dataesr/scientific-paragraphs-categorization huggingface dataset:
Such systems make it easier machine-readable documentation, and allow for computerized comparisons of the outcomes of different treatments for the same diagnosis  [13, 14]. In the early 2000s, no consensus-standardized nomenclature for dental diagnoses and treatment outcomes was available  [13]. The lack of a collective strategy among governments, health centers, and software developers strongly limited progress in this area  [15]. Moreover, the most widely used coding system at the time, the International Classification of Diseases (ICD-9  [16] ), provides limited coding for dentistry and is inadequate for making appropriate dental diagnoses  [17]. Several studies have attempted to overcome this problem by proposing different coding systems, including EZCode  [18] , SNODENT, Ontology for Dental Research  [19] , Oral Health and Disease Ontology  [20] , etc.
The available literature on coding systems in dentistry is confusing at first glance. Some of the proposed classifications have been redefined or renamed several times, and, in some cases, they have been merged with other coding systems to fit the needs of dentistry. In addition to standardization issues, clinical dental coding usage is mainly considered as an academic concern whereas private practitioners should also be concerned by this  [2]. Difficulties in capturing standardized data may explain why private practitioners in dentistry have failed to adopt SCCSs. Indeed, making the capture of standardized data more efficient is essential to improve usability, workflow integration, but also data quality. The reuse of EDR data holds much promise in the area of research. Not only can it diminish the costs and inefficiencies associated with clinical research, but shared EDR data warehouses can surpass many registries and data repositories in volume.
Moreover, EDRs are realworld data sources that can be used in studies to produce real-world evidence, which in turn can help accelerate advances in care, improve outcomes for patients, and provide important insights for daily practice. Like other forms of retrospective research, EDR-based retrospective studies require neither patient recruitment nor the collection of new data, both of which are expensive and time-consuming. While the reuse of EDR data is a promising step towards decreasing research costs, facilitating patient-centered research, and speeding the rate of new medical discoveries  [21] , it is nevertheless limited by data quality concerns. Indeed, it is generally accepted that due to differences in priorities between clinical practice and research, clinical data are not recorded with the same care as research data  [21].
Thus, in addition to proper ergonomics and workflow integration, there is a need for data capture forms that can intercept basic errors and provide real-time feedback to keep the user informed of what is going on, thus ensuring that the most accurate and complete information is collected. In addition, EDR data can be used in clinical decision support systems (CDSSs) to provide real-time patientcentered clinical recommendations. They can also be used in educational settings to monitor students' technical and theoretical knowledge as well as their clinical activity. The primary objective of this scoping review was to summarize studies on SCCSs and EDR data capture in dentistry. The secondary objective was to explore the practical implications of reusing EDR data in CDSSs, quality measure development and clinical research.
Methods Based on the definition of HISs  [22] , the literature search was divided into three specifics searches: 1. HISs in dentistry and SCCSs 2. HISs in dentistry and data capture 3. HISs in dentistry and reuse of routine patient care data For each of the searches, a review of the literature was conducted in August 2020 and then updated on January 2021 following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) protocol. PubMed was used to search the MEDLINE bibliographical database, and Web of Science was used to search all databases. Studies published between 1 January 2000 and 9 January 2021 were selected. This long period of inclusion helped to account for developments in the field and for the current state of knowledge on each of the subjects discussed.
Evaluation and validation of standardized clinical coding systems In 2005, Goldberg et al. [24]  used a software-based method to evaluate the internal quality of SNODENT. This method consisted of searching for errors in ontology by comparing different ways of extracting information from terms, concepts, descriptions, and definitions. The authors found that SNODENT had quality issues, mainly due to confusion between terms and concept codes (for example, unclear relationships between terms and concepts, polysemic concepts, subsumption problems, etc. ). Practice-based evaluations were performed only for Z codes  [18] , the Dental Diagnostic System (DDS)  [25, 28, 30] , and SNODENT  [31]. Some studies evaluated diagnostic code entry by determining the plausibility of the entered diagnostic code based on the entered treatment procedure code  [18, 25, 28, 30] , while others compared written diagnoses to diagnostic codification  [31].
User interface and workflow integration Improving user interfaces is an important concern  [10, 11, 39, 40, 42, 43]. The following issues should be addressed: unintuitive interfaces, complex navigation Capture technique Development of a natural language processing application to automatically annotate clinical notes with unified medical language system codes within the interfaces, insufficient user feedback, complex structured data capture. Several user interface evaluation techniques were identified in the literature (Table  6 ). In their 2014 article, Walji et al. [42]  evaluated 3 different methods (user testing, semi-structured interviews, and surveys) for detecting usability problems in an EDR. They concluded that the user testing method is better at detecting usability problems than the other two methods but that a combination of different complementary techniques is needed to provide a more comprehensive picture of EDR usability challenges.
