dataesr/scientific-paragraphs-categorization huggingface dataset:
Single and double mutations of these two arginines impairs the interaction with XIAP-BIR2 domain (Fig. 4B ),  (Hrdinka et al, 2018). Our structure shows that these residues are involved in the RIP2K-BIR2 interaction, and they are positioned at the kinase dimerization interface (Fig. 3E ). Indeed, any perturbation of this zone might prevent binding between the two proteins by affecting either the binding itself or by destabilising the kinase dimer. Crystal structures of RIP2K in complex with Ponatinib, GSK583 or CSLP18, show that inhibitor binding perturbs the DFG-in conformation and disorders the activation loop beyond residue 164, whilst in the active conformation residues 164-171 can still be traced (PDB IDs: 4C8B, 5J7B and 6FU5, SI Appendix Fig. S10 )  (Canning et al, 2015; Haile et al, 2016; He et al, 2017).
All NMR experiments were performed at 25°C on Bruker Avance IIIHD spectrometers operating at magnetic field strengths of 850 or 950 MHz ( 1 H frequency), equipped with cryogenically cooled triple-resonance probes. 1 H-15 N correlation spectra were recorded using a BEST-TROSY pulse scheme  (Favier et al, 2011) , while chemical shift assignments were obtained from a set of 3D BEST-TROSY HNC correlation experiments  (Solyom et al, 2013). diffusion constants of the proteins in solution were measured by 1D 1 H DOSY experiments  (Johnson, 1999). NMR data processing and analysis was performed using TopSpin 3. 5 (Bruker BioSpin) and CCPNMR V3 software tools.
Cryo-EM specimen preparation Cryo-EM specimens were prepared on UltrAuFoil R1. 2/1. 3 holey gold grids (Quantifoil) that were glow-discharged for 20 s at 25 mA on both sides (PELCO easy glow). Vitrobot (Vitrobot Mk IV, Thermo Fisher Scientific) was set to 4 °C and 100% humidity. A drop of 2 µl sample was applied to each grid side and blotting was run at force 0, for a total time of 3. 5-4. 5 s. Grids were then vitrified by plunging into liquid ethane at liquid N2 temperature. Grids were clipped into autoloader cartridges and screened using a Glacios cryo electron microscope (Thermo Fisher Scientific) equipped with a Falcon 3 detector. Promising grids showing visible particles by eye at -1 µM defocus, were used for data collection on CM01, ESRF Grenoble France (SI Appendix Fig. S4 ).
Cryo-EM Data Collection and Processing The RIP2K 1-317 -XIAP BIR2 154-240 dataset was acquired using a Titan Krios operating at 300 keV, equipped with K2 Quantum detector (Gatan) and a GIF Quantum energy filter (Gatan) at CM01 (ESRF, Grenoble, France)  (Kandiah et al, 2019). 7178 movies were collected in untilted mode, at 165K magnification, corresponding to a pixel size of 0. 87 px/Å for a total dose of 47. 8 (1. 2 e-/A2 per frame, fractionated in 40 frames). A total of 3698 movies were recorded in tilted mode (1870 micrographs at 20 degrees, 1825 micrographs at 25 degrees), at the same magnification, for a total dose of 45. 7 (1. 1 e-/A2 per frame, fractionated in 40 frames) (SI Appendix Fig. S4 , Table  S2 ). Movies were imported into Relion, aligned and dose-weighted using MotionCor2 in Relion 3.
1  (Zheng et al, 2017; Fernandez-Leiro & Scheres, 2017). Micrographs were then imported into CryoSPARC  (Punjani et al, 2017)  were CTF estimation has been run with Patch CTF and tilted micrographs were manually curated according to CTF based estimated resolution (<10Å) and estimated ice thickness (<1. 1). Any attempts of processing of the untilted dataset alone or in combination with the tilted datasets with a series of 2D and 3D classifications, resulted in poorly resolved cryo-EM maps indicating preferred particle orientations. Therefore, we modified our processing approach. We firstly processed only the tilted data. The two tilted datasets (collected at 20 degrees and 25 degrees respectively) were kept separately and processed similarly (SI Appendix Fig. S5 ). Particles were firstly picked on 100 representative micrographs using Topaz  (Bepler et al, 2019)  and they were extracted with a box size of 300 x 300 pixels.
