BUSCADOR RECOLECTA

Elemental analysis data; theoretical elemental composition; comparison of the DSC and TGA traces of 1, 2, and 3; NMR spectra; DLS size distributions; and comparison of the SEC traces of “Staudinger” SCNPs., Peer reviewed

To describe the incorporation of monoclonal antibodies (mAb) in real-world (RW) practice for the treatment of patients with relapsed refractory multiple myeloma (RRMM) in a setting with other treatment alternatives. This was an observational, multicenter, ambispective study of RRMM treated with or without a mAb. A total of 171 patients were included. For the group treated without mAb, the median (95% CI) progression-free survival (PFS) to relapse was 22.4 (17.8-27.0) months; partial response or better (≥PR) and complete response or better (≥CR) was observed in 74.1% and 24.1% of patients, respectively; and median time to first response in first relapse was 2.0 months and in second relapse was 2.5 months. For the group of patients treated with mAb in first or second relapse, the median PFS was 20.9 (95% CI, could not be evaluated) months; the ≥ PR and ≥ CR rates were 76,2% and 28.6%, respectively; and the median time to first response in first relapse was 1.2 month and in second relapse was 1.0 months. The safety profiles for the combinations were consistent with those expected. The incorporation of mAb in RW practice for the treatment of RRMM has shown good quality and speed of response with a similar safety profile shown in randomized clinical trials., This study was sponsored by Janssen-Cilag. Janssen-Cilag participated in the study design, data analysis and drafting of the manuscript, Peer reviewed

4 files, Supplementary material for the article http://dx.doi.org/10.3390/biology9100337, Doc file: Figure S1: Number of turbot cells and ciliates in the peritoneal cavity; Figure S2: Micrographs of ciliates at different stages of infection; Figure S3: qPCR validation of RNA-seq findings; Table S1: Sample information; Table S2: Primer sequences used in the qPCR analysis.-- File S1: Excel file showing the contigs that were DE in P. dicentrarchi at 1, 2, 4 hpi, the fold change, p-value, and the gene names.-- File S2: Excel file showing the contigs that were DE in turbot peritoneal cells at 1, 2, 4 hpi, the fold change, p-value, and the gene names.-- File S3: Excel file showing the contigs that were DE in turbot peritoneal cells at 12 and 48 hpi, the fold change, p-value, and the gene names, Peer reviewed

Additional file 1: Text S1. Translated questionnaire to include donor in Cohort II. Fig. S1. Impact of genetic background on numbers of circulating immune cells. Each color and symbol indicate members of one family. Fully open symbols represent a centenarian. Semi-open symbol (orange) represents a sibling of a centenarian. Dashed lines indicate the available age-matched reference values produced with flow cytometry panels highly similar to the panels used in this study (earlier or later prototypes of these panels). For B- and T-cell subsets, reference lines indicate a cohort aged 60–79 years. For innate myeloid populations, reference lines indicate a cohort > 55 years old. In plots without dashed lines, no published reference values from highly similar flow cytometry panels were available. Fig. S2. Results of the pilot study to evaluate the calcium flux upon stimulation of the B-cell receptor (BCR) with IgG and IgM Fab fragments. (A) Measurement of calcium release (‘flux’) after B-cell stimulation with IgM Fabs in pre-GC B cells (CD27-IgA-IgG-) or unswitched memory B cells (CD27+IgA-IgG-). (B) Measurement of calcium release (‘flux’) after B-cell stimulation with IgG Fabs in CD27-IgG+ memory B cells (CD27-IgD-IgA-) or CD27+IgG+ memory B cells (CD27+IgD-IgA-). Ionomycin was added to calculate maximum calcium release. N = 14. Pre-GC; pre-Germinal Center, MBC; memory B cell. Fig. S3. Assessