Machine learning in marine ecology: an overview of techniques and applications

Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.Machine learning in marine ecology: an overview of techniques and applicationspublishedVersio

Machine learning in marine ecology: an overview of techniques and applications

Machine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets

IPAAC Rapport WP4 : Cancer control policy interview survey

From July 2018 to January 2020, the Innovative Partnership for Action Against Cancer (iPAAC) Work Package 4 (WP4) performed a survey among European Union (EU) Member States to capture their experience and challenges regarding the implementation of cancer control policies. In total, 28 countries were visited, and the meeting minutes were inductively coded using NVivo qualitative analysis software to provide the core data for this report (https://www.ipaac.eu/res/file/outputs/wp4/ipaac_wp4_ccpis_methodological&#8230;). Two important and consistent rationale for action were found: quality and equity. Through all cancer control domains, the objectives are the same: ensure quality and tackle&nbsp;inequities. When it comes to primary prevention, all countries reported having pursued innovative approaches to better inform and communicate with key stakeholders, especially related to children, adolescents and young adults (AYAs) and lower socio-economic groups. A recurrent issue concerns the sustainability of primary prevention actions. A vicious circle exists due to the difficulty in measuring short-term impacts, which in turn, does not provide support for the provision of structural budgets. Register-based collection of structured and validated data of lifestyles and interventions from electronic data sources in health care would be a key to evaluation and to generate evidence-based&nbsp;recommendations. A second important challenge relates to the interference of the corporate giants of the tobacco, alcohol and food industries. Regulatory actions as well as inter-ministerial and inter-sectorial platforms have proven their efficacy to mitigate the influence of these corporate interests and promote the pursuit and maintenance of healthy&nbsp;lifestyles. Regarding cancer screening, the extent of implementation of screening programs varies widely among EU Member States. The most often reported challenges concern test selection, non-appropriate governance and/or legal frameworks and the effectiveness of population-based screening programs. Some countries, as well as the scientific community, are investigating the possibility of shifting to high-risk stratified screening programme. Some groups have been found to have systematically lower compliance to organized screening programs. Special attention should be given to the means of reaching, informing and inviting these specific populations. The involvement of community health professionals (pharmacists or nurses) and the training of community lay workers have been reported by several countries to better inform the population and raise the participation of target groups to&nbsp;screening. Cancer diagnostics and treatment are of high importance for both quality and equity. Most countries struggle with controlling the rise of the costs of innovation that put the sustainability of their systems at risk. Also, the rapid pace of some innovations can require regular adjustments in reimbursement schemes and decision-making processes. EU cooperation on these two matters is highly sought and&nbsp;needed. Cancer care provision and organization is at the heart of action in most EU countries. It regulates the ‚what and how‘ for cancer patients and their family. Waiting times, lack of cancer care professionals, cultural habits and quality control are recurrent challenges reported by EU countries. In addition, the lack of knowledge and the persistent need to identify best practices, especially for long-term care have been raised. Comprehensive cancer care networks, patient pathways and coordinated activities have been reported as the current ways to improve and ensure quality and equity in the provision of cancer care. More efforts are needed to investigate (evidence-based) improvements that focus on a more patient-centered provision of care, especially for rehabilitation and palliative care. Rare cancers are specific priorities for these networks, especially in relation to European Reference Networks (ERNs). Cancer information systems intersect all dimensions of cancer control and are mainly organized through cancer registries. However, their mandate and subsequent ability to support evidence-based cancer control policy varies widely. The possibility to link with other health, administrative or socio-economical information sources is key but requires legal, ethical and technical adjustments. Enhancing digitalization, data integration and interoperability ‘by design’ is crucial and requires global strategies and resources. In a context of increasing prevalence the lack of data on the whole disease trajectory, including quality of life and survivorship, is considered critical. Also, patient and carers perspectives need to be integrated to ensure meeting their needs and support development of patient-centered&nbsp;interventions. Overall, EU countries are engaged in many cancer control efforts, with differing foci according to specific national needs, political agendas and resources. However, maximum capacity seem to have been reached in many domains and the support from the European Commission (EC) would help to overcome persistent challenges. Three types of support are required. First support for research, including epidemiology and health services research leading to the identification of best practices and the development of guidance. Second, support for knowledge exchange among EU countries on cancer control policy implementation. Third, legal frameworks, i.e. regulations, have the power to ensure coherent activities and provide binding force to expected good quality practice. To ensure improved effectiveness and cost-effectiveness, these three key types of support need to be organized and developed in parallel, integrated and well&nbsp;documented.</p

