Dispersal Dynamics in a Wind-Driven Benthic System

Bedload and water column traps were used with simultaneous wind and water velocity measurements to study postlarval macrofaunal dispersal dynamics in Manukau Harbour, New Zealand. A 12-fold range in mean wind condition resulted in large differences in water flow (12-fold), sediment flux (285-fold), and trap collection of total number of individuals (95-fold), number of the dominant infaunal organism (84-fold for the bivalve Macomona liliana), and number of species (4-fold). There were very strong, positive relationships among wind condition, water velocity, sediment flux, and postlarval dispersal, especially in the bedload. Local density in the ambient sediment was not a good predictor of dispersal. Results indicate that postlarval dispersal may influence benthic abundance pat- terns over a range of spatial scales

The iBRA (implant breast reconstruction evaluation) study: protocol for a prospective multi-centre cohort study to inform the feasibility, design and conduct of a pragmatic randomised clinical trial comparing new techniques of implant-based breast reconstruction.

BACKGROUND: Implant-based breast reconstruction (IBBR) is the most commonly performed reconstructive procedure in the UK. The introduction of techniques to augment the subpectoral pocket has revolutionised the procedure, but there is a lack of high-quality outcome data to describe the safety or effectiveness of these techniques. Randomised controlled trials (RCTs) are the best way of comparing treatments, but surgical RCTs are challenging. The iBRA (implant breast reconstruction evaluation) study aims to determine the feasibility, design and conduct of a pragmatic RCT to examine the effectiveness of approaches to IBBR. METHODS/DESIGN: The iBRA study is a trainee-led research collaborative project with four phases:Phase 1 - a national practice questionnaire (NPQ) to survey current practicePhase 2 - a multi-centre prospective cohort study of patients undergoing IBBR to evaluate the clinical and patient-reported outcomesPhase 3- an IBBR-RCT acceptability survey and qualitative work to explore patients' and surgeons' views of proposed trial designs and candidate outcomes.Phase 4 - phases 1 to 3 will inform the design and conduct of the future RCT All centres offering IBBR will be encouraged to participate by the breast and plastic surgical professional associations (Association of Breast Surgery and British Association of Plastic Reconstructive and Aesthetic Surgeons). Data collected will inform the feasibility of undertaking an RCT by defining current practice and exploring issues surrounding recruitment, selection of comparator arms, choice of primary outcome, sample size, selection criteria, trial conduct, methods of data collection and feasibility of using the trainee collaborative model to recruit patients and collect data. DISCUSSION: The preliminary work undertaken within the iBRA study will determine the feasibility, design and conduct of a definitive RCT in IBBR. It will work with the trainee collaborative to build capacity by creating an infrastructure of research-active breast and plastic surgeons which will facilitate future high-quality research that will ultimately improve outcomes for all women seeking reconstructive surgery. TRIAL REGISTRATION: ISRCTN37664281

Experimenting with ecosystem interaction networks in search of threshold potentials in real-world marine ecosystems

Thresholds profoundly affect our understanding and management of ecosystem dynamics, but we have yet to develop practical techniques to assess the risk that thresholds will be crossed. Combining ecological knowledge of critical system interdependencies with a large-scale experiment, we tested for breaks in the ecosystem interaction network to identify threshold potential in real-world ecosystem dynamics. Our experiment with the bivalves Macomona liliana and Austrovenus stutchburyi on marine sandflats in New Zealand demonstrated that reductions in incident sunlight changed the interaction network between sediment biogeochemical fluxes, productivity, and macrofauna. By demonstrating loss of positive feedbacks and changes in the architecture of the network, we provide mechanistic evidence that stressors lead to break points in dynamics, which theory predicts predispose a system to a critical transition

Organism-sediment interactions govern post-hypoxia recovery of ecosystem functioning

