Intercalibration of assessment methods for macrophytes in lowland streams: direct comparison and analysis of common metrics

The results of four macrophyte assessment methods (French Indice Biologique Macrophytique en Rivière, German Reference Index, British Mean Trophic Rank and Dutch Macrophyte Score) were compared, based on plant survey data of medium-sized lowland streams in Central Europe. To intercalibrate the good quality class boundaries two alternative methods were applied: direct comparison and the use of “common metrics”. While the French and British methods were highly related (R²>0.75), the German RI showed less (0.20<R²<0.55) and the Dutch DMS least correlation (R²<0.10) with other methods. Of 70 macrophyte metrics tested only Ellenberg_N was considerably related to three of the national assessment methods, thus representing a potential common metric for intercalibration. Comparison of quality class boundaries via regression analysis using both intercalibration approaches revealed major differences between classifications of the French, German and British methods, which are, in addition, related in a nonlinear way.     

A fish-based index of estuarine ecological quality incorporating information from both scientific fish survey and experts knowledge

In the Water Framework Directive (European Union) context, a multimetric fish based index is required to assess the ecological status of French estuarine water bodies. A first indicator called ELFI was developed, however similarly to most indicators, the method to combine the core metrics was rather subjective and this indicator does not provide uncertainty assessment. Recently, a Bayesian method to build indicators was developed and appeared relevant to select metrics sensitive to global anthropogenic pressure, to combine them objectively in an index and to provide a measure of uncertainty around the diagnostic. Moreover, the Bayesian framework is especially well adapted to integrate knowledge and information not included in surveys data. In this context, the present study used this Bayesian method to build a multimetric fish based index of ecological quality accounting for experts knowledge. The first step consisted in elaborating a questionnaire to collect assessments from different experts then in building relevant priors to summarize those assessments for each water body. Then, these priors were combined with surveys data in the index to complement the diagnosis of quality. Finally, a comparison between diagnoses using only fish data and using both information sources underlined experts knowledge contribution. Regarding the results, 68% of the diagnosis matched demonstrating that including experts knowledge thanks to the Bayesian framework confirmed or slightly modified the diagnosis provided by survey data but influenced uncertainty around the diagnostic and appeared especially relevant in terms of risk management.     

Vision-Based Framework of Single Master Dual Slave Semi-Autonomous Surgical Robot System

BackgroundIn the traditional Robot assisted minimally invasive surgery (RMIS) scenario, the instruments are fully controlled by the surgeon through tele-operation. Recent works have widely explored the surgical intelligence by integrating advanced approaches to enhance the surgical operating room (OR) outcomes.MethodsWe propose a novel single-master dual-slave framework for semi-autonomous suturing task, laparoscope information is introduced to feed back into the robotic control loop to guide the movement of surgical instrument.ResultsExperimental results demonstrate that the proposed method can handle the single-master dual-slave semi-autonomous suturing subtask. Furthermore, the framework exhibits compelling performance leading to the efficiency of surgical OR.ConclusionsAdding vision information into the robotic control loop can achieve the semi-autonomous operation, improve the surgical OR efficiency, this capability yields new level of intelligence for the RMIS.     

Macroinvertebrate indicators of lake acidification: analysis of monitoring data from UK, Norway and Sweden

Although the acid sensitivity of many invertebrate species in lakes is well known, methods for assessment of lake acidification based on macroinvertebrate samples are less developed than for rivers. This article analyses a number of existing metrics developed for assessment of river acidification, and evaluates their performance for assessment of lake acidification. Moreover, new species-based indicators of lake acidification were developed and tested. The selected dataset contains 668 samples on littoral macroinvertebrates from 427 lakes with almost 60% of the samples from Sweden and the rest from UK and Norway. Flexible, non-parametric regression models were used for explorative analyses of the pressure–response relationships. The metrics have been assessed according to their response to pH, the degree of non-linearity of the response and the influence of humic compounds. Acid-sensitive metrics often showed a threshold in response to pH between 5.8 and 6.5. Highly acid-tolerant metrics were typically dominant across the whole pH range. Humic level had a positive effect for most acid-sensitive metrics. Generally, most metrics showed a more non-linear response pattern for the humic lakes than for clear lakes. The significant relationship between these macroinvertebrate metrics and acidification shows that there is a potential for developing further the assessment systems for ecological quality of lakes based on these metrics, although the metrics explained a low % of the variation (<30%). In order to improve the predictive power of the biotic metrics across the acidified part of Europe, further harmonization and standardisation of sampling effort and taxa identification are needed.     

Development of an estuarine multi-metric fish index and its application to Irish transitional waters

An estuarine multi-metric fish index (EMFI) was developed and applied to Irish transitional waters. The index comprised a balanced and complimentary set of 14 metrics that represent four fish community attributes: species diversity and composition, species abundance, estuarine utilisation, and trophic composition. Reference conditions and metric scoring thresholds were developed using a combination of historical records, best available data, and expert judgement. The index was applied using representative and robust fish monitoring data collected using a suite of methods designed to cover a range of habitats and conditions. To ensure consistency and comparability, all systems were considered at the whole estuary level. A sensitivity analysis was carried out to assess the response of the EMFI under various scenarios of metric change; five metrics were consistently among the most influential on the EMFI in all scenarios of metric manipulation. The overall EMFI was significantly correlated with environmental condition as measured by two separate indicators of ecological state. Ecological status classes were also established based on the relationship between the EMFI and an index of human pressure. The EMFI provides a robust, sensitive, and integrated measure of the ecological status of fishes in transitional waters and meets the requirements of the EU Water Framework Directive.     

Influence of canonical structure determining residues on antibody affinity and stability

A number of light and heavy chain canonical residue core redesigns were made in a therapeutic antibody (AQC2, anti-VLA1) Fab to explore the consequences to binding affinity and stability. These positions are all loop supporting, primarily CDR1 residues which do not directly contact the antigen. Structure based methods were used with and without consensus sequence information. 30 constructs were made, 24 expressed, and 70% of the designs using consensus sequence information retained binding affinity. Some success maintaining stability with more extreme redesigns suggests a surprising tolerance to mutation, though it often comes at the cost of loss of binding affinity and presumed loop conformation changes. In concordance with the expected need to present an ordered surface for binding, a relationship between decreased affinity and decreased stability was observed. Overpacking the core tends to destabilize the molecule and should be avoided.     

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.