According to  [39, 42] , issues related to EDR usability can be divided into three categories: user interface-related themes, SCCS-related themes, and work domain-and workflow-related themes. More generally, the problems identified in the selected articles were: the lack of intuitiveness of the EDR interface, inadequate user guidance, and poorly organized controls. All of these were shown to impair users' ability to determine how to perform a desired action and on which object the action should be performed  [35, 40]. Lastly, the lack of easy and consistent access to patient data in most EDRs, and in particular the absence of an integrated view of the patient, requires users to switch between separate screens to see radiographs, intraoral photos, and clinical notes. This makes navigation cumbersome and introduces breakdowns in workflow  [11, 38, 43, 44].
Greater standardization of EDR data and increased adoption of public health databases and registries are needed to make EDR data more accessible in dental research  [57]. In the US, a shared data warehouse named BigMouth was launched in August 2012, making data on 1. 1 million patients available to users in the four contributing dental schools  [58]. Nowadays, ten institutions have contributed to BigMouth by providing data on more than 3 million patients  [63].
Moreover, the complexity of SCCSs makes them difficult to navigate from the EDR user interface, which can negatively impact data capture. Many issues can thwart data capture: a lack of universally accepted documentation standards and information needs, incomplete or inaccurate record practices, lack of usability of EDR user interfaces, a lack of easy and consistent access to patient data, and inaccurate workflow integration  [10, 12, 39, 44]. These various problems, both technical and socio-organizational, condition the usability of EDRs  [11, 35, 39]. One of the main challenges of data capture is to ensure the customization of EDRs according to dental department needs or user expectations  [11, 43]. Practitioners typically spend more time than they would like in properly documenting clinical information, which reduces the time available for patient care or other activities  [10].
Although it is difficult to customize EDRs to each practitioner, there is a need for EDRs that can adapt to the most common situations. No study on the specifics of dental practitioners' working environment was identified in our review. This is unfortunate, as the dental chair would benefit from being interfaced with the EDR. This would greatly facilitate the integration of data capture into processes at multiple levels (care, radio examination, etc. ). As regards care data reuse, EDRs have received increased attention because they help to expand evidence-based knowledge  [57] , assess needs, and improve quality of care. The most obvious obstacles to the widespread reuse of EDR data are the lack of standards in dentistry and data availability and quality issues  [55, 57, 58]. The reuse of EDR data can complement traditional research methods or can function in synergy with them  [57].
Limitations The main limitation of this review lies in the search strategy, which may have prevented us from identifying all studies of interest due to limitations in database coverage and to the particularities of article indexing. To compensate this limitation a manual bottom-up search of the references of each selected article was performed. Regarding the reuse of routine patient care data, our work aimed only to include studies addressing data reuse in view of information system. Therefore, studies that reuse electronic data without consideration of HIS were excluded from this scoping review. Another area of research related to data reuse is the Dental Practice-Based Research Network (DPBRN). The DPBRN brings together solo and large group practitioners to accelerate the development and conduct of clinical studies on important issues in oral health care  [68].
Efforts in terms of standardization and interoperability have led to concrete progress that allows EDR data to be aggregated with other health and non-health data (e. g. , geographic data) to generate new broader knowledge. Despite these advances, strong governance seems fundamental to achieve concrete achievements such as inter-university data warehouses  [71]. Some studies selected in this review assessed the educational value of HISs, but only in relation to SCCSs. The latter can indeed be used to evaluate students' diagnostic abilities in a clinical situation. Clinical data linked to care provided by students would benefit from being exploited. They could be used to monitor the acquisition of student skills at both the technical and intellectual levels or to ensure that students properly perform enough procedures to be able to have their own private practice.
Excisional skin wounding, bacterial infections and measurement of wound areas After anesthesia by an intraperitoneal injection of a xylazine (10 mg/ml)/ketamine (1 mg/ml) solution (100 ml of this solution/ 10 g of animal weight), the back skin of mice was shaved and remaining hairs were removed using a depilatory cream (Veet@, Reckitt Benckiser, France). Four excisional wounds were performed by puncturing the skin with a 4 mm-round punch (Stiefel) and removing the skin biopsy. Twenty microliters of the bacterial suspension (5X10 6 CFU) or the PBS control solution were directly applied on each wound. After spreading of the bacterial mixture on the wound, mice were housed individually to avoid grooming behavior of infected wounds. To follow wound healing kinetics, the surface of each wound was measured daily using Image J software on pictures of back skin of mice including a meter stick as reference.
