dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistics and reproducibility. Data are expressed either as absolute numbers or percentages ± s. d. An unpaired, two-tailed Student's t-test was used to analyse datasets with two groups. A paired, two-tailed Student's t-test was used to analyse datasets across different time points. Actual P-values were provided in the legends when available. NS denotes no significance. Statistical calculations were performed using Prism v. 8. 0. 0 (GraphPad). No statistical method was used to pre determine sample size (n). Sample sizes are represented as distinct biological replicates in all experiments. Panels showing representative images are representative of two to five independent experiments, as indicated in the figure legends. *P < 0. 05, **P < 0. 01, ***P < 0. 001 and ****P < 0. 0001 indicate significant differences.
Negative control (gray) gated on cells negative for epithelial cell marker K14 H2B-Cerulean and immune cell markers for LCs (CD207) and DETCs. Unpaired, two-tailed Student's t-test (n=3 mice respectively). Data presented as absolute values +/-SD. g-h, The expression levels of E-cadherin, a mediator of cell-cell interaction known to be down regulated in activated LCs, from LCs of Cdkn1b;rtTA mice (closed red) and those from Cdkn1b control mice (solid black) in the epidermis. Negative control (gray) gated on cells negative for the epithelial cell marker K14-H2B-Cerulean and immune cell markers for LCs (CD207) and DETCs. Unpaired, two-tailed Student's t-test (n= 3 mice respectively). Data presented as absolute values +/-SD. a, Ears and lymph nodes were taken from mice 7 days post induction with 2mg dose of tamoxifen given on 5 consecutive days.
Epidermal and lymph node single cell suspensions were processed for flow cytometry and gated for LCs using anti-langerin antibody (CD207). K14-H2B-Cerulean was used to gate out the epithelial cells. b-e, LC Rac1KO (open red) show no significant difference in the expression levels of the known activation markers MHCII and CD86 compared to LC wt (solid black) in either the epidermis or draining lymph nodes showing that LC  Rac1KO  are not activated in this model. Unpaired, two-tailed Student's t-test (data is representative n=4 for huLangerin-CreER; Rac1 +/+ mice, n=5 for huLangerin CreER; Rac1 fl/fl mice in c and n=4 for both groups in e). Data presented as absolute values +/-SD. f, Epidermal cell suspensions were processed for flow cytometry and gated for LCs using anti-langerin antibody (CD207).
Acknowledgements We thank  A. Anderson  of  Life Science Editors  for critical feedback on the manuscript;  N. Anandasabapathy  for the Lang-eGFP mice;  S. Beronja  for the Hras G12V mice; and  Akiko Iwasaki  for the Tcrd KO mice. This work is supported by the  Howards Hughes Medical   Institute Scholar award ,  National Institutes if Health  grants no. 1R01AR072668-01. S. P. was supported by  The New York Stem Cell Foundation  ( NYSCF-D-F58 ). Y. B. is supported by the  Centre National de la recherche Scientifique , The  Institut Curie  and the  Institut National de la santé et de la recherche médicale (INSERM). E. M. was supported in part by the  National Institute of Health  ( T32 GM007499 ). D. P. M. was supported by The  National Insitutes of Health  ( T32-GM007223-44 ). J. L. M. was supported by  Lo Graduate Fellowship  for Excellence in Stem Cell Research and The  National Institutes of Health  ( T32 GM 7499-41 A1  and  T32 HD 7149-40 ).
Data availability Additional source data for Figs. 4 , 5, and Extended Data Figs. 1, 2, 4, 6, 8 have been deposited at Figshare and are accessible from https://doi. org/10. 6084/m9. figshare. 14199746, https://figshare. com/s/ 6855f86218f9026b0250, https://figshare. com/s/016423de8cf0ce293c1e, https:// figshare. com/s/5c97c32da91f8810fed7, https://figshare. com/s/78598f01a1438569eb9b, https://figshare. com/s/03291104075fbb3492e7, https://figshare. com/s/ f4ccb37bd6bd4557dbe2, https://figshare. com/s/c199699135ff4b446dc8 and https:// figshare. com/s/336af7d8ebf313fcb2a5. Source data are provided with this paper. All other data that support the conclusions are available from the authors upon reasonable request.
