Search

Cancer is associated with increased muscle weakness, reduced physical functioning, increased fatigue, but also sleep disturbances, including insomnia, that affect quality of life (QoL). Physical activity demonstrated benefits on functional capacity, resilience and cancer-related fatigue, but there is a paucity of available data regarding its effects on insomnia in patients with cancer. This systematic review aims to examine the efficacy of exercise levels with insomnia in cancer patients. A systematic search was performed for articles published in PubMed and Cochrane Library databases from December 2013 to February 2023. Included studies explored insomnia during or after cancer treatment, with various exercise interventions. The search identified nine studies included in this review. Due to substantial heterogeneity in the interventions across studies, meta-analysis was not performed. Three studies reported positive results for insomnia reduction by self-reported outcomes under a supervised aerobic exercise program alone or combined with strength training. The present systematic review establishes the role of exercise interventions for reducing cancer-related insomnia. Further studies are indeed warranted to improve the level of evidence for exercise interventions for implementation in the care of cancer-related insomnia.

The increasing number of articles on adverse interactions that may occur when specific foods are consumed with certain drugs makes it difficult to keep up with the latest findings. Conflicting information is available in the scientific literature and specialized knowledge bases because interactions are described in an unstructured or semi-structured format. The FIDEO ontology aims to integrate and represent information about food-drug interactions in a structured way. This article reports on the new version of this ontology in which more than 1700 interactions are integrated from two online resources: DrugBank and Hedrine. These food-drug interactions have been represented in FIDEO in the form of precompiled concepts, each of which specifies both the food and the drug involved. Additionally, competency questions that can be answered are reviewed, and avenues for further enrichment are discussed., (© 2024. The Author(s).)

Drug repositioning is a faster and more affordable solution than traditional drug discovery approaches. From this perspective, computational drug repositioning using knowledge graphs is a very promising direction. Knowledge graphs constructed from drug data and information can be used to generate hypotheses (molecule/drug - target links) through link prediction using machine learning algorithms. However, it remains rare to have a holistically constructed knowledge graph using the broadest possible features and drug characteristics, which is freely available to the community. The OREGANO knowledge graph aims at filling this gap. The purpose of this paper is to present the OREGANO knowledge graph, which includes natural compounds related data. The graph was developed from scratch by retrieving data directly from the knowledge sources to be integrated. We therefore designed the expected graph model and proposed a method for merging nodes between the different knowledge sources, and finally, the data were cleaned. The knowledge graph, as well as the source codes for the ETL process, are openly available on the GitHub of the OREGANO project ( https://gitub.u-bordeaux.fr/erias/oregano )., (© 2023. The Author(s).)

Objectives: To introduce the 2023 International Medical Informatics Association (IMIA) Yearbook by the editors., Methods: The editorial provides an introduction and overview to the 2023 IMIA Yearbook where the special topic is "Informatics for One Health". The special topic, survey papers and some best papers are discussed. The section changes in the Yearbook editorial committee are also described., Results: IMIA Yearbook 2023 provides many perspectives on a relatively new topic called "One Digital Health". The subject is vast, and includes the use of digital technologies to promote the well-being of people and animals, but also of the environment in which they evolve. Many sections produced new work in the topic including One Health and all sections included the latest themes in many specialties in medical informatics., Conclusions: The theme of "Informatics for One Health" is relatively new but the editors of the IMIA Yearbook have presented excellent and thought-provoking work for biomedical informatics in 2023., Competing Interests: Disclosure The authors report no conflicts of interest in this work., (IMIA and Thieme. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/).)

Introduction: Despite the benefits of an active lifestyle on health, there are still difficulties for patients, during and beyond cancer treatment, to initiate and maintain physical activity. A workshop was organized based on cooperation, coordination of the collective for and with the patient., Methods: Ninety-six people - patients, relatives and professionals - were divided into five workgroups according to the cancer care continuum or according to specific clinical situations. Subgroups had to develop a common reflection around a representative fictive patient in order to (i) identify the factors that are in favor or not of physical activity practice, (ii) estimate at what extent it is possible to act on these factors, and (iii) to guide the fictive patient in the initiation and the maintenance of physical activity. Finally, the participants were asked to propose actions, strategies and tools to facilitate this process. The participants' writings and the moderators' summaries were collected and transcribed., Results: Offers exist on the territory and their variety, plebiscited, is effective. However, their knowledge and the coordination allowing patients to access them must be reinforced through multidisciplinary network integrating patient-experts, training, digital technology use, and implementation research., Discussion: The workshop has initiated a part of the conditions for collective empowerment which, if the process was created, could act on the structural determinants of patients' health., (Copyright © 2023 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.)

Background: Up to 70% of breast cancer patients report symptoms of insomnia during and after treatment. Despite the ubiquity of insomnia symptoms, they are under-screened, under-diagnosed and poorly managed in breast cancer patients. Sleep medications treat symptoms but are ineffective to cure insomnia. Other approaches such as cognitive behavioral therapy for insomnia, relaxation through yoga and mindfulness are often not available for patients and are complex to implement. An aerobic exercise program could be a promising treatment and a feasible option for insomnia management in breast cancer patients, but few studies have investigated the effects of such a program on insomnia., Methods: This multicenter, randomized clinical trial evaluate the effectiveness of a moderate to high intensity physical activity program (45 min, 3 times per week), lasting 12 weeks, in minimizing insomnia, sleep disturbances, anxiety/depression, fatigue, and pain, and in enhancing cardiorespiratory fitness. Patients with breast cancer be recruited from six hospitals in France and randomly allocated to either the "training" or the "control" group. Baseline assessments include questionnaires [Insomnia Severity Index (ISI), Pittsburgh Sleep Quality Index questionnaire (PSQI), Hospital Anxiety Depression Scale (HADS), Epworth Sleepiness Scale (ESS)], home polysomnography (PSG), and 7-day actigraphy coupled with completion of a sleep diary. Assessments are repeated at the end of training program and at six-month follow-up., Discussion: This clinical trial will provide additional evidence regarding the effectiveness of physical exercise in minimizing insomnia during and after chemotherapy. If shown to be effective, exercise intervention programs will be welcome addition to the standard program of care offered to patients with breast cancer receiving chemotherapy., Trial Registration: National Clinical Trials Number (NCT04867096)., (© 2023. The Author(s).)

