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Background: Messages from an Internet forum are raw material that emerges in a natural setting (i.e., non-induced by a research situation)., Aims: The FLARE-IBD project aimed at using an innovative approach consisting of collecting messages posted by patients in an Internet forum and conducting a machine-learning study (data analysis/language processing) for developing a patient-reported outcome measuring flare in inflammatory bowel disease meeting international requirements., Methods: We used web-based and machine learning approaches, in the following steps. 1) Web-scraping to collect all available posts in an Internet forum (23 656 messages) and extracting metadata from the forum. 2) Twenty patients were randomly assigned 50 extracted messages; participants indicated whether the message corresponded or not to the flare phenomenon (labeling). If yes, participants were asked to identify excerpts from the text they considered significant flare markers (annotation). 3) The set of annotated messages underwent a vocabulary analysis., Results: The phenomenon of flare was circumscribed with the identification of 20 surrogate flare markers classified into five dimensions with their frequency within extracted labeled data: impact on life, symptoms, extra-intestinal manifestations, drugs and environmental factors. Web-based and machine-learning approaches met international recommendations to inform the content and structure for the development of patient-reported outcomes., Competing Interests: Declaration of Competing Interest None declared, (Copyright © 2021. Published by Elsevier Ltd.)

Background: Transfer learning aims at enhancing machine learning performance on a problem by reusing labeled data originally designed for a related, but distinct problem. In particular, domain adaptation consists for a specific task, in reusing training data developedfor the same task but a distinct domain. This is particularly relevant to the applications of deep learning in Natural Language Processing, because they usually require large annotated corpora that may not exist for the targeted domain, but exist for side domains., Results: In this paper, we experiment with transfer learning for the task of relation extraction from biomedical texts, using the TreeLSTM model. We empirically show the impact of TreeLSTM alone and with domain adaptation by obtaining better performances than the state of the art on two biomedical relation extraction tasks and equal performances for two others, for which little annotated data are available. Furthermore, we propose an analysis of the role that syntactic features may play in transfer learning for relation extraction., Conclusion: Given the difficulty to manually annotate corpora in the biomedical domain, the proposed transfer learning method offers a promising alternative to achieve good relation extraction performances for domains associated with scarce resources. Also, our analysis illustrates the importance that syntax plays in transfer learning, underlying the importance in this domain to privilege approaches that embed syntactic features., (© 2021. The Author(s).)

Introduction: Crohn's disease and ulcerative colitis, the two major forms of inflammatory bowel disease (IBD), are chronic disabling conditions characterised by flares followed by periods of remission. However, patients with IBD are seen every 3-6 months in the outpatient clinic, and the occurrence of a flare between two outpatient visits is not captured. To our knowledge, there is no validated patient-reported outcome (PRO) tool to measure the phenomenon of flare in IBD. This study aimed to use an innovative methodology to collect messages posted by patients in an internet forum for developing and validating a PRO measuring flare in IBD., Methods and Analysis: The design involves (1) computer engineering sciences for scraping extraction of messages posted in an internet forum and for identification of messages related to flare; (2) qualitative methods for thematic content analyse of the messages posted, for candidate items generation, for items selection (Delphi process) and for items adjustment ('think-aloud' interviews) and (3) quantitative methods for psychometric validation of the PRO., Ethics and Dissemination: Ethical approval was obtained from the Comité de Protection des Personnes (CPP) CPP Nord-Ouest I (19.07.15.44139) in November 2019. The project aims to provide a tool to evaluate IBD flare in current medical practice that is constructed with patients' perspectives. Items generation from a source corresponding to exchanges in an internet forum is an innovative method in this field and provides a wider coverage of qualitative data. If such a forum can result in interesting material, then this could be a new methodological perspective for generating items for questionnaires. Findings will be reported and disseminated widely through international peer-reviewed journal publications, oral and poster presentations at scientific conferences., Trial Registration Number: NCT04180345., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Pharmacogenomics (PGx) studies how individual gene variations impact drug response phenotypes, which makes PGx-related knowledge a key component towards precision medicine. A significant part of the state-of-the-art knowledge in PGx is accumulated in scientific publications, where it is hardly reusable by humans or software. Natural language processing techniques have been developed to guide experts who curate this amount of knowledge. But existing works are limited by the absence of a high quality annotated corpus focusing on PGx domain. In particular, this absence restricts the use of supervised machine learning. This article introduces PGxCorpus, a manually annotated corpus, designed to fill this gap and to enable the automatic extraction of PGx relationships from text. It comprises 945 sentences from 911 PubMed abstracts, annotated with PGx entities of interest (mainly gene variations, genes, drugs and phenotypes), and relationships between those. In this article, we present the corpus itself, its construction and a baseline experiment that illustrates how it may be leveraged to synthesize and summarize PGx knowledge.

