warming) may lead to a general decline of marine trematodes, with possible beneficial effects for the involved hosts.

Description: This article reviews extensive geophysical survey data, ocean drilling results and long-term seafloor monitoring that constrain the distribution and concentration of gas hydrates within the accretionary prism of the northern Cascadia subduction margin, located offshore Vancouver Island in Canada. Seismic surveys and geologic studies conducted since the 1980s have mapped the bottom simulating reflector (BSR), detected gas hydrate occurrence and estimated gas hydrate and free gas concentrations. Additional constraints were obtained from seafloor-towed, controlled-source electromagnetic surveying. A component of these studies has been the examination of low-temperature seafloor vents and seeps that emit gas and fluids into the ocean. These features are identified seismically as chimney-like zones of reduced acoustic reflectivity within the sediment stratigraphy, functioning as conduits for gas and fluid migration from below the BSR to the seafloor. Gas hydrates have been recovered from the seafloor and from sediment cores at vent sites, mostly in massive (nodular) form and as a vein-like fracture filling. The Ocean Networks Canada cabled NEPTUNE observatory has gathered extensive continuous, long-term observations on gas hydrate dynamics at the seafloor and in boreholes at two nodes on the continental slope featuring high gas hydrate concentrations. Measurements taken at the observatory include a time-series of gas bubble emission rates, changes in the near-seafloor electromagnetic structure and seafloor compliance linked to gas hydrate formation and dissociation. Two Integrated Ocean Drilling Program (IODP) expeditions collected cores, measured downhole properties and deployed downhole instruments within the central accretionary prism. At IODP Site U1364, pore pressures are being monitored above and below the base of the gas hydrate stability zone at a slope setting using an “Advanced Circulation Obviation Retrofit Kit” (A-CORK). Downhole pore pressures, temperatures and electrical resistivities also are being monitored at IODP Site U1416 using the “Simple Cabled Instrument for Measuring Parameters In Situ” (SCIMPI) tool at a vent site from near-seafloor to just above the base of the gas hydrate stability zone.

Description: The southern African subcontinent and its surrounding oceans accommodate globally unique ecoregions, characterized by exceptional biodiversity and endemism. This diversity is shaped by extended and steep physical gradients or environmental discontinuities found in both ocean and terrestrial biomes. The region’s biodiversity has historically been the basis of life for indigenous cultures and continues to support countless economic activities, many of them unsustainable, ranging from natural resource exploitation, an extensive fisheries industry and various forms of land use to nature-based tourism. Being at the continent’s southern tip, terrestrial species have limited opportunities for adaptive range shifts under climate change, while warming is occurring at an unprecedented rate. Marine climate change effects are complex, as warming may strengthen thermal stratification, while shifts in regional wind regimes influence ocean currents and the intensity of nutrient-enriching upwelling. The flora and fauna of marine and terrestrial southern African biomes are of vital importance for global biodiversity conservation and carbon sequestration. They thus deserve special attention in further research on the impacts of anthropogenic pressures including climate change. Excellent preconditions exist in the form of long-term data sets of high quality to support scientific advice for future sustainable management of these vulnerable biomes.

Description: Environmental factors shape the structure and functioning of benthic communities. In coastal zones of the southwestern Baltic Sea, boulder fields represent one of the most productive habitats, supporting diverse benthic communities that provide many ecosystem services. In this study, the influence of the geological characteristics of boulder fields on the biodiversity of associated hard-bottom communities was investigated at two different spatial scales (few kilometers and tens of kilometers). The analyses on overall richness (taxonomic and functional) and community composition revealed how: (i) locally the size of boulders and (ii) regionally site-specific factors like the boulder density distribution and the sediment distribution can act as environmental driving forces. The overall richness of assemblages was shown to increase with increasing surface area of boulders, by up to 60% for species and up to 40% for functional richness. At both investigated scales, differences in compositional variability (β diversity) of the communities were detected. Locally, smallest boulders hosted more variable communities (β diversity up to 2 times higher), while at the regional level, indications of a larger habitat heterogeneity featuring the highest β diversity were observed. This study exemplifies how geological habitat characteristics shape the biodiversity of boulder field communities. The obtained information could be considered in assessment strategies, in order to avoid misclassifications of habitats naturally limited in biodiversity, making a step forward to the desired objective of protecting, conserving, and managing boulder field communities in the study area and at other comparable sites.