Abstract: Garbellotto, L, Petit, E, Brunet, E, Guirronnet, S, Clolus, Y, Gillet, V, Bourdin, H, and Mougin, F. Gradual advance of sleep-wake schedules before an eastward flight and phase adjustment after flight in elite cross-country mountain bikers: effects on sleep and performance. J Strength Cond Res 37(4): 872-880, 2023-Strategies, for alleviating jet lag, specifically targeted to competitive athletes have never been studied, in ecological conditions. This study aimed to assess the effects of a phase advance before a 7-hour eastward flight followed by a strategy of resynchronization at destination on sleep and physical performance in professional mountain bikers. Six athletes participated in this study divided into 4 periods: (i) baseline (usual sleep-wake rhythm); (ii) phase advance (advance sleep-wake schedules of 3 hours for 6 days); (iii) travel (flight: Paris-Tokyo); and (iv) phase adjustment (resynchronization of sleep-wake schedules). Melatonin pills and light therapy were administrated during the phase advance and phase adjustment. Sleep was recorded by polysomnography and actigraphy, core body temperature (CBT) rhythm was assessed by ingestible capsules, and physical performances were tested by the Wingate and 5-minute maximal exercise tests. Results showed that bedtime was advanced by 2.9 hours at the end of the phase advance ( p ≤ 0.01) with a batyphase of CBT advanced by 2.5 hours ( p = 0.07). Bedtime was similar at destination compared with baseline. Total sleep time and sleep composition were unchanged at the end of the phase advance or at destination, compared with baseline. Physical performances were maintained after phase advance and at destination. The phase advance enabled to preshift part of the time zones without disturbing sleep and physical performances and contributed to preserving them once at destination. A phase advance before eastward travel represents an effective strategy to counter harmful effects of jet lag., (Copyright © 2022 National Strength and Conditioning Association.)

Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Background: Trastuzumab is used, alone or in conjunction with standard chemotherapy, to treat HER2-positive breast cancer (BC). Although it improves cancer outcomes, trastuzumab. can lead to cardiotoxicity. Physical exercise is a safe and effective supportive therapy in the management of side effects, but the cardioprotective effects of exercise are still unclear., Objectives: The primary aim of this study was to test whether trastuzumab-induced cardiotoxicity [left ventricular ejection fraction (LVEF) under 50%, or an absolute drop in LVEF of 10%] was reduced after a supervised exercise program of 3 months in patients with HER2-positive breast cancer. Secondary endpoints were to evaluate (i) cardiotoxicity rates using other criteria, (ii) cardiac parameters, (iii) cardiorespiratory fitness and (iv) whether a change in LVEF influences the cardiorespiratory fitness., Methods: 89 women were randomized to receive adjuvant trastuzumab in combination with a training program (training group: TG; n = 46) or trastuzumab alone (control group: CG; n = 43). The primary and secondary endpoints were evaluated at the end of the supervised exercise program of 3 months (T3)., Results: After exercise program, 90.5 % of TG patients and 81.8% of CG patients did not exhibit cardiotoxicity. Furthermore, whatever the used criterion, percentage of patients without cardiotoxicity were greater in TG (97.6 and 100% respectively) than in CG (90.9 and 93.9% respectively). LVEF and GLS values remained stable in both groups without any difference between the groups. In contrast, at T3, peak VO 2 (+2.6 mL.min -1 .kg -1 ; 95%CI, 1.8 to 3.4) and maximal power (+21.3 W; 95%CI, 17.3 to 25.3) increased significantly in TG, whereas they were unchanged in CG (peak VO 2 : +0.2 mL.min -1 .kg -1 ; 95%CI, -0.5 to 0.9 and maximal power: +0.7 W, 95%CI, -3.6 to 5.1) compared to values measured at T0. No correlation between LVEF changes and peak VO 2 or maximal power was observed., Conclusion: A 12-week supervised exercise regimen was safe and improved the cardiopulmonary fitness in particular peak VO 2 , in HER2-positive BC patients treated with adjuvant trastuzumab therapy. The study is under powered to come to any conclusion regarding the effect on cardiotoxicity., Clinical Trial Registration: www.ClinicalTrials.gov, identifier: NCT02433067., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Jacquinot, Meneveau, Falcoz, Bouhaddi, Roux, Degano, Chatot, Curtit, Mansi, Paillard, Bazan, Chaigneau, Dobi, Meynard, Vernerey, Pivot and Mougin.)

Objectives: To introduce the 2022 International Medical Informatics Association (IMIA) Yearbook by the editors., Methods: The editorial provides an introduction and overview to the 2022 IMIA Yearbook whose special topic is "Inclusive Digital Health: Addressing Equity, Literacy, and Bias for Resilient Health Systems". The special topic, survey papers, section editor synopses and some best papers are discussed. The sections' changes in the Yearbook Editorial Committee are also described., Results: As shown in the previous edition, health informatics in the context of a global pandemic has led to the development of ways to collect, standardize, disseminate and reuse data worldwide. The Corona Virus Disease 2019 (COVID-19) pandemic has demonstrated the need for timely, reliable, open, and globally available information to support decision making. It has also highlighted the need to address social inequities and disparities in access to care across communities. This edition of the Yearbook acknowledges the fact that much work has been done to study health equity in recent years in the various fields of health informatics research., Conclusion: There is a strong desire to better consider disparities between populations to avoid biases being induced in Artificial Intelligence algorithms in particular. Telemedicine and m-health must be more inclusive for people with disabilities or living in isolated geographical areas., Competing Interests: Disclosure The authors report no conflicts of interest in this work., (IMIA and Thieme. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/).)

New use cases and the need for quality control and imaging data sharing in health studies require the capacity to align them to reference terminologies. We are interested in mapping the local terminology used at our center to describe imaging procedures to reference terminologies for imaging procedures (RadLex Playbook and LOINC/RSNA Radiology Playbook). We performed a manual mapping of the 200 most frequent imaging report titles at our center (i.e. 73.2% of all imaging exams). The mapping method was based only on information explicitly stated in the titles. The results showed 57.5% and 68.8% of exact mapping to the RadLex and LOINC/RSNA Radiology Playbooks, respectively. We identified the reasons for the mapping failure and analyzed the issues encountered.

Secondary use of health data is made difficult in part because of large semantic heterogeneity. Many efforts are being made to align local terminologies with international standards. With increasing concerns about data privacy, we focused here on the use of machine learning methods to align biological data elements using aggregated features that could be shared as open data. A 3-step methodology (features engineering, blocking strategy and supervised learning) was proposed. The first results, although modest, are encouraging for the future development of this approach.