We applied 2D classification with a tight mask (100 Å) and select 2D-classes showing particle features. These particles were used to train Topaz and the resulting topaz_model was used to pick particles in the remaining micrographs. After extraction, 2D classification was applied to eliminate bad particles and to select 2D class averages with lower background noise and stronger features. We then performed ab-initio reconstruction with two models followed by non-uniform (NU) refinement using the best model as reference and all the particles. The resulting map, denoted the tilted map, showed a better orientation distribution than for previous maps. In order to maintain a balance between the number of particles from the tilted dataset and the number of particles from the untilted dataset, only 2000 micrographs of the later were selected.
Further 3D classification using either heterogeneous refinement or 3D classification (beta) with different masks size did not improve particle selection nor the clarity of final map. A processing workflow, comprising data statistics, is shown in SI Appendix Fig. S5. For map sharpening, we used the sharpening tool in CryoSPARC. For manual reconstruction in Coot, the map was sharpened and blurred using the mrc_to_mtz tool in ccpem  (Wood et al, 2015; Burnley et al, 2017).
Model building and refinement The atomic model of RIP2K 1-317 in complex with XIAP BIR2 154-240 was obtained by fitting with rigid-body refinement the existing crystal structures of both proteins. For RIP2K 1-317 , we firstly fit the structure of active RIP2K (PDB ID: 5NG0)  (Pellegrini et al, 2017)  which displays RIP2K residues from 5 to 310. For XIAP BIR2, we used the crystal structure 4J3Y, chain C  (Lukacs et al, 2013). We firstly fit the two structures in the cryo-EM map, using ChimeraX  (Pettersen et al, 2021). After removal of waters, ions and nucleotide analogue, we then proceeded with rigid-body refinement in Phenix  (Liebschner et al, 2019). In Coot, we mutated back to cysteine residues 202 and 212 in the BIR2 domain, manually adjusted loop 210-214, built the αL-helices (residues 299-312) using as template the structure of RIP2K-ponatininb (PDB ID: 4C8B)  (Canning et al, 2015) , and deleted the regions obviously outside of the density as well as the N-termini β-strand interaction.
Alphafold2 For the Alphafold2 calculations we used Local ColabFold  (Evans et al, 2022; Jumper et al, 2021; Mirdita et al, 2022)  installed on an in house server. To compute the complex structure of XIAP BIR2 with RIP2K (residues 154-240, 1-317 respectively) we used 3 cycles, model 'multimer-2' and 5 models. Neither increasing the number of cycles nor changing module improved the prediction. We applied the same calculation to RIP2K-cIAP1 BIR2 and RIP2K-cIAP2 (SI Appendix Fig. S11C ). As for RIP2K-XIAP BIR2 complex, the prediction does not show any significant interaction between the two proteins.
Acknowledgements We thank  Katrin Rittinger  ( Francis Crick Institute, UK ) for the kind plasmids gift. We acknowledge  Alice Aubert  and  Martine Pelosse  for support in using the  Eukaryotic Expression Facility. We acknowledge  Sarah Schneider  and  Wojtek Galej  for support in using the EM facility at the  EMBL in Grenoble. We thank the  European Synchrotron Radiation Facility  for provision of beam time on CM01. We acknowledge the EM platform in HD, for further data collections not here reported, but project connected. We thank the IT assistant of the IBS-EMBL shared processing cluster. This work used the platforms of the Grenoble Instruct-ERIC Center (ISBG;  UAR 3518 CNRS-CEA-UGA-EMBL ) within the  Grenoble Partnership for Structural Biology  (PSB), supported by  FRISBI  ( ANR-10-INBS-0005-02 ) and GRAL, financed within the  University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS  ( ANR-17-EURE-0003 ).
