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Microsatellite data for Atlantic Mackerel

Background: Pre-eclampsia is a leading cause of maternal and perinatal mortality and morbidity. Early identification of women at risk is needed to plan management. Objective : To assess the performance of existing pre-eclampsia prediction models and to develop and validate models for pre-eclampsia using individual participant data meta-analysis. We also estimated the prognostic value of individual markers. Design: This was an individual participant data meta-analysis of cohort studies. Setting: Source data from secondary and tertiary care. Predictors: We identified predictors from systematic reviews, and prioritised for importance in an international survey. Primary outcomes Early-onset (delivery at = 34 weeks' gestation) and any-onset pre-eclampsia. Analysis: We externally validated existing prediction models in UK cohorts and reported their performance in terms of discrimination and calibration. We developed and validated 12 new models based on clinical characteristics, clinical characteristics and biochemical markers, and clinical characteristics and ultrasound markers in the first and second trimesters. We summarised the data set-specific performance of each model using a random-effects meta-analysis. Discrimination was considered promising for C-statistics of >= 0.7, and calibration was considered good if the slope was near 1 and calibration-in-the-large was near 0. Heterogeneity was quantified using l(2) and tau(2). A decision curve analysis was undertaken to determine the clinical utility (net benefit) of the models. We reported the unadjusted prognostic value of individual predictors for pre-eclampsia as odds ratios with 95% confidence and prediction intervals. Result The International Prediction of Pregnancy Complications network comprised 78 studies (3,570,993 singleton pregnancies) identified from systematic reviews of tests to predict pre-eclampsia. Twenty-four of the 131 published prediction models could be validated in 11 UK cohorts. Summary C-statistics were between 0.6 and 0.7 for most models, and calibration was generally poor owing to large between-study heterogeneity, suggesting model overfitting. The clinical utility of the models varied between showing net harm to showing minimal or no net benefit. The average discrimination for IPPIC models ranged between 0.68 and 0.83. This was highest for the second-trimester clinical characteristics and biochemical markers model to predict early-onset pre-eclampsia, and lowest for the first-trimester clinical characteristics models to predict any pre-eclampsia. Calibration performance was heterogeneous across studies. Net benefit was observed for International Prediction of Pregnancy Complications first and second-trimester clinical characteristics and clinical characteristics and biochemical markers models predicting any pre-eclampsia, when validated in singleton nulliparous women managed in the UK NHS. History of hypertension, parity, smoking, mode of conception, placental growth factor and uterine artery pulsatility index had the strongest unadjusted associations with pre-eclampsia. Limitations: Variations in study population characteristics, type of predictors reported, too few events in some validation cohorts and the type of measurements contributed to heterogeneity in performance of the International Prediction of Pregnancy Complications models. Some published models were not validated because model predictors were unavailable in the individual participant data. Conclusion: For models that could be validated, predictive performance was generally poor across data sets. Although the International Prediction of Pregnancy Complications models show good predictive performance on average, and in the singleton nulliparous population, heterogeneity in calibration performance is likely across settings. Future work: Recalibration of model parameters within populations may improve calibration performance. Additional strong predictors need to be identified to improve model performance and consistency. Validation, including examination of calibration heterogeneity, is required for the models we could not validate.

BACKGROUND: Pre-eclampsia is a leading cause of maternal and perinatal mortality and morbidity. Early identification of women at risk during pregnancy is required to plan management. Although there are many published prediction models for pre-eclampsia, few have been validated in external data. Our objective was to externally validate published prediction models for pre-eclampsia using individual participant data (IPD) from UK studies, to evaluate whether any of the models can accurately predict the condition when used within the UK healthcare setting. METHODS: IPD from 11 UK cohort studies (217,415 pregnant women) within the International Prediction of Pregnancy Complications (IPPIC) pre-eclampsia network contributed to external validation of published prediction models, identified by systematic review. Cohorts that measured all predictor variables in at least one of the identified models and reported pre-eclampsia as an outcome were included for validation. We reported the model predictive performance as discrimination (C-statistic), calibration (calibration plots, calibration slope, calibration-in-the-large), and net benefit. Performance measures were estimated separately in each available study and then, where possible, combined across studies in a random-effects meta-analysis. RESULTS: Of 131 published models, 67 provided the full model equation and 24 could be validated in 11 UK cohorts. Most of the models showed modest discrimination with summary C-statistics between 0.6 and 0.7. The calibration of the predicted compared to observed risk was generally poor for most models with observed calibration slopes less than 1, indicating that predictions were generally too extreme, although confidence intervals were wide. There was large between-study heterogeneity in each model's calibration-in-the-large, suggesting poor calibration of the predicted overall risk across populations. In a subset of models, the net benefit of using the models to inform clinical decisions appeared small and limited to probability thresholds between 5 and 7%. CONCLUSIONS: The evaluated models had modest predictive performance, with key limitations such as poor calibration (likely due to overfitting in the original development datasets), substantial heterogeneity, and small net benefit across settings. The evidence to support the use of these prediction models for pre-eclampsia in clinical decision-making is limited. Any models that we could not validate should be examined in terms of their predictive performance, net benefit, and heterogeneity across multiple UK settings before consideration for use in practice. TRIAL REGISTRATION: PROSPERO ID: CRD42015029349 .