Beads with the cloned amplicons were then enriched, loaded on a 454 picotiter plate, and sequenced on the Roche GS Junior Sequencer according to the protocol of the manufacturer (Sequencing Method Manual, GS Junior Titanium Series, Roche). Image analysis and base calling of the raw sequencing data were performed using the default "shotgun" Roche GS Junior data analysis pipeline. To obtain the position of transgene insertions in genomic DNA, sequence reads were aligned to the 50 bp of each end of the transgene primary sequence using BWASW, an algorithm designed for long reads with more errors. Aligned sequences were then aligned against C57BL/6NJ genomic sequences to obtain scaffold at both ends of the transgene sequence. A 10 kb for each region was extracted and amplified by long range PCR (LR-PCR).
Enzyme-Linked Immunospot Assay IFNg-ELISpot assays were achieved as previously reported  (21). Spots were counted using Bioreader 5000 Pro Sf (BioSys GmbH). Splenocytes from mice were stimulated overnight with peptides and Il-2 (5 U/ml final). The enzyme-linked immunospot (ELISpot) assay was performed using mouse g-ELISpot antibody pair, from U-CyTech biosciences. Data are the mean of triplicate wells. The background of IFNg responses was evaluated in the absence of peptide. Specific IFNg responses were expressed as spot-forming cells (SFC) per 10 6 cells after normalization of the background. Positive controls were triplicates of cells stimulated by 1 mg/ml ConA (Sigma-Aldrich) and negative controls by pyruvate dehydrogenase (PDHase 208-216 ) irrelevant peptide.
Immunohistochemistry and Fluorescence Immunofluorescence stainings were performed on formalin-fixed paraffin pancreas sections that were deparaffinized in xylene and dehydrated by ethanol. After washing, antigen retrieval was realized by hot incubation in citrate buffer, followed by permeabilization (20 min in PBS 1×/0. 4% Triton X-100) and saturation (30 min PBS 1×/1% horse serum) before immunostaining with biotinylated rat anti-human CD3e(AbD Serotec) and polyclonal rabbit anti-glucagon (DAKO) antibodies overnight. Slides were washed with PBS 1×/1% BSA/0. 1% Triton X-100 and stained with an anti-rabbit Ig-FITC antibody (Abcam) and SAV-Cy3 (Abcam) at RT. Sections were mounted in Vectashield mounting medium for fluorescence with DAPI (Vector Laboratories). Observations were made with a spinning disk confocal apparatus at the Cochin Institute Imaging Platform and pictures analyzed with the ImageJ software.
Stable immunohistochemical stainings were performed on paraffin-embedded pancreas sections and stained with polyclonal guinea-pig anti-human insulin (DAKO) or rat antimouse CD4 biotin (eBioscience), followed by incubation with peroxidase-labeled antibodies. All reactions were revealed with diaminobenzidine (DAB, Genemed). Sections were counterstained with hematoxylin and mounted. Observations were made with Zeiss AxioObserver Z1 microscope coupled with MRm Axiocam Zeiss and pictures analyzed with the ImageJ software. Assessment of total b-cell mass was performed on scanstained microscope slides with Inform software using a guinea pig anti-human insulin antibody (DAKO) as the ratio between bcell surface (µm 2 )/pancreas surface (µm 2 ) multiplied by pancreas weight (mg)  (24). Assessment of total a-cell mass was performed on scan-stained microscope slides with Inform software using a rabbit anti-glucagon antibody (DAKO) as the ratio between acell surface (µm 2 )/pancreas surface (µm 2 ) multiplied by pancreas weight (mg).