Information about drugs is numerous and varied, and many drugs can share the same information. Grouping drugs that have common characteristics can be useful to avoid redundancy and facilitate interoperability. Our work focused on the evaluation of the relevance of classes allowing this type of grouping: the "Virtual Drug". Thus, in this paper, we describe the process of creating this class from the data of the French Public Drug Database, which is then evaluated against the codes of the Anatomical Therapeutic Chemical classification associated with the drugs. Our evaluation showed that 99.55% of the "Virtual Drug" classes have a good intra-class consistency.

Background: Despite growing interest in athletes' sleep, few studies have focused on professional athletes, especially in individual sports. Moreover, limited investigations included female athletes. This study aimed to evaluate sleep chronotype, as well as objective and subjective sleep characteristics in male and female professional cross-country mountain bikers., Methods: Thirteen athletes (7 males and 6 females) of the French national team took part in this study. The Chronotype was assessed by the Horne and Östberg Morningness-Eveningness Questionnaire and sleep by actigraphy for one month, by ambulatory polysomnography (PSG) for one night and by the Pittsburgh Sleep Quality Index., Results: Most athletes (77%) are classified as moderately morning type and a minority of athletes (23%) are intermediate type. Athletes sleep on average 8 hours per night and during the night recorded by PSG, N3 and REM sleep stages represented 21.2±3.4% and 20.9±3.1% of the total sleep time, respectively. These good sleep parameters were confirmed by subjective data with 77% good sleepers. Except the poorer subjective sleep quality in female athletes (5.7±1.6) compared to male athletes (2.6±1.7, P<0.05), no significant sex difference was found for all characteristics evaluated., Conclusions: The professional status of these athletes and the organization of mountain bike calendar may explain their good sleep characteristics.

Objectives: To introduce the 2021 International Medical Informatics Association (IMIA) Yearbook by the editors., Methods: The editorial provides an introduction and overview to the 2021 IMIA Yearbook whose special topic is "Managing Pandemics with Health Informatics - Successes and Challenges". The Special Topic, the keynote paper, and survey papers are discussed. The IMIA President's statement and the IMIA dialogue with the World Health Organization are introduced. The sections' changes in the Yearbook Editorial Committee are also described., Results: Health informatics, in the context of a global pandemic, led to the development of ways to collect, standardize, disseminate and reuse data worldwide: public health data but also information from social networks and scientific literature. Fact checking methods were mostly based on artificial intelligence and natural language processing. The pandemic also introduced new challenges for telehealth support in times of critical response. Next generation sequencing in bioinformatics helped in decoding the sequence of the virus and the development of messenger ribonucleic acid (mRNA) vaccines., Conclusions: The Corona Virus Disease 2019 (COVID-19) pandemic shows the need for timely, reliable, open, and globally available information to support decision making and efficiently control outbreaks. Applying Findable, Accessible, Interoperable, and Reusable (FAIR) requirements for data is a key success factor while challenging ethical issues have to be considered., Competing Interests: Disclosure The authors report no conflicts of interest in this work., (IMIA and Thieme. This is an open access article published by Thieme under the terms of the Creative Commons Attribution-NonDerivative-NonCommercial License, permitting copying and reproduction so long as the original work is given appropriate credit. Contents may not be used for commercial purposes, or adapted, remixed, transformed or built upon. (https://creativecommons.org/licenses/by-nc-nd/4.0/).)

As the capacity for generating large-scale molecular profiling data continues to grow, the ability to extract meaningful biological knowledge from it remains a limitation. Here, we describe the development of a new fixed repertoire of transcriptional modules, BloodGen3, that is designed to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome data. The construction of this repertoire is based on co-clustering patterns observed across sixteen immunological and physiological states encompassing 985 blood transcriptome profiles. Interpretation is supported by customized resources, including module-level analysis workflows, fingerprint grid plot visualizations, interactive web applications and an extensive annotation framework comprising functional profiling reports and reference transcriptional profiles. Taken together, this well-characterized and well-supported transcriptional module repertoire can be employed for the interpretation and benchmarking of blood transcriptome profiles within and across patient cohorts. Blood transcriptome fingerprints for the 16 reference cohorts can be accessed interactively via:  https://drinchai.shinyapps.io/BloodGen3Module/ ., (© 2021. The Author(s).)

Objective: Our study consists in aligning the interface terminology of the Bordeaux university hospital (TLAB) to the Logical Observation Identifiers Names and Codes (LOINC). The objective was to facilitate the shared and integrated use of biological results with other health information systems., Materials and Methods: We used an innovative approach based on a decomposition and re-composition of LOINC concepts according to the transversal relations that may be described between LOINC concepts and their definitional attributes. TLAB entities were first anchored to LOINC attributes and then aligned to LOINC concepts through the appropriate combination of definitional attributes. Finally, using laboratory results of the Bordeaux data-warehouse, an instance-based filtering process has been applied., Results: We found a small overlap between the tokens constituting the labels of TLAB and LOINC. However, the TLAB entities have been easily aligned to LOINC attributes. Thus, 99.8% of TLAB entities have been related to a LOINC analyte and 61.0% to a LOINC system. A total of 55.4% of used TLAB entities in the hospital data-warehouse have been mapped to LOINC concepts. We performed a manual evaluation of all 1-1 mappings between TLAB entities and LOINC concepts and obtained a precision of 0.59., Conclusion: We aligned TLAB and LOINC with reasonable performances, given the poor quality of TLAB labels. In terms of interoperability, the alignment of interface terminologies with LOINC could be improved through a more formal LOINC structure. This would allow queries on LOINC attributes rather than on LOINC concepts only., (© The Author(s) 2021. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

This paper presents a prototype for the visualization of food-drug interactions implemented in the MIAM project, whose objective is to develop methods for the extraction and representation of these interactions and to make them available in the Thériaque database. The prototype provides users with a graphical visualization showing the hierarchies of drugs and foods in front of each other and the links between them representing the existing interactions as well as additional details about them, including the number of articles reporting the interaction. The prototype is interactive in the following ways: hierarchies can be easily folded and unfolded, a filter can be applied to view only certain types of interactions, and details about a given interaction are displayed when the mouse is moved over the corresponding link. Future work includes proposing a version more suitable for non-health professional users and the representation of the food hierarchy based on a reference classification.

The aim of our study was to create a graph model for the description of LOINC ® concepts. The main objective of the constructed structure is to facilitate the alignment of French local terminologies to LOINC. The process consisted of automatically incorporating the naming rules of LOINC labels, based on punctuation. We implemented these rules and applied them to the French variants of LOINC and then created attributes and concepts described with synonymous labels. When comparing the created attributes to the stated ones, the multiple mappings led to the identification of errors that must be corrected for improving the translation quality. These mappings are consecutive to semantic errors generated during the translation process. They mainly corresponded to misinterpretations of LOINC concepts and/or LOINC attributes., (©2020 AMIA - All rights reserved.)