Additional file 1: Supplementary methods: Additional details for handling missing data and evaluating predictive performance of models. Table S1: Search strategy for pre-eclampsia prediction models. Table S2: Predictors evaluated in the models externally validated in the IPPIC-UK cohorts. Table S3: Prediction models and equations identified from the literature search. Table S4: Study level characteristics of IPPIC-UK cohorts. Table S5: Patient characteristics of IPPIC-UK cohorts. Table S6: Number and proportion missing for each predictor in each cohort used for external validation. Table S7: Risk of bias assessment of the IPPIC-UK cohorts using the PROBAST tool. Table S8: Summary of linear predictor values and predicted probabilities for each model in each cohort. Table S9: Predictive performance statistics for models in the individual IPPIC-UK cohorts. Table S10: Predictive performance statistics for models in nulliparous women in all cohorts and in the POP cohort. Fig. S1: Decision curves for early pre-eclampsia models in SCOPE, UPBEAT and POP. Fig. S2: Decision curves for late pre-eclampsia models in SCOPE, Allen 2017, UPBEAT and POP.

L'édition des Guides du chef de mission des campagnes halieutiques vise en particulier les campagnes inscrites dans des séries de relevés pluri-annuels (campagnes benthiques, démersales et pélagiques). Mais elle concerne également toutes les campagnes halieutiques dont les données sont déposées auprès du Système d'information halieutique - campagnes à la mer. Cette documentation sur la campagne PELGAS est publiée pour répondre aux objectifs suivants : - Constituant le complément opérationnel aux manuels des protocoles des campagnes halieutiques, les Guides du chef de mission fournissent aux chefs de mission et aux équipes embarquées une documentation de base leur permettant de maîtriser l'ensemble des opérations à conduire pendant les campagnes. Ils contribuent ainsi à la cohérence de la conduite des observations et de l'acquisition des relevés au cours des séries, même dans le cas de changement de responsable des opérations. - Les Guides du chef de mission viennent en complément au guide des opérations navales édité par la DMON (http://www.ifremer.fr/guideopnav/) et qui rassemble l’ensemble des règles, procédures et formulaires pour les demandes de campagnes, leur préparation, leur exécution et l’exploitation de leurs résultats. - Les Guides du chef de mission fournissent aux responsables de la mise en œuvre des campagnes toutes les informations nécessaires à la préparation des campagnes, à leur réalisation à bord des navires d'observation et au transfert des produits des campagnes à leurs destinataires finaux. - Comme les manuels des protocoles, les Guides du chef de mission sont révisés autant que de besoin, après approbation du responsable de la campagne concerné. Chaque édition est attachée à une campagne ou une série de campagnes. Les révisions sont référencées pour en permettre le suivi. - L'édition des révisions permet d'adapter le guide aux évolutions prévues dans le manuel des protocoles correspondant, ainsi qu'à celles de l'environnement technique dans lequel les campagnes sont conduites. Elle permet en outre de documenter et de suivre toute modification éventuelle du système d'observation des séries concernées. - La réalisation des Guides du chef de mission s'inscrit dans la démarche Qualité du projet SIH-Campagnes à la mer de l'Ifremer.

PELGAS2012 sea cruise summary, including a multi-sensor characterisation of the marine particles in the Gironde mouth, Rapport de la campagne à la mer PELGAS2012, incluant une caractérisation multicapteurs des particules présentes dans l'estuaire de la Gironde

Individual fish growth depends on internal population factors such as phenotypic variability as well as external factors such as past environmental conditions (temperature, food) and selective mortality (predation or fishing). In the anchovy, growth in the first year is key to population dynamics as it determines the potential energy allocated to reproduction as well as the capacity to occupy off-shore habitats. Further, in the recent past, the anchovy in the bay of Biscay has experienced collapse and recovery and the role played by growth in this history is unknown. Since 2001 with the spring acoustic survey series PelGas, we have monitored individual fish growth by measuring in the otolith the increments between annual rings, in addition to age determination. These data now allow to analyse the growth patterns in the population as well as the effects of environmental parameters and fishing on the apparent growth of individuals. We show that growth is related to a spatial pattern where smaller and lower growing individuals are more coastal than off-shore larger and faster growers. We evidence a temperature effect on the growth pattern where warm years are also those of faster growth. In contrast, fishing does not seem to affect the apparent growth. We also account for the variability of growth between individuals, which has stayed high throughout the series. The study implies a spatial substructure and segregation in this population where particular habitats could have played a fundamental role for the recovery of the population after its collapse.