A reliable DNA barcode reference library for the identification of benthic invertebrates: essential for biomonitoring of the North Sea

Benthic macroinvertebrates are key components in environmental impact assessments. Nevertheless, their use as bioindicators can be constrained by the time- and cost-consuming processes needed for their morphological identification. The recent advances in high-throughput sequencing, particularly DNA metabarcoding can provide an alternative to morphology-based approaches. The main limitation for DNA-based tools to be implemented in biomonitoring projects is the considerable investment needed to build high-quality and curated taxonomic reference DNA sequence libraries for species identification. To begin addressing this shortage, Interreg NSR project GEANS aim in developing a curated DNA reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for the North Sea macrobenthos that will serve as the backbone of all the molecular protocols. For the collection of the macroinvertebrates, a targeted sampling campaign is underway across the North Sea Region, while existing collections are being scanned. Macrobenthic specimens are being processed following a series of standardised work flows covering sampling, morphological identifications, molecular lab processing and data handling. GEANS' reference library, currently holds DNA barcodes for 3443 specimens collected from various areas of the North Sea. In total 11 phyla, 28 classes, 80 orders, 280 families, 428 genera and 586 species (37 non-indigenous species) are represented within the library. Species-level identification is taxonomically verified for over 90 % of the species, while genus-level identifications are verified for almost 100 % of the genera. GEANS reference library covers so far over 30 % of North Sea species and its constantly enriched. All specimens are photographed and together with the accompanying sequences, collection and taxonomic data are archived in a dedicate BOLD project. Voucher specimens and DNA extracts are archived at three different institutes in Germany (Senckenberg am Meer), the Netherlands (Naturalis) and Belgium (ILVO). Once available, this DNA-library will be based on taxonomically well-curated specimens and it will support the implementation of fast, cost-efficient and reliable DNA-based identifications and subsequently environmental health assessments in the North Sea

Towards harmonization of DNA metabarcoding for monitoring marine macrobenthos : the effect of technical replicates and pooled DNA extractions on species detection

DNA-based monitoring methods are potentially faster and cheaper compared to traditional morphological benthic identification. DNA metabarcoding involves various methodological choices which can introduce bias leading to a different outcome in biodiversity patterns. Therefore, it is important to harmonize DNA metabarcoding protocols to allow comparison across studies and this requires a good understanding of the effect of methodological choices on diversity estimates. This study investigated the impact of DNA and PCR replicates on the detection of macrobenthos species in locations with high, medium and low diversity. Our results show that two to three DNA replicates were needed in locations with a high and medium diversity to detect at least 80% of the species found in the six DNA replicates, while three to four replicates were needed in the location with low diversity. In contrast to general belief, larger body size or higher abundance of the species in a sample did not increase its detection prevalence among DNA replicates. However, rare species were less consistently detected across all DNA replicates of the location with high diversity compared to locations with less diversity. Our results further show that pooling of DNA replicates did not significantly alter diversity patterns, although a small number of rare species was lost. Finally, our results confirm high variation in species detection between PCR replicates, especially for the detection of rare species. These results contribute to create reliable, time and cost efficient metabarcoding protocols for the characterization of macrobenthos

To blend or not to blend? The role of morphological traits for the detection of marine macrobenthos in bulk DNA and eDNA from the ethanol preservative