Objectives: Pediatric obesity and sleep-disordered breathing (SDB) are strongly associated, and both promote metabolic impairments. However, the effects of a lifestyle intervention on the overall metabolic syndrome (MetS) are unknown. The objectives were i) to evaluate the effects of a lifestyle intervention on cardiometabolic risk (CMR), assessed with a dichotomous (MetS) and a continuous (MetScore FM ) instrument, in obese adolescents with and without SDB and ii) to compare the post-intervention cardiometabolic responses between adolescents with persistent (apnea-hypopnea index; AHI≥2) or normalized-SDB (AHI<2)., Methods: Seventy-six adolescents with obesity recruited from two specialized institutions underwent a 9-12month diet and exercise intervention. Sleep and SDB (AHI≥2) were studied by polysomnography. Anthropometric parameters, fat mass (FM), glucose, insulin, lipid and leptin profiles, blood pressure (BP), MetScore FM and MetS were assessed pre- and post-intervention. We performed comparisons between Non-SDB and SDB groups and between Normalized-SDB and Persistent-SDB subgroups., Results: Fifty participants completed the study. Pre-intervention, twenty youth had SDB (40%) with higher insulin concentrations and systolic BP than Non-SDB participants (p < 0.01), for a similar degree of obesity. Post-intervention, MetScore FM (p < 0.001) and MetS prevalence (p < 0.05) were decreased in both groups. Eleven participants (55%) normalized SDB along with a decrease in insulin concentrations and BP (p < 0.05). Triglycerides, total cholesterol and LDL-cholesterol concentrations (p < 0.01) improved equally in the Normalized and Persistent-SDB subgroups., Conclusion: SDB was associated with lower insulin sensitivity and higher BP but did not affect the lipid profile. A diet and exercise lifestyle intervention is effective in decreasing the CMR whether or not SDB was normalized in obese adolescents., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Early adiposity rebound (EAR) predicts paediatric overweight/obesity, but current approaches do not consider both the starting point of EAR and the BMI trajectory. We compared the clinical characteristics at birth, age 3-5 and 6-8 years of children, according to the EAR and to its type (type A/type B-EAR). We assessed the children's odds of being classified as overweight/obese at age 6-8 years, according to the type of EAR as defined at age 3-5 years. As part of this two-wave observational study, 1055 children were recruited and examined at age 3-5 years. Antenatal and postnatal information was collected through interviews with parents, and weight and height from the health records. Type A and type B-EAR were defined in wave 1 according to the BMI nadir and the variation of BMI z-score between the starting point of the adiposity rebound and the last point on the curve. At 6-8 years (wave 2), 867 children were followed up; 426 (40·4 %) children demonstrated EAR. Among them, 172 had type A-EAR, higher rates of parental obesity (P < 0·05) and greater birth weight compared with other children (P < 0·001). Odds for overweight/obesity at 6-8 years, when adjusting for antenatal and postnatal factors, was 21·35 (95 % CI 10·94, 41·66) in type A-EAR children and not significant in type B-EAR children (OR 1·76; 95 % CI 0·84, 3·68) compared with children without EAR. Classification of EAR into two subtypes provides physicians with a reliable approach to identify children at risk for overweight/obesity before the age of 5 years.

Background and Aims: Pediatric obesity and sleep-disordered breathing (SDB) are associated with cardiometabolic risk (CMR), but the degree of severity at which SDB affects cardiometabolic health is unknown. We assessed the relationship between the CMR and the apnea-hypopnea index (AHI), to identify a threshold of AHI from which an increase in the CMR is observed, in adolescents with obesity. We also compared the clinical, cardiometabolic and sleep characteristics between adolescents presenting a high (CMR+) and low CMR (CMR-), according to the threshold of AHI., Methods and Results: 114 adolescents with obesity were recruited from three institutions specialized in obesity management. Sleep and SDB as assessed by polysomnography, anthropometric parameters, fat mass (FM), glucose and lipid profiles, and blood pressure (BP) were measured at admission. Continuous (MetScore FM ) and dichotomous (metabolic syndrome, MetS) CMR were determined. Associations between MetScore FM and AHI adjusted for BMI, sex and age were assessed by multivariable analyses. Data of 82 adolescents were analyzed. Multivariable analyses enabled us to identify a threshold of AHI = 2 above which we observed a strong and significant association between CMR and AHI (Cohen's d effect-size = 0.57 [0.11; 1.02] p = 0.02). Adolescents with CMR+ exhibited higher MetScore FM (p < 0.05), insulin resistance (p < 0.05), systolic BP (p < 0.001), sleep fragmentation (p < 0.01) and intermittent hypoxia than CMR- group (p < 0.0001). MetS was found in 90.9% of adolescents with CMR+, versus 69.4% in the CMR- group (p < 0.05)., Conclusions: The identification of a threshold of AHI ≥ 2 corresponding to the cardiometabolic alterations highlights the need for the early management of SDB and obesity in adolescents, to prevent cardiometabolic diseases., Clinical Trials: NCT03466359, NCT02588469 and NCT01358773., (Copyright © 2019 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.)

Background: Pediatric obesity is closely associated with obstructive sleep apnea (OSA) and short sleep duration. While multidisciplinary weight loss interventions are recommended for pediatric obesity management, the evidence for their effects on OSA severity and overall sleep in youth have not been systematically examined., Objectives: To conduct a systematic review and meta-analysis investigating the effects of multidisciplinary weight loss interventions on OSA severity and prevalence, and on overall sleep health in youth with obesity., Methods: A systematic search of interventional studies (participants age range: 10-19 yrs) was performed using PubMed, CENTRAL and Embase, from inception to May 2019. The quality of the evidence was assessed using the Cochrane risk of bias tool., Results: Ten studies were included by the end of the screening process. Ninety percent of the included studies reported a decrease in OSA prevalence post-intervention, and OSA was normalized for 46.2-79.7% of the youth. The meta-analysis comprising seven longitudinal studies revealed significant reductions in apnea-hypopnea index (effect size: -0.51, 95%CI -0.94 to -0.08, p = 0.019), and oxygen desaturation index (effect size: -0.28, 95%CI = -0.50 to -0.05, p = 0.016). Seventy-five percent of the studies reported improved sleep duration in youth with OSA., Conclusions: Evidence suggests that multidisciplinary weight loss interventions result in improvements in OSA severity and sleep duration in youth with obesity. Future randomized controlled trials are warranted to better assess and understand the independent implications of weight loss, fat mass decrease and chronic exercise on OSA and sleep health in this population.

