it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed.The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge.Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers journal seriesThe Frontiers journal series is a multi-tier and interdisciplinary set of openaccess, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing.All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community.At the same time, the Frontiers journal series operates on a revolutionary invention, the tiered publishing system, initially addressing specific communities of scholars, and gradually climbing up to broader public understanding, thus serving the interests of the lay society, too. Dedication to qualityEach Frontiers article is a landmark of the highest quality, thanks to genuinely collaborative interactions between authors and review editors, who include some of the world's best academicians.Research must be certified by peers before entering a stream of knowledge that may eventually reach the public -and shape society; therefore, Frontiers only applies the most rigorous and unbiased reviews.Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view.By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new generation.

This study provides the first implementation of environmental risk assessment (ERA) regarding marine plastic accumulation (environmental threat) in the water body of small islands in the Indonesian Coral Triangle region (a case study in Ambon Bay of Ambon Island). Ambon Bay is a tropical fjord system with outer Ambon Bay (OAB) separated from inner Ambon Bay (IAB) by a shallow sill. The emphasis of ERA was to combine coastal demography determining the probability of occurrence of the threat and flushing capacity of Ambon Bay determining the vulnerability of the system to the threat to evaluate risk during the peak rainfall season (easterly monsoon, June–August). Supplementarily, ERA considered the coral ecosystem in the bay contributing to the vulnerability parameter. This study only calculated flushing time (τ) of OAB due to available information on IAB flushing, and used three simple flushing models: 1D numerical advection–diffusion, salt-exchange and land–ocean​ interaction in coastal zone (LOICZ) models. The flushing time of the entire OAB was found to be 1–1.5 weeks. Inshore OAB was found to be flushed within 1.5–2 weeks while τ of mid OAB was 1–1.5 weeks. The flushing time of offshore OAB was ≤1 week. Regarding the ERA implementation, the probability of occurrence of marine plastics was very high in IAB and inshore OAB (linked to dense-populated areas) compared to in mid and offshore OAB (i.e. moderate-to-low, where sparsely population areas are located). It was also true for the vulnerability of Ambon Bay to marine plastic accumulation that was found to be high in IAB and inshore OAB, linked to slower flushing in these locations than in mid and offshore OAB, located close to the open ocean. Combining this, IAB and inshore OAB showed a high risk of marine plastic contamination than mid and offshore OAB. The knowledge of ERA regarding marine plastic accumulation presented here is informative for other embayments in Indonesia’s Coral Triangle region due to their similarity to Ambon Bay in shape and demographic aspects.

Surface water flushing of the tropical fjord of Ambon Bay is linked to stratification and frontogenesis that vary with tidal and seasonal cycles. Tidal-and seasonal-based deployments of CTD casts and bottom-mounted current meters in 2019 coupled with an analytical model were employed to investigate estuarine circulation (i.e. flood/ebb-mean transport) at the sill of Ambon Bay. Spring tides produce a large (flood/ebb-mean) horizontal salinity gradient, 8S/8x, (up to 13 x 10-4 parts per thousand/m) across the sill, intensifying estuarine circulation. This intensification of 8S/8x is driven by strong (flood/ebb-mean) stratification at the inshore sill, associated with buoyant frontogenesis (indicated by densimetric Froude number, Fo2 >= 0.3) during the related strong flood tides. Estuarine circulation is stronger in the easterly monsoon (July) than in the transitional monsoon (October) since buoyant fronts are larger in thickness and horizontal extension along the sill in the easterly monsoon following high freshwater input. The estuarine circulation was intensified by a deep-water renewal process in which deep water from the adjacent open sea is upwelled to the sill by internal waves.Flushing of inner Ambon Bay (IAB, the fjord basin) due to estuarine circulation at the sill only occurs at the surface layer of IAB. Within a spring-neap sequence (similar to 2 weeks), the net oceanic inflow due to estuarine circulation at the sill replenished 73% and 41% volume of the surface layer of IAB in the easterly monsoon and the transitional season, respectively. The knowledge of flushing of IAB due to net oceanic inflow presented here has application for the mitigation of pollution build-up and for understanding of oceanic nutrient supply in the basin.(c) 2022 Elsevier B.V. All rights reserved.

