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"Benoit, Vincent"
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Marine robotics and applications
This book reports on findings at the intersection between two related fields, namely coastal hydrography and marine robotics. On one side, it shows how the exploration of the ocean can be performed by autonomous underwater vehicles; on the other side, it shows how some methods from hydrography can be implemented in the localization and navigation of such vehicles, e.g. for target identification or path finding. Partially based on contributions presented at the conference Quantitative Monitoring of Underwater Environment, MOQESM, held on October 11-12, 2016, Brest, France, this book includes carefully revised and extended chapters presented at the conference, together with original papers not related to the event. All in all, it provides readers with a snapshot of current methods for sonar track registration, multi-vehicles control, collective exploration of underwater environments, and optimization of propulsion systems, among others. More than that, the book is aimed as source of inspiration and tool to promote further discussions and collaboration between hydrographers, robotic specialists and other related communities.
Book
A methodological framework for characterizing fish swimming and escapement behaviors in trawls
Knowledge about fish behavior is crucial to be able to influence the capture process and catch species composition. The rapid expansion of the use of underwater cameras has facilitated unprecedented opportunities for studying the behavior of species interacting with fishing gears in their natural environment. This technological advance would greatly benefit from the parallel development of dedicated methodologies accounting for right-censored observations and variable observation periods between individuals related to instrumental, environmental and behavioral events. In this paper we proposed a methodological framework, based on a parametric Weibull mixture model, to describe the process of escapement attempts through time, test effects of covariates and estimate the probability that a fish will attempt to escape. We additionally proposed to better examine the escapement process at the individual level with regard to the temporal dynamics of escapement over time. Our approach was used to analyze gadoids swimming and escapement behaviors collected using a video set up in front of a selective device known to improve selectivity on gadoids in the extension of a bottom trawl. Comparison of the fit of models indicates that i) the instantaneous rate of escape attempts is constant over time and that the escapement process can be modelled using an exponential law; ii) the mean time before attempting to escape increases with the increasing number of attempts; iii) more than 80% of the gadoids attempted to escape through the selective device; and iv) the estimated probability of success was around 15%. Effects of covariates on the probability of success were investigated using binomial regression but none of them were significant. The data set collected is insufficient to make general statements, and further observations are required to properly investigate the effect of intrinsic and extrinsic factors governing gadoids behavior in trawls. This methodology could be used to better characterize the underlying behavioral process of fish in other parts of a bottom trawl or in relation to other fishing gears.
Journal Article
Two new species of the Neotropical Lophocampa hyalinipuncta (Rothschild) group (Lepidoptera, Erebidae, Arctiinae)
Two new species of Lophocampa Harris are described and illustrated, Lophocampaazuayensis sp. n. , and Lophocampacarpishensis sp. n. Both new species were confused with Lophocampahyalinipuncta (Rothschild, 1909), and a comparative diagnosis is provided.
Journal Article
Procalcitonin detection in human plasma specimens using a fast version of proximity extension assay
An exciting trend in clinical diagnostics is the development of easy-to-use, minimally invasive assays for screening and prevention of disease at the point of care. Proximity Extension Assay (PEA), an homogeneous, dual-recognition immunoassay, has proven to be sensitive, specific and convenient for detection or quantitation of one or multiple analytes in human plasma. In this paper, the PEA principle was applied to the detection of procalcitonin (PCT), a widely used biomarker for the identification of bacterial infection. A simple, short PEA protocol, with an assay time suitable for point-of-care diagnostics, is presented here as a proof of concept. Pairs of oligonucleotides and monoclonal antibodies were selected to generate tools specifically adapted to the development of an efficient PEA for PCT detection. The assay time was reduced by more than 13-fold compared to published versions of PEA, without significantly affecting assay performance. It was also demonstrated that T4 DNA polymerase could advantageously be replaced by other polymerases having strong 3’>5’ exonuclease activity. The sensitivity of this improved assay was determined to be about 0.1 ng/mL of PCT in plasma specimen. The potential use of such an assay in an integrated system for the low-plex detection of biomarkers in human specimen at the point of care was discussed.
Journal Article
Influence of knot strength on the mechanical performance of a biodegradable gillnet
Ghost fishing is a global issue that can be addressed using fishing gear materials that do not persist in the marine environment. However, for these alternatives to be widely adopted, they must meet the same mechanical specifications as current commercial materials while degrading without any negative impact. The objective of this study was to compare a conventional gillnet made of polyamide 6 (PA6) with an alternative made of poly(butylene succinate-co-adipate-co-terephthalate) (PBSAT) at three different scales: monofilament, knot, and net. While the PBSAT monofilament’s strength was half that of the conventional PA6 net, knot and net losses were even more significant. This indicates a greater sensitivity of the material to the knot. Since the results between the knot and net scales were coherent, testing whole net panels is not necessary. Studying the curvature and the behaviour of the knot revealed its complex geometry and mechanical behaviour. Testing the weaver’s knot is a good indicator for studying the relevance of an alternative to conventional fishing gear materials. This should be considered when developing biodegradable nets in order to reduce ghost fishing at sea.
