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

SCoRS -- a content and collaborative based recommender system

We designed and built a web-based movie recommender system. We used association rule mining to implement two data filtering methods. Content-based filtering identifies sets of common attributes of the movies that the user has liked in the past, while collaborative filtering associates users with each other based on similarities in taste. By combining content- and collaborative-base filtering, we obtained recommendations with a higher precision than either method individually

Compatibilité du citrate de caféine injectable avec plusieurs autres médicaments

RésuméObjectif : Établir la compatibilité du citrate de caféine injectable avec 99 autres médicaments lors d’une administration en Y.Méthode : Le citrate de caféine dosé à 20 mg/mL (équivalant à 10 mg/mL de caféine base) a été combiné (ratio 1:1) à 99 médicaments injectables non dilués (10 mL chacun) à la température ambiante. Chaque préparation a été réalisée deux fois. La première a subi une évaluation visuelle et un test de dénombrement des particules par obstruction de lumière immédiatement après le mélange. Ces tests ont été répétés quatre heures après le mélange en utilisant la seconde préparation. Pour être considérés comme compatibles, les mélanges ne devaient pas présenter de précipitation ou tout autre changement observable (turbidité, cristaux, formation de gaz, changement de couleur) et devaient respecter la spécification établie par la norme USP <788> 1.B, à la fois au temps zéro et quatre heures après le mélange.Résultats : Au total, 80 des 99 médicaments injectables testés avec le citrate de caféine se sont révélés compatibles à la fois visuellement à l’oeil nu et à l’aide du compteur de particules selon la norme USP <788>. L’incompatibilité des 19 autres médicaments a pu être vérifiée visuellement, car elles étaient nettement visibles. Mais dans le cas du propofol, il n’a pas été possible de démontrer sa compatibilité.Conclusion : Un certain nombre de médicaments se sont révélés compatibles lorsqu’ils sont mélangés dans un ratio de 1:1 avec le citrate de caféine. Il faut cependant prendre en considération le fait que seuls les critères physiques ont été pris en compte dans cette étude.AbstractObjective: To determine the compatibility of injectable caffeine citrate with 99 other drugs during Y-site administration.Method: Caffeine citrate solution 20 mg/mL (equivalent to 10 mg/mL of caffeine base) was combined (1:1 ratio) with 99 undiluted injectable drugs (10 mL each) at room temperature. Each preparation was made in duplicate. One of the test samples underwent a visual evaluation and a light obscuration particle count test immediately after mixing. Four hours after mixing, these tests were repeated on the other test sample. To be considered compatible, a mixture had to be free of precipitate or any other observable change (turbidity, crystals, gas formation or colour change) and had to meet the specification for Test 1.B of standard USP <788>, both at time 0 and 4 hours after mixing.Results: In all, 80 of the 99 injectable drugs tested with caffeine citrate were found to be compatible with it, both visually, with the unaided eye, and with the particle counter, as per standard USP <788>. We were able to ascertain the incompatibility of the other 19 drugs visually because it was visibly evident. The compatibility of propofol could, however, not be determined.Conclusion: A certain number of drugs tested were found to be compatible with caffeine citrate when they were mixed in a ratio of 1:1. We must take into consideration that only physical criteria were used in this evaluation

Nano-composites Argile/polyéthylène avec propriétés barrière améliorées pour la conservation à long terme des graines