Tetramer Assays and Single-Cell RT-PCR Tetramers (TMrs) associating the chimeric HLA-A*02:01-H-2K b and the human b2-microglobulin to hPPI peptides were obtained from the NIH Tetramer Core Facility. Stainings were performed as previously reported  (11). Incubation of cells with TMrs was performed for 30 min at RT. The following antibodies were used: anti-mouse CD3e-AlexaFluo700, anti-mouse CD8a-APC, anti-mouse CD19-PerCP-Cy5, and anti-mouse CD14-PercP-Cy5 antibodies (BD/Pharmingen and eBioscience). Cells were analyzed with a BD LSR-Fortessa flow cytometer and the FlowJo 9. 2 software (Tree Star Inc. ). For single-cell RT-PCR assays, CD8 + /TMr + T cells were sorted with a FACSAria II at 1 cell/well into 96-well PCR plates containing 5 ml PBS 1× treated with diethyl pyrocarbonate (DEPC) (Sigma) and immediately frozen at -80°C.
Islet Isolation Procedure Islets of Langerhans were isolated as described previously  (25). Islets were dissociated with Cell Dissociation Solution Non-Enzymatic (Sigma) for 30 min at RT. Cells were filtered and stained with anti-HLA-DQ-FITC (BD Biosciences), anti-human b2m-PE (BD Biosciences), guinea pig anti-human insulin (DAKO), anti-guinea pig Ig-Biot and SAV-PECy7, anti-mouse CD4-AlexaFluo700, anti-mouse CD8a-APC, anti-mouse CD19-Percp-Cy5. 5, and/or anti-mouse TCRb-efluo450 antibodies (eBioscience). Acquisition was done with a BD FACSAria flow cytometer and analyzed using FlowJo 10. 7. 1 software.
We did not evidence hot spots of enhancer transcripts close to the LV-RIP-hB7. 1 insertions using the mouse ENCODE database from UCSC Genome Bioinformatics (GSE101551 and GSE151644 GEO data accession numbers). We screened 128 mice from the progeny for the selected insertion sites in order to stabilize the lineage at a homozygote status using a classical progeny test.
Reactivity Against Spliced hPPI in YES-RIP-hB7. 1 Mice and HLA-DQ8 and DQ2/ DQ8 Patients Based on the observation of insulin mRNA alternative splicing events when reanalyzing databases generated in the context of human islet inflammation  (28, 29) , we designed an HLA-A*02:01-restricted spliced hPPI peptide, sp-hPPI 60-68 , and three HLA-DQ8-restricted spliced peptides, named sp-hPPI 55-74 , sp-hPPI 52-74 , and sp-hPPI 51-77 using HLA-restrictor and NetMHCII 2. 3 server, respectively (Figure  6A ). Using an IFNg-ELISpot assay, we detected HLA-A*02:01-restricted IFNg responses against sp-hPPI 60-68 peptide (Figure  6B ) and HLA-DQ8-restricted responses to the sp-hPPI 51-77 peptide (p ≤ 0. 05) in splenocytes from diabetic YES-RIP-hB7. 1 mice as compared with non-diabetic YES-RIP-hB7. 1 or YES mouse controls (Figure  6C ).
ACKNOWLEDGMENTS We acknowledge the  NIH tetramer core facility  for provision of MHC class I tetramers;  Francina Langa Vives  and the  CIGM platform at Institut Pasteur, Paris ;  Beátrice Durel  and the imaging platform at  Institut Cochin, Paris ;  Yannick Marie  and the genotyping and sequencing platform at ICM, Paris;  Sebastien Jacques ,  Florent Dumont , and the genotyping platform at  Institut Cochin ; and  Camille Huet  for the staining to evaluate the alpha and beta masses.
