dataesr/scientific-paragraphs-categorization huggingface dataset:
However, we failed to observe a change in grunt duration during the anticipation of pen mates; as their grunts remained as short as during the initial phase. Two non-exclusive hypotheses can be raised to explain this result: (1) piglets learned that something positive was going to happen when entering the room (either the arrival of its pen mates or the arrival of a human with positive contacts, but not remaining in isolation) and began by expressing a non-specific positive state during the initial phase, so that grunts produced during the initial phase were already 'non-specific positive grunts' , and (2) the anatomical constraints of piglets' vocal tract does not allow them to shorten the grunts. In a recent study, Briefer et al. 19  showed that vocalisations (but not specifically grunts although they are usually over represented in datasets) recorded in positive contexts lasted 0.
Acknowledgements We acknowledge all the technical staff at UEPR: especially  Patrick Touanel  and  Marie-Hélène Lohat , who largely participated in handling the piglets. We thank  Eric Siroux  who helped building the acoustic chamber at the beginning of the experiment and  Remi Resmond  for great discussion about statistics. We thank  Ursula Kwong-Brown  for English edition of the manuscript. All the authors acknowledge  Camille Noûs , affirming the collective and open character of the creation and dissemination of knowledge (Cogitamus Laboratory https ://www. cogitamus. fr/indexen. html). This project is part of the  SoundWel  project in the framework of the  Anihwa Eranet and  funded by  ANR 30001199.
Chronic pulmonary aspergillosis (CPA) is a chronic fungal infection of the lung associated with high morbidity and mortality. The CPA Research network (CPAnet) registry established in 2018 is an international multicenter collaboration aiming to improve CPA knowledge and patient care. This study's aim was to describe the data collection process and content of CPAnet registry with preliminary clinical data. In the CPAnet registry, clinical data are collected through a web-based questionnaire. Data include CPA phenotype, comorbidities, treatment, outcome, and follow-up from several international centers. An exemplary descriptive analysis was performed on 74 patients, who were registered online before April 2020. CPA patients were predominantly (72%) male, 39% had chronic obstructive pulmonary disease, and 68% had a history of smoking.
Chronic obstructive pulmonary disease (COPD), prior tuberculosis (TB), non-tuberculous mycobacterial (NTM) infection, sarcoidosis, prior pneumothorax, and allergic bronchopulmonary aspergillosis (ABPA) comprise over 90% of the other underlying conditions  [9] [10] [11]. Physicians' unawareness or negligence of CPA in a patient is an important risk factor for diagnostic and therapeutic delay, which partly explains the increased mortality and the observed low single-site prevalence. Since many aspects of this underestimated disease are unknown, a prerequisite for improving the lack of knowledge is to join experience and expand data gathering across CPA reference centers worldwide. On this basis, the international CPA Research Network (CPAnet) was founded in 2017, followed by the creation of its multinational and multicenter CPAnet registry launched in 2018  [12, 13].
The main objective of the CPAnet registry is to assess the worldwide epidemiology of CPA, while the secondary objectives include the evaluation of diagnostic performance and treatment outcome measures across the different participating centers. Eventually, this registry will enable longitudinal studies monitoring the disease burden and clinically oriented research in order to improve the management and outcome of CPA patients  [14]. The aim of this article is to describe the CPAnet registry and present preliminary multicentric data on CPA patients to illustrate the clinical value and importance of such an international registry.
Materials and Methods The CPAnet registry is an open international registry containing individual and pseudonymized data from CPA patients from the participating reference centers, eventually giving rise to epidemiological and clinical non-interventional multicenter studies. CPAnet registry was officially launched in 2018 and data collection is ongoing without an endpoint. As the registry is open, treating physicians from various specialties (e. g. , pulmonology or infectious diseases) and microbiologists are invited to participate in the registry to further expand the extent of clinical data collection.
