Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Interactions entre insectes floricoles et cultures de fenouil aromatique (Foeniculum vulgare) : influences des variables locales et paysagères et implications pour la production d’anéthole

Fennel is an aromatic mass-flowering crop cultivated in Provence (France), characterized by lavender crops, for its essential oil that contains anethole, a compound of food and economical interest for the elaboration of anise drinks. The realization of controlled pollinations (flowers pollinated by insects and flowers not accessible to insects) demonstrated a drop in fruit production of 86% in the absence of flying insects. The use of coloured pan-traps and net captures in fennel field revealed that the landscape configuration and the vicinity of fennel fields to semi-natural habitats (SNH) positively influence the richness of flying insects. This richness influences then positively the amount of essential oil but negatively the amount of anethole. At the field level, bee visitation rate (mainly driven by honey bees) and species richness positively influence the amount of anethole. The nectar production dynamic of lavender and fennel was also explored thanks to simulation model to identify how insect foraging behaviours could change the daily nectar production. We showed that nectar production for both species is insect visitation driven, but the nectar of lavandin flowers is replenished more quickly. However, visits were more frequent on fennel, probably due to the general nature of the flower and its pollen supply. From a management point of view, we suggest maintaining complex landscape configurations of diversified habitats, to sustain both the crop production of fennel and insect biodiversity.Le fenouil est une plante aromatique à floraison massive cultivée en Provence (France), caractérisé par la culture de lavandin, pour son huile essentielle (HE) contenant de l’anéthole d’intérêt économique pour la fabrication du pastis. La réalisation de pollinisations contrôlées (fleurs pollinisées par les insectes et fleurs non-accessibles aux insectes) a démontré une chute de la production de fruits de 86% en absence d’insectes floricoles. L’utilisation de pièges colorés et de captures au filet dans les parcelles de fenouil a révélé que la configuration du paysage et la proximité des parcelles de fenouil à des habitats semi-naturels (SNH) influencent positivement la richesse d’insectes floricoles, laquelle influence positivement la quantité d’HE mais négativement la quantité d’anéthole. Au niveau de la parcelle, la fréquence de visites des abeilles (surtout domestiques) et leur richesse spécifique affectent positivement la quantité d’anéthole. La dynamique de la production de nectar du lavandin et du fenouil a aussi été explorée grâce à un modèle de simulations afin d’identifier comment les comportements de butinage peuvent changer la production journalière de nectar. Nous avons montré que la production de nectar pour les deux plantes était influencée par les visites d’insectes, mais le nectar des fleurs de lavandin se reconstitue plus rapidement. Cependant, les visites étaient plus fréquentes sur le fenouil, probablement dû au caractère généraliste de la fleur et à sa fourniture en pollen. Enfin en termes de gestion, nous proposons de maintenir une configuration d’habitats diversifiés afin de préserver la diversité des insectes floricoles et la production du fenouil

Interaction between flower-visiting insects and aromatic fennel crops (Foeniculum vulgare) : influence of local and landscape variables and implications for anethole production

Le fenouil est une plante aromatique à floraison massive cultivée en Provence (France), caractérisé par la culture de lavandin, pour son huile essentielle (HE) contenant de l’anéthole d’intérêt économique pour la fabrication du pastis. La réalisation de pollinisations contrôlées (fleurs pollinisées par les insectes et fleurs non-accessibles aux insectes) a démontré une chute de la production de fruits de 86% en absence d’insectes floricoles. L’utilisation de pièges colorés et de captures au filet dans les parcelles de fenouil a révélé que la configuration du paysage et la proximité des parcelles de fenouil à des habitats semi-naturels (SNH) influencent positivement la richesse d’insectes floricoles, laquelle influence positivement la quantité d’HE mais négativement la quantité d’anéthole. Au niveau de la parcelle, la fréquence de visites des abeilles (surtout domestiques) et leur richesse spécifique affectent positivement la quantité d’anéthole. La dynamique de la production de nectar du lavandin et du fenouil a aussi été explorée grâce à un modèle de simulations afin d’identifier comment les comportements de butinage peuvent changer la production journalière de nectar. Nous avons montré que la production de nectar pour les deux plantes était influencée par les visites d’insectes, mais le nectar des fleurs de lavandin se reconstitue plus rapidement. Cependant, les visites étaient plus fréquentes sur le fenouil, probablement dû au caractère généraliste de la fleur et à sa fourniture en pollen. Enfin en termes de gestion, nous proposons de maintenir une configuration d’habitats diversifiés afin de préserver la diversité des insectes floricoles et la production du fenouilFennel is an aromatic mass-flowering crop cultivated in Provence (France), characterized by lavender crops, for its essential oil that contains anethole, a compound of food and economical interest for the elaboration of anise drinks. The realization of controlled pollinations (flowers pollinated by insects and flowers not accessible to insects) demonstrated a drop in fruit production of 86% in the absence of flying insects. The use of coloured pan-traps and net captures in fennel field revealed that the landscape configuration and the vicinity of fennel fields to semi-natural habitats (SNH) positively influence the richness of flying insects. This richness influences then positively the amount of essential oil but negatively the amount of anethole. At the field level, bee visitation rate (mainly driven by honey bees) and species richness positively influence the amount of anethole. The nectar production dynamic of lavender and fennel was also explored thanks to simulation model to identify how insect foraging behaviours could change the daily nectar production. We showed that nectar production for both species is insect visitation driven, but the nectar of lavandin flowers is replenished more quickly. However, visits were more frequent on fennel, probably due to the general nature of the flower and its pollen supply. From a management point of view, we suggest maintaining complex landscape configurations of diversified habitats, to sustain both the crop production of fennel and insect biodiversit