FUNDING This work was performed within the  Deṕartement Hospitalo-Universitaire (DHU) AUToimmune and HORmonal diseaseS  and supported by  ANR  grant  R11189KK-RPV11189KKA ,  ANR2010-Biot-00801 ,  EFSD  grant  1-2008-106 , and  INNODIA  grant  E15179KK. DE was supported by grants from the  Fonds National de la Recherche 420 Scientifiques (FNRS) -Welbio   CR-2015A-06 ,  Belgium , and the  Innovative Medicines Initiative 2 Joint Undertaking  under grant agreement No. 115797  (INNODIA). This joint undertaking receives support from the  Union 's  Horizon 2020 research and innovation program  and  EFPIA ,  JDRF , and  The Leona M. and Harry B. Helmsley Charitable Trust.
Acknowledgement The study was supported by a  German Research Foundation (DFG) -funded project called " Establishment of a national database for alveolar echinococcosis"  (Ref. No. KA 4356/3-1 ) and " Implementation of interfaces for the standardization of national database systems for alveolar echinococcosis and its transformation processes " (Ref. No. KR 5204/1-2 );  Natural Science Foundation of China (NSFC) ,  81260232 ,  Multiple imaging study of the Hepatic Alveolar Echinococcosis after albendazole treatment ; the  Qinghai Science & Technology Department  (Ref. No. 2017-SF-158 ); and the  Müller Holding Ltd. & Co. KG Ulm.
to capture patients' experiences of signs, symptoms and impacts of psoriasis. Methods: Pooled, blinded, 16-week data from 1002 patients in the BE VIVID and BE READY bimekizumab phase 3 trials were analysed. The suitability of the P-SIM missing score rule (weekly scores considered missing if C 4 daily scores were missing) was assessed. Test-retest reliability was evaluated using intraclass correlation coefficients (ICCs). Convergent validity was assessed between P-SIM and relevant patient-reported outcome (PRO) (Dermatology Life Quality Index [DLQI], DLQI item 1 [skin symptoms], Patient Global Assessment of Psoriasis) and clinician-reported outcome (ClinRO) scores (Psoriasis Area and Severity Index [PASI], Investigator's Global Assessment  [IGA] ) at baseline and week 16. Known-groups validity was assessed, comparing P-SIM scores between patient subgroups predefined using PASI/IGA scores.
In these analyses, the psychometric properties of the P-SIM were evaluated using data pooled from the first 16 weeks of the BE VIVID and BE READY phase 3 trials investigating bimekizumab in the treatment of moderate to severe plaque psoriasis. What was learned from this study? In these analyses, the 14 item scores of the P-SIM demonstrated good reliability, validity and sensitivity to change in the assessment of patients' experiences of key psoriasis signs, symptoms and impacts when completed daily on a handheld device over a period of 16 weeks.
To date, no RD thresholds have been reported for the P-SIM. Here, the psychometric properties of the P-SIM are assessed using data from the BE VIVID (NCT03370133) and BE READY (NCT03410992) phase 3 trials, as well as the suitability of the weekly missing data rule that is currently applied to the instrument. RD thresholds for the P-SIM items are also estimated.
Study Design Blinded data were pooled from the first 16 weeks of the BE VIVID and BE READY phase 3 trials investigating bimekizumab in the treatment of moderate to severe plaque psoriasis. BE VIVID was a randomised, double-blinded, placebo-and active comparator-controlled phase 3 study (Supplementary Fig. 1a ). Patients in BE VIVID were randomised 4:2:1 to bimekizumab 320 mg every 4 weeks (Q4W), ustekinumab 45/90 mg (by weight) administered at baseline and then every 12 weeks (Q12W) from week 4, or placebo for initial treatment (weeks 0-16). BE READY was a double-blinded, placebo-controlled, randomised withdrawal phase 3 study (Supplementary Fig. 1b ). Patients in BE READY were randomised 4:1 to bimekizumab 320 mg Q4W or placebo for initial treatment (weeks 0-16). Both trials enrolled adult patients with a diagnosis of moderate to severe plaque psoriasis C 6 months prior to screening, with baseline Psoriasis Area and Severity Index (PASI) C 12 (on a scale from 0-72), C 10% body surface area (BSA) affected and an Investigator's Global Assessment (IGA) score C 3 on a 5-point scale.