Seasonal-varying internal tidal dynamics have a critical role in deep-water renewal in tropical shallow-silled fjords (e.g. Ambon Bay, Indonesia). Seasonal- and tidal-based longitudinal CTD casts from the slope of outer Ambon Bay (OAB) to the sill of Ambon Bay coupled with bottom-mounted current meters at the sill and in inner Ambon Bay (IAB, the fjord basin), were employed to investigate the internal tidal-sill slope interaction and the characteristics of deep-water inflow. Weaker stratification in the easterly monsoonal season than the transitional monsoonal season (dT/dz = -0.02 ?C/m cf. dT/dz = -0.06 ?C/m) drives the predominant sub-critical slope condition at the OAB slope causing more frequent tidal upwelling events in the easterly monsoonal season (13 events in a spring-neap sequence) than in the transitional monsoonal season (5 events). The magnitude of tidal upwelling in Ambon Bay, as measured by the depth from which water upwells, is stronger in the easterly monsoonal season (up to 200 m) than in the transitional monsoonal season (maximum: 115 m). The influx of upwelled water across the sill was controlled by the tidal excursion of the deep-water plume in the easterly monsoonal season and by the deep-water/sill density difference in the transitional monsoonal season. A series of deep-water renewal events in IAB within a spring-neap sequence (-2 weeks) in the easterly monsoonal season supplied a total inflow volume of 0.09 ? 0.02 km3 which can replenish approximately 80% volume of the IAB deep layer. This total inflow volume was smaller in the transitional monsoonal season (0.05 ? 0.01 km3), hence, only flushing 40% volume of the IAB deep layer. The knowledge of internal tidal waves and deep-water inflow in Ambon Bay presented here will be a key reference for future studies focused on water transport in Ambon Bay and other shallow-silled tropical fjords.

Robotic weed control has seen increased research of late with its potential for boosting productivity in agriculture. Majority of works focus on developing robotics for croplands, ignoring the weed management problems facing rangeland stock farmers. Perhaps the greatest obstacle to widespread uptake of robotic weed control is the robust classification of weed species in their natural environment. The unparalleled successes of deep learning make it an ideal candidate for recognising various weed species in the complex rangeland environment. This work contributes the first large, public, multiclass image dataset of weed species from the Australian rangelands; allowing for the development of robust classification methods to make robotic weed control viable. The DeepWeeds dataset consists of 17,509 labelled images of eight nationally significant weed species native to eight locations across northern Australia. This paper presents a baseline for classification performance on the dataset using the benchmark deep learning models, Inception-v3 and ResNet-50. These models achieved an average classification accuracy of 95.1% and 95.7%, respectively. We also demonstrate real time performance of the ResNet-50 architecture, with an average inference time of 53.4 ms per image. These strong results bode well for future field implementation of robotic weed control methods in the Australian rangelands.

This study reports palynological and geochemical results for modern and ancient sediments from 19 lakes on a rainfall gradient (784-1880 mm), across a range of savannas in Northern Australia. All proxies varied significantly across the range of sites examined, providing a robust envelope of values that can reliably be employed to identify a savanna signature in the sedimentary record. While the results indicate it is possible to identify a savanna, we found only three statistically significant relationships between any proxy measured in surface sediments and the major climate driver of savanna vegetation composition (rainfall amount). This is because edaphic factors play a dominant role in determining vegetation composition and also potentially because of the impact of land use change. Measures of fire determined by charcoal counting were positively correlated with geochemical measures of pyrogenic carbon abundance, suggesting both record a similar signal. While measures of fire incidence were not correlated with rainfall, there was a significant positive correlation between charcoal abundance and number of fires early in the dry season, suggesting that charcoal abundance is controlled more by the number/timing of fires than climate. There was also a significant correlation between the delta C-13-value of pyrogenic carbon and tree:grass ratio derived from palynological indicators, indicating that the delta C-13-value of PyC is a reliable indicator of savanna 'woodiness'. Comparison of the carbon isotope composition of total organic carbon, PyC and n-alkanes between modern and Holocene sediments suggest that the savannas of the region have remained either similar in 'woodiness' or have thickened over the last millennia. (C) 2018 Elsevier Ltd. All rights reserved.