Data availability Coordinates for RIP2K-XIAP BIR2 complex are in the protein data bank) PDB with accession code 8AZA. The cryo-EM map has accession code EMD-15757. Movies have been deposited in EMPIAR with accession code ###. The NMR chemical shift assignments of XIAP BIR2 AG 124-240 have been deposited with the Biological Magnetic Resonance Bank (BMRB) under accession number 51600.
, Rockford, IL, USA) to label cell membranes were added to the cell medium. Then, cells were rinsed twice with D-PBS and then covered with 1. 5 mL of FluoroBrite (Life Technologies) for imaging using a Leica SP5-SMD confocal microscope (objective Leica HCS PL Apo CS 63x/1. 4 NA oil objective; Hoechst 33342: λex = 405 nm/λem = 415-485 nm; TAMRA: λex = 561 nm/λem = 571-611 nm; Alexa488: λex = 488 nm/λem = 498-548 nm). After the acquisition, the images were processed under the same conditions and parameters using ImageJ software.
These results suggested that after 1. 5 h of incubation, the majority of the peptide internalized by endocytosis was found in late endosomes or lysosomes, confirming the internalization via endocytosis-dependent pathways. (1 μM =  [1] ) and compared to non-treated cells (NT) in the absence or presence of chloroquine (CQ, 100 μM). After cell trypsinization (to remove external peptides), the fluorescence and cell viability were assessed via flow cytometry. Graphical representation of data obtained from four independent measurements (mean ± SD, n = 4). A statistically significant difference was noticed between the incubation conditions without and with CQ for TatRI-iCAL36 and Pen-iCAL36 at 5 μM, whereas no statistical difference was revealed for TatRI-iCAL36 at 1 μM (one-way ANOVA with Bonferroni test, statistical relevance given as **** p < 0.
0001 and ns > 0. 05). (B) Caco-2 cells were incubated with Tamra-TatRI-iCAL36 (5 μM) and Tamra-Pen-iCAL36 (1 μM) at 4 °C or in the presence of either ATPdepleting reagents (NaN3/DG) or endocytosis inhibitors (CPZ, NYS or MBCD) at 37 °C. The same conditions were used on cells without peptides (w/o peptide) to determine the effect of the endocytosis inhibition. For all conditions, fluorescence and cell viability were acquired via flow cytometry after cell trypsinization (to remove membrane externally bound peptides). Graphical representation of data obtained from four independent measurements (mean ± SD, n = 4). A statistically significant difference compared to untreated condition was noticed for ATP depletion and 4 °C incubation for TatRI-iCAL36 and Pen-iCAL36 Because a number of these chemical endocytosis inhibitors lack specificity, it was possible that they could give misleading results  [44, 45].
Therefore, we further evaluated (1 µM =  [1] ) and compared to non-treated cells (NT) in the absence or presence of chloroquine (CQ, 100 µM). After cell trypsinization (to remove external peptides), the fluorescence and cell viability were assessed via flow cytometry. Graphical representation of data obtained from four independent measurements (mean ± SD, n = 4). A statistically significant difference was noticed between the incubation conditions without and with CQ for TatRI-iCAL36 and Pen-iCAL36 at 5 µM, whereas no statistical difference was revealed for TatRI-iCAL36 at 1 µM (one-way ANOVA with Bonferroni test, statistical relevance given as **** p < 0. 0001 and ns > 0. 05). (B) Caco-2 cells were incubated with Tamra-TatRI-iCAL36 (5 µM) and Tamra-Pen-iCAL36 (1 µM) at 4 • C or in the presence of either ATP-depleting reagents (NaN 3 /DG) or endocytosis inhibitors (CPZ, NYS or MBCD) at 37 • C.