International audienceThere are numerous threats to the biodiversity of commercial and non-commercial plant species. The easiest way to prevent biodiversity loss is to conserve their genetic resources in seed banks. Depending on seeds sensitivity, it is vital to provide seeds packaging protection with high water vapor barrier components. Currently, most of container materials for seed banking are made from glass or tri-laminated foil. Glass containers are heavy and easily broken during handling and transport, whereas tri-laminated foil pouches are opaque and subjected to puncture by sharp seeds. High density polyethylene (HDPE) containers are rarely used for long term seed storage due to their permeability to moisture vapor. Considering the numerous advantages of HDPE such as low cost, lightweight, chemical inertness and easy processing, HDPE with enhanced barrier properties is suitable for long-term seed storage. According to previous research work, the addition of nanoclays into polymer matrix leads to the tortuous path that delayed the diffusion of gaseous molecules as water vapour. The present study aims to evaluate the effect of different clays on the overall properties of HDPE, especially water vapor barrier properties. The water vapor barrier of tested samples was found to be influenced by several factors: the aspect ratio of clays, the crystallinity of HDPE, the interface between clays and HDPE and the storage conditions.Il y a des nombreuses menaces qui pèsent sur la biodiversité des espèces végétales commerciales et non commerciales. La meilleure façon de prévenir la perte de biodiversité est de conserver leurs ressources génétiques dans des banques de semences. Selon la sensibilité des graines, il est essentiel d’utiliser des contenants composés de matériaux faisant hautement barrage à la vapeur d’eau. Actuellement, la plupart des conteneurs pour les banques de semences est en verre ou en complexe laminé aluminium /plastique. Les récipients en verre sont lourds et fragiles pendant les manutentions et le transport, alors que les sachets laminés aluminium/plastique sont opaques et sensibles à la perforation par des graines acérées. Les contenants en polyéthylène haute densité (PEHD) sont rarement utilisés pour le stockage long terme de semences en raison de leur perméabilité à la vapeur d’eau. Étant donné les nombreux avantages du PEHD tels que l’inertie chimique, la légèreté, leur faible coût ainsi que leur mise en oeuvre facile, le PEHD doté de propriétés de barrière renforcées est adapté au stockage à long terme des semences. Comme démontré dans les travaux de recherche précédents, l’ajout de nano-argiles dans la matrice polymère conduit à la mise en place de chemins tortueux qui retardent la diffusion des molécules gazeuses comme la vapeur d’eau. La présente étude vise à évaluer l’effet des différentes argiles sur les propriétés globales de HDPE et en particulier les propriétés de barrière de vapeur d’eau. La capacité barrière de vapeur d’eau des échantillons testés s’est avérée être influencée par plusieurs facteurs : l’allongement des argiles, la cristallinité du PEHD, l’interface entre les argiles et le PEHD ainsi que les conditions de stockage

Conception et fabrication d'un contenant à base de PEHD/Nanoparticules d'argile Application: conservation sécuritaire des semences

National audienceLa conservation de la diversité végétale est un enjeu crucial en raison des changements climatiques appréhendés. Une des façons de conserver cette diversité est de créer des banques de semences. Or, pour assurer la qualité de la conservation, il faut que le contenant utilisé limite les échanges entre l’ambiance de conservation (congélateur) et les semences. Des mesures d’activité de l’eau effectuées sur des semences forestières en conservation depuis près de 40 ans ont montré que les contenants sont perméables à l’humidité ambiante, induisant à moyen terme une perte de germination. Un nouveau contenant a été conçu à base d’un système hybride polyéthylène haute densité /Nanoparticules d’argile (PEHD/Argile). De forme lamellaire, les nanoparticules d’argiles, lorsqu’elles sont exfoliées, ont pour fonction de diminuer l’échange d’eau entre le milieu extérieur et les semences en créant un effet de barrière à la diffusion, appelé phénomène de tortuosité. Différents mélanges PEHD/Argiles ont été préparés par extrusion double vis puis soumis à des tests de caractérisations morphologiques (XRD,TEM), thermiques (DSC, TGA), mécaniques (Traction, DMA) et des propriétés barrières (perméabilité à l’eau) avant l’étape finale de fabrication des contenants par extrusion soufflage. Selon la nature et le type d’argiles utilisées, la réduction de la perméabilité et la rigidité ont été modifiées à des degrés variables

Stability of ex situ biological methanation of H2/CO2 with a mixed microbial culture in a pilot scale bubble column reactor

International audienceBiological methanation is a promising technology for gas and carbon valorisation. Therefore, process stability is required to allow its scale up and development. A pilot scale bubble column reactor was used for ex situ biological methanation with Mixed Microbial Culture (MMC). A 16S rRNA high throughput sequencing analysis revealed the MMC reached a stable composition with 50-60% Methanobacterium in closed liquid mode, a robust genus adapted to large scale constraints. Class MBA03 was identified as an indicator of process stability. Methanogenic genera moved toward 50% of Methanothermobacter when intensifying the process, and proteolytic activity was identified while 94% of H2/CO2 was converted into methane at 4NL.L-1.d-1. This study gives clarifications on the origin of volatile fatty acids (VFA) apparitions. Acetate and propionate accumulated when methanogenic activity weakened due to nutritive deficiency, and when PH2 reached 0.7 bar. The MMC withstood a storage period of 34d at room temperature indicating its suitability for industrial constraints