The impact of methodological choices on the reliability and reproducibility of DNA metabarcoding need to be well understood to allow successful implementation in routine monitoring frameworks. For macrobenthos communities, the metabarcoding protocol focuses on a fragment of the mitochondrial COI gene and depending on the primer set used for amplification of COI, different taxa can be detected. To identify the primer set that allows the best diversity estimates for macrobenthos in the North Sea region, we sampled four distinct and well characterised communities and identified macrobenthos using traditional morpho-taxonomy before molecular processing. Of the five primer sets tested, the Leray primer set yielded the highest number of non-chimeric reads, detected the highest number of macrobenthos species and best recovered beta diversity patterns. Despite the availability of a nearly complete reference database, 19 out of the 59 morphological species were not picked up with DNA metabarcoding. Next to primer choice, the DNA source used in metabarcoding studies can affect whether or not a species is detected. DNA can be extracted from bulk specimens or from the ethanol preservative in which the macrobenthos sample was preserved. The latter DNA source would greatly speed up processing time of samples in the laboratory. We therefore compared species detection in bulk DNA and eDNA from the ethanol preservative from the four macrobenthos communities in the North Sea. Our results show that community composition differed significantly between bulk DNA and eDNA samples, but both sample types are able to differentiate the four macrobenthos communities from the North Sea. Of the 49 species that are detected in both sample types, 27 are also found in the morphological dataset. The 14 species that are exclusively detected in the ethanol preservative are mainly pelagic species. In view of the low read numbers allocated to these species (at most 153 reads) they most likely represent “contaminant” DNA molecules that are attached to the specimens or the organic debris. To better understand the different results between bulk DNA and eDNA from the ethanol preservative, we investigated the importance of four categorical traits in explaining the probability of detecting a species in the two sample types: body, larval stage (benthic or pelagic), longevity and body skeleton (chitin, CaCO3 or soft tissue). A generalized linear mixed effects model approach shows that the probability of detecting a species in the eDNA from the ethanol preservative is significantly lower than for bulk DNA for macrobenthos species having small to medium body size and for species having chitine or CaCO3 in their skeleton. In contrast, detection in the bulk DNA samples is not affected by the investigated traits. Although the ethanol preservative can be used to characterize beta diversity patterns, our results show that monitoring of macrobenthos species will be most robust when using bulk DNA as template for metabarcoding

Testing repeatability, testing repeatability, testing repeatability: harmonization of the DNA metabarcoding protocol for macrobenthos across Europe

Macrobenthos is a good indicator to evaluate the potential effects of human activities on the marine benthic ecosystem. In environmental impact assessments (EIAs), macrobenthic species identification is typically based on morphological characteristics, a time-consuming and labor-intensive process for which specific taxonomic knowledge and experts are needed. DNA metabarcoding can circumvent most of these shortcomings. However, to be applicable in EIAs and to be adapted by policy, a standardized protocol that allows for reproducible and reliable DNA metabarcoding results is a prerequisite. Here, three research questions were investigated as part of the international Interreg NSR project GEANS: 1) “How many replicates of DNA extractions and PCR products are needed to capture most of the macrobenthic species in a sample?”, 2) “Is a ‘fixed’ DNA metabarcoding protocol repeatable across different institutes?” and 3) “What is the impact of small changes in this DNA metabarcoding protocol on alpha diversity?”. These are important steps to convince stakeholders that this efficient and quick method generates reliable and comparable results.First, variation in macrobenthic species across technical replicates was investigated in three biological replicates from three macrobenthic communities in the Belgian Part of the North Sea (BPNS) with high, medium and low diversity. For each biological replicate, six DNA replicates were taken and one of these DNA replicates was used to assess variation between three replicates for PCR amplification. Three DNA replicates were needed in locations with a high and medium diversity to pick up at least 80% of the species diversity present in the six replicates, while four DNA replicates were needed in the location with low diversity. Variation in the detected species between PCR replicates was high, illustrating the importance of including at least three PCR replicates in the lab protocol. Second, we conducted a ring test where subsamples of 12 bulk macrobenthos samples, originating from four different macrobenthic communities in the BPNS (differing in species density and diversity), were distributed to four institutes located in Belgium, the Netherlands, Germany and Denmark. Samples were processed using the same standardized lab protocol and the resulting datasets were processed bioinformatically by one institute. The number of ASVs and the number of species reflected the morphological diversity patterns, i.e. highest values for the replicates from the highly diverse macrobenthic community, lowest numbers in the low diversity replicates and intermediate values in the samples from the medium diversity community. These patterns were identical between the four institutes, showing high repeatability for alpha diversity when using the same protocol. In total, 100 macrobenthic species were detected through DNA metabarcoding, of which 60 species were picked up by all four institutes, while 0-14 species were recorded by only one of the four institutes. Beta diversity patterns were also comparable between the four institutes, as the nMDS plot clearly showed clustering based on the macrobenthic communities, independent of the institute that conducted the work. Finally, small changes to the lab protocol (different DNA extraction kit, different high fidelity polymerases for PCR amplification, different reagents for clean-up) resulted in only minor changes in alpha diversity: similar number of species were detected as with the fixed protocol in all samples and 70% - 75% of the species were shared between the ‘fixed’ and adjusted protocols.This study shows for the first time that DNA metabarcoding offers a highly repeatable assessment of alpha and beta diversity patterns, which supports the suitability of DNA metabarcoding for monitoring of marine macrobenthos. These results are highly valuable to establish a harmonized and uniform DNA metabarcoding protocol, to be used by all institutions in Europe when implemented as a new standard method in EIAs of the benthic ecosystem