The revolution in new sequencing technologies is greatly leading to new understandings of the relations between genotype and phenotype. To interpret and analyze data that are grouped according to a phenotype of interest, methods based on statistical enrichment became a standard in biology. However, these methods synthesize the biological information by a priori selecting the over-represented terms and may suffer from focusing on the most studied genes that represent a limited coverage of annotated genes within a gene set. Semantic similarity measures have shown great results within the pairwise gene comparison by making advantage of the underlying structure of the Gene Ontology. We developed GSAn, a novel gene set annotation method that uses semantic similarity measures to synthesize a priori Gene Ontology annotation terms. The originality of our approach is to identify the best compromise between the number of retained annotation terms that has to be drastically reduced and the number of related genes that has to be as large as possible. Moreover, GSAn offers interactive visualization facilities dedicated to the multi-scale analysis of gene set annotations. Compared to enrichment analysis tools, GSAn has shown excellent results in terms of maximizing the gene coverage while minimizing the number of terms., (© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)

The W3C project, "Linking Open Drug Data" (LODD), linked several publicly available sources of drug data together. So far, French data, like marketed drugs and their summary of product characteristics, were not integrated and remained difficult to query. In this paper, we present Romedi (Référentiel Ouvert du Médicament), an open dataset that links French data on drugs to international resources. The principles and standard recommendations created by the W3C for sharing information were adopted. Romedi was connected to the Unified Medical Language System and DrugBank, two central resources of the LODD project. A SPARQL endpoint is available to query Romedi and services are provided to annotate textual content with Romedi terms. This paper describes its content, its services, its links to external resources, and expected future developments.

Clinical information in electronic health records (EHRs) is mostly unstructured. With the ever-increasing amount of information in patients' EHRs, manual extraction of clinical information for data reuse can be tedious and time-consuming without dedicated tools. In this paper, we present SmartCRF, a prototype to visualize, search and ease the extraction and structuration of information from EHRs stored in an i2b2 data warehouse.

The objectives of this study were to assess the relationship between inflammation and obstructive sleep apnea (OSA) and determine whether the lifestyle program's effects on inflammatory markers are associated with changes in anthropometric parameters, cardiorespiratory fitness, sleep duration, and OSA severity in severely obese adolescents. Participants were aged 14.6 (SD 1.2) yr, with a body mass index (BMI) of 40.2 (SD 6.5) kg/m 2 . Sleep, anthropometric parameters, glucose metabolism, inflammatory profile, and cardiorespiratory fitness [V̇o 2peak relative to body weight (V̇o 2peakBW ) and fat-free mass (V̇o 2peakFFM )] were assessed at admission and at the end of a 9-mo lifestyle intervention program (LIP). Associations between C-reactive protein (CRP) concentrations and BMI, sex, oxygen desaturation index (ODI), sleep fragmentation, total sleep time (TST), and V̇o 2peak were assessed via ANCOVA. Twenty-three subjects completed the study. OSA subjects ( n = 13) exhibited higher CRP concentrations and a trend for higher BMI than non-OSA subjects ( P = 0.09) at admission. After intervention, OSA was normalized in six subjects, and CRP significantly decreased in the OSA group and in the whole population. In both groups, leptin levels significantly decreased, whereas adiponectin concentrations increased. At admission, BMI adjusted for sex, arousal index, ODI, TST, and V̇o 2peakBW was associated with CRP levels (adjusted r 2  = 0.32, P < 0.05). The decrease in CRP concentrations postintervention was associated with enhanced V̇o 2peakFFM adjusted for sex, weight loss, and changed sleep parameters (adjusted r 2  = 0.75, P < 0.05). Despite higher amounts of CRP in OSA subjects, obesity severity outweighs the proinflammatory effects of OSA, short sleep duration, and low cardiorespiratory fitness. However, enhanced cardiorespiratory fitness is associated with the decrease of inflammation after controlling for the same parameters.

Aim: To evaluate the impact of an aerobic fitness program on disease activity, defined by the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) and on C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and the Bath Ankylosing Spondylitis Functional Index (BASFI) in case of axial spondyloarthritis., Methods: A systematic review of the literature, following the Prisma recommendations, was performed by two reviewers on the PubMed and Embase databases. Controlled trials assessing the efficacy of aerobic exercises compared to physiotherapy on axial spondyloarthritis disease activity were included. The diagnosis of axial spondyloarthritis was meeting the New York criteria and/or the Assessment in Axial Spondyloarthritis International Working Group criteria. Aerobic fitness was defined as an exercise performed at 50%-90% of the maximal heart rate or between 50% and 80% oxygen consumption (VO 2 ) peak., Results: Five hundred and twenty abstracts were identified and 93 abstracts were analyzed. Eight studies met the selection criteria and 6 were finally included in this study because of the presence of a control group. Both groups were similar in terms of age, sex ratio, disease duration. Aerobic exercise provided a positive impact on the BASDAI in the intervention group (148 patients) (weighted mean difference [WMD]: -0.52 [95% CI: -0.9 to -0.13]) (I 2 : 10.3%, P = 0.35). However, when compared to a control group (152 patients), the improvement of BASDAI didn't reach significance (WMD: -0.25 [95% CI: -0.83 to 0.32]) (I 2 : 0%, P = 0.41). Aerobic exercise did not improve BASFI, CRP or ESR., Conclusion: Aerobic exercise did not provide beneficial effects either on disease activity or on physical function and biological parameters when compared to a control group in axial spondyloarthritis., (© 2018 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.)

Motivation: The recent revolution in new sequencing technologies, as a part of the continuous process of adopting new innovative protocols has strongly impacted the interpretation of relations between phenotype and genotype. Thus, understanding the resulting gene sets has become a bottleneck that needs to be addressed. Automatic methods have been proposed to facilitate the interpretation of gene sets. While statistical functional enrichment analyses are currently well known, they tend to focus on well-known genes and to ignore new information from less-studied genes. To address such issues, applying semantic similarity measures is logical if the knowledge source used to annotate the gene sets is hierarchically structured. In this work, we propose a new method for analyzing the impact of different semantic similarity measures on gene set annotations., Results: We evaluated the impact of each measure by taking into consideration the two following features that correspond to relevant criteria for a "good" synthetic gene set annotation: (i) the number of annotation terms has to be drastically reduced and the representative terms must be retained while annotating the gene set, and (ii) the number of genes described by the selected terms should be as large as possible. Thus, we analyzed nine semantic similarity measures to identify the best possible compromise between both features while maintaining a sufficient level of details. Using Gene Ontology to annotate the gene sets, we obtained better results with node-based measures that use the terms' characteristics than with measures based on edges that link the terms. The annotation of the gene sets achieved with the node-based measures did not exhibit major differences regardless of the characteristics of terms used., Competing Interests: The authors have declared that no competing interests exist.