CPA Case Documentation, Definitions, and Data Collection CPAnet developed a case report form using the ClinicalSurveys. net online survey platform (QuestBack GmbH, Cologne, Germany). Investigators log into the system with username and password and are able to view and modify their own contributions. All data transmissions are encrypted via transport layer security (TLS) 1. 2 with an advanced encryption standard (AES) 256 Galois/Counter mode (GCM) bit key and ephemeral elliptic curve Diffie-Hellman (ECDHE) Rivest-Shamir-Adleman (RSA) key exchange. Data are documented pseudonymously or anonymously on QuestBack servers. Adult patients with a diagnosis of CPA are included either prospectively or retrospectively. The population is selected based on the following four diagnostic criteria  [1, 15] : (1) Radiology: one or more cavities with or without a fungal ball present or nodules on thoracic imaging; (2) Mycology: any direct or indirect mycological evidence from respiratory samples or from blood of Aspergillus spp.
g. , smoking, abuse of drugs or alcohol), other chronic diseases (e. g. , diabetes; heart-, liver-, and kidney disease), pulmonary co-infection at CPA diagnosis time point. Regarding the secondary endpoint of CPA diagnostic performance, clinical signs and symptoms, weight, height, lung function test(s), result of clinical scores (e. g. , St. George's Respiratory Questionnaire (SGRQ), Medical Research Council dyspnea scale (MRC)), result of imaging and mycological testing leading to CPA diagnosis (e. g. , microscopy, culture, polymerase chain reaction (PCR), histology, Aspergillus precipitins, Aspergillus-specific IgG antibody, galactomannan assay, beta-D-glucan assay), result of antifungal susceptibility testing are being collected. As treatment outcome measures, the following data are requested: antifungal treatment of CPA (e.
CPA Case Recruitment Eligible CPA cases are identified at sites participating in the CPAnet registry, mostly clinical departments or centers responsible for the diagnosis, treatment, and follow-up of CPA in their respective regions or countries (Table  1 ). Additional reference centers are being welcomed to join the CPAnet registry. At each center, cases are identified using relevant diagnosis codes (e. g. , ICD-10) for Aspergillus-related disease, local CPA registries, and medical records. Incident CPA cases fulfilling the above-mentioned diagnostic criteria are included both prospectively and retrospectively in the registry. The investigators at each site including patients and entering data are all specialists within the field of CPA. Diagnostic tools, treatment, and monitoring at each site are applied in accordance with current international guidelines and recommendations.
Ethical Considerations and Approvals The CPAnet registry is approved by the Institutional Review Board and Ethics Committee (EC) of the University Hospital Cologne (procedure ID 17-263), Cologne, Germany, as well as by the local ECs of the other participating centers. For prospectively included cases, oral and written informed consent from the patients has to be provided in order to participate. Approval for inclusion of retrospective cases has been obtained locally at each site in accordance with the different local requirements. All patient data are pseudonymized and stored in accordance with the General Data Protection Regulation (GDPR).
Funding At the time of the writing of this manuscript, the CPAnet registry has not received any financial support. Support for the initial programming and maintenance of the database was provided by Excellence Center of Medical Mycology (ECMM), Hospital Cologne, Cologne, Germany. Up to date, sites participating in CPAnet do not receive any financial support or compensation for their participation in the registry. As of February 2020, the CPAnet registry was awarded a Clinical Research Collaboration (CRC) by the European Respiratory Society (ERS) for the next three years.
g. , clarification of causes to diagnostic latency. Another strength is that the main proportion of CPA data is based on multidisciplinary team discussions involving experts of different backgrounds who follow international consensus on CPA management. By linking data from other registries with the CPAnet registry, specific research questions can be uncovered, such as pharmaco-epidemiological studies on medication patterns giving rise to or increasing the risk of CPA development, e. g. , combination of certain immunosuppressants in chronic underlying diseases. The major limitation is that not all CPA patients are entered in the CPAnet registry, which makes the data subject to selection bias. As such, one may claim that data are not generalizable but only concern patients from tertiary care centers, thereby inducing referral bias.
