dataesr/scientific-paragraphs-categorization huggingface dataset:
E3 Specifically, following Hanley computation  E4  and assuming the null hypothesis, the SE equals sqrt(0. 25 1 (n 1 1 n 2 -2)/(12 n 1 n 2 ), where n 1 and n 2 are the number of patients in each group. The z ratio is then equal to (area under the curve 5 0. 5)/SE, which follows a 2-tailed normal distribution, from which the P value is derived. Optimal thresholds were obtained by maximization of Youden index. All tests were 2 sided, and a P value less than. 05 was considered statistically significant. Correction for multiple testing was obtained by using false discovery rate algorithms (Cai and Liu's procedure  E5  in the case of correlation data [adapted to the high level of dependencies] and Benjamini-Hochberg procedure for all other instances [shown as q values]). Analyses were performed by using R, version 3.
Supported by the  Fonds IMMUNOV, for Innovation in Immunopathology ; the  Institut national de la sant e et de la recherche m edicale (Inserm) ; a government grant managed by the  Agence national de la recherche  as part of the  Investment for the Future program  ( ANR-10-IAHU-01 ); and by grants from the  Agence national de la recherche (ANRflash COVID-19 ''AIROCovid'' and ''CoVarImm''). We also acknowledge funding from the  Institut Pasteur  for COVID-19 Research and an  Institut Imagine MD-PhD  Fellowship Program award supported by the  Fondation Bettencourt Schueller  (to J. H. ). Disclosure of potential conflict of interest: The authors declare that they have no relevant conflicts of interest.
Patientreported HRQoL outcomes included Functional Assessment of Chronic Illness Therapy (FACIT)-Fatigue and European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 [EORTC QLQ-C30] scores. 2] [33]  Work-related outcomes were derived from the Work Productivity and Activity Impairment (WPAI) questionnaire, which is psychometrically validated and designed for adaptation to specific illnesses (See Table  S1  for full survey questions). 34, 35 3 | Ethics statement and data confidentiality PAG representatives sent email invitations for a 25-min one-time survey to potential participants through patient organisations; a unique link allowed participants to enter the survey. After providing informed consent in accordance with the Helsinki Declaration, survey participants completed the screener (inclusion/exclusion criteria).
| Statistical analysis We used aggregated data from all countries for total study population analysis. According to pre-specified analysis in the study protocol, we stratified results by treatment type (eculizumab or ravulizumab), combined data from each country for total study population analysis and categorised patients who reported Hb levels for additional subgroup analyses (Hb <10. 5 g/dL versus ≥10. 5 g/dL); the subgroup cut-off of 10. 5 g/dL was selected to generally reflect the median of real-world PNH populations and clinical trial inclusion criteria. 24, 26, 27 We used descriptive statistics to analyse results, with means, medians and standard deviations (SDs) for continuous variables and counts and proportions for categorical variables. We assessed statistical differences between treatment subgroup means in demographic and other dependent variables using one-way analysis of variance (ANOVA) and differences in proportions using Chi-squared tests.
Hb, haemoglobin. a Hinz. 33 *Not statistically significant. Unless otherwise noted, all differences were statistically significant as compared with general population means, calculated using 95% CIs (see Supplementary Table  S5 ). conducted in 2015 (before the introduction of ravulizumab). 42 Conversely, our ravulizumab subgroup mean FACIT-F score was considerably lower than the range reported at weeks 26 and 52 in a post hoc analysis of a phase 3 trial and its extension (33. 8 vs. 41. 1-43. 3, respectively). 43 This variation may be attributable to population differences: the former comparator was conducted with survey data from patients selected from the Aplastic Anemia and MDS International Foundation database versus our PAGs that may have selected for patients with more severe cases, and the latter comparator analysed data from a clinical trial with more stringent inclusion criteria.
Background: Viral and bacterial sexually transmitted infections (STIs) are public health concerns worldwide, but surveillance systems are not comprehensive enough to design and monitor accurately STI control strategies in most countries. In 2016, 320 STI clinics (CeGIDDs in French) were implemented in France, primarily targeting most exposed populations, although access is free of charge for anybody. Objective: This article describes the mandatory surveillance system (SurCeGIDD) based on CeGIDD's individual data aiming to better guide STI prevention.
Methods: A decree ensured the use of software to manage consultations in CeGIDDs and to transfer surveillance data. A web service was implemented to secure data transfer from CeGIDDs' software to a centralized database. CeGIDDs can also transfer data in CSV format via a secured data-sharing platform. Then, data are automatically checked before integration. Data on sociodemographic variables, sexual exposure, blood exposure, symptoms, STI tests, STI diagnoses, and sexual health services delivery were collected for the previous year (n-1). Preliminary and descriptive analyses of 2017-2018 data transmitted in 2018 and 2019, respectively, were performed using numbers and proportions for qualitative variables.
Before the implementation of the CeGIDDs, the surveillance systems were based on the sentinel networks for bacterial STI and the mandatory notification for HIV and HBV infections  [22] [23] [24]. However, their representativeness, sensitivity, timeliness, and flexibility remained challenges even after several decades  [22] [23] [24] [25] [26]. Indeed, these surveillance systems provided a reliable information at the national level but these indicators could neither describe accurately the epidemics at a lower level, nor give a relevant insight about the CeGIDD users by subregions  [12, 27]. Since 2016, the CeGIDDs submit a mandatory activity report to the regional health authority each year  [16]. As the aggregated data of this report are insufficient to guide the policies  [8] , the decree of July 2015 ensures that each CeGIDD uses a software "to manage the patients' records and facilitate the mandatory transmission of case-based data" to Santé publique France (SpF)  [21] , to establish a comprehensive surveillance of the CeGIDDs.
Principles of the SurCeGIDD Surveillance The SurCeGIDD surveillance was developed through a collaborative and iterative approach launched in 2015 (Figure  1 ). First, the stakeholders engaged in STI clinics, infectious diseases, sexual health promotion, epidemiological surveillance, regional and national health administration, and population representatives were identified through a national concertation meeting held by the French Ministry of Health. The software companies were not engaged in the working groups to prevent any conflict of interest, assuming that the CeGIDDs will contract the implementation of the specifications for SurCeGIDD afterward. Among the stakeholders, volunteers-regional health agencies (n=3), former STI clinics and HIV-hepatitis testing centers (n=4), charities (n=2), regional response coordination consortium for HIV infection (n=1), SpF, the Health Care and Health Directorates of the Ministry of Health-defined the core principles for the SurCeGIDD surveillance: • to produce the most relevant epidemiological indicators to guide, implement, and monitor the national sexual health strategy at national, subnational, and local levels; • to better understand the drivers of these epidemics in France; • to cover STIs that are not targeted by the classical surveillance in France (genital warts, herpes, Mycoplasma genitalium); • to collect the tests and diagnoses to monitor the positivity rates of STI; • to cover all sexual health services provided by the CeGIDDs (eg, contraception, HIV preexposure prophylaxis [PrEP], HIV postexposure prophylaxis, vaccination); • to use patients' records routinely collected for consultation purposes; • to use computer-based protocols to facilitate a timely transmission of the required data (no paper form, no online form) and to maximize the coverage of the surveillance; • to conform to the SurCeGIDD metadata set to enable the comparisons of CeGIDDs, subnational regions, and exposed populations; • to guarantee patients' confidentiality by collecting and sharing anonymous data; and.
An intermittent data workflow is generated yearly by the screening centers, by activating a specific command on their computer  [33]. Then, incoming data are checked and merged using SAS (SAS Institute Inc. )  [33]. Another approach is an automated data extraction from 3 multisite laboratories (3Labos surveillance) including tests and diagnoses for 11 pathogens  [34]. The 3Labos surveillance relies on a daily/monthly transmission (depending on pathogens) of individual data (sex, age, residence, test, and diagnosis) to SpF through a web service (a protocol enabling the communication between 2 electronic devices via internet)  [34]. The incoming data are checked and merged using a Stata (StataCorp) script  [34]. The literature review also showed the advantages and limitations of surveillance systems based on data extraction in other countries as well as the development stages of these surveillance systems: GUMCAD (the Genitourinary Medicine Clinic Activity Dataset) in England; CIDR (Computerised Infectious Disease Reporting) in Ireland; SSuN (STD Surveillance Network) in the United States; MIBA (the Danish Microbiology Database) in Denmark; ACCESS (Australian Collaboration for Coordinated Enhanced Sentinel Surveillance) in Australia; eCR (Electronic Case Reporting) in Utah, USA; SOAP (Dutch STI Database) in the Netherlands; and MAVEN (Massachusetts Virtual Epidemiologic Network) in the United States  [35] [36] [37] [38] [39] [40] [41] [42] [43] [44].