Description: In addition to being a major threat to biodiversity and ecosystem functioning, biological invasions also have profound impacts on economies and human wellbeing. However, the threats posed by invasive species often do not receive adequate attention and lack targeted management. In part, this may result from different or even ambivalent perceptions of invasive species which have a dual effect for stakeholders—being simultaneously a benefit and a burden. For these species, literature that synthesizes best practice is very limited, and analyses providing a comprehensive understanding of their economics are generally lacking. This has resulted in a critical gap in our understanding of the underlying trade-offs surrounding management efforts and approaches. Here, we explore qualitative trends in the literature for invasive species with dual effects, drawing from both the recently compiled InvaCost database and international case studies. The few invasive species with dual roles in InvaCost provide evidence for a temporal increase in reporting of costs, but with benefits relatively sporadically reported alongside costs. We discuss methods, management, assessment and policy frameworks dedicated to these species, along with lessons learned, complexities and persisting knowledge gaps. Our analysis points at the need to enhance scientific understanding of those species through inter- and cross-disciplinary efforts that can help advance their management.

Description: Interannual sea surface temperature (SST) variations in the tropical Atlantic Ocean lead to anomalous atmospheric circulation and precipitation patterns with important ecological and socioeconomic consequences for the semiarid regions of sub-Saharan Africa and northeast Brazil. This interannual SST variability is characterized by three modes: an Atlantic meridional mode featuring an anomalous cross-equatorial SST gradient that peaks in boreal spring; an Atlantic zonal mode (Atlantic Nino mode) with SST anomalies in the eastern equatorial Atlantic cold tongue region that peaks in boreal summer; and a second zonal mode of variability with eastern equatorial SST anomalies peaking in boreal winter. Here we investigate the extent to which there is any seasonality in the relationship between equatorial warm water recharge and the development of eastern equatorial Atlantic SST anomalies. Seasonally stratified cross-correlation analysis between eastern equatorial Atlantic SST anomalies and equatorial heat content anomalies (evaluated using warm water volume and sea surface height) indicate that while equatorial heat content changes do occasionally play a role in the development of boreal summer Atlantic zonal mode events, they contribute more consistently to Atlantic Nino II, boreal winter events. Event and composite analysis of ocean adjustment with a shallow water model suggest that the warm water volume anomalies originate mainly from the off-equatorial northwestern Atlantic, in agreement with previous studies linking them to anomalous wind stress curl associated with the Atlantic meridional mode.

Description: Cristamonadea is a large class of parabasalian protists that reside in the hindguts of wood-feeding insects, where they play an essential role in the digestion of lignocellulose. This group of symbionts boasts an impressive array of complex morphological characteristics, many of which have evolved multiple times independently. However, their diversity is understudied and molecular data remain scarce. Here we describe seven new species of cristamonad symbionts from Comatermes, Calcaritermes, and Rugitermes termites from Peru and Ecuador. To classify these new species, we examined cells by light and scanning electron microscopy, sequenced the symbiont small subunit ribosomal RNA (rRNA) genes, and carried out barcoding of the mitochondrial large subunit rRNA gene of the hosts to confirm host identification. Based on these data, five of the symbionts characterized here represent new species within described genera: Devescovina sapara n. sp., Devescovina aymara n. sp., Macrotrichomonas ashaninka n. sp., Macrotrichomonas secoya n. sp., and Macrotrichomonas yanesha n. sp. Additionally, two symbionts with overall morphological characteristics similar to the poorly-studied and probably polyphyletic ‘joeniid’ Parabasalia are classified in a new genus Runanympha n. gen.: Runanympha illapa n. sp., and Runanympha pacha n. sp.

Description: Background: Spliceosomal introns are parts of primary transcripts that are removed by RNA splicing. Although introns apparently do not contribute to the function of the mature transcript, in vertebrates they comprise the majority of the transcribed region increasing the metabolic cost of transcription. The persistence of long introns across evolutionary time suggests functional roles that can offset this metabolic cost. The teleosts comprise one of the largest vertebrate clades. They have unusually compact and variable genome sizes and provide a suitable system for analysing intron evolution. Results: We have analysed intron lengths in 172 vertebrate genomes and show that teleost intron lengths are relatively short, highly variable and bimodally distributed. Introns that were long in teleosts were also found to be long in mammals and were more likely to be found in regulatory genes and to contain conserved sequences. Our results argue that intron length has decreased in parallel in a non-random manner throughout teleost evolution and represent a deviation from the ancestral state. Conclusion: Our observations indicate an accelerated rate of intron size evolution in the teleosts and that teleost introns can be divided into two classes by their length. Teleost intron sizes have evolved primarily as a side-effect of genome size evolution and small genomes are dominated by short introns (〈256 base pairs). However, a non-random subset of introns has resisted this process across the teleosts and these are more likely have functional roles in all vertebrate clades.