Hypoxia represents one of the major causes of biodiversity and ecosystem functioning loss for coastal waters. Since eutrophication-induced hypoxic events are becoming increasingly frequent and intense, understanding the response of ecosystems to hypoxia is of primary importance to understand and predict the stability of ecosystem functioning. Such ecological stability may greatly depend on the recovery patterns of communities and the return time of the system properties associated to these patterns. Here, we have examined how the reassembly of a benthic community contributed to the recovery of ecosystem functioning following experimentally-induced hypoxia in a tidal flat. We demonstrate that organism-sediment interactions that depend on organism size and relate to mobility traits and sediment reworking capacities are generally more important than recovering species richness to set the return time of the measured sediment processes and properties. Specifically, increasing macrofauna bioturbation potential during community reassembly significantly contributed to the recovery of sediment processes and properties such as denitrification, bedload sediment transport, primary production and deep pore water ammonium concentration. Such bioturbation potential was due to the replacement of the small-sized organisms that recolonised at early stages by large-sized bioturbating organisms, which had a disproportionately stronger influence on sediment. This study suggests that the complete recovery of organism-sediment interactions is a necessary condition for ecosystem functioning recovery, and that such process requires long periods after disturbance due to the slow growth of juveniles into adult stages involved in these interactions. Consequently, repeated episodes of disturbance at intervals smaller than the time needed for the system to fully recover organism-sediment interactions may greatly impair the resilience of ecosystem functioning.

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

BACKGROUND: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data was donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Impacts of a novel shellfishing gear on macrobenthos in a marine protected area: pump-scoop dredging in Poole Harbour, UK

Understanding the impact of bottom-fishing gears at various scales and intensities on habitats and species is necessary to inform management. In Poole Harbour, UK, a multiple use marine protected area, fishermen utilise a unique “pump-scoop” dredge to harvest the introduced Manila clam Ruditapes philippinarum. Managers need to balance the socio-economic benefits of the fishery with ecological concerns across the region, which has required a revision of by-laws that include both spatial and temporal measures. Within an operational fishery, we used a Before-After-Control-Impact sampling design to assess the impacts of pump-scoop dredging on benthic physical characteristics and community structure in an area where there was no dredging, an area newly opened to dredging and an area subject to high levels of historic dredging. A sampling grid was used in each area to best capture any fishing effort in the newly opened area. Core samples were taken to a depth of 30 cm within intertidal mudflats. A significant loss of fine sediments was observed in the site subject to high intensity dredging and a significant change in community structure also occurred in both dredged sites throughout the study period. In the newly opened site this was characterised by a relative increase in species richness, including increased abundance of annelid worms, notably Hediste diversicolor and Aphelochaeta marioni and a decline in the abundance of the bivalve mollusc Abra tenuis. These changes, albeit relatively small, are attributed to physical disturbance as a direct result of pump-scoop dredging, although no difference in the classification of the biotope of the site was observed. This is of particular interest to managers monitoring site condition within areas under the new bylaws as the Manila clam is spreading to other protected estuaries in the region

Scale and ecosystem-based management: Navigating mismatches between socio-ecological systems

\ua9 2025Ecosystem Based Management (EBM) is a dynamic process, focused on understanding and managing human interactions with ecosystems across a range of organisational, spatial and temporal scales. Scale-dependency in different disciplines and the interactions between them will affect both the decision-making process and its success. Unsurprisingly, many of the problems encountered by societies in managing natural ecosystems arise because of a mismatch between the scale of management and the scale(s) of the ecological processes being managed. This research therefore aims to produce new knowledge to better understand and communicate scale-dependencies for EBM. We evaluate scale-dependencies in social-ecological systems and provide case study examples where scale is explicitly recognised resulting in ‘scale fit’. Case studies include research that acknowledges ecological heterogeneity when scaling up information and place-based customary practices. We do this against a background of the organisations and legal instruments that are responsible for managing marine systems to ensure social-ecological resilience. Opportunities to align policy and law with marine ecosystems include a series of legal and policy innovations to set high-level, cross-sectoral and cross-scalar policy intention for oceans management which could collectively support EBM approaches across sectors and scales. This research aims to facilitate the development of decision-making practices that explicitly identify scale-dependencies to increase the success of EBM decision-making processes

Intermittent bioirrigation and oxygen dynamics in permeable sediments: An experimental and modeling study of three tellinid bivalves

