The effect of uncertain river forcing on the thermohaline properties of the North West European Shelf Seas

Modeling studies and observations show that the thermohaline properties of the North West European Shelf Seas (NWESS) are sensitive to surface wind and heat flux forcing, as well as river outflows that transport fresh water from land to the ocean. In previous studies, it was assumed that the variability of the thermohaline properties in response to river outflow could be adequately sampled with a high-resolution, submesoscale permitting, long-term (i.e., 30-year) deterministic hindcast. In this study, we assume that the statistical distribution of the river forcing, rather than the time series of forcing itself, is adequately constrained by a 28-year history (1991 to 2018) of river forcing created specifically for our domain. In this way, we created an ensemble of 10 lower-resolution ( 7-km), short-term (i.e., 2.5 years) hindcast models that are forced with randomly perturbed river outflows and an ensemble of surface fluxes from the 10-member ECMWF ERA5 reanalysis (the ‘Test’ ensemble) as well with a companion ensemble that is forced with the ERA5 surface forcing fluxes but unperturbed river outflows (the ‘Base’ ensemble) for the June 2016 through December 2018 time period. In both ensembles, the modeled evolution of 25-hour averaged (to partially filter out tides) temperature and salinity is realistic with peaks in summer for sea surface temperature and in winter for salinity, and annual amplitudes that are comparable to those found in other studies of the NWESS. The increased mean and standard deviation of the sea surface and bottom salinity in the Test ensemble are partly an artifact of the assumption that the errors in river forcing have a log-normal distribution that mimics the episodic nature of river outflow with a positive mean and an asymmetrical shape with a long tail towards large values. For surface density, the standard deviation in the Test ensemble was below 0.5 kg/m3, covering an areal extent larger than that for the Base ensemble throughout the year. The annual cycle of the areal extent of density in that range had a peak in summer and minima in winter, in phase with that of the river outflow forcing. Overall, the effect of uncertain river forcing on the thermohaline properties in this study is small. In order to understand the true impact of river forcings, better temporal and spatial observations of river outflow are needed

X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)(2) molecules by a bis(9-aminoacridine-4-carboxamide) derivative

Acridine-4-carboxamides form a class of known DNA mono-intercalating agents that exhibit cytotoxic activity against tumour cell lines due to their ability to inhibit topoisomerases. Previous studies of bis-acridine derivatives have yielded equivocal results regarding the minimum length of linker necessary between the two acridine chromophores to allow bis-intercalation of duplex DNA. We report here the 1.7 angstrom resolution X-ray crystal structure of a six-carbon-linked bis(acridine-4-carboxamide) ligand bound to d(CGTACG)(2) molecules by non-covalent duplex cross-linking. The asymmetric unit consists of one DNA duplex containing an intercalated acridine-4-carboxamide chromophore at each of the two CG steps. The other half of each ligand is bound to another DNA molecule in a symmetry-related manner, with the alkyl linker threading through the minor grooves. The two crystallographically independent ligand molecules adopt distinct side chain interactions, forming hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast to the semi-disordered state of mono-intercalators bound to the same DNA molecule. The complex described here provides the first structural evidence for the non-covalent cross-linking of DNA by a small molecule ligand and suggests a possible explanation for the inconsistent behaviour of six-carbon linked bis-acridines in previous assays of DNA bis-intercalation

Variations in hydrological connectivity of Australian semiarid landscapes indicate abrupt changes in rainfall-use efficiency of vegetation

[1] Dryland vegetation frequently shows self‐organized spatial patterns as mosaic‐like structures of sources (bare areas) and sinks (vegetation patches) of water runoff and sediments with variable interconnection. Good examples are banded landscapes displayed by Mulga in semiarid Australia, where the spatial organization of vegetation optimizes the redistribution and use of water (and other scarce resources) at the landscape scale. Disturbances can disrupt the spatial distribution of vegetation causing a substantial loss of water by increasing landscape hydrological connectivity and consequently, affecting ecosystem function (e.g., decreasing the rainfall‐use efficiency of the landscape). We analyze (i) connectivity trends obtained from coupled analysis of remotely sensed vegetation patterns and terrain elevations in several Mulga landscapes subjected to different levels of disturbance, and (ii) the rainfall‐use efficiency of these landscapes, exploring the relationship between rainfall and remotely sensed Normalized Difference Vegetation Index. Our analyses indicate that small reductions in the fractional cover of vegetation near a particular threshold can cause abrupt changes in ecosystem function, driven by large nonlinear increases in the length of the connected flowpaths. In addition, simulations with simple vegetation‐thinning algorithms show that these nonlinear changes are especially sensitive to the type of disturbance, suggesting that the amount of alterations that an ecosystem can absorb and still remain functional largely depends on disturbance type. In fact, selective thinning of the vegetation patches from their edges can cause a higher impact on the landscape hydrological connectivity than spatially random disturbances. These results highlight surface connectivity patterns as practical indicators for monitoring landscape health

Australian non-perennial rivers: Global lessons and research opportunities

Non-perennial rivers are valuable water resources that support millions of humans globally, as well as unique riparian ecosystems. In Australia, the Earth’s driest inhabited continent, over 70% of rivers are non-perennial due to a combination of ancient landscape, dry climates, highly variable rainfall regimes, and human interventions that have altered riverine environments. Here, we review Australian non-perennial river research incorporating geomorphology, hydrology, biogeochemistry, ecology, and Indigenous knowledges. The dominant research themes in Australia were drought, floods, salinity, dryland ecology, and water management. Future research will likely follow these themes but must address emerging threats to river systems due to climate change and other anthropogenic impacts. Four high level opportunities for future research are identified, namely: (1) integrating Indigenous and western scientific knowledge; (2) quantifying climate change impacts on hydrological and biological function; (3) clarifying the meaning and measurement of “restoration” of non-perennial systems; and (4) understanding the role of groundwater. These challenges will require inter- and multi-disciplinary efforts supported by technological advances. The evolving body of knowledge about Australian rivers provides a foundation for comparison with other dryland areas globally where recognition of the importance of non-perennial rivers is expanding

Perspectives and Integration in SOLAS Science

Why a chapter on Perspectives and Integration in SOLAS Science in this book? SOLAS science by its nature deals with interactions that occur: across a wide spectrum of time and space scales, involve gases and particles, between the ocean and the atmosphere, across many disciplines including chemistry, biology, optics, physics, mathematics, computing, socio-economics and consequently interactions between many different scientists and across scientific generations. This chapter provides a guide through the remarkable diversity of cross-cutting approaches and tools in the gigantic puzzle of the SOLAS realm. Here we overview the existing prime components of atmospheric and oceanic observing systems, with the acquisition of ocean–atmosphere observables either from in situ or from satellites, the rich hierarchy of models to test our knowledge of Earth System functioning, and the tremendous efforts accomplished over the last decade within the COST Action 735 and SOLAS Integration project frameworks to understand, as best we can, the current physical and biogeochemical state of the atmosphere and ocean commons. A few SOLAS integrative studies illustrate the full meaning of interactions, paving the way for even tighter connections between thematic fields. Ultimately, SOLAS research will also develop with an enhanced consideration of societal demand while preserving fundamental research coherency. The exchange of energy, gases and particles across the air-sea interface is controlled by a variety of biological, chemical and physical processes that operate across broad spatial and temporal scales. These processes influence the composition, biogeochemical and chemical properties of both the oceanic and atmospheric boundary layers and ultimately shape the Earth system response to climate and environmental change, as detailed in the previous four chapters. In this cross-cutting chapter we present some of the SOLAS achievements over the last decade in terms of integration, upscaling observational information from process-oriented studies and expeditionary research with key tools such as remote sensing and modelling. Here we do not pretend to encompass the entire legacy of SOLAS efforts but rather offer a selective view of some of the major integrative SOLAS studies that combined available pieces of the immense jigsaw puzzle. These include, for instance, COST efforts to build up global climatologies of SOLAS relevant parameters such as dimethyl sulphide, interconnection between volcanic ash and ecosystem response in the eastern subarctic North Pacific, optimal strategy to derive basin-scale CO2 uptake with good precision, or significant reduction of the uncertainties in sea-salt aerosol source functions. Predicting the future trajectory of Earth’s climate and habitability is the main task ahead. Some possible routes for the SOLAS scientific community to reach this overarching goal conclude the chapter

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Soil Salinity and pH Drive Soil Bacterial Community Composition and Diversity Along a Lateritic Slope in the Avon River Critical Zone Observatory, Western Australia

Soils are crucial in regulating ecosystem processes, such as nutrient cycling, and supporting plant growth. To a large extent, these functions are carried out by highly diverse and dynamic soil microbiomes that are in turn governed by numerous environmental factors including weathering profile and vegetation. In this study, we investigate geophysical and vegetation effects on the microbial communities of iron-rich lateritic soils in the highly weathered landscapes of Western Australia (WA). The study site was a lateritic hillslope in southwestern Australia, where gradual erosion of the duricrust has resulted in the exposure of the different weathering zones. High-throughput amplicon sequencing of the 16S rRNA gene was used to investigate soil bacterial community diversity, composition and functioning. We predicted that shifts in the microbial community would reflect variations in certain edaphic properties associated with the different layers of the lateritic profile and vegetation cover. Our results supported this hypothesis, with electrical conductivity, pH and clay content having the strongest correlation with beta diversity, and many of the differentially abundant taxa belonging to the phyla Actinobacteria and Proteobacteria. Soil water repellence, which is associated with Eucalyptus vegetation, also affected beta diversity. This enhanced understanding of the natural system could help to improve future crop management in WA since the physicochemical properties of the agricultural soils in this region are inherited from laterites via the weathering and pedogenesis processes