Interactions entre insectes floricoles et cultures de fenouil aromatique (Foeniculum vulgare) : influences des variables locales et paysagères et implications pour la production d’anéthole

Fennel is an aromatic mass-flowering crop cultivated in Provence (France), characterized by lavender crops, for its essential oil that contains anethole, a compound of food and economical interest for the elaboration of anise drinks. The realization of controlled pollinations (flowers pollinated by insects and flowers not accessible to insects) demonstrated a drop in fruit production of 86% in the absence of flying insects. The use of coloured pan-traps and net captures in fennel field revealed that the landscape configuration and the vicinity of fennel fields to semi-natural habitats (SNH) positively influence the richness of flying insects. This richness influences then positively the amount of essential oil but negatively the amount of anethole. At the field level, bee visitation rate (mainly driven by honey bees) and species richness positively influence the amount of anethole. The nectar production dynamic of lavender and fennel was also explored thanks to simulation model to identify how insect foraging behaviours could change the daily nectar production. We showed that nectar production for both species is insect visitation driven, but the nectar of lavandin flowers is replenished more quickly. However, visits were more frequent on fennel, probably due to the general nature of the flower and its pollen supply. From a management point of view, we suggest maintaining complex landscape configurations of diversified habitats, to sustain both the crop production of fennel and insect biodiversity.Le fenouil est une plante aromatique à floraison massive cultivée en Provence (France), caractérisé par la culture de lavandin, pour son huile essentielle (HE) contenant de l’anéthole d’intérêt économique pour la fabrication du pastis. La réalisation de pollinisations contrôlées (fleurs pollinisées par les insectes et fleurs non-accessibles aux insectes) a démontré une chute de la production de fruits de 86% en absence d’insectes floricoles. L’utilisation de pièges colorés et de captures au filet dans les parcelles de fenouil a révélé que la configuration du paysage et la proximité des parcelles de fenouil à des habitats semi-naturels (SNH) influencent positivement la richesse d’insectes floricoles, laquelle influence positivement la quantité d’HE mais négativement la quantité d’anéthole. Au niveau de la parcelle, la fréquence de visites des abeilles (surtout domestiques) et leur richesse spécifique affectent positivement la quantité d’anéthole. La dynamique de la production de nectar du lavandin et du fenouil a aussi été explorée grâce à un modèle de simulations afin d’identifier comment les comportements de butinage peuvent changer la production journalière de nectar. Nous avons montré que la production de nectar pour les deux plantes était influencée par les visites d’insectes, mais le nectar des fleurs de lavandin se reconstitue plus rapidement. Cependant, les visites étaient plus fréquentes sur le fenouil, probablement dû au caractère généraliste de la fleur et à sa fourniture en pollen. Enfin en termes de gestion, nous proposons de maintenir une configuration d’habitats diversifiés afin de préserver la diversité des insectes floricoles et la production du fenouil

Interactions entre insectes floricoles et cultures de fenouil aromatique (Foeniculum vulgare) : influences des variables locales et paysagères et implications pour la production d’anéthole