After washing, cells were resuspended in complete RPMI and stimulated for 4 hours in the presence of phorbol myristate acetate (PMA, 50 ng/ml), ionomycin (750 ng/ml) and Golgi Plug (1 μl for/10 6 cells; BD Biosciences). Before extracellular staining, cells were incubated with Fc Block (BD Biosciences) for 10 minutes and then for 15 minutes at 4°C with the following antibodies: V500-conjugated anti-CD45, BV421-conjugated anti-CD3ϵ, FITC-conjugated anti-TCRgd (all from BD Biosciences) and Zombie NIR for cell viability (BioLegend, San Diego,CA). For intracellular staining, cells were permeabilized with the Cytofix/Cytoperm kit and labelled for 15 min at 4°C with PE-conjugated anti-IL-17A (BD Biosciences) and PercP-eFluor710-conjugated anti-IL-22 (eBioscience) antibodies. Data were collected on a FACS Verse instrument (BD Bioscience) and analyzed using FlowJo software.
Acknowledgments We thank  Martine Garnier  for her excellent technical support,  Adriana Delwail  ( ImageUP platform, University of Poitiers ) for technical help for flow cytometry and the members of the animal facility of the  University of Poitiers (Prebios)  and  CNRS/University of Orleáns. We thank  Jeffrey Arsham  ( CHU Poitiers, France ) for careful reviewing and editing the original English language manuscript. The authors thank the  European Union  for benefiting from its equipment grant program for research laboratories and platforms and the  Poitiers University Hospital  ( CHU ) for his grant for publication support.
Objectives Development of a Community Engagement Package composed of (1) database of community engagement (CE) experiences from different contexts, (2) CE learning package of lessons and tools presented as online modules, and (3) CE workshop package for identifying CE experiences to enrich the CE database and ensure regular update of learning resources. The package aims to guide practitioners to promote local action and enhance skills for CE. Setting and participants The packages were co-created with diverse teams from WHO, Social Innovation in Health Initiative, UNICEF, community practitioners, and other partners providing synergistic contributions and bridging existing silos. Methods The design process of the package was anchored on CE principles. Literature search was performed using standardised search terms through global and regional databases.
Interviews with CE practitioners were also conducted. Results A total of 356 cases were found to fit the inclusion criteria and proceeded to data extraction and thematic analysis. Themes were organised according to rationale, key points and insights, facilitators of CE and barriers to CE. Principles and standards of CE in various contexts served as a foundation for the CE learning package. The package comprises four modules organised by major themes such as mobilising communities, strengthening health systems, CE in health emergencies and CE as a driver for health equity. Conclusion After pilot implementation, tools and resources were made available for training and continuous collection of novel CE lessons and experiences from diverse socio-geographical contexts.
CEP project design and components The design of the CEP involved the creation of a database of relevant CE cases. These cases were categorised and analysed, and themes and concepts were used to develop the CELP with contributions from CE subject matter experts (SMEs). The CEWP was designed to document 'newer' CE experiences that can be incorporated into the database, ensuring regular updates of the learning resources (see figure  1 ). Table  1  summarises the three components of the CEP. Given the uniqueness, relevance and value of the harmonised CEP in the context of health emergencies and the overall global health sphere, this paper seeks to document the processes and the innovative ways by which the CEP was developed at the height of COVID-19 restrictions.
Development of the CELP The CELP is a curation of CE lessons and tools presented as online (asynchronous) modules designed to capacitate learners on basic concepts, principles and applications of CE, and explore best practice experiences in solving health problems and promoting health through CE. In-depth analysis done with the contents of the database identified important CE principles, practices, lessons, challenges, and barriers encountered in different contexts and regions. Existing CE frameworks, toolkits and guides were also surveyed. Emerging themes and concepts were used as the basis for the development of the CELP. SMEs contributed to the contents of the CELP designed to be delivered in an online learning management system. Initial outline and plans for the CELP were also vetted among the CEP WG, and stakeholders and partners who have extensive experience in engaging and mobilising communities, both at the regional and global levels.
Categories of cases in the CE database There are 356 cases in the database (290 identified from published literature, 57 from grey literature and 9 from CE practitioner interviews) from all six WHO regions, categorised according to the health topic (table  3 ). In addition, a total of 56 cases dealing with health emergencies were identified with 30 cases on COVID-19, 12 on Ebola, 9 on environmental risk and disaster, and 5 on humanitarian crises.
Community engagement workshop package The CEWP provides tools and templates for identifying other CE experiences in a workshop format. The contents are similar to the CELP, with a special focus on documenting 'new' CE experiences and a walk-through of using and submitting case studies for the CE database. The target participants are practitioners who are interested in sharing their CE experiences. The CEWP allows the continuous collection of evidence and discussions with stakeholders on CE principles, practices and frameworks. These resources will be catalogued, categorised, and used to update the database and the learning and workshop packages. Participants and observers of the CEWP pilot were satisfied with the introduction and ice-breaking activities which set the stage for conducive training sessions.