The co-primary endpoints for both studies were 90% improvement in PASI (PASI 90) and IGA 0/1 (0 [clear] or 1 [almost clear] with C 2-category improvement from baseline) responses at week 16. Full study designs and efficacy and safety outcomes have been reported previously  [17, 18]. The study protocols, amendments and patient informed consent were reviewed by a national, regional or independent ethics committee or institutional review board. BE VIVID (NCT03370133) and BE READY (NCT03410992) were conducted in accordance with the current version of the applicable regulatory and International Conference on Harmonisation (ICH)-Good Clinical Practice (GCP) requirements, the ethical principles that have their origin in the principles of the Declaration of Helsinki, and the local laws of the countries involved.
DLQI item 1 (Question: ''over the last week, how itchy, sore, painful, or stinging has your skin been?''; answer: ''not at all'', ''a little'', ''a lot'', or ''very much'') is specific to skin symptoms commonly seen in psoriasis and is considered individually in these analyses. The PGAP consists of a multiple-choice question (''How severe are your psoriasis-related symptoms right now?''), with answers scored from 1 to 5 (1, ''no symptoms''; 2, ''mild symptoms''; 3, ''moderate symptoms''; 4, ''severe symptoms''; 5, ''very severe symptoms''). Both the DLQI item 1 and PGAP represent verbal rating scales. Details of PASI and IGA score measurements can be found in the Supplementary Methods  [19, 20]. The PGAP was completed on the same electronic device as the P-SIM; all other outcome data were collected on a tablet during on-site study visits (week 0, 1, 2, 4, 8, 12 and 16).
Confirmation of Weekly Scoring Rule Analyses were conducted to establish whether alternatives to the currently applied weekly scoring rule for the P-SIM, in which weekly item scores are considered missing for patients in weeks where they had C 4 missing daily scores in that item, impacted the variability of weekly item scores. Patients with no missing data were included for analysis of each item. Scenarios for the number of days missing (1, 2, 3, 4, 5 or 6 days missing) were simulated using a bootstrapping method with replacement by randomly sampling the appropriate number of daily scores for that missing day scenario and calculating average weekly scores. For each missing day scenario for a given item, each patient's simulated weekly score was the mean of 100 replications of a random selection of daily scores.
Sensitivity to Change Over Time Spearman's correlation coefficients and p values were calculated between changes from baseline to week 16 in P-SIM item scores and in other clinically relevant outcomes (PASI, IGA, PGAP, DLQI item 1 and DLQI). Correlations using the change from baseline to week 12 for PGAP were assessed as a sensitivity analysis; this was because a large amount of PGAP data were missing at week 16 as a result of technical limitations of the electronic device. A Spearman correlation C 0. 30 was considered to demonstrate acceptable responsiveness  [24].
Patient Disposition and Baseline Characteristics In BE VIVID, 567 patients were randomised at baseline: 321 to bimekizumab, 163 to ustekinumab and 83 to placebo. In BE READY, 435 patients were randomised at baseline: 349 to bimekizumab and 86 to placebo. Blinded 16-week data were pooled for the 1002 patients randomised across both studies. Demographics and baseline disease characteristics are shown in Table  2. No major differences were noted between studies, except for race/region; BE VIVID included patients from.
This was because its change from baseline to week 16 generally had the highest correlation with those of P-SIM items, it is patient-reported, it is measured on an ordinal scale with directly interpretable verbal descriptors, and eCDF and PDF findings supported the thresholds obtained using it. Results obtained using anchors based on PASI total score, IGA change from baseline and DLQI total score were also considered in the triangulation process, though were deprioritised as they did not meet all of the above criteria. IGA absolute score and PGAP change from baseline-derived thresholds were considered as supportive only (IGA had only one improvement level, and PGAP had a substantial amount of missing data at week 16 leading to week 12 being used). The P-SIM item RD thresholds found using mean score changes ranged from -2.