Fennel is an aromatic mass-flowering crop cultivated in Provence (France), characterized by lavender crops, for its essential oil that contains anethole, a compound of food and economical interest for the elaboration of anise drinks. The realization of controlled pollinations (flowers pollinated by insects and flowers not accessible to insects) demonstrated a drop in fruit production of 86% in the absence of flying insects. The use of coloured pan-traps and net captures in fennel field revealed that the landscape configuration and the vicinity of fennel fields to semi-natural habitats (SNH) positively influence the richness of flying insects. This richness influences then positively the amount of essential oil but negatively the amount of anethole. At the field level, bee visitation rate (mainly driven by honey bees) and species richness positively influence the amount of anethole. The nectar production dynamic of lavender and fennel was also explored thanks to simulation model to identify how insect foraging behaviours could change the daily nectar production. We showed that nectar production for both species is insect visitation driven, but the nectar of lavandin flowers is replenished more quickly. However, visits were more frequent on fennel, probably due to the general nature of the flower and its pollen supply. From a management point of view, we suggest maintaining complex landscape configurations of diversified habitats, to sustain both the crop production of fennel and insect biodiversity.Le fenouil est une plante aromatique à floraison massive cultivée en Provence (France), caractérisé par la culture de lavandin, pour son huile essentielle (HE) contenant de l’anéthole d’intérêt économique pour la fabrication du pastis. La réalisation de pollinisations contrôlées (fleurs pollinisées par les insectes et fleurs non-accessibles aux insectes) a démontré une chute de la production de fruits de 86% en absence d’insectes floricoles. L’utilisation de pièges colorés et de captures au filet dans les parcelles de fenouil a révélé que la configuration du paysage et la proximité des parcelles de fenouil à des habitats semi-naturels (SNH) influencent positivement la richesse d’insectes floricoles, laquelle influence positivement la quantité d’HE mais négativement la quantité d’anéthole. Au niveau de la parcelle, la fréquence de visites des abeilles (surtout domestiques) et leur richesse spécifique affectent positivement la quantité d’anéthole. La dynamique de la production de nectar du lavandin et du fenouil a aussi été explorée grâce à un modèle de simulations afin d’identifier comment les comportements de butinage peuvent changer la production journalière de nectar. Nous avons montré que la production de nectar pour les deux plantes était influencée par les visites d’insectes, mais le nectar des fleurs de lavandin se reconstitue plus rapidement. Cependant, les visites étaient plus fréquentes sur le fenouil, probablement dû au caractère généraliste de la fleur et à sa fourniture en pollen. Enfin en termes de gestion, nous proposons de maintenir une configuration d’habitats diversifiés afin de préserver la diversité des insectes floricoles et la production du fenouil

Flux de pollen chez Astragalus tragacantha (Fabaceae) et réseaux d’interactions de pollinisation pour la conservation de ses populations au sein du Parc National des Calanques.

The increase of habitat fragmentation impacts plant-pollinator interactions and threatens the sustainability of plant species. Astragalus tragacantha (Fabaceae), is a rare endangered plant endemic to the Mediterranean coastal habitats mainly located in the Calanques National Park (CNP, Marseille, France). Its fragmented populations present important regressive demographic dynamics. Using controlled pollination treatments, observations and captures of pollinators within six populations, we studied (1) the self- versus cross-reproduction, and within- versus between-populations crossings, (2) the presence of inbreeding and/or outbreeding depressions, and (3) the role of pollinators on the reproductive performance of A. tragacantha. Here we showed a dependence of this plant to pollinators for its reproduction and no pollen limitation. We showed a clear difference in pollinator guilds among populations and some populations presented a predominance of a single species (Bombus terrestris, Anthophora plumipes and Eucera caspica). These species are suspected to be especially efficient in the pollination of A. tragacantha because the populations with their predominance presented a good reproduction performance. Moreover, there was better reproductive success of A. tragacantha for within-population crossings than between-population crossings. Indeed, the population with the higher reproductive success seems to favor autogamy. However, this population presents evidences of inbreeding depression. So autogamy strategy seems to be not viable to a medium-term. To make A. tragacantha reproductive success viable in a longer-term, pollinators which realize preferentially cross-pollination within populations (like Anthophora and Eucera genus) have to be favored. Results from these studies were discussed in light of A. tragacantha populations’ restoration in the LIFE project context. Particularly, the conservation of A. tragacantha has to take into account the protection of its pollinator’s network integrity, including both A. tragacantha, wild pollinators, and Mediterranean coastal habitat conservation

Syrphidae rares ou nouveaux dans les Alpes-de-Haute-Provence (Diptera)