DISCUSSION The CEP and its development showcase innovative elements in the project design, the human resources involved and way of working, and the inter-relationships of the different CEP components. The CEP conceptualisation and design involved broad consultations and co-creation with a community of diverse teams of WHO, SIHI hubs, UNICEF, and other implementing partners and frontline responders. The process and products of the package were vetted among stakeholders and partners at the regional and global levels. In addition, community practitioners were consulted regarding the screening criteria of cases to be included in the database, shared undocumented CE practices, and participated in the pilots of the learning and workshop packages to provide user feedback. This multistakeholder consultative processes allowed for the creation of a grounded, contextualised, relevant and integrated package.
Working on the CEP project during the COVID-19 pandemic did not deter the WHO and SIHI from Open access intensifying collaboration. The use of online platforms enabled the team to engage and mobilise relevant resources and develop the CEP components despite the absence of face-to-face consultations and other limitations. Creative use of online platforms was also maximised for the different components of the CEP (eg, online database, online modules) while still providing templates for possible face-to-face delivery, allowing for flexibility in engagement methods. The three components of the CEP feed into each other. The thematic analysis of the materials in the CE database guided the design of the CELP and CEWP. Selected cases were also used to reinforce and provide real-world application to the CE frameworks and related concepts in the online modules.
The CEWP facilitates the discussion of CE principles and practices among practitioners and the collection of new information for updating the database and CELP with 'new' CE experiences. The merit of the current CEP project over existing documentation is that the CEP is broad based-not limited to health emergencies, but includes other public health and social developmental activities such as routine immunisation, neglected tropical diseases, city and urban development, nutritional interventions and disaster risk management, among others. An operational challenge during the documentation was the language barrier. The cases were limited to English, French and Spanish. Future researchers can explore relevant documented and undocumented experiences in other languages, which will make the database more comprehensive and unifying at the same time.
CONCLUSION The design of the CEP emphasised inter-relationships among its components-CE database, learning package and workshop package. The CELP contents were taken from the comprehensive thematic analysis of the database. The CEWP facilitates the documentation of 'new' CE experiences and their nuances, ensuring timely updates of the database by CE practitioners themselves. Most of the cases included in the CEP database presented key insights on CE including its basic principles and the role of individual and community agency, building on local capacity, multidirectional communication, inclusion and multistakeholder engagement. Barriers to CE including issues of access, acceptability and adoption in the setting of weak health systems and societal issues were also identified. The learning and workshop packages were then developed to guide health professionals and other stakeholders based on these grounds.
At the time of extubation, the following data were recorded: body mass index, sequential organ failure assessment (SOFA) scores  [18] , previous duration of MV, number of previous SBTs without extubation, ventilator settings, quality of cough strength and amount of secretions assessed by nurses  [19]. Variables recorded after extubation included the following: treatment with noninvasive ventilation (NIV) and high-flow oxygen therapy (HFOT), time and reason for reintubation, length of ICU stay, and ICU and hospital mortality. Extubation failure was defined as a need for reintubation within the 7 days following extubation. The main reasons for intubation, risk factors for extubation failure, underlying chronic respiratory diseases, underlying cardiac diseases, obesity, weaning groups, the amount of secretions scoring and quality of cough, and reason for reintubation are defined in the supplemental material.
Patients From February 1, 2018 to December 12, 2020, 895 patients received more than 24 h of MV, among whom 623 patients (69%) were screened for the study because they performed at least one SBT. Of note, 38 subjects (6%) were excluded from the study because they had PS8 ZEEP SBT after inclusion in the Tip-Ex study  [21]. Five hundred and twenty-nine subjects with no missing data were observed, and their data were analysed. Among the 529 subjects, 303 subjects (57%) underwent 1-hour T-piece SBT, and 226 subjects (43%) underwent 1-h PS0 ZEEP SBT before being extubated (Fig. 1 ). The characteristics of subjects before extubation, day of extubation, and NIV received after extubation were compared to determine whether subjects underwent 1-hour T-piece SBT or 1-h PS0 ZEEP SBT before extubation, and the results are listed in Table  1.
In a physiologic meta-analysis assessing and comparing respiratory effort during T-piece SBT with various modalities of PS ventilation, the authors concluded the equivalence of T-piece and PS0 trials  [8]. Indeed, the "physiological" rationale existed to consider that evaluation of extubation readiness and success by 1-hour T-piece SBT and 1-h PS0 ZEEP SBT could provide similar results. However, to our knowledge, this comparison has not been previously realized during a clinical study. The results of repeated respiratory and cardiac parameters recorded and compared between the two types of SBTs suggest that one is not more effort-demanding than the other. Our study has several limitations. First, it was conducted at a single site; thus, the results may not be applicable to other ICUs. Second, the  investigator who recorded data (AG) was not blinded to the type of SBT and issue of extubation.