Ce document présente l'état des principaux stocks exploités par les flottes françaises en termes de mortalité par pêche et de biomasse de reproducteurs. La situation fin 2010 (début 2011) par rapport aux points de référence (de précaution et Fmsy) est indiqué lorsque les indicateurs sont estimés et que les références sont définies. Les grandes tendances en matière d'évolution des mortalités et biomasses sont également indiquées.

Estimer la biomasse d'un stock de poissons par acoustique nécessite de combiner des données de nature diverse collectées le long du parcours d'échantillonnage (Woillez et al., 2009). Il s'agit essentiellement de combiner trois champs de données spatialisées : une carte de densités acoustiques attribuées aux poissons, une carte de proportions d'espèces et une carte de longueurs moyennes.

The main objective of Ifremer's pelagic sea surveys (Pelgas in the Bay of Biscay and Pelmed in the Gulf of Lion) is to assess the biomass of anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) populations, based on fisheries acoustic data. Complementary data on the whole pelagic ecosystem (hydrology, plankton, fish eggs and larvae, other fish species, seabirds and marine mammals) are also collected during the cruises. This document describes the procedures used to derive stock abundance estimates from acoustic and fishing data collected during sea cruises, the Pelgas sea survey being used as an example.

Ifremer est sollicité pour fournir des éléments utiles à la prise de décision d’attribuer de nouvelles licences de pêche à la bolinche dans le Parc Naturel Marin d’Iroise. Il lui est notamment demandé d’établir : - un état des lieux sur le stock de sardine - un état des lieux de la pêcherie de bolinche - un état des lieux des frayères connues de la baie de Douarnenez

Le sondeur multifaisceaux Simrad ME70 (ou SMFH) (Trenkel et al., 2008) a été utilisé pour la première fois en routine en parallèle des sondeurs monofaisceaux ER60 lors de la campagne Pelgas09 (25/04-05/06/2009). Le premier objectif était de tester la faisabilité d'une utilisation en routine du ME70 lors d'une campagne visant à évaluer par acoustique les stocks d'anchois et de sardine du Golfe de Gascogne. A terme, les données récoltées lors de cette campagne permettront d'étudier l'apport du sondeur multifaisceaux ME70 à l'estimation de biomasse, en comparant les estimations de stocks obtenues en mono et multifaisceaux. Les données acoustiques 3D collectées au moyen du ME70 dans l'ensemble du Golfe de Gascogne lors de Pelgas09 doivent également permettre d'avancer sur la définition de types de structures agrégatives 3D de petits poissons pélagiques. A terme, l'analyse 3D des structures doit permettre de mieux comprendre le comportement des bancs et leurs liens avec les paramètres de l'environnement, par exemple pour une meilleure définition des habitats et des relations entre espèces.

International audience; Probabilistic models for inferring species mixture from acoustic data in a multi-specific envionment