Another important limitation is the different follow-up times of the enrolled patients and the non-standardized (timing of) response evaluation. Of note, the registry currently integrates retrospective and prospective data as some patients were already under follow-up at the time of informed consent or only referred to the CPA reference center after failure of first-line treatment. As the project progresses, however, a shift toward more prospective follow up might be anticipated. Data quality might vary between centers due to different reasons, such as infrastructural or interpersonal differences. Although patient numbers remain too low to draw any firm conclusions, this first analysis already revealed the unavailability of some diagnostic techniques (such as galactomannan) or therapeutic options (such as certain antifungals or the availability of interventional radiology for bronchial artery embolization) in certain regions.
Data on referral patterns may also reveal bottlenecks for the apparent diagnostic delay or neglect that seems to exist in low-prevalence countries where the prevalence of comorbidities on the other hand is similar to that of countries with a higher CPA prevalence. This interim analysis lifts a first tip from the veil of the wealth of structured information embedded within the CPAnet registry. Additional clinical sites and reference centers are highly welcomed to join this clinical research collaboration. In the near future, this registry will indefinitely allow for multicentric clinical and epidemiological research on CPA of crucial importance, aiming to fill the lack of previous evidence on disease management.
Acknowledgments: We thank all study patients and study staff at the different CPAnet sites. We acknowledge  Korkut Avsar ,  Asklepios Pulmonary Clinic Gauting, Munich, Germany; Chris Kosmidis, Division of Infection, Immunity and Respiratory Medicine, University of Manchester , Manchester, UK; and  Fabian Leo ,  Department of Respiratory Medicine, Evangelical Lung Clinic, Berlin, Germany  for the inclusion of patient cases into the registry.
Patients with significant language barriers, complex medical consultations, or a vaccine catch-up already performed or in progress (recorded in our medical database), were excluded. Medical consultations were conducted by general practitioners and residents in French or English, or sometimes with the help of a companion speaking French or English. Every included patient was duly informed of the study's aim and asked to sign a written consent form. The following information was collected from our medical database used in PASS (ORBIS software): -Age and sex, -Country of origin and urban or rural environment in the country of origin, -Spoken language, literacy, level of education, -Professional occupation in the country of origin  (  All the above information was part of the regular anamnesis asked at the PASS.
Patients were asked if they recall being vaccinated during childhood, adolescence and/or adulthood. During the medical consultation, a TQS Ò test was performed on the patient (the TQS Ò test was not usually realized at the PASS); the presence or not of a Bacillus Calmette-Guérin (BCG) scar was also verified. The TQS Ò test's result and the presence or not of a BCG scar were recorded in the medical database.
Characteristics of the studied population (Tables The BCG scar was verified for 218 patients with 105 patients having had a BCG scar. Serologies were available for 266 patients: six were HIV positive, 7 were HCV positive and 26 were antigen HBs positive. Regarding vaccination declarations, 73. 2% declared having previous vaccination(s) during their childhood. This number decreased for vaccinations reported in adolescence (35. 5%) and adulthood (41%); 33. 5% reported receiving vaccines at all ages. As a reminder, only patients without proof of vaccination were included: patients having a vaccination report seen by the investigator or already vaccinated in the service (catch-up done or in progress and recorded in the medical database) were not included.
A French study conducted in an emergency room has also shown that the TQS Ò test was a better tool than the interview to appreciate vaccination status  [38]. Furthermore, during the study, type of vaccine was not specified when asking for previous vaccinations. However, most of the vaccines administered during adolescence and adulthood due to the need for boosters are the dt-IPV. Missed opportunities were high in our study after one month. Each medical visit must be an occasion of vaccine catch-up, which should be started as soon as possible. To prevent these missed opportunities, a special section specific to vaccinations is present in the medical database with each vaccination noted as well as the date of the next booster, serving as a reminder for the practitioner. A regular supply of vaccine must be ensured to avoid a shortage of stocks (which happened during our study).