Hypersaline water is the very common feature in the Great Barrier Reef (GBR) during winter season as evaporation exceeds precipitation. The baroclinic circulation of this saltier water is unknown and thus, some numerical investigation is required. The baroclinic circulation on transporting the hypersaline water to the off shore GBR prevails at deeper bathymetrydue to the insignificance of southeast winds-driven well-mixed condition; the vertical mixing is mostly profound at the shallow inshore GBR. The degree of the baroclinic circulation on at the GBR deep inshore waters was also related to the SE winds-induced alongshore transports of hypersalinity. NF-POGO Alumni E-Newsletter, Vol. 13 December 2017 P: 21-22

Sampling issues represent a persistent problem in shell matrix research, particularly for large shell deposits. When small samples are taken from large buried deposits it is almost impossible, under current research practices, to understand how representative that sample is of the overall deposit. This case study tests a novel method for creating a better understanding of the buried deposits from which excavated samples are taken, thereby allowing for improved sampling strategies and a better understanding of how representative those samples are of the overall site. The case study employs two geophysical survey methods, ground‐penetrating radar (GPR) and electrical resistivity, to investigate buried shell deposits under experimental conditions. The survey results were used to create volume estimations and three‐dimensional (3D) models of buried shell deposits. This method is novel to shell matrix research and the current case study was designed to test the viability of the method under differing conditions. As well as testing the two geophysical methods, surveys were conducted under different moisture levels, soil types and survey transect spacings. Results showed that the 3D models and volume estimates of the deposit were successful in creating a representative understanding of the nature of the buried deposit, but with varying degrees of accuracy. GPR results created more accurate volume estimates and 3D models than the electrical resistivity results. Both geophysical methods produced more accurate results under drier conditions, though the electrical resistivity produced more visually distinct results with higher moisture levels. Analysis of the volume results revealed an error margin (to a confidence level of 95%) of 9.5% ± 15.5% for the GPR, and 44.5% ± 31.5% to 56 ± 70.5% for the electrical resistivity, depending on the interpretation method used to create the models.

Research science used to inform public policy decisions, herein defined as “Policy-Science”, is rarely subjected to rigorous checking, testing and replication. Studies of biomedical and other sciences indicate that a considerable fraction of published peer-reviewed scientific literature, perhaps half, has significant flaws. To demonstrate the potential failings of the present approaches to scientific Quality Control (QC), we describe examples of science associated with perceived threats to the Great Barrier Reef (GBR), Australia. There appears a serious risk of efforts to improve the health of the GBR being directed inefficiently and/or away from the more serious threats. We suggest the need for a new organisation to undertake quality reviews and audits of important scientific results that underpin government spending decisions on the environment. Logically, such a body could also examine policy science in other key areas where governments rely heavily upon scientific results, such as education, health and criminology.

Sedimentation is considered the most widespread contemporary, human-induced perturbation on reefs, and yet if the problems associated with its estimation using sediment traps are recognized, there have been few reliable measurements made over time frames relevant to the local organisms. This study describes the design, calibration and testing of an in situ optical backscatter sediment deposition sensor capable of measuring sedimentation over intervals of a few hours. The instrument has been reconfigured from an earlier version to include 15 measurement points instead of one, and to have a more rugose measuring surface with a microtopography similar to a coral. Laboratory tests of the instrument with different sediment types, colours, particle sizes and under different flow regimes gave similar accumulation estimates to SedPods, but lower estimates than sediment traps. At higher flow rates (9–17 cm s −1 ), the deposition sensor and SedPods gave estimates >10× lower than trap accumulation rates. The instrument was deployed for 39 d in a highly turbid inshore area in the Great Barrier Reef. Sediment deposition varied by several orders of magnitude, occurring in either a relatively uniform (constant) pattern or a pulsed pattern characterized by short-term (4–6 h) periods of ‘enhanced’ deposition, occurring daily or twice daily and modulated by the tidal phase. For the whole deployment, which included several very high wind events and suspended sediment concentrations (SSCs) >100 mg L −1 , deposition rates averaged 19 ± 16 mg cm −2 d −1 . For the first half of the deployment, where SSCs varied from <1 to 28 mg L −1 which is more typical for the study area, the deposition rate averaged only 8 ± 5 mg cm −2 d −1 . The capacity to measure sedimentation rates over a few hours is discussed in terms of examining the risk from sediment deposition associated with catchment run-off, natural wind/wave events and dredging activities.

[Extract] The Great Barrier Reef is often used to show the imminent crisis we are supposedly facing from climate change. It is photogenic, the water sparkles blue, the fish and corals are beautiful and delicate, and most who see it - particularly marine biologists - fall in love with it. It is abhorrent to even contemplate that it could be destroyed or damaged by humanity. The claimed imminent peril faced by the Great Barrier Reef has captured the public's imagination. When then US president Barack Obama visited Australia, he remarked that he wanted global action on climate change, so that maybe his daughters would have a changed to see the Great Barrier Reef. A visiting architect to my university revealed that his daughter, on discussing the latest reef bleaching event at school, came home depressed that she would probably never be able to see the Great Barrier Reef. Most of the world's population seems to have been persuaded that it has no more than a few years left. There is no doubt that every decade or so, abnormally high seawater temperatures can cause corals to bleach (Marshall & Schuttenberg 2006). Bleaching is when the coral expels the symbiotic algae (zooxanthellae) which normally live inside an individual coral polyp. The polyps are the animals, generally a few millimetres across, that make the calcium carbonate structure of the coral. Thousands or even millions of polyps make up an indificual coral. The symbiotic algae live inside the polyp and make energy from sunlight; they share this energy with the polyp in exchange for a comfortable environment. However, when the water gets much hotte than normal, something goes wrong with the symbionts and they effectively become poisonous to the polyp. The polyp expels the symbionts and - because it is the symbionts that give the polyp its colour - the coral turns white. Without the symbionts, the polyp will run out of energy and die within a few weeks or months, unless it takes on more symbionts that float around naturally in the water surrounding the coral. The ghastly white skeletons of bleached coral, particularly when seen on a massive scale, make graphic and compelling images to demonstrate the perils of climate change. The fact that this only happens when the water gets much hotter than normal makes it a plausible hypothesis that coral bleaching is caused by anthropogenic climate change. It is also often claimed by scientists that mass bleaching has only occurred since the 1970s, and that it is a recent phenomenon that did not occur 100 years ago when the water temperature of the Great Barrier Reef was 0.5°°C to 1.0C degrees cooler (Hughes 2016). Despite this apparently plausible hypothesis, it will be argued in this chapter that there is perhaps no ecosystem on Earth better able to cope with rising temperatures than the Great Barrier Reef. Irrespective of one's views about the role of carbon dioxide (CO₂) in warming the climate, it is remarkable that the Great Barrier Reef has become the ecosystem, more than almost all others, that isused to illustrate and claim environmental disaster from the modest warming we have seen over the course of the last century.

Despite the large number of dredging projects worldwide and the perceived environmental threats caused by dredging, there are few large scale water quality studies into the distance to dredge effects, which limits our knowledge of dredging impacts and leads to contentious public interest. Fortunately, we now have access to the largest (spatial and temporal) water quality dataset ever collected during a large scale capital dredging operation providing, for the first time, a comprehensive multi-variate study of the distance to dredge effects. Changes in turbidity, light attenuation and sediment deposition at increasing distances north and south of the dredge zone, and compared to baseline conditions, revealed that significant dredging impacts were confined to sites within 2 - 5 km south of the dredge zone at Barrow Island, Western Australia. Conditions gradually decreased at sites 5 - 10 km south, while all northern sites and sites > 10 km south (including the dredge spoil disposal sites) were unaffected by dredging. The site locations of the Gorgon project allowed us for the first time to determine the spatial extent of the dredge impacts because there were many sites (10 of 26) located within a few kilometres of the dredge.

The coastal hypersaline system of the Great Barrier Reef (GBR) in the dry season, was investigated for the first time using a 3D baroclinic model. In the shallow coastal embayments, salinity increases to c.a. 1‰ above typical offshore salinity (~35.4‰). This salinity increase is due to high evaporation rates and negligible freshwater input. The hypersalinity drifts longshore north-westward due to south-easterly trade winds and may eventually pass capes or headlands, e.g. Cape Cleveland, where the water is considerably deeper (c.a. 15m). Here, a pronounced thermohaline circulation is predicted to occur which flushes the hypersalinity offshore at velocities of up to 0.08m/s. Flushing time of the coastal embayments is around 2–3weeks. During the dry season early summer, the thermohaline circulation reduces and therefore, flushing times are predicted to be slight longer due to the reduced onshore-offshore density gradient compared to that in the dry season winter period.