The same conditions were used on cells without peptides (w/o peptide) to determine the effect of the endocytosis inhibition. For all conditions, fluorescence and cell viability were acquired via flow cytometry after cell trypsinization (to remove membrane externally bound peptides). Graphical representation of data obtained from four independent measurements (mean ± SD, n = 4). A statistically significant difference compared to untreated condition was noticed for ATP depletion and early and late endosomes, as well as lysosomes. As shown in Figure  4A ,B, neither peptide fully colocalized with early endosome markers. Instead, they showed strong degrees of colocalization with late endosomes and with lysosomes (see arrows). These results suggested that after 1. 5 h of incubation, the majority of the peptide internalized by endocytosis was found in late endosomes or lysosomes, confirming the internalization via endocytosis-dependent pathways.
0001 and ns > 0. 05). (B) Caco-2 cells were incubated with Tamra-TatRI-iCAL36 (5 μM) and Tamra-Pen-iCAL36 (1 μM) at 4 °C or in the presence of either ATPdepleting reagents (NaN3/DG) or endocytosis inhibitors (CPZ, NYS or MBCD) at 37 °C. The same conditions were used on cells without peptides (w/o peptide) to determine the effect of the endocytosis inhibition. For all conditions, fluorescence and cell viability were acquired via flow cytometry after cell trypsinization (to remove membrane externally bound peptides). Graphical representation of data obtained from four independent measurements (mean ± SD, n = 4). A statistically significant difference compared to untreated condition was noticed for ATP depletion and 4 °C incubation for TatRI-iCAL36 and Pen-iCAL36 (2-way ANOVA with Bonferroni test, statistical relevance given as * p < 0.
0001 and ns > 0. 05). (B) Caco-2 cells were incubated with Tamra-TatRI-iCAL36 (5 µM) and Tamra-Pen-iCAL36 (1 µM) at 4 • C or in the presence of either ATP-depleting reagents (NaN 3 /DG) or endocytosis inhibitors (CPZ, NYS or MBCD) at 37 • C. The same conditions were used on cells without peptides (w/o peptide) to determine the effect of the endocytosis inhibition. For all conditions, fluorescence and cell viability were acquired via flow cytometry after cell trypsinization (to remove membrane externally bound peptides). Graphical representation of data obtained from four independent measurements (mean ± SD, n = 4). A statistically significant difference compared to untreated condition was noticed for ATP depletion and 4 • C incubation for TatRI-iCAL36 and Pen-iCAL36 (2-way ANOVA with Bonferroni test, statistical relevance given as * p < 0.
Acknowledgments: Peptide synthesis was performed with excellent technical support from the  Synbio3 platform , which is supported by the  GIS IBISA/ITMO Cancer  ( Plan Cancer   2014-2019 ) and  Chimie Balard Cirimat Carnot Institute. We acknowledge the  Montpellier Ressources Imagerie (MRI) , a member of the national infrastructure  France-BioImaging  supported by the  French National Research Agency  ( ANR-10-INBS-04 , " Investments for the Future "), especially for technical support from  Myriam Boyer  (flow cytometry) and  Baptiste Monterroso  (confocal microscopy). We also thank  Karidia Konate  and  Sébastien Deshayes  for their discussion and critical reading of the manuscript.
4 • 4 Figure 3. Dissecting the internalization mechanism of TatRI-iCAL36 and Pen-iCAL36. (A) Caco-2 cells were incubated with Tamra-TatRI-iCAL36 (1 µM = [1] or 5 µM) = [5] and Tamra-Pen-iCAL36(1 µM = [1] ) and compared to non-treated cells (NT) in the absence or presence of chloroquine (CQ, 100 µM). After cell trypsinization (to remove external peptides), the fluorescence and cell viability were assessed via flow cytometry. Graphical representation of data obtained from four independent measurements (mean ± SD, n = 4). A statistically significant difference was noticed between the incubation conditions without and with CQ for TatRI-iCAL36 and Pen-iCAL36 at 5 µM, whereas no statistical difference was revealed for TatRI-iCAL36 at 1 µM (one-way ANOVA with Bonferroni test, statistical relevance given as **** p < 0.