Acknowledgements We thank  INGEN Ò laboratory  who freely provided all the TQS Ò tests needed for the study. We also like to acknowledge all members of the medical team of the  Hôtel-Dieu 's PASS who participate in the study as investigators:  Dr. de Champs Léger ,  Dr. Rieutord ,  Dr. Lelong ,  Dr. Giorno ,  Dr. Hass ,  Dr. Boyer ,  Dr. Lamache ,  Dr. Durel ,  Dr. Chicheportiche ,  Dr. Bouzouita ,  Dr. Renier ,  Dr. Paul Petit ,  Dr. de Willencourt ,  Dr. Blaes ,  Dr. Olivier  and  Dr. Bu. Also we would like to thank  Mrs. PIETRI Marie-Pierre  and  ALABA Marie , who helped with setting up the study and following up with the study.
Materials and Methods We conducted a retrospective, observational, bicentric study that included all cases of PA treated at the University Hospital Center of Toulouse and at the Intercommunal Center of Créteil between January 2000 and December 2018. The study protocol was approved by the Institutional Review Board, the Comité d'éthique de la recherche en obstétrique et gynécologie (CEROG) (N • 2020-GYN-0204, date of approval March 5th, 2020). The diagnosis of PA was based on the association of one of several clinical criteria (fever, metrorrhagia, leukorrhea, pelvic pain) and paraclinical criteria (inflammatory syndrome, imaging abnormalities) with bacteriological and/or histopathological confirmation. All data were collected retrospectively via computerized and archived records. All patients with a finding of Actinomyces in the abdominal-pelvic region, determined via histopathological and/or bacteriological examination and meeting the above definition, were included.
All patients carrying an asymptomatic Actinomyces-like organism (ALO) were excluded, as were those with a possible differential diagnosis: proven neoplasia or proven sexually transmitted disease. Phone contact was made with patients in the case of missing data concerning follow-up and the evolution of symptoms, and to identify recurrences or complications. The following clinical data were collected: age, obstetric-gynecological and digestive history, immunodepression status (immunosuppressive treatment, diabetes), the presence of an IUD and duration of use, fever, metrorrhagia, pelvic pain, and leukorrhea. Concerning biologic paraclinical data, the following were noted: the presence of an inflammatory syndrome (hyperleucocytosis associated with an increase in C-reactive protein (CRP)), the assay of the CA125 marker, positive results of diagnostic tests (bacteriological samples: vaginal smear, endocervix, hemocultures, IUD per-operative; cytological samples: targeted biopsy, endometrial biopsy, Pap smear, operative specimen).
With regard to imaging examinations, conclusions of ultrasound, computed tomography scanners (CT scans), and MRIs were collected. Data on treatment choices (surgeries/antibiotics), their duration, and means of administration, as well as events (recoveries, relapses, sequelae) were collected. Due to the great heterogeneity of the clinical pictures, the patients were classified into six categories according to the type of infiltration they presented at imaging: endometritis, tubo-ovarian abscess, infiltrating mass without involvement of adjacent organs, infiltrating mass with involvement to adjacent organs, chorioamnionitis, or unknown. Lacking recommendations, the choice of diagnostic tool was left up to the clinician according to the clinical picture. These tools were grouped into two categories: bacteriological (vaginal and endocervical swab, bacteriological culture of the IUD, and blood cultures) and histopathological (Pap smear, endometrial biopsy, and biopsy of the lesion under imaging guidance).
In addition to the standard staining with hematoxylin and eosin, a stain with a periodic acid and methenamine-silver-borate solution (Grocott's stain procedure) (Figure  1 ) was used to visualize Actinomyces. Recovery was considered achieved when there was disappearance of symptoms, regression of the inflammatory syndrome, or disappearance of ultrasound or scan image findings. Follow-up varied by doctor (laboratory examinations, imaging, interval between consultations). The database was managed using Excel (14. 7. 7 version, Microsoft Corporation, Redmond, WA, USA) and statistical analyses were performed using R software (3. 3. 1 version, available online). Statistical analysis was based on Fisher's exact test for our categorical variables. Values of p < 0. 05 were considered to denote significant differences.