Dredging poses a potential risk to tropical ecosystems, especially in turbidity-sensitive environments such as coral reefs, filter feeding communities and seagrasses. There is little detailed observational time-series data on the spatial effects of dredging on turbidity and light and defining likely footprints is a fundamental task for impact prediction, the EIA process, and for designing monitoring projects when dredging is underway. It is also important for public perception of risks associated with dredging. Using an extensive collection of in situ water quality data (73 sites) from three recent large scale capital dredging programs in Australia, and which included extensive pre-dredging baseline data, we describe relationships with distance from dredging for a range of water quality metrics. Using a criterion to define a zone of potential impact of where the water quality value exceeds the 80th percentile of the baseline value for turbidity-based metrics or the 20th percentile for the light based metrics, effects were observed predominantly up to three km from dredging, but in one instance up to nearly 20 km. This upper (~20 km) limit was unusual and caused by a local oceanographic feature of consistent unidirectional flow during the project. Water quality loggers were located along the principal axis of this flow (from 200 m to 30 km) and provided the opportunity to develop a matrix of exposure based on running means calculated across multiple time periods (from hours to one month) and distance from the dredging, and summarized across a broad range of percentile values. This information can be used to more formally develop water quality thresholds for benthic organisms, such as corals, filter-feeders (e.g. sponges) and seagrasses in future laboratory- and field-based studies using environmentally realistic and relevant exposure scenarios, that may be used to further refine distance based analyses of impact, potentially further reducing the size of the dredging footprint.

Maintenance and capital dredging represents a potential risk to tropical environments, especially in turbidity-sensitive environments such as coral reefs. There is little detailed, published observational time-series data that quantifies how dredging affects seawater quality conditions temporally and spatially. This information is needed to test realistic exposure scenarios to better understand the seawater-quality implications of dredging and ultimately to better predict and manage impacts of future projects. Using data from three recent major capital dredging programs in North Western Australia, the extent and duration of natural (baseline) and dredging-related turbidity events are described over periods ranging from hours to weeks. Very close to dredging i.e. <500 m distance, a characteristic features of these particular case studies was high temporal variability. Over several hours suspended sediment concentrations (SSCs) can range from 100-500 mg L-1. Less turbid conditions (10-80 mg L-1) can persist over several days but over longer periods (weeks to months) averages were <10 mg L-1. During turbidity events all benthic light was sometimes extinguished, even in the shallow reefal environment, however a much more common feature was very low light 'caliginous' or daytime twilight periods. Compared to pre-dredging conditions, dredging increased the intensity, duration and frequency of the turbidity events by 10-, 5- and 3-fold respectively (at sites <500 m from dredging). However, when averaged across the entire dredging period of 80-180 weeks, turbidity values only increased by 2-3 fold above pre-dredging levels. Similarly, the upper percentile values (e.g., P99, P95) of seawater quality parameters can be highly elevated over short periods, but converge to values only marginally above baseline states over longer periods. Dredging in these studies altered the overall probability density distribution, increasing the frequency of extreme values. As such, attempts to understand the potential biological impacts must consider impacts across telescoping-time frames and changes to extreme conditions in addition to comparing central tendency (mean/median). An analysis technique to capture the entire range of likely conditions over time-frames from hours to weeks is described using a running means/percentile approach.

Histograms of Oriented Gradients (HOGs) have proven to be a robust feature set for many visual object recognition applications. In this paper we investigate a simple but powerful approach to make use of the HOG feature set for in situ leaf classification. The contributions of this work are threefold. Firstly, we present a novel method for segmenting leaves from a textured background. Secondly, we investigate a scale and rotation invariant enhancement of the HOG feature set for texture based leaf classification - whose results compare well with a multi-feature probabilistic neural network classifier on a benchmark data set. And finally, we introduce an in situ data set containing 337 images of Lantana camara - a weed of national significance in the Australian landscape - and neighbouring flora, upon which our proposed classifier achieves high accuracy (86.07%) in reasonable time and is thus viable for real-time detection and control of Lantana camara.