Post-lunch sleepiness belongs to biological rhythms. Athletes take a nap to counteract afternoon circadian nadir, in prevision of disturbed sleep. This study examined the effects of brief post-lunch nap on vigilance in young and healthy athletes. The P300 components, physiological and cognitive performances were assessed either after nap or rest, following a night of normal sleep (NSC) or simulated jet lag condition (5-h advance-JLC). P300 wave is the positive deflection at about 300 ms in response to a rare stimulus, representing higher information processing. P300 amplitude reflects the amount of attention allocated whereas P300 latency reflects time spent on stimulus classification. P300 amplitude was significantly increased (Fz:11.14±3.0vs9.05±3.2 µV; p<0.05) and P300 latency was shorter (Pz:327.16±18.0vs344.90±17.0 ms; p<0.01) after nap in NSC. These changes were accompanied by lower subjective sleepiness (19.7±9.6vs27.5±16.5; p<0.05) and decrease in mean reaction times (MRT: divided attention, 645.1±74.2vs698±80.4 ms; p<0.05). In contrast, in JLC, only P300 amplitudes (Fz:10.30±3.1vs7.54±3.3 µV; p<0.01 and Cz: 11.48±3.1vs9.77±3.6 µV; p<0.05) increased but P300 latencies or MRT did not improve. These results indicated improvements in speed of stimulus evaluation time. Napping positively impacts on cognitive processing, especially when subjects are on normal sleep schedules. A nap should be planned for athletes whose performance requires speedy and accurate decisions., Competing Interests: The authors declare no conflict of interest., (© Georg Thieme Verlag KG Stuttgart · New York.)

Study Objectives: Physical exercise and lifestyle modification are recognized as adjunct therapy for obstructive sleep apnea (OSA) in overweight adults. The objectives of this study were to investigate the effects of long-term physical exercise combined with a balanced diet on sleep architecture, sleep duration, and OSA in adolescents with severe obesity., Methods: This interventional study was conducted in a nursing institution. Participants were aged 14.6 ± 1.2 years with obesity (body mass index (BMI) = 40.2 ± 6.5 kg/m 2 ). At admission and at 9 months, participants underwent ambulatory polysomnography and incremental maximal exercise testing to determine cardiorespiratory fitness., Results: Twenty-four subjects completed the study. Analyses were performed on the whole population and on a subgroup of subjects with OSA (OSA-subgroup). OSA, defined as obstructive apnea-hypopnea index (OAHI) ≥ 2 events/h, was diagnosed in 58.3% of the population. OAHI was only associated with fat mass in males ( r = .75, P < .05). At 9 months postintervention, weight loss (-11.1 kg, P < .0001) and improved cardiorespiratory fitness (VO 2 peak: +4.9 mL/min/kg, P < .001) were found in the whole population. Sleep duration was increased (+34 minutes, P < .05) and sleep architecture was changed with an increase of rapid eye movement sleep (+2.5%, P < .05) and a decrease of stage N3 sleep (-3.1%, P < .001). Similar results were found in the OSA subgroup. However, OAHI remained unchanged ( P = .18)., Conclusions: A combination of supervised aerobic exercise and a balanced diet led to weight loss, improved aerobic capacity, and modified sleep architecture without changes in OSA., Commentary: A commentary on this article appears in this issue on page 907., Clinical Trial Registration: Registry: ClinicalTrials.gov, Title: Exercise and Venous Compression on Upper Airway Resistance in Obese Teenagers With OSA (OBESOMAC), URL: https://clinicaltrials.gov/ct2/show/NCT02588469, Identifier: NCT02588469., (© 2018 American Academy of Sleep Medicine.)

Life sciences are currently going through a great number of transformations raised by the in-going revolution in high-throughput technologies for the acquisition of data. The integration of their high dimensionality, ranging from omics to clinical data, is becoming one of the most challenging stages. It involves inter-disciplinary developments with the aim to move towards an enhanced understanding of human physiology for caring purposes. Biologists, bioinformaticians, physicians and other experts related to the healthcare domain have to accompany each step of the analysis process in order to investigate and expertise these various data. In this perspective, methods related to information visualization are gaining increasing attention within life sciences. The softwares based on these methods are now well recognized to facilitate expert users' success in carrying out their data analysis tasks. This article aims at reviewing the current methods and techniques dedicated to information visualisation and their current use in software development related to omics or/and clinical data., (Copyright © 2017 Elsevier Inc. All rights reserved.)

In oncology, the reuse of data is confronted with the heterogeneity of terminologies. It is necessary to semantically integrate these distinct terminologies. The semantic integration by using a third terminology as a support is a conventional approach for the integration of two terminologies that are not very structured. The aim of our study was to use SNOMED CT for integrating ICD-10 and ICD-O3. We used two complementary resources, mapping tables provided by SNOMED CT and the NCI Metathesaurus, in order to find mappings between ICD-10 or ICD-O3 concepts and SNOMED CT concepts. We used the SNOMED CT structure to filter inconsistent mappings, as well as to disambiguate multiple mappings. Based on the remaining mappings, we used semantic relations from SNOMED CT to establish links between ICD-10 and ICD-O3. Overall, the coverage of ICD-O3 and ICD10 codes was over 88%. Finally, we obtained an integration of 24% (203/852) of ICD-10 concepts with 86% (888/1032) of ICD-O3 morphology concepts combined to 39% (127/330) of ICD-O3 topography concepts. Comparing our results with the 23,684 ICD-O3 pairs mapped to ICD-10 concepts in the SEER conversion file, we found 17,447 pairs of ICD-O3 concepts in common among which 11,932 pairs were integrated with the same ICD-10 concept as the SEER conversion file. The automated process leverages logical definitions of SNOMED CT concepts. While the low quality of some of these definitions impacted negatively the integration process, the identification of such situations made it possible to indirectly audit the structure of SNOMED CT., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Background: The overexpression of human epidermal growth factor receptor-2 (HER2) in breast cancer is a poor prognosis. Trastuzumab improves overall survival but is associated with cardiotoxicity, especially a decline in left ventricular ejection fraction (LVEF). In addition, chemotherapy and radiotherapy increase fatigue and pain, decrease physical capacity and health-related quality of life. To date, no study has evaluated the benefits of physical activity on the side effects of treatment in patients with HER2 positive breast cancer. The aim of this study is to evaluate the impact of 3 months' exercise intervention on myocardial function and in particular on the rate of cardiotoxicity., Methods: This multicenter, randomized clinical trial will include 112 patients treated by adjuvant trastuzumab for HER2 positive breast cancer to investigate the effects of a 3 months' supervised exercise program (intermittent exercise, combining moderate and high intensities; 55 minutes duration, 3 times per week), on the rate of cardiotoxicity [defined by either a decrease of the LVEF under 50% or an absolute drop of LVEF of 10%] between baseline and at 3 months and on strength, aerobic capacity, metabolic, inflammatory and hormonal parameters. Health-related quality of life, fatigue, pain and level of physical activity will also be assessed. Participants are randomly allocated to one of the two groups ("training group" vs "standard oncological care"). Performance-based and self-reported outcomes are assessed at baseline, at the end of supervised exercise program and at six months follow-up., Discussion: Although physical exercise is recommended to reduce the side effects of adjuvant treatments in breast cancer patients, no randomized study has been conducted to assess the benefits of a physical training program in patients with HER2 overexpressing breast cancer. Cardiac toxicity of trastuzumab may be minimized with an exercise program combining high and moderate intensities. This type of program may be safe, feasible and effective but also increase cardiorespiratory fitness and improve health-related quality of life. If these benefits are confirmed, this exercise intervention could be systematically proposed to patients during the course of treatment by trastuzumab in addition to standard oncological care., Trial Registration: National Clinical Trials Number ( NCT02433067 ); Registration 28 april 2015.