The spatial pattern in hydro-plankton and fish distributions and their relationship were analysed based on the spring 2000 fisheries acoustic survey. The importance of this survey was that it was a multi-disciplinary platform which collected an extensive set of parameters in the hydro-plankton leading to a potentially finer description of hydro-plankton conditions and fish habitats. More than 50 variables were measured on a grid of stations, in four compartments of the ecosystem: hydrology, nutrients, primary producers and meso-zooplankton. First, a joint analysis of all hydro-plankton compartments was performed using multiple factor analysis (MFA). The method was used to estimate a compromise factorial space common to all compartments in which the stations were grouped by hierarchical clustering. The groups were represented spatially and a strong spatial pattern was evidenced. The fish and their spawned eggs were sampled along transect lines using acoustics and CUFES (continuous underway fish egg samplers). The distribution of the fish and their eggs was analysed in relation to the hydro-plankton groups of stations and difference in fish density across hydro-plankton conditions was tested by a pair-wise multiple comparison procedure. Anchovy was associated with a lesser number of hydro-plankton conditions than sardine. Eggs of both species were also associated with a lesser number of conditions than the fish. Finally, the gain provided by using the extensive set of hydro-plankton parameters for mapping large-scale hydro-plankton conditions was analysed in comparison with the situation in which a small set of parameters was available. The extensive set of parameters allowed more hydro-plankton conditions to be identified but only in the coastal area and not on the shelf. Size fractionated chlorophyll was determinant for tracking river plume hydro-plankton condition. However, the fish did not respond to the variety of the coastal hydro-plankton conditions., Este artículo analiza la relación espacial entre los peces pelágicos y su medio ambiente utilizando datos de la campaña acústica francesa del año 2000. Esta campaña fue multidisciplinaria y permitió la colección de una lista extensa de parámetro en el hidro-plancton. Mas de 50 variables fueron muestreadas sobre la misma red de estaciones. Estas variables se agrupan en cuatro compartimientos del ecosistema: hidrología, nutrientes y materia en suspensión, bacterias y fitoplancton, mesozooplancton. En primer lugar se hizo una análisis conjunto a todas las variables reagrupadas en los cuatros compartimientos aplicando el método MFA (Análisis Factorial Múltiple). El método permitió estimar el espacio factorial común a todos los compartimientos en el que se hizo un agrupamiento de las estaciones. Los grupos tenían una distribución espacial bien estructurada. Durante la campaña, los peces fueron muestreados sobre líneas de muestreo usando el método acústico y sus huevos fueron muestreado al mismo tiempo con la bomba CUFES (continuous underway fish egg sampler). Las diferencias de abundancia de peces y de sus huevos, relativas a los grupos del hidro-plancton, se comprobaron estadísticamente. La anchoa estaba limitada a grupos de hidro-plancton particulares mientras que la sardina no lo estaba. Las puestas de las dos especies estaban limitadas a menos grupos que los adultos. El beneficio de usar una lista extensiva de variables en el hidro-plancton fue analizado. La clorofila por clases de tamaño era determinante en identificar grupos de hidro-plancton relacionados con las plumas de los ríos. Pero el pez no estaba relacionado solamente con estos grupos.

The objective of PELGAS surveys is to study the abundance and distribution of pelagic fish in the Bay of Biscay. The main target species is anchovy but it will be considered in a multi-specific context. To assess an optimum horizontal and vertical description of the area, two types of actions are combined : 1) Continuous acquisition by storing acoustic data from five different frequencies and pumping sea-water under the surface in order to evaluate the number of fish eggs using a CUFES system (Continuous Under-water Fish Eggs Sampler)), and 2) discrete sampling at stations (by trawls, plankton nets, CTD). Satellite imagery (temperature and sea colour) and modelisation will be also used before and during the cruise to recognise the main physical and biological structures and to improve the sampling strategy. Concurrently, a visual counting and identification of cetaceans (from board) and of birds (by plane) will be carried out in order to characterise the higher level predators of the pelagic ecosystem. This task is formally included in the first priorities defined by the Commission regulation (EC) No 1639/2001 of 25 July 2001 establishing the minimum and extended Community programmes for the collection of data in the fisheries sector and laying down detailed rules for the application of Council Regulation (EC) No 1543/2000. These surveys must be considered in the frame of the Ifremer fisheries ecology action "resources variability" which is the French contribution to the international Globec programme. Thesesurveys are planned with Spain and Portugal in the frame of the ICES working group WGACEGG in order to have most of the small pelagic fish potential area to be covered from Gibraltar to Brest with the same protocol for sampling strategy. The results will be used during ICES working group WGHMSA in charge of the assessment of sardine, anchovy, mackerel and horse mackerel., L'objectif des campagnes PELGAS est de suivre la répartition et l'abondance des espèces pélagiques exploitées dans le golfe de Gascogne. Si l'anchois est l'espèce cible, elle est considérée dans son contexte multi-spécifique et au centre de l'écosystème pélagique. Afin de contribuer à une caractérisation de l'écosystème pélagique au sens de l'"approche écosystémique des ressources exploitées", ces campagnes s'attachent à récolter le maximum de paramètres à chaque niveau du réseau tropique. Afin de caractériser au mieux la distribution horizontale et verticale de la communauté pélagique, les actions sont menées 1) en continu, selon un réseau de radiales standardisé, par prospection acoustique sur 5 fréquences différentes, associée à des pêches d'identification et par l'étude de la distribution de la ponte grâce au système de pompage en surface CUFES. et 2) selon une grille de stations, par des pêches planctoniques et des profils verticaux établissant les paramètres physiques par bathysonde. Ces mesures sont associées aux images satellites et aux résultats de modèles hydrodynamiques. Simultanément, les oiseaux et mammifères marins sont répertoriés et comptabilisés pour caractériser les prédateurs supérieurs. Ces campagnes sont rattachées aux programmes "Systèmes d'information & techniques d'observation, économie et diagnostic de l'évolution des ressources et de leur usage" et "Démarche écosystémique pour une gestion intégrée des ressources halieutiques" du thème 4 de l'IFREMER : "Ressources halieutiques, exploitation durable et valorisation". Elles sont menées dans le cadre de la DCR (Data Collection Regulation) qui définit le programme communautaire minimum de collecte des données relatives à la pêche de l'Union européenne (règlement CE No 1639/2001 du 25 juillet 2001). Les résultats sont mis à disposition du groupe de travail annuel du CIEM chargé de suivre les stocks exploités de sardine, anchois, maquereau et chinchard. Ces actions sont considérées comme la contribution française au programme international GLOBEC. Elles sont coordonnées au niveau international dans le cadre du groupe de travail du CIEM WGACEGG auquelparticipent la France, l'Espagne et le Portugal afin de couvrir autant que possible l'ensemble de l'aire potentielle de présence de petits pélagiques au printemps, entre Brest et Gibraltar. Les résultats sont directement utilisés par le groupe de travail WGHMSA du CIEM chargé de suivre les stocks exploités de sardine, anchois, chinchard et maquereau.

