PREDICT identifies precipitating events associated with the clinical course of acutely decompensated cirrhosis

Background & Aims: Acute decompensation (AD) of cirrhosis may present without acute-on-chronic liver failure (ACLF) (ADNo ACLF), or with ACLF (AD-ACLF), defined by organ failure(s). Herein, we aimed to analyze and characterize the precipitants leading to both of these AD phenotypes. Methods: The multicenter, prospective, observational PREDICT study (NCT03056612) included 1,273 non-electively hospitalized patients with AD (No ACLF = 1,071; ACLF = 202). Medical history, clinical data and laboratory data were collected at enrolment and during 90-day follow-up, with particular attention given to the following characteristics of precipitants: induction of organ dysfunction or failure, systemic inflammation, chronology, intensity, and relationship to outcome. Results: Among various clinical events, 4 distinct events were precipitants consistently related to AD: proven bacterial infections, severe alcoholic hepatitis, gastrointestinal bleeding with shock and toxic encephalopathy. Among patients with precipitants in the AD-No ACLF cohort and the AD-ACLF cohort (38% and 71%, respectively), almost all (96% and 97%, respectively) showed proven bacterial infection and severe alcoholic hepatitis, either alone or in combination with other events. Survival was similar in patients with proven bacterial infections or severe alcoholic hepatitis in both AD phenotypes. The number of precipitants was associated with significantly increased 90day mortality and was paralleled by increasing levels of surrogates for systemic inflammation. Importantly, adequate first-line antibiotic treatment of proven bacterial infections was associated with a lower ACLF development rate and lower 90-day mortality. Conclusions: This study identified precipitants that are significantly associated with a distinct clinical course and prognosis in patients with AD. Specific preventive and therapeutic strategies targeting these events may improve outcomes in patients with decompensated cirrhosis. Lay summary: Acute decompensation (AD) of cirrhosis is characterized by a rapid deterioration in patient health. Herein, we aimed to analyze the precipitating events that cause AD in patients with cirrhosis. Proven bacterial infections and severe alcoholic hepatitis, either alone or in combination, accounted for almost all (96-97%) cases of AD and acute-on-chronic liver failure. Whilst the type of precipitant was not associated with mortality, the number of precipitant(s) was. This study identified precipitants that are significantly associated with a distinct clinical course and prognosis of patients with AD. Specific preventive and therapeutic strategies targeting these events may improve patient outcomes. (c) 2020 European Association for the Study of the Liver. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Insect interaction analysis based on object detection and CNN

International audienceDirect observation to study biodiversity can be time consuming, however, other methods often provide indirect measurements and are possibly biased. To solve these problems, images can be a useful tool and ecologists have started to rely more and more on images as a source of data and on automated image analysis. However, the existing methods mostly perform image classification. In this paper we present an efficient method based on object detection to access deeper information the content of an image. Using high resolution images, we built a pipeline to slice the original images, perform detections and later refine these observations. We illustrate the interest of this pipeline by using it on-field images taken in agroforestery banana-coffee systems to study invertebrate communities around the banana pests Cosmopolites sodidus and Metamasius sp. and the interactions between the different animals within this community. Experimental results show that our pipeline reaches 87.8% F1-score and allows us to successfully detect and identify 23 species and ant castes. These 23 species are divided into 7 super-classes, but the ant super-class, that shows more individuals and interactions is described more precisely. We are then able to study the interaction network between different species of this community and identify major predators of banana pests within this ecosystem

Hierarchical Classification of Very Small Objects: Application to the Detection of Arthropod Species

International audienceAutomated image analysis and deep learning tools such as object detection models are being used increasingly by biologists. However, biological datasets often have constraints that are challenging for the use of deep learning. Classes are often imbalanced, similar, or too few for robust learning. In this paper we present a robust method relying on hierarchical classification to perform very small object detection. We illustrate our results on a custom dataset featuring 22 classes of arthropods used to study biodiversity. This dataset shows several constraints that are frequent when using deep learning on biological data with a high class imbalance, some classes learned on only a few training examples and a high similarity between classes. We propose to first perform detection at a super-class level, before performing a detailed classification at a class level. We compare the obtained results with our proposed method to a global detector, trained without hierarchical classification. Our method succeeds in obtaining a mAP of 75 %, while the global detector only achieves a mAP of 48 %. Moreover, our method shows high precision even on classes with the less train examples. Confusions between classes with our method are fewer and are of a lesser impact. We are able achieve a more robust object classification with the use of our proposed method. This method can also enable better control on the model's output which can be particularly valuable when handling ecological, biological or medical data for example

Corigan testing dataset

93 images from on-field sentinel experiments. These image files are associated with labelled files. These files have been used to test the Yolov3 detection model (Redmon & Farhadi 2018), which constitutes the core of the CORIGAN pipeline. For more details on data and CORIGAN, see the related manuscript and supplementary materials in Methods in Ecology & Evolution

CORIGAN: Assessing multiple species and interactions within images

International audienceImages are resourceful data for ecologists and can provide a more complete information than other methods to study biodiversity and the interactions between species. Automated image analysis however often relies on extensive datasets, not implementable by small research teams. We are here proposing an object detection method that allows the analysis of high-resolution images containing many animals interacting in a small dataset. 2. We developed an image analysis pipeline named 'CORIGAN' to extract the characteristics of animal communities. CORIGAN is based on the YOLOv3 model as the core of object detection. To illustrate potential applications, we use images collected during a sentinel prey experiment. 3. Our pipeline can be used to detect, count and study the physical interactions between various animals. On our example dataset, the model reaches 86.6% precision and 88.9% recall at the species level or even at the caste level for ants. The training set required fewer than 10 hr of labelling. Based on the pipeline output, it was possible to build the trophic and non-trophic interactions network describing the studied community. 4. CORIGAN relies on generic properties of the detected animals and can be used for a wide range of studies and supports. Here, we study invertebrates on high-resolution images, but the same processing can be transferred for the study of larger animals on satellite or aircraft images

Corigan training dataset

95 images from on-field sentinel experiments. These image files are associated with labelled files. These files have been used to train the Yolov3 detection model (Redmon & Farhadi 2018), which constitutes the core of the CORIGAN pipeline. For more details on data and CORIGAN, see the related manuscript and supplementary materials in Methods in Ecology & Evolution

Number of predation events per hour for different predator species.

The shaded area represents night time.</p