Then, SpF organized a concertation meeting with several clinicians, biologists, and public health specialists to share the findings of the literature review and the interviews, and to discuss the informatics capabilities of the CeGIDDs as well as the levers and obstacles that could impact the implementation of the SurCeGIDD principles in each subnational region. Fourth, in May 2016, SpF conducted a feasibility survey, by sending an electronic questionnaire to all CeGIDDs. This questionnaire was used to collect information on the computerization of the CeGIDDs, the specifications of their software for the management of the patients records, and their capability to export or recode and transfer a data set in a predefined CSV format. The response rate was 57. 2% (183/320). Among the respondents, most CeGIDDs (147/183, 80.
3%) used informatic tools to manage their patients/users. A majority of them could export individual data (117/183, 63. 9%). Less than half of the CeGIDDs (79/183, 43. 2%) were capable of recoding a data set but only 21. 9% (40/183) reported being able to recode and transfer data according to a template. The CeGIDDs used mainly 6 software and numerous "homemade" applications. Interestingly, 2 major software companies decided to apply the SurCeGIDD principles at this stage, and communicated their decision to use the surveillance specifications as soon as they would be published. Few months after the feasibility study, one of these companies covered half of the CeGIDDs.
Surveillance Architecture Fifth, the findings of the feasibility assessment were used to adjust the SurCeGIDD metadata set, taking into account the day-to-day practices in the CeGIDDs and their informatic limitation. Then, the order of November 23, 2016, stated the mandatory format for the SurCeGIDD data as well as the procedures for data transfer  [46]. The specifications for the surveillance were subsequently published on the SpF website  [46]. Considering the SurCeGIDD specifications, the literature review, and the results of the feasibility survey, a web service was designed for the data transmission  [42, 47]. If any software provider developed an access to the web service using the specifications shared by SpF, the CeGIDD can automatically transfer its individual database to SpF (Figure  2 ).
Otherwise, the CeGIDDs can export and recode their data in the expected CSV format before their transmission to SpF via a secured data-sharing platform. Then, the structure of the data is automatically checked and validated before its integration in the SurCeGIDD repository or its return to the CeGIDDs if this control stage fails. During this stage, empty variables are accepted. Warning messages pop-up if the data specifications are not applied. In such a case, SpF helps the CeGIDDs to correct its data set. A pilot study conducted by SpF among 12 voluntary CeGIDDs helped to test, correct, redesign, and implement the surveillance system between March and April 2017. During the pilot development, 6 CeGIDDs failed to extract their data. Among the 6 data sets that were transmitted to SpF, only 3 were extracted and transferred according to the SurCeGIDD specifications.
Ethical Consideration The protocol was reviewed and approved by the data protection officer of SpF. Then, ethical approval was granted by the French Personal Data Protection Authority (CNIL authorization no. 2049450). Data are collected with patients' consent. Only anonymized data are transmitted through the SurCeGIDD system. Subsequently, any potential identifying information is aggregated or suppressed after the elimination of duplicates to ensure patients confidentiality. Access to database is strictly restricted to the authorized agents of SpF.
Results The number of CeGIDD respondents increased from 54/320 (16. 9%) in 2017 to 143/320 (44. 7%) in 2018. In 2018, 65. 7% (94/143) of respondent CeGIDDs transmitted their data using the web service versus 41%  (22/54)   identifiers for the consultations of the same person, whereas others attributed a unique identifier to the same person regardless of the number of his/her visits. Consequently, it was not possible to link repeated consultations of the same person in SurCeGIDD. An advisory committee for SurCeGIDD was set up to better guide the construction of algorithms enabling effective data management and analyses. Accurate analyses will be performed afterward. Nevertheless, the first analyses showed that attendees were mostly men 227,326/379,921 (59. 84%), whereas 151,963/379,921 (40%) were women and 632/379,921 (0.