Western cultural practices and values have largely shaped advance care planning (ACP) policies across the world. Low uptake of ACP among ethnic minority groups in Western countries has been interpreted with reference to cultural differences. This paper adopts a life-history approach to explore attitudes towards ACP among older, first-generation Dutch-Australian and Italian-Australian migrants. Thirty people participated in extended ethnographic interviews (N = 17) and group discussions (N = 13) during 2012. Transcripts were thematically analyzed and interpreted using a Foucauldian perspective on knowledge and power. Migration experiences, ongoing contact with the native country and participation in migrant community support networks influenced attitudes towards ACP. Dutch participants framed ACP discussions with reference to euthanasia, and adopted a more individualist approach to medical decision-making. Italian participants often spoke of familial roles and emphasized a family-based decision making style. The importance of migrant identity has been neglected in previous discussions of cultural factors influencing ACP uptake among ethnic minority groups. The unique migration experience should be considered alongside culturally appropriate approaches to decision-making, in order to ensure equitable access to ACP among migrant groups., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Objective: To analyse the interaction between visual restrictions and somatosensory disturbances on unipedal control equilibrium with or without classical dance training., Methods: The support (computerized force platform) was disturbed during roll and pitch sways in association with restriction of the left and right visual hemifields (selective nasal and temporal hemiretina goggles). The effect of training by comparing spontaneous dynamic equilibrium (spectral analysis of body sways) between 14 healthy female right-sided untrained and expert dancers was assessed. The foot of the supporting leg was placed on the unstable platform center in the same way for all the participants., Results: In pitch sways, analysis of variance showed that, regardless of the supporting leg used, dancers oscillated significantly less than untrained participants (p<0.01). Furthermore, all participants were significantly less stable in pitch sways if the left visual field was occluded (p<0.001). However, in roll sways, equilibrium was disturbed by covering the eyes only in dancers (p<0.001)., Conclusion: When classical dancers' feet were in an unusual position during the experimental task (a somatosensory constraint for them but not for untrained participants), dancers shifted their spatial reference frame from somesthetic to visual cues. The elimination of this visual reference may have created imbalance, indicating that right hemispheric visual dominance is particularly useful for postural control in complex equilibrium conditions.

To investigate the influence of vision and motor imagery styles on equilibrium control, displacements of the supporting foot during spontaneous whole-body rotations ("pirouette") by expert female ballet dancers were analyzed using three-dimensional kinematics. Four turn types were defined according to direction (clockwise, CW vs. counterclockwise, CCW) and supporting foot (SF, left vs. right). Visual influences were examined by including two visual conditions (blindfolded vs. full-vision). Motor imagery styles were determined using the Vividness of Movement Imagery Questionnaire (VMIQ) (Kinesthetic, n = 4 vs. Visual/Kinesthetic, n = 6). Turning direction preference was assessed by a closed-response questionnaire in which all dancers indicated that they preferred CW turn direction. Kinesthetic dancers showed more SF displacement during CCW (non-preferred direction) than CW (preferred direction) pirouettes. However, Visual/Kinesthetic dancers showed no significant effect of turn direction. Furthermore, Kinesthetic dancers showed no significant effect of vision on SF displacement whereas Visual/Kinesthetic dancers showed significantly higher SF displacement when vision was occluded. Thus there appears to be a selective effect of vision on Visual/Kinesthetic dancers, and a selective effect of turn direction on Kinesthetic dancers. These results suggest that perceptual styles should be taken into consideration when training tasks that require fine equilibrium control because the factors that perturb balance differ depending on perceptual style.