DNA metabarcoding on repeat: Sequencing data of marine macrobenthos are reproducible and robust across labs and protocols

DNA metabarcoding can be used in marine environmental monitoring if results are reproducible between labs and robust against modifications to the lab protocol. In this interlaboratory study, we conducted a ring test where subsamples of blended macrobenthos samples were distributed to four laboratories located in Belgium, the Netherlands, Germany and Denmark. Samples were processed by a standardized lab protocol and by an adapted protocol, and the resulting datasets were analyzed with the same bioinformatics pipeline. Different biodiversity indicators were calculated. Our results show that bulkDNA metabarcoding of marine macrobenthos offers a highly reproducible assessment of alpha diversity patterns when using a standardized protocol, since comparable species numbers, Shannon indices and Inverse Simpson indices were found between laboratories. Especially high abundant species and species with large body sizes were shared between the laboratories. The need for using a standardized protocol to enhance comparability in alpha diversity between different studies was shown. Beta diversity patterns are less subjected to changes in the metabarcoding protocol and were almost identical between different laboratories, as the main clustering was always based on the macrobenthic community, independent of the used protocol or the laboratory that conducted the work. We conclude that DNA metabarcoding for marine environmental monitoring is an appropriate method when the aim is to study changes in community patterns and advocate its implementation in routine monitoring programs of national and European authorities, providing that a standardized protocol is implemented and/or a detailed description of the protocol is available

Reduced humoral immune response after BNT162b2 coronavirus disease 2019 messenger RNA vaccination in cancer patients under antineoplastic treatment

BACKGROUND: Cancer patients are at higher risk of developing severe COVID-19. However, safety and efficacy of COVID-19 vaccination in cancer patients undergoing treatment is unclear. PATIENTS AND METHODS: In this interventional prospective multi-cohort study, priming and booster doses of the BNT162b2 COVID-19 vaccine were administered 21 days apart to solid tumor patients receiving chemotherapy, immunotherapy, targeted- or hormonal therapy, and patients with a hematologic malignancy receiving rituximab or after allogeneic hematopoietic stem cell transplantation. Vaccine safety and efficacy (until three months post-booster) were assessed. Anti-SARS-CoV-2 receptor binding domain (RBD) antibody levels were followed over time (until 28 days post-booster) and in vitro SARS-CoV-2 50% neutralization titers (NT50) towards the wild-type Wuhan strain were analyzed 28 days post-booster. RESULTS: Local and systemic adverse events (AEs) were mostly mild to moderate (only 1-3% of patients experiencing severe AEs). Local, but not systemic, AEs occurred more frequently after booster dose. 28 days post-booster vaccination of 197 cancer patients, RBD-binding antibody titers and NT50 were lower in the chemotherapy group (234.05IU/mL [95%CI 122.10-448.66] and NT50 of 24.54 [95% CI 14.50-41.52]) compared to healthy individuals (1844.93IU/mL [95% CI 1383.57-2460.14] and NT50 of 122.63 [95% CI 76.85-195.67]), irrespective of timing of vaccination during chemotherapy cycles. Extremely low antibody responses were seen in hematology patients receiving rituximab, only two patients had RBD-binding antibody titers necessary for 50% protection against symptomatic SARS-CoV-2 infection (<200IU/mL) and only one had NT50 above the limit of detection. During the study period, five cancer patients tested positive for SARS-CoV-2 infection, including a case of severe COVID-19 in a patient receiving rituximab, resulting in a 2-week hospital admission. CONCLUSION: The BNT162b2 vaccine is well-tolerated in cancer patients under active treatment. However, the antibody response of immunized cancer patients was delayed and diminished, mainly in patients receiving chemotherapy or rituximab, resulting in breakthrough infections