Recovery was considered achieved when there was disappearance of symptoms, regression of the inflammatory syndrome, or disappearance of ultrasound or scan image findings. Follow-up varied by doctor (laboratory examinations, imaging, interval between consultations). The database was managed using Excel (14. 7. 7 version, Microsoft Corporation, Redmond, WA, USA) and statistical analyses were performed using R software (3. 3. 1 version, available online). Statistical analysis was based on Fisher's exact test for our categorical variables. Values of p < 0. 05 were considered to denote significant differences.
search strategy We systematically searched PubMed, Embase via Ovid and Web of Science to identify the guidelines published in English language in peer-reviewed journals before 10 January 2018 (the day the search was conducted), using appropriate terms for each database optimised from the following search string (as can be found in the protocol  6  ): (guideline OR recommendation OR recommendations) AND ('preclinical model' OR 'preclinical models' OR 'disease model' OR 'disease models' OR 'animal model' OR 'animal models' OR 'experimental model' OR 'experimental models' OR 'preclinical study' OR 'preclinical studies' OR 'animal study' OR 'animal studies' OR 'experimental study' OR 'experimental studies'). 6 urthermore, as many of the researchers participating in the European Quality in Preclinical Data project (http:// eqipd.
screening and data management We combined the search results from all sources and identified duplicate search returns and the publication of identical guidelines by the same author group in several based on the PubMed ID, DOI, and the title, journal and author list. Unique references were then screened in two phases: (1) screening for eligibility based on title and abstract, followed by (2) screening for definitive inclusion based on full text. Screening was performed using the Systematic Review Facility (SyRF) platform (http:// syrf. org. uk). Ten reviewers contributed to the screening phase; each citation was presented to two independent reviewers with a real-time computergenerated random selection of the next citation to be reviewed. Citations remained available for screening until two reviewers agreed that it should be included or excluded.
If the first two reviewers had disagreed the citation was offered to a third, but reviewers were not aware of previous screening decisions. A citation could not be offered to the same reviewer twice. Reviewers were not blinded to the authors of the presented record. In the first stage, two authors screened the title and abstract of the retrieved records for eligibility based on predefined inclusion criteria (see above). The title/ abstract screening stage aimed to maximise sensitivity rather than specificity-any paper considered to be of any possible interest was included. Articles included after the title-abstract screening were retrieved as full texts. Articles for which no fulltext version could be obtained were excluded from the review. Full texts were then screened for definite inclusion and data extraction.
Data collection Data collection was carried out on four commercial dairy farms with 55-71 Holstein cows, located in the region Pays-de-la-Loire (France), during the summer of 2017, and the spring and summer of 2018. On each farm, cows that were equipped with a collar were selected based on stage of lactation (days in milk) and number of calvings (parity), as these factors are known to affect the time spent in different behaviours. Therefore, we selected cows between 60 and 300 days in milk, and representative of the herd in terms of parity. A total of 86 cows were equipped with a sensor through the study. Further details on farms and animals are presented in Table  1. An RF-Track datalogger (RF-Track, Rennes, France) with a LSM9DS1 three-axis accelerometer (STMicroelectronics, Geneva, Switzerland) ± 2 g was used.
Data were collected at 59. 5 Hz. The accelerometer was powered with two 3. 7 V lithium batteries (2. 6 Ah). Data were stored on a SD card and downloaded after the experiment. The dataloggers were 98. 2 × 51. 60 × 36. 0 mm in size and weighed 250 g. The three-axis accelerometer was fixed on a collar and positioned on the right side of the neck as recommended by  Smith et al. (2016). Collars were tightly adjusted and a 500 g counterweight was added to prevent them from turning around (Fig. 2 )  (Robert et al. , 2009). The x-axis detected the up-down direction, the y-axis detected the backward-forward direction and the z-axis detected the left-right direction. Each selected cow was equipped with the collar during one day of grazing on the first and second farm, 2, 4 or 6 days of grazing on the third farm depending on the cow, and 3 days of grazing on the last farm.