Background: The alarming progression of pediatric obesity is associated with the development of sleep-disordered breathing (SDB), and both exhibit similar adverse cardiometabolic health outcomes. Physical activity level (PAL) may counteract sleep and metabolic disturbances. The present study investigates i) the association between the metabolic syndrome in childhood obesity and SDB, ii) the impact of SDB severity on cardiometabolic risk scores and PAL in children with obesity., Methods: Maturation status (Tanner stages), anthropometric (height, weight, body mass index, waist circumference, body adiposity index) and cardiometabolic characteristics (systolic and diastolic blood pressure, lipid and glycemic profiles) were assessed in 83 obese children (mean±SD, age: 10.7±2.7years). PAL and SDB were investigated with a step test and interviews, and an overnight sleep monitor, respectively. The presence or absence of metabolic syndrome (MS) was established and continuous cardiometabolic risk scores were calculated (MetScore BMI and MetScore WC )., Results: Obese children with (61.4%) and without (38.6%) MS present similar SDB. SDB severity is associated with increased insulin concentrations, MetScore BMI and MetScore WC (p<0.05) in obese children. There is no association between SDB and PAL., Conclusions: In a context where no consensus exists for SDB diagnosis in children, our results suggest the influence of SDB severity on cardiometabolic risk factors. Further studies are needed to explore the association between PAL and both metabolic and sleep alterations in obese children., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Background: Identifying incident cancer cases within a population remains essential for scientific research in oncology. Data produced within electronic health records can be useful for this purpose. Due to the multiplicity of providers, heterogeneous terminologies such as ICD-10 and ICD-O-3 are used for oncology diagnosis recording purpose. To enable disease identification based on these diagnoses, there is a need for integrating disease classifications in oncology. Our aim was to build a model integrating concepts involved in two disease classifications, namely ICD-10 (diagnosis) and ICD-O-3 (topography and morphology), despite their structural heterogeneity. Based on the NCIt, a "derivative" model for linking diagnosis and topography-morphology combinations was defined and built. ICD-O-3 and ICD-10 codes were then used to instantiate classes of the "derivative" model. Links between terminologies obtained through the model were then compared to mappings provided by the Surveillance, Epidemiology, and End Results (SEER) program., Results: The model integrated 42% of neoplasm ICD-10 codes (excluding metastasis), 98% of ICD-O-3 morphology codes (excluding metastasis) and 68% of ICD-O-3 topography codes. For every codes instantiating at least a class in the "derivative" model, comparison with SEER mappings reveals that all mappings were actually available in the model as a link between the corresponding codes., Conclusions: We have proposed a method to automatically build a model for integrating ICD-10 and ICD-O-3 based on the NCIt. The resulting "derivative" model is a machine understandable resource that enables an integrated view of these heterogeneous terminologies. The NCIt structure and the available relationships can help to bridge disease classifications taking into account their structural and granular heterogeneities. However, (i) inconsistencies exist within the NCIt leading to misclassifications in the "derivative" model, (ii) the "derivative" model only integrates a part of ICD-10 and ICD-O-3. The NCIt is not sufficient for integration purpose and further work based on other termino-ontological resources is needed in order to enrich the model and avoid identified inconsistencies.

Background: The aim of this study was to validate a measurement scale for perceived exertion, named the Childhood Obesity Perceived Exertion Scale (COPE-10), by evaluating concurrent validity, reliability and sensitivity in obese adolescents., Methods: Thirty obese adolescents (BMI 36.2±0.8 kg.m-2), aged 14.2±0.3 years, performed two incremental exercise tests (maximal followed by submaximal) before and after a multidisciplinary obesity management program. To standardize workload, physiological variables [heart rate (HR), ventilation (E) and gas exchange (O2)] and perceived exertion (RPE) were modelized (fHR, fVE, fVO2, fRPE). At a rank of 6 on the COPE-10 Scale (RPE6) and at fixed second ventilatory threshold (VT2), we determined respectively the associated power (WPRPE6, WPVT2) and HR (HRRPE6, HRVT2)., Results: During maximal exercise, we observed significant correlations between fRPE and each of fHR (r=0.88 ; r=0.91), fVE (r=0.93 ; r=0.94) and fVO2 (r=0.87 ; r=0.89) before and after management respectively, indicating the concurrent validity of the COPE-10 Scale to estimate exercise intensity in obese adolescents. During submaximal exercise, we observed intraclass correlation coefficients of 0.77 before and 0.86 after management, showing reliability. After management, WPVT2 and WPRPE6 increased significantly (+23W and +21W ; P<0.001), and there was a significant correlation between HRVT2 and HRRPE6 (r=0.90), illustrating the scale's sensitivity to change., Conclusions: The COPE-10 Scale is a valid tool to measure perceived exertion in obese adolescents. This inexpensive and non-invasive instrument could be widely used in rehabilitation programs for obese youths.