Principal Findings Despite numerous challenges, SurCeGIDD surveillance was successfully implemented. The effectiveness of this system to collect automatically important volumes of data was demonstrated by 143/320 (44. 7%) CeGIDDs that reported simultaneously the STI tests, diagnoses, clinical details, and patients' socioeconomic characteristics for the first time in France. Although these data need further consolidation, the preliminary analysis confirmed that CeGIDDs' attendees are particularly exposed to STI with high positivity rates: 0. 37% for HIV, 1. 31% for HBV, 7. 16% for Ct, 2. 83% for gonorrhea, 1. 04% for syphilis, and 5. 96% for M. genitalium. These results also gave the first insight into M. genitalium testing in the CeGIDDs. Further analyses will better describe their situation.
However, a selection of CeGIDDs with greater human, informatic, or financial resources compared with the nonparticipating structures cannot be ruled out. But the participation rate of 143/320 (44. 7%) will probably increase in the next years, considering the growing interest of the CeGIDDs and software providers for SurCeGIDD data. Experiences in STI surveillance in Denmark, England, Ireland, Australia, and United Sates seem to confirm this expectation  [35] [36] [37] [38] 44]. Moreover, the increasing computerization of the CeGIDDs and the adapted support provided by SpF in the use of the specifications might contribute to a better representativeness of the data in the medium term. This support is also an opportunity for SpF to correct the metadata set, taking into account the operational feedback from the structures.
Nevertheless, the time to develop or modify the informatic platforms was underestimated by SpF and stakeholders, delaying the use of the updated metadata set in data collection. This was also observed in other contexts, and it must be better anticipated in informatic development  [35] [36] [37] [38] 44]. Moreover, difficulties to extract or recode data by CeGIDDs according to the specifications hampered the surveillance implementation. Indeed, some CeGIDDs selected a range of variables considering feasibility burden. Consequently, nonprioritized variables were mostly missing. gonorrhoeae. Some patient's records could not be recoded despite the CeGIDDs' willingness to conform to the surveillance specifications. For example, some CeGIDDs only recorded trademarks of vaccines instead of the names and doses that enable the monitoring of vaccination coverage.
Some adjustment might be necessary in the data format to better take CeGIDDs' needs into account. This also underlines the need for appropriate human and financial resources to support CeGIDDs' adherence to the specifications. Nevertheless, data transmission will require no extra labor burden once the specifications have been implemented, in contrast to the use of paper or electronic forms  [35, 41, 42]. Because of the legal context in France, it was not possible to engage software companies in the SurCeGIDD working groups. In England, software providers contributed to the early stage of the surveillance project, applying GUMCAD specification in the development of their tools  [36]. Moreover, the lack of specific funding for information systems in CeGIDDs might limit SurCeGIDD's expansion and evolution because each structure has to pay for the implementation of the specification changes.
Conversely, incentives and additional funding contributed to ensure the largest and long-term coverage in other contexts  [35, 37, 41, 42]. Mandatory use of national specifications by all software companies might be a solution. It might not only enable database transmission by all CeGIDDs, but can also facilitate the implementation of any change simultaneously in all CeGIDDs (additional information)  [35, 36]. Regarding SurCeGIDD coverage, the list of CeGIDDs including emails and telephone numbers was not updated since 2016, despite the creation of new structures and closures of other ones by regional health agencies  [8]. Therefore, it was not possible to engage with noninformed CeGIDDs in the surveillance. SpF advocates for a systematic transmission of updated phone books by regional public health agencies each year, to ensure the best representativeness of the surveillance data.
Considering the volumes of data shared, SpF needs to upgrade its tools and procedures, using algorithms to automatize data monitoring, quality checking, and epidemiological reports at national and subnational levels. There is also a need to formalize rules and process for data sharing and analyses  [35, 48, 49]. Despite its limitations, SurCeGIDD surveillance creates new opportunities for research collaboration on sexual health in France  [35, 41, 50]. Availability of a wide range of individual characteristics (health insurance, occupation) in this database will be an opportunity to better understand the impact of social health inequalities on STI epidemics in France. SurCeGIDD will also help to fill the gap in our knowledge of M. genitalium,   [8]. Generating a continuous data workflow instead of a yearly transmission of data might be the next improvement of SurCeGIDD, to timely detect and investigate STI events (multidrug resistance, uncommon anatomic location, upsurge, clusters)  [41, 44, [51] [52] [53].
RenderX Subsequently, the stakeholders mapped the information needs at the national, subnational, and local levels (Textbox 1 [28]). Finally, SpF used this mapping exercise to propose a detailed metadata set that was discussed, amended, and agreed upon by all the stakeholders. JMIR FORMATIVE RESEARCH Ndeikoundam Ngangro et al • to secure the data transfer and repository. https://formative. jmir. org/2022/10/e31136 JMIR Form Res 2022 | vol. 6 | iss. 10 | e31136 | p. 2 XSL • FO (page number not for citation purposes).
The separation flow rate was set at 300 nL/min. The mass spectrometer operated in positive ion mode at a 2. 0 kV needle voltage. Data were acquired using Xcalibur 4. 1 software in a data-dependent mode. MS scans (m/z 375-1500) were recorded at a resolution of R = 120000 (@ m/z 200) and an AGC target of 4×10 5 ions was collected within 50 ms, followed by a top speed duty cycle of up to 3 s for MS/MS acquisition. Precursor ions (2 to 7 charge states) were isolated in the quadrupole with a mass window of 1. 6 Th and fragmented with HCD@30% normalized collision energy. MS/MS data were acquired in the ion trap with rapid scan mode, AGC target of 3x10 3 ions, and a maximum injection time of 35 ms. Selected precursors were excluded for 60 s. Protein identification and Label-Free Quantification (LFQ) were done in Proteome Discoverer 2.
4. MS Amanda 2. 0, Sequest HT, and Mascot 2. 5 algorithms were used for protein identification in batch mode by searching against a Toxoplasma gondii GT1 strain protein database (8 459 entries, release 48, https://toxodb. org/website). Two missed enzyme cleavages were allowed for the trypsin. Mass tolerances in MS and MS/MS were set to 10 ppm and 0. 6 Da. Oxidation (M), acetylation (K), and biotinylation (K) were searched as dynamic modifications, and carbamidomethylation (C) as a static modification. Peptide validation was performed using Percolator algorithm  (Käll et al. , 2007)  and only "high confidence" peptides were retained corresponding to a 1% false discovery rate at the peptide level. Minora feature detector node (LFQ) was used along with the feature mapper and precursor ions quantifier.
The quantification parameters were selected as follows: (1) Unique peptides (2) Precursor abundance based on intensity (3) No normalization was applied (4) Protein abundance calculation: summed abundances (5) Protein ratio calculation: pairwise ratio based and (6) Hypothesis test: t-test (background based). Quantitative data were considered for master proteins, quantified by a minimum of 2 unique peptides, fold changes above 2, and a statistical p-value lower than 0. 05. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE  (Deutsch et al. , 2020)  partner repository with the dataset identifier PXD035106.
Competition assays BCC1-mAID-3HA/MyoJ-2Ty parasites were mixed with GFP-expressing parasites at a ratio of about 1:1. This ratio was then determined over 5 passages (14 days) by IFA using a-GAP45. At each passage, 100 vacuoles were counted in duplicate from three independent biological replicates. The ratios have been normalized to 50% at t0. The data are presented as mean ± SD.
Videomicroscopy Human osteosarcoma cells (U2OS) cells obtained from Sigma-Aldrich were plated on 18 mm diameter and poly-L-lysine -coated glass coverslips. The next day, cells were infected with a single parasite and incubated for 36 to 42 h at 37°C under a 5% CO2 atmosphere to allow several cycles of parasite multiplication. Samples were then installed on an appropriate chamber that fits the platform of the Eclipse Ti inverted confocal microscope (Nikon France Instruments, Champigny sur Marne, France) coupled to a CMOS Prime camera (Photometrics, Tucson, AZ, USA) and a CSU X1 spinning disk (Yokogawa Roper Scientific, Lisses, France). To select for cells ready to spontaneously release the tachyzoite progeny, images were captured with a 60x Planneofluar objective (NA: 1. 46) using the multi-stage position in the MetaMorph software (Molecular Devices, Sunnyvale, USA).