Since IMD is notifiable in many countries and the disease is severe enough to warrant hospitalisation in most people, it is unlikely that poor surveillance measures/lack of notification accounted for the decline of IMD in 2020. This is particularly unlikely in countries where IMD surveillance is well established. Overall, the data suggest that the observed reduction in hyperinvasive meningococcal transmission was more likely a result of COVID-19 control measures. A recent analysis of invasive disease cases associated with Streptococcus pneumoniae, Haemophilus influenzae , and N. meningitidis was conducted in 26 countries during the period Jan 1, 2018-May 31, 2020. Case data associated with the non-respiratory pathogen Streptococcus agalactiae were also collected. All countries experienced a large reduction in cases due to the respiratory pathogens between Jan 1, 2020 and May 31, 2020.
48 ltered penA alleles are frequently associated with penicillin resistance and can be broadly categorised into two discrete types: 'mosaic or altered' with an MIC ≥0. 125 μg/mL and 'wildtype' (MIC < 0. 125 μg/mL). 42 In PubMLST (Public Database for Molecular Typing and Microbial Genome Diversity), the most frequently identified alleles are harboured by a genetically diverse set of isolates. 49 rom recent data in the Republic of Ireland, the frequency of isolates with high MICs and mosaic alleles has increased since the late 1990s, especially amongst MenB strains. 50 A similar increase has been reported in Australia. 51 However, given the isolate diversity associated with these alleles, there remains no significant evidence of clonal expansion or horizontal spread of a specific penA allele.
54 urther data indicate that NmCV-5 boosts both anti-tetanus toxoid and anti-diphtheria toxoid (DT) responses ∼10 fold (manuscript in preparation). However, Menactra (DT carrier) boosts DT responses to a somewhat higher extent than NmCV-5 (CRM 197 carrier). Following this Phase II programme there are now several ongoing or planned Phase III studies to further assess the immunogenicity and safety of NmCV-5. The first is an observer-blind, randomised, controlled study amongst healthy individuals (2-29 years) in Mali and The Gambia, with 168-day follow-up postvaccination. 62 A total of 1800 participants were randomised to receive either NmCV-5 or Menactra as part of the trial. The primary objective is to demonstrate non-inferiority of NmCV-5 to Menactra in terms of SBA assay (using rabbit complement, rSBA) seroresponse or geometric mean titres (GMTs) to MenA, MenC, MenY and MenW.
RMD Open RMD Open RMD Open Force checked the list of papers and abstracts included for correctness and completeness and could add relevant papers not retrieved during the search. Additionally, snowballing was performed. Details on the search strategy are displayed in figure  1A-C. Data were extracted from eligible papers using a standardised extraction form and listed in summary of evidence tables (see online supplemental file 2) by one reviewer and checked by a second reviewer. Disagreement between the reviewers was discussed with the methodologists. Risk of bias assessment of individual studies was performed using the A Measurement Tool to Assess Systematic Reviews 2 for systematic reviews,  17  Cochrane Risk of Bias 2 tool for randomised controlled trials (RCTs),  18  the Quality in Prognosis Studies tool  19  and the Newcastle-Ottowa Scale for observational (cohort and case-control) studies,  20  the Quality Assessment of Diagnostic Accuracy Studies  21  for diagnostic studies and the Consensus on Health Economic Criteria  22  for economic evaluations (online supplemental files 2 and 3).