Background: With the large and increasing volume of textual data, automated methods for identifying significant topics to classify textual documents have received a growing interest. While many efforts have been made in this direction, it still remains a real challenge. Moreover, the issue is even more complex as full texts are not always freely available. Then, using only partial information to annotate these documents is promising but remains a very ambitious issue., Methods: We propose two classification methods: a k-nearest neighbours (kNN)-based approach and an explicit semantic analysis (ESA)-based approach. Although the kNN-based approach is widely used in text classification, it needs to be improved to perform well in this specific classification problem which deals with partial information. Compared to existing kNN-based methods, our method uses classical Machine Learning (ML) algorithms for ranking the labels. Additional features are also investigated in order to improve the classifiers' performance. In addition, the combination of several learning algorithms with various techniques for fixing the number of relevant topics is performed. On the other hand, ESA seems promising for this classification task as it yielded interesting results in related issues, such as semantic relatedness computation between texts and text classification. Unlike existing works, which use ESA for enriching the bag-of-words approach with additional knowledge-based features, our ESA-based method builds a standalone classifier. Furthermore, we investigate if the results of this method could be useful as a complementary feature of our kNN-based approach., Results: Experimental evaluations performed on large standard annotated datasets, provided by the BioASQ organizers, show that the kNN-based method with the Random Forest learning algorithm achieves good performances compared with the current state-of-the-art methods, reaching a competitive f-measure of 0.55 % while the ESA-based approach surprisingly yielded unsatisfactory results., Conclusions: We have proposed simple classification methods suitable to annotate textual documents using only partial information. They are therefore adequate for large multi-label classification and particularly in the biomedical domain. Thus, our work contributes to the extraction of relevant information from unstructured documents in order to facilitate their automated processing. Consequently, it could be used for various purposes, including document indexing, information retrieval, etc.

Introduction: Rheumatoid arthritis (RA) is the most common chronic inflammatory joint disease and is associated with an excess risk of cardiovascular disease. For the general population, the World Health Organization has issued detailed recommendations on the type of physical activity appropriate for decreasing the cardiovascular risk. The objective of this work is to review available data on the effects of physical activity in patients with RA., Results: RA is responsible for a marked decrease in physical activity. Physical activity significantly diminishes both the cardiovascular risk and the DAS 28. Vascular benefits from physical activity include improved endothelial function and slowing of the atherosclerotic process. Physical activity also has favorable effects on bone, slowing radiographic disease progression in small joints and increasing bone mineral density at the femoral neck, although these effects are not statistically significant. Finally, engaging in physical activity increases self-esteem, alleviates symptoms of depression, improves sleep quality, and decreases pain perception. Aerobic exercise is the most commonly advocated type of physical activity. Most interventions were of short duration (4 weeks) and involved aerobic activity (running or cycling) for 60minutes a day 5 days a week. Resistance training has been shown to decrease systemic inflammation and increase muscle strength. The main obstacles to physical activity in patients with RA are related to both the patients, who lack both motivation and knowledge, and the rheumatologists, who also lack knowledge and place insufficient emphasis on promoting physical activity., Conclusion: Physical activity provides many benefits in patients with RA and should be widely performed. Promoting physical activity should be among the objectives of therapeutic patient education for RA., (Copyright © 2015 Société française de rhumatologie. Published by Elsevier SAS. All rights reserved.)

With the recent and intensive research in the biomedical area, the knowledge accumulated is disseminated through various knowledge bases. Links between these knowledge bases are needed in order to use them jointly. Linked Data, SPARQL language, and interfaces in Natural Language question-answering provide interesting solutions for querying such knowledge bases. We propose a method for translating natural language questions in SPARQL queries. We use Natural Language Processing tools, semantic resources, and the RDF triples description. The method is designed on 50 questions over 3 biomedical knowledge bases, and evaluated on 27 questions. It achieves 0.78 F-measure on the test set. The method for translating natural language questions into SPARQL queries is implemented as Perl module available at http://search.cpan.org/ thhamon/RDF-NLP-SPARQLQuery.

Significant efforts have been undertaken for providing the Gene Ontology (GO) in a computable format as well as for enriching it with logical definitions. Automated approaches can thus be applied to GO for assisting its maintenance and for checking its internal coherence. However, inconsistencies may still remain within GO. In this frame, the objective of this work was to audit GO relationships. First, reasoning over relationships was exploited for detecting redundant relations existing between GO concepts. Missing necessary and sufficient conditions were then identified based on the compositional structure of the preferred names of GO concepts. More than one thousand redundant relations and 500 missing necessary and sufficient conditions were found. The proposed approach was thus successful for detecting inconsistencies within GO relations. The application of lexical approaches as well as the exploitation of synonyms and textual definitions could be useful for identifying additional necessary and sufficient conditions. Multiple necessary and sufficient conditions for a given GO concept may be indicative of inconsistencies.

Clinical data recorded in modern EHRs are very rich, although their secondary use research and medical decision may be complicated (eg, missing and incorrect data, data spread over several clinical databases, information available only within unstructured narrative documents). We propose to address the issue related to the processing of narrative documents in order to detect and extract numerical values and to associate them with the corresponding concepts (or themes) and units. We propose to use a CRF supervised categorisation for the detection of segments (themes, numerical sequences and units) and a rules-based system for the association of these segments among them in order to build semantically meaningful sequences. The average results obtained are competitive (0.96 precision, 0.78 recall, and 0.86 F-measure) and we plan to use the system with larger clinical data.

Travel across time zones causes jet lag and is accompanied by deleterious effects on sleep and performance in athletes. These poor performances have been evaluated in field studies but not in laboratory conditions. The purpose of this study was to evaluate, in athletes, the impact of 5-h phase advance on the architecture of sleep and physical performances (Wingate test). In a sleep laboratory, 16 male athletes (age: 22.2 ± 1.7 years, height: 178.3 ± 5.6 cm, body mass: 73.6 ± 7.9 kg) spent 1 night in baseline condition and 2 nights, 1 week apart, in phase shift condition recorded by electroencephalography to calculate sleep architecture variables. For these last 2 nights, the clock was advanced by 5 h. Core body temperature rhythm was assessed continuously. The first night with phase advance decreased total sleep time, sleep efficiency, sleep onset latency, stage 2 of nonrapid eye movement (N2), and rapid eye movement (REM) sleep compared with baseline condition, whereas the second night decreased N2 and increased slow-wave sleep and REM, thus improving the quality of sleep. After phase advance, mean power improved, which resulted in higher lactatemia. Acrophase and bathyphase of temperature occurred earlier and amplitude decreased in phase advance but the period was not modified. These results suggest that a simulated phase shift contributed to the changes in sleep architecture, but did not significantly impair physical performances in relation with early phase adjustment of temperature to the new local time.