Survey data from 2000 to 2004 were used to analyse whether sardine show a preferential distribution in relation to bottom depth and/or latitude. For this analysis, four strata were considered; North or South of latitude 46°N (separating VIIIa and VIIIb) and bottom depths deeper or shallower than 110m. Sardine length distributions are plotted as the proportion of small (< 18.5 cm) or big (larger than 18.5 cm) fish on the samples over the years. This division was chosen to take into account the bimodal structure of sardine length distributions (usually with a "valley" at 18.5 cm fish length). Small fish (mainly 1 year old) are generally found close to the coast and preferentially in the southern part. The year 2003 is different to the others but this year was totally atypical for all species and sardine was rather absent of the Bay of Biscay at the time of the survey.

An acoustic survey was carried out in the bay of Biscay from May 3rd to June 1st on board the French research vessel Thalassa. The objective of PELGAS05 survey was to study the abundance and distribution of pelagic fish in the Bay of Biscay. The target species were mainly anchovy and sardine and were considered in a multi-specific context. The results have to be used during ICES working groups in charge of the assessment of sardine, anchovy, mackerel and horse mackerel and in the frame of the Ifremer fisheries ecology program "resources variability"., Une campagne acoustique a été organisée dans le golfe de Gascogne du 3 mi au 1er juin 2005, à bord du navire océanographique français, Thalassa. L'objectif de cette campagne Pelgas 06 était d'étudier l'abondance et la distribution des poissons pélagiques dans le golfe de Gascogne. Les deux espèces cibles étaient principalement l'anchois et la sardine. Les résultats ont été utilisés lors des groupes de travail en charge de l'estimation des stocks de sardine, anchois, maquereau et chinchard et dans le cadre du programme d'écologie des pêcheries de l'Ifremer, "ressources variability".

An acoustic survey was carried out in the bay of Biscay from April 27th to May 25th on board the French research vessel Thalassa. The objective of PELGAS04 survey was to study the abundance and distribution of pelagic fish in the Bay of Biscay. The target species were mainly sardine and anchovy but had to be considered in a multi-specific context. The results have to be used during ICES working groups in charge of the assessment of sardine, anchovy, mackerel and horse mackerel and in the frame of the Ifremer fisheries ecology program "resources variability"., Une campagne acoustique a été organisée dans le golfe de Gascogne du 27 avril au 25 mai 2004, à bord du navire océanographique français, Thalassa. L'objectif de cette campagne Pelgas 06 était d'étudier l'abondance et la distribution des poissons pélagiques dans le golfe de Gascogne. Les deux espèces cibles étaient principalement l'anchois et la sardine. Les résultats ont été utilisés lors des groupes de travail en charge de l'estimation des stocks de sardine, anchois, maquereau et chinchard et dans le cadre du programme d'écologie des pêcheries de l'Ifremer, "ressources variability".

The french fishery of anchovy is divided in two groups defined by gears : purse seine and pelagic trawl. The average length of these vessels is about 20m. This fleet is very opportunistic : all trawlers are using several trawls during the year, to catch sometimes bass, tuna, hake, or scampi, and purse seine are mainly fishing sardine. Each year, the main anchovy catches are provided by pair trawlers. Purse seiners operate often in coastal areas (