The link between supporting leg stability and individual trunk strategies used during spontaneous whole-body rotations was studied according to visual and kinesthetic imagery styles for classical dancers and untrained female participants. Shoulders-hip angles in the horizontal plane and supporting leg (SL) displacements were analyzed with three-dimensional kinematic at the beginning and end of the four turns, identified according to their SL (left vs. right) and turn direction (clockwise, CW vs. counterclockwise, CCW). To begin a turn in CCW on left SL, all the participants turned shoulders before hips (-25 degrees angle), p<0.01. Untrained participants yielded the reverse (+30 degrees angle) in CW - their non-preferred turn - whereas dancers maintained their trunk en bloc. In the turn slow down, in their preferred direction all the participants adopted en bloc behavior to avoid imbalance. Dancers kept this pattern in CCW but untrained participants separated shoulders and hips, p<0.01; on left SL (+20 degrees angle) hips finished before shoulders and on right SL (-25 degrees angle), shoulders finished before hips. Both mental imagery styles and spatial context link reduction of shoulder-hip angle and stability of SL. Daily expertise, not only dance training, facilitates the en bloc shoulder-hip coordination to maintain equilibrium.

A bias in spontaneous turning has been observed in several animal species, at the individual or group level. There has been no consensus so far on the existence of such a bias in humans, probably due to lack of control of the factors likely to modulate this bias. We tested the spontaneous behavior of thirteen human adults required to run around a circle in an empty, symmetrical space, as a function of starting position (from the left, the center, or the right), and gaze direction (to one of five targets going from left to right). A clear significant overall tendency to turn counterclockwise across all conditions was observed. This was particularly striking when the participants were required to start from the center position and look straight ahead before starting, with more than 80% of the participants turning counterclockwise in this perfectly symmetrical condition. Starting position, gaze and head direction modulated the bias, without masking the counterclockwise tendency. We discuss some of the factors likely to be partly responsible for this clear turning bias, including cognitive space representation, and preference for keeping the peripheral vision to one's left visual field during running due to hemispheric asymmetry.

Without vision, keeping a straight-ahead direction while stepping on the spot is almost impossible, everybody deviates more or less. Several explanations for this, such as laterality, vestibulo-spinal influence, dopamine system, have been proposed. The aims of the experiment presented here were (1) to quantify the lateral deviation when stepping using a modified Fukuda test apparatus, and (2) to determine the factors potentially underlying such deviation. Twenty-five young adults, blindfolded, performed the experiment which consisted in stepping while holding a rotating vertical roll bar fixed on the wall. Four experimental conditions (i.e., normal, with an imposed pace, dual-task, or with the neck bent) were tested. All participants deviated towards one side or the other in all conditions. Adding an attentional load or imposing a particular pace did not change the amount of deviation. For three conditions (normal, with an imposed pace and dual-task), the deviation towards one side was not significantly larger than towards the other side at the group level. In the bent-neck condition, the deviation was significantly larger than in the other conditions. Furthermore, in this condition the deviation towards the left was significantly larger than the deviation towards the right at the group level. We discussed the results regarding the role of vestibular information and proprioceptive feedback from neck muscles in correcting a spontaneous deviation. Our results, however, go against the idea that sensorimotor lateral preferences are among the factors underlying such deviations, since we found no relationship between lateral preferences (hand, foot, and eye) and the side of deviation.