Immunogenicity of biopharmaceuticals Immunogenicity is an important pharmacodynamic factor in treatment with most biopharmaceuticals, especially with therapeutic monoclonal antibodies. There is evidence for the association of low biopharmaceutical blood concentrations with the presence of ADAb detected using a drug-sensitive assay for all anti-TNF therapeutic monoclonal antibodies, certolizumab pegol, sarilumab and rituximab. 10 51 53 56 63 65 67 71 76 91  96 106-116 or tocilizumab and other biopharmaceuticals such as secukinumab or ixekizumab, there are some data available; however, data in these papers were presented with insufficient amount of detail to properly extract these from the papers. Receptor constructs such as etanercept and abatacept do not appear to be immunogenic.
Treatments Treatments Treatments on the induction phase of treatment with infliximab and compares to standard care in the achievement of remission after 30 weeks of treatment. Patients with different immune-mediated inflammatory diseases were enrolled, including RA, PsA and SpA. TDM was not superior to standard care, although a reduced number of infusion-related reactions were observed with TDM. The authors conclude that TDM is not indicated in the induction phase of treatment with infliximab. Results of the maintenance phase (NOR-DRUM B) and costeffectiveness analyses were not available within the search period of this SLR. Several observational studies addressed proactive TDM. Only one study included sufficient data for this SLR; however, it was a small study and lacked a standard care comparator.
Furthermore, current evidence is also inconsistent with regard to the use of biopharmaceutical blood concentrations and/or ADAb measurement at the time of treatment failure to assist the choice of subsequent treatment. Data surrounding ADAb utility is particularly conflicting in this regard, although there is a strong association between the detection of ADAb and loss of response to treatment and some association with hypersensitivity reactions. Measurement of infliximab, adalimumab and, probably, certolizumab pegol blood concentrations early in the course of treatment may aid in predicting future treatment response. High biopharmaceutical blood concentrations may be associated with a higher risk of infections, although evidence is limited. There is currently insufficient evidence for the routine use of proactive TDM, in part because published costeffectiveness analyses do not incorporate the current landscape of biopharmaceutical costs and usage.
Acknowledgements The authors thank the librarians of the  Paris Descartes University , the  Spanish Society of Rheumatology , the  Medical Library, Division of Rheumatology and Research, Diakonhjemmet Hospital , and the  Amsterdam Rheumatology and immunology Centre|Reade  for their assistance in defining the terms of the search on the technical aspects of therapeutic drug monitoring. MJ is funded by a  National Institute for Health Research (NIHR)   Advanced Fellowship  ( NIHR301413 ). Work in JI's laboratory is supported by the  NIHR Newcastle Biomedical Research Centre  and the  Research Into Inflammatory Arthritis Centre vs Arthritis. JI is an  NIHR  senior investigator. Contributors All authors where involved in planning and reporting of the work. CK, BH-B JEG, GlM, VN-C, JI and AvT conducted the study.
Selection of patients Patients with suspected TMA who were admitted to the Tours university hospital (France) between January 1 st , 2009 and December 31 st , 2016 were included. As previously described  [14] , patients were identified using 2 modes of detection: the presence of schistocytosis in the laboratory results and/or the presence of specific keywords in hospitalization discharge summaries (HDS). All patients' records were reviewed individually (manually) using all available data by 4 physicians (AB, GB, FVT, BT), including medical reports and electronic databases and diagnosis of TMA was confirmed or ruled out. TMA was suspected based on the presence of at least 3 of the following criteria: hemoglobin <12 g/dL, increased LDH, low haptoglobin and schistocytosis ≥0. 5% associated with thrombocytopenia (platelets count <150 G/L)  [1, 2].
Statistical analyses Quantitative data are presented as median and interquartile range (IQR). Qualitative data are described with percentages. Comparisons were made using Chi square test or Fischer test as appropriate for qualitative data and Wilcoxon test for quantitative data. Univariate and multivariate logistic regressions were performed for the identification of parameters associated with the risk of ESRD. SAS software (version 9. 3) was used.