International audienceWe report here data on 55 species of Syrphidae found in the department of Alpes-de-Haute-Provence, France,of which nine are reported here for the first time. Four rare saproxylic species were found : Sphiximorpha garibaldii Rondani, Brachypalpoides lentus (Meigen), Caliprobola speciosa (Rossi) and Spilomyia saltuum (Fabricius

Pollination insights for the conservation of a rare threatened plant species, Astragalus tragacantha (Fabaceae)

International audienceThe increase in habitat fragmentation impacts plant-pollinator interactions and threatens the sustainability of plant species. Astragalus tragacantha (Fabaceae), is a rare endangered plant species along the coastal habitats where the plant populations have undergone considerable fragmentation and decline of size. Controlled pollination treatments, the observation of pollinator activity, and pollinator captures, have been conducted to study: (1) the mating system of A. tragacantha and the potential for inbreeding depression and/or out-breeding depression based on controlled pollination treatments, (2) the pollinator composition among populations using a correspondence analysis and a hierarchical clustering, and (3) the link between pollinators and the plant reproductive success using a path-analysis model. In this study, we demonstrated that this plant was not autogamous self-pollinating and depended on pollinators for its reproduction. The absence of difference between manual and open pollinations regarding the reproductive success showed an absence of pollen limitation in our populations. We showed that populations differed in the composition of their pollinator guilds. Some pollinator species were predominant in certain populations. The pollination treatments revealed the existence of a mixed mating system in A. tragacan-tha populations. We showed an inbreeding depression potentially linked to a predominant pollinator-facilitated selfing, and the existence of outbreeding depression between some distant populations. These differences in pollinator guild and plant mating systems among populations must be considered during the restoration of populations along the Mediter-ranean coastal habitats in order to enhance the reproductive success and sustainability of A. tragacantha

Land cover composition, local plant community composition and honeybee colony density affect wild bee species assemblages in a Mediterranean biodiversity hot-spot

International audienceIdentifying environmental drivers which structure wild bee species assemblages appears essential in a context of worldwide pollinator decline. During a two-year survey, we studied wild bee species assemblages in an 85km 2 protected area dominated by Mediterranean scrubland, the Calanques National Park, located in southern France. Our objectives were (i) to assess the composition of the wild bee species assemblages, and (ii) to explore the effect of a) land cover composition (anthropogenic zone, low scrubland, forest and rocky land cover), b) local plant community composition, and c) honeybee colony density on wild bee species assemblages. On 17 circular 100m 2 plots, we collected 541 specimens belonging to 87 wild bee species. We found that large bee species were significantly influenced by land cover composition within a 1000m radius. More specifically, we observed that the presence of a diversified land cover composition within a 1000m radius maximized large wild bee species richness, whereas large bee abundance and richness were negatively affected by honeybee colony density. Small wild bee species were structured by the local plant community composition within 100m 2 plots and by land cover composition within a 1000m radius. Their occurrence were related to the local composition of plants growing on deep soils in scrublands. The Calanques National Park, which is the only European park located at the interface with a large city and consequently suffers from anthropic pressure, encompasses several types of land cover which are beneficial for a wide diversity of bees. However, we would like to raise awareness among park managers regarding beekeeping activities within this territory which includes diverse types of land cover favorable for wild bee species

To what extent is fennel crop dependent on insect pollination?

The importance of insects for global food crop production is starting to be well-known but the level of dependence on insects is less referenced, especially for some aromatic crops. Fennel (Foeniculum vulgare, Mill.) is an aromatic mass-flowering crop cultivated in the south of France for its essential oil that contains anethole. This compound is of food and economical interest because of its anise flavour, which is used to elaborate anise drinks. Here, we have characterized the dependence of fennel on insect pollination. We used four controlled pollination treatments to compare the reproductive success (fruit initiation rate, fruit weight), and the fennel yield (fruit weight and amount of anethole per hectare) between insect pollinated flowers and bagged flowers. We also checked the ability of reproduction by self-pollination in this species, and the existence of a reproductive limitation linked to insect activity. We have shown that pollination without insects leads to reproductive failure in fennel. At the field level, insect pollination is fundamental to improve the fruit initiation rate, the fruit weight and the amount of anethole per hectare leading to an estimated 86 % dependence of fennel on insect pollination. Finally, we showed no reproductive limitation with the current state of insect activity. This study adds new evidence of the importance of insects in agroecosystems to sustain food production