Journal Article
Spinopelvic parameters in greater trochanteric pain syndrome: a retrospective case-control study
PurposeGreater trochanteric pain syndrome (GTPS) is a condition resulting in lateral hip pain, most commonly caused by tendinosis or tear of the gluteus medius and minimus tendons, and greater trochanteric bursitis. Our aim was to assess pelvic parameters and proximal femoral anatomy in patients suffering from surgical-stage GTPS compared with a control group.MethodsThis retrospective, case-control study assessed 43 patients suffering from GTPS, matched according to age, gender, body mass index and level of sport and physical activity to 43 control patients, between 2013 and 2018. Pelvic parameters, including pelvic incidence (PI), pelvic tilt (PT) and sacral slope (SS), and proximal femoral anatomy, including femoral offset (FO) and neck-shaft angle (NSA), were measured using the EOS Imaging™ system.ResultsGTPS patients had a significantly lower mean (± SD) SS than control patients (33.1 ± 10.4 vs. 39.6 ± 9.7°, respectively; p < 0.05). There was no significant difference in PT (21.3 ± 7.1 vs. 19.0 ± 7.2°), PI (53.5 ± 11.6 vs. 57.7 ± 10.5°), FO (40.4 ± 8 vs. 42.2 ± 6.8°) or NSA (125.1 ± 5.8 vs. 124.4 ± 4.7°). There was no difference in lower back pain symptoms in a subgroup analysis of GTPS patients.ConclusionsSacral slope was lower in patients with surgical-stage GTPS than in asymptomatic hip patients, using the EOS Imaging™ system.
Journal Article
The biology and ecology of Necrodes littoralis, a species of forensic interest in Europe
Necrodes littoralis
(Linnaeus, 1758) (Coleoptera: Silphidae), also known as the “shore sexton beetle,” is a common silphid beetle that visits and breeds on large vertebrate cadavers. This study describes, for the first time, the involvement of
N. littoralis
on human corpses based on a large dataset of 154 French forensic cases. Various parameters regarding corpse location, decomposition stages, and entomofauna were extracted from each file. Compared to all of the forensic entomology cases analyzed between 1990 and 2013 (1028),
N. littoralis
was observed, on average, in one case out of eight; most of these cases occurred during spring and summer (73.5 %). More than 90 % of the cases were located outdoors, especially in woodlands, bushes, and fields. The decomposition stage of the corpse varied among cases, with more than 50 % in the advanced decomposition stage, 36 % in the early decomposition stage, and less than 10 % in the fresh, mummified, or skeletonized stages. Regarding other necrophagous species sampled with
N. littoralis
, Calliphorid flies were found in 94 % of the cases and Fanniidae/Muscidae in 65 % of the cases.
Chrysomya albiceps
, a heliophilic species mostly located in the Mediterranean area, was present in 34 % of the cases (only 20 % in the whole dataset). The most common coleopteran species were
Necrobia
spp. (Coleoptera: Cleridae) and
Creophilus maxillosus
(Coleoptera: Staphylinidae); these beetles were observed in 27 % of the cases. The over-representation of these species is likely due to similar requirements regarding the climate and decomposition stage. As
N. littoralis
is frequently observed and tends to become more common, we conclude that the developmental data for this species would be a precious tool for forensic entomologists in Europe.
Journal Article
Stratigraphic Modelling of the Lower/Middle Oxfordian (Upper Jurassic) Outer Ramp Deposits from the NE Paris Basin (France)
We investigate herein the lateral and vertical lithological heterogeneities of the Lower/Middle Oxfordian deposits (“Terrain à Chailles” and “Marnes des Eparges” formations) in the north-eastern Paris Basin. This new detailed stratigraphic framework documents the evolution at high resolution of an outer ramp based on regional correlations in order to constrain the evolution of petrological properties between the clayey “Argiles de la Woëvre” Formation and the more calcareous “Marnes et Calcaires à Coraux de Foug Formation. The “Argiles de la Woëvre” Formation is targeted for the deep storage of nuclear waste in north-eastern France. Nine wells are correlated over the “Zone of Interest for Further Research” (ZIRA), defined by the French agency for radioactive waste management (Andra), with a resolution of 0.5–1.0 m. The architecture and the age control of these formations have been refined, revealing that the “Terrain à Chailles” Formation is characterised by a regular slightly inclined sedimentation gently deeping in the SW direction and shows a lithological evolution from silty claystones to an increased occurrence of its calcareous content towards the top (Lower Oxfordian, uppermost mariae and cordatum ammonite zones). The above “Marnes des Eparges” Formation, characterised by claystone limestone alternations, is assigned to the Middle Oxfordian (plicatilis ammonite zone), deposited during a slightly enhanced subsidence phase in the SE part of the basin and documented and associated with onlaps geometries on the more proximal areas. However, this change in geometry does not affect petrological properties over ZIRA, as this is not accompanied by lithological changes. The environmental factors controlling petrological heterogeneities over ZIRA are also discussed. The stepwise increase in the carbonate content and the decrease in the detrital content towards the Lower to Middle Oxfordian deposits was likely triggered by a climate change towards drier conditions, modulated by sea level changes on a ramp morphology. A major condensation phase encompassing most of the Lower Oxfordian cordatum ammonite zone is also highlighted. The occurrence of a maximum regressive surface associated with gentle slope topography is a probable trigger for condensation. Changes in geometries are, however, associated with the activity of the Metz Fault, which potentially had an influence on the subsidence rates of the basin at that time.
Journal Article
Next generation phenotyping using narrative reports in a rare disease clinical data warehouse
Background
Secondary use of data collected in Electronic Health Records opens perspectives for increasing our knowledge of rare diseases. The clinical data warehouse (named Dr. Warehouse) at the Necker-Enfants Malades Children’s Hospital contains data collected during normal care for thousands of patients. Dr. Warehouse is oriented toward the exploration of clinical narratives. In this study, we present our method to find phenotypes associated with diseases of interest.
Methods
We leveraged the frequency and TF-IDF to explore the association between clinical phenotypes and rare diseases. We applied our method in six use cases: phenotypes associated with the Rett, Lowe, Silver Russell, Bardet-Biedl syndromes, DOCK8 deficiency and Activated PI3-kinase Delta Syndrome (APDS). We asked domain experts to evaluate the relevance of the top-50 (for frequency and TF-IDF) phenotypes identified by Dr. Warehouse and computed the average precision and mean average precision.
Results
Experts concluded that between 16 and 39 phenotypes could be considered as relevant in the top-50 phenotypes ranked by descending frequency discovered by Dr. Warehouse (resp. between 11 and 41 for TF-IDF). Average precision ranges from 0.55 to 0.91 for frequency and 0.52 to 0.95 for TF-IDF. Mean average precision was 0.79. Our study suggests that phenotypes identified in clinical narratives stored in Electronic Health Record can provide rare disease specialists with candidate phenotypes that can be used in addition to the literature.
Conclusions
Clinical Data Warehouses can be used to perform Next Generation Phenotyping, especially in the context of rare diseases. We have developed a method to detect phenotypes associated with a group of patients using medical concepts extracted from free-text clinical narratives.
Journal Article
Effect of low temperature in the development cycle of Lucilia sericata (Meigen) (Diptera, Calliphoridae): implications for the minimum postmortem interval estimation
Knowledge of necrophagous insects' developmental data is necessary for the forensic entomologist to estimate a reliable minimum postmortem interval (PMI
min
). Among the most represented necrophagous species, Lucilia sericata (Diptera, Calliphoridae) is particularly interesting. It is regularly identified in samples, with a predominance in summer, and is commonly used by analysts of our entomology department (Institut de Recherche Criminelle de la Gendarmerie Nationale) to estimate the PMI
min
with the accumulated degree days (ADD) method. This method requires the mathematical lower thermal threshold to be known. This value dictates the quality of the applied ADD method but cannot be considered as fixed, especially when insect development occurs at temperatures close to the biological threshold. In such conditions, it is necessary to study the influence of such temperatures on development rate, as well as the consequences of estimating the period of first oviposition on cadavers, when using the ADD method. Seven replicate rearings were conducted at six different temperatures: 30 °C, 24 °C, 18 °C, 15 °C, 12 °C and 10 °C. Time of development and time of emergence were recorded. The effect of low temperature on the development cycle and the reliability of the ADD method under this entire temperature spectrum were studied using different linear regression models. Calculated durations of total insect time development and experimental rearing duration were then compared. A global linear model cannot be used on the whole temperature spectrum experienced by L. sericata without resulting in an overestimation at some temperatures. We found a combination of two linear regression models to be suitable for the estimation of the total development time, depending on the temperature experienced by L. sericata. This approach allowed us to obtain a variation lower than 2% at 12 °C and 10 °C between the calculated duration and experimental duration of development. In comparison, the results obtained with a global model show a variation higher than 3% at 12 °C and 10% at 10 °C.
Journal Article