Somatic cell recovery by microfiltration technologies: a novel strategy to study the actual impact of somatic cells on cheese matrix

The actual impact of the somatic cells in the dairy technology is still ill-defined, because the increase inmilk somatic cell count, usually correlated with mastitis factors, impairs the raw milk composition,through mainly unwanted proteolysis and lipolysis. This study used microfiltration technologies forrecovering high quantity of somatic cells and for clarifying their role in cheese quality. Three series ofSwiss-type cheeses were manufactured by adding 0 (control), 4 105 and 9 105 somatic cells mL 1.These cells were traced for the first time during the cheese making process by using adapted flowcytometry and real-time quantitative PCR. Proteolysis and lipolysis indices were measured throughoutripening time. Only a weak increase in lipolysis (þ28%) and proteolysis (þ8%) was observed in thehighest somatic cell count cheese, despite 73% of the cells trapped within the cheeses. Our approachgives a new view of somatic cell role in cheese milk alteration

Desirable Somatic Cell Role on Swiss-type Cheese Making Properties and Final Quality

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Safety and efficacy of subcutaneous night-time only apomorphine infusion to treat insomnia in patients with Parkinson’s disease (APOMORPHEE): a multicentre, randomised, controlled, double-blind crossover study

International audienceBACKGROUND: Insomnia is a frequent complaint of patients with Parkinson’s disease, and it negatively affects quality of life. Drugs that improve both sleep and parkinsonism would be of major benefit to patients with Parkinson’s disease-related insomnia. We aimed to test the safety and efficacy of subcutaneous night-time only apomorphine infusion in patients with Parkinson’s disease and insomnia. METHODS: We did a randomised, multicentre, double-blind, placebo-controlled, crossover trial in 11 expert centres in Parkinson’s disease and sleep centres in France. Participants aged 35-90 years with fluctuating Parkinson’s disease and moderate to severe insomnia (Insomnia Severity Index score ≥15) were randomly assigned to either first receive night-time subcutaneous apomorphine (up to 5 mg/h) or matching placebo. Randomisation was done using a computer-generated plan in blocks of four, stratified by centre. This first intervention was followed by a 14-night washout period, then crossover to the other intervention. The treatment periods consisted of a 10-night titration phase followed by a 7-night fixed-dose phase. The dose was adjusted during the titration phase on the basis of a daily telephone call assessing sleep quality and treatment tolerability. The primary efficacy endpoint was the difference in Parkinson’s disease sleep scale (PDSS) scores from the beginning to the end of each treatment period. Analysis was done on an intention-to-treat basis. This trial is registered with ClinicalTrials.gov, NCT02940912. FINDINGS: Between Jan 31, 2017, and Jan 29, 2021, 46 participants were enrolled. 25 (54%) patients were randomly assigned to receive apomorphine first and 21 (46%) patients to receive placebo first. Mean change in PDSS score was significantly greater with night-time apomorphine infusion (15·18 [SD 24·34]) compared with placebo (5·23 [21·52]; treatment effect 9·95 [95% CI 0·88-19·03]; p=0·041). Adverse events were reported in 25 (54%) participants during the apomorphine period and in 17 (37%) participants during the placebo period (p=0·16). Apomorphine was associated with more frequent dizziness than was placebo (seven [15%] vs 0; p=0·041). INTERPRETATION: Subcutaneous night-time only apomorphine infusion improved sleep disturbances according to difference on PDSS score, with an overall safety profile consistent with previous studies in Parkinson’s disease. This treatment might be useful to manage sleep disturbances in patients with advanced Parkinson’s disease and moderate to severe insomnia. FUNDING: Orkyn and Aguettant Pharma. TRANSLATION: For the French translation of the abstract see Supplementary Materials section