The pharmacovigilance databases consist of several case reports involving drugs and adverse events (AEs). Some methods are applied consistently to highlight all signals, i.e. all statistically significant associations between a drug and an AE. These methods are appropriate for verification of more complex relationships involving one or several drug(s) and AE(s) (e.g; syndromes or interactions) but do not address the identification of them. We propose a method for the extraction of these relationships based on Formal Concept Analysis (FCA) associated with disproportionality measures. This method identifies all sets of drugs and AEs which are potential signals, syndromes or interactions. Compared to a previous experience of disproportionality analysis without FCA, the addition of FCA was more efficient for identifying false positives related to concomitant drugs.

Skin lesions in the allergic form of atopic dermatitis (AD) are induced by allergen-specific T cells that infiltrate the skin at the site of allergen exposure. Although Th2-type CD4+ T cells appear to be crucial in AD pathophysiology, little is known about the contribution of CD8+ T cells in the development of the allergic skin inflammation. In the present study, we have analyzed the respective role of CD8+ and CD4+ T cells in the development of AD skin lesions in a mouse model of allergen-induced AD. In sensitized mice, CD8+ T cells are rapidly and transiently recruited to the allergen-exposed site and initiate the inflammatory process leading to skin infiltration with eosinophils and Th1/Th2-producing cells. CD8+ T cell-depleted mice show no inflammation, demonstrating that these cells are mandatory for the development of AD. In contrast, CD4+ T cell-depleted mice develop a severe form of eczema. Furthermore, adoptive transfer of CD8+ T cells from sensitized mice into naive recipient mice leads to skin inflammation soon after allergen exposure. These data indicate that allergen-primed CD8+ T cells are required for the development of AD-like lesions in mice.

Necrotizing encephalitis of the Yorkshire terrier is a chronic non-suppurative encephalitis that was reported in approximately 15 cases worldwide. We report the case of a 10-year-old female Yorkshire terrier with gross evidence of severe cortical degeneration and necrosis. Microscopically, affected areas were mainly located in the cortical white matter and in the mesencephalon without implication of the cerebellum. Cavitation necrosis, demyelination, gemistocytic astrocytosis, marked perivascular lymphocytic cuffing with a diffuse lymphocytic/histiocytic/gitter cell infiltration characterized the lesions. Immunohistochemical analysis identified the major infiltration of T lymphocytes and macrophages with implication of some cytotoxic lymphocytes and IgG-producing plasma cells; depositions of IgG in the affected white matter were also observed. Specific stains did not reveal fungal, protozoal or bacterial organisms and reverse transcriptase-polymerase chain reaction analysis for distemper virus was also negative. The lympho-histiocytic inflammation suggests a T-cell-mediated and a delayed-type immune reaction as a possible pathogenic mechanism for this brain disorder.

West Nile virus (WNV) is a mosquito-transmitted Flavivirus with a transmission cycle involving birds as amplifying hosts. Wild birds are also believed to carry WNV over large distances and are able to introduce it into new areas during migration and dispersal. In this paper, our objective is to provide lists of birds potentially involved in the introduction, the amplification and the spread of WNV in the Camargue, a Mediterranean wetland in the south of France where several WNV outbreaks have occurred since the 1960s. Bird species were classified according to the following ecological factors: migratory status and provenance area, used biotopes, abundance and period of presence in the Camargue. The obtained lists of bird species potentially involved in the introduction, amplification and spread of WNV should prove useful to determine target species on which further studies on WNV ecology in birds could be focused.

Three additional techniques (Ziehl-Neelsen, auramine O/rhodamine and immunostaining using polyclonal anti-Mycobacterium bovis) to hematoxylin-eosin histopathology were evaluated for bovine tuberculosis diagnosis on 39 samples from several slaughterhouses. The immunohistochemichal technique was more sensitive and could detect a greater number of positive cattle. It has about the same sensibility as the bacteriology but it was faster.