To explore the dynamic nature of geochemical conditions in bioirrigated marine permeable sediments, we studied the hydraulic activity of three tellinacean bivalve molluscs (the Pacific species Macoma nasuta and Macomona liliana, and the northern Atlantic and Pacific species Macoma balthica). We combined porewater pressure sensing, time-lapse photography and oxygen imaging to quantify the durations and frequencies of tellinid irrigation activity and the associated oxygen dynamics in the sediment. Porewater pressure records of all tellinids were dominated by intermittent porewater pressurization, induced by periodic water injection into the sediment through their excurrent siphons, which resulted in intermittent oxygen supply to subsurface sediments. The irrigation (two–12 minutes long) and intervals between subsequent irrigation bouts (1.5–13 minutes) varied among tellinid species and individual sizes. For large M. liliana and M. nasuta, the average intervals between irrigation bouts were sufficiently long (10 minutes and four minutes, respectively) to allow complete oxygen consumption in between irrigation bouts in all tested sediment types. Irrigation patterns of smaller conspecifics and the smaller species M. balthica were characterized by significantly shorter separation of irrigation bouts, which resulted in more continuous oxygenation of the sediment. Transport-reaction modeling confirmed these species- and size-specific geochemical signatures and indicated that the geochemical character of the sediment is largely conditioned by the interplay between temporal irrigation patterns and sedimentary oxygen consumption rates. For large tellinids, model simulations indicated that oscillatory rather than stationary geochemical conditions are prevalent in a wide range of sediment types, with oxic pockets collapsing completely between periods of active irrigation. Based on the model results we developed analytical approximations that allow estimation of spatio-temporal characteristics of sediment oxygenation for a wide range of sediment types and infaunal activity patterns. Our results emphasize the need to consider the intermittent nature of bioirrigation when studying the geochemical impact of infauna in permeable sediments

The applications of complex network analysis in aquaculture and capture fisheries: a systematic review of trends, challenges, and future directions

The rapid growth of the aquaculture and capture fisheries sector has made a significant contribution to global food security and economic development. However, increasing complexity in managing ecological sustainability, disease control, production efficiency, and supply chain resilience presents ongoing challenges. To address these, complex network analysis (CNA) has been applied to explore interactions among fish species, farms, environmental factors, and stakeholders. This approach provides operational insights, such as identifying vulnerable points in production systems, ecological insights into species and environmental linkages, and economic insights into trade and supply chains, all of which can inform more sustainable management practices. This paper presents a comprehensive review of CNA applications in aquaculture and fisheries, including modelling of disease transmission pathways, gene co-expression networks, trade systems, and production flows. A systematic literature review was conducted following PRISMA guidelines using the Web of Science and Scopus databases. Four major thematic areas emerged from the synthesis: (1) disease spread and control, (2) ecological analysis, (3) genetic analysis, and (4) production and resource flow. Within these themes, researchers used diverse network modelling approaches such as disease transmission models, ecological interaction frameworks, and trade flow networks alongside metrics like centrality measures, clustering coefficients, and modularity to assess structural properties. The review also highlights recurring challenges, including limited data availability, difficulties in model validation, and reliance on static networks that fail to capture temporal dynamics. Future research directions include developing dynamic network models, improving interdisciplinary data integration, and applying machine learning techniques to enhance analytical capabilities. These priorities reflect both the current limitations and the potential for CNA to inform more resilient and adaptive aquaculture and fisheries systems. As the sector continues to expand, CNA offers a valuable framework to support research and management practices that address critical challenges and promote long-term sustainability

Predicting spatio-temporal dynamics in aquaculture networks: An extended Katz index approach

The effective surveillance of the distribution of live fish between aquaculture farms is crucial for maintaining food security and preventing disease outbreaks. However, existing conventional models often assume the network is static and do not incorporate other factors that contribute to movement between farms, lacking the ability to accurately predict future movements, especially given the dynamic interactions within aquaculture networks. This study addresses this gap by developing the Edge-Weighted Katz Index (EWKI), an extension of the traditional Katz index that integrates spatial information to improve the accuracy of predicting fish distribution between farms. Using a comprehensive dataset on the distribution of live fish between farms in England and Wales from the year 2010 and 2023, the study evaluates the performance of the EWKI model in comparison to other similarity-based link prediction methods. The results indicate that the EWKI model significantly outperforms other methods, achieving a precision of 92.89%, a recall of 81.09%, and an F1-score of 86.59%, alongside an AUPR of 93.44% and an AUROC of 99.97%. This research has practical implications, as the developed method can accurately predict the distribution of fish between farms, supporting predictions of disease spread and facilitating targeted interventions. Furthermore, the integration of spatial information into the network analysis has broader applications across various fields where understanding and predicting spatially influenced network dynamics are crucial, including transportation networks