Blinded data were used for the psychometric validation and RD analyses, removing sources of potential bias. The applied weekly missing score rule, in which weekly item scores were set to 'missing' if C 4 daily scores were missing for that item, was found to be adequate. The P-SIM item scores were shown to have excellent test-retest reliability, with all ICCs C 0. 91, well above the acceptability threshold of 0. 70; this demonstrates that the P-SIM is consistent in its measurement of signs, symptoms and impacts of plaque psoriasis in patients whose disease state has not changed, and that results are repeatable. The P-SIM demonstrated strong inter-item correlations at both baseline and week 16, apart from item 14 (choice of clothing), which had a moderate correlation with items 3 (skin pain) and 4 (burning) at baseline.
These results support the use of the P-SIM to define efficacy endpoints measuring patient experiences of signs, symptoms and impacts of psoriasis. The use of a four-point RD threshold over an 11-point numeric rating scale throughout all 14 items represents a simple and stringent criterion for defining marked clinical improvement; however, responder analyses using this threshold to assess treatment effect will be restricted to patients reporting a score of [ 4 at baseline. Complementary analyses or endpoints, such as attaining a P-SIM score of 0 or 1, could be considered, as has been done for similar instruments in trials of other compounds approved in plaque psoriasis  [31, 32]. This would allow all symptomatic patients to be taken into account. Lower RD thresholds for items 1, 3 and 5 (itch, skin pain and scaling, respectively) were determined previously in preliminary phase 2b data analyses (1.
3% of those excluded versus 28. 8% of those included]; Supplementary Table  6 ). Furthermore, while the daily nature of P-SIM completion helps to capture how patients' experiences may change from day to day, the regularity of assessment may affect overall completion rates; however, the simulation to confirm the weekly scoring rule demonstrated that the results do not vary substantially when the number of days included in the weekly score change, thus showing that the weekly scores are robust with respect to variation between days. Additionally, completion rates were high in this study even when using the 4-day missing weekly score rule. Additionally, there were substantial amounts of missing data for the PGAP at week 16, limiting its use in analyses to a 12-week period instead. However, the RD analysis utilised several robust anchors (both patient-and clinicianreported), each yielding relatively similar results (predominantly between 3 and 5 points).
CDF curves for each anchor showed separation between those who experienced an improvement and those who experienced no change at a four-point improvement in P-SIM item scores. Thus, it is likely that conclusions would be similar if there had not been missing data on the PGAP at week 16. A large proportion of the 1002 patients enrolled in the phase 3 BE VIVID and BE READY trials were male (71. 8%) and white (82. 1%). It has been suggested that male patients generally have greater severity of psoriasis  [35] , leading to a greater proportion being included in the trials; however, another study has indicated that female patients experience greater impact on their quality of life  [36] , and the vast majority of clinical trials exclude pregnant women, meaning that they do not appear in true proportion  [37].
Additionally, while the majority of patients in the general moderate to severe psoriasis disease population are white, this study Fig. 3  eCDF curves of observed changes from baseline to week 16 in P-SIM item scores by PASI absolute score category. a P-SIM item 1 (itching). b P-SIM item 3 (skin pain). c P-SIM item 5 (scaling). Data were pooled from BE VIVID and BE READY. Negative changes from baseline in P-SIM item scores indicate improvement. Dotted lines show median values. eCDFs for itching, skin pain and scaling items are shown as these items were used as efficacy endpoints in the BE VIVID and BE READY trials; findings for other items were similar. eCDF empirical cumulative distribution function, PASI Psoriasis Area and Severity Index, P-SIM Psoriasis Symptoms and Impacts Measure b may not fully represent the experiences of patients with skin of colour, who may have increased impact of psoriasis on quality of life  [38, 39] ; for example, post-inflammatory hyperpigmentation has a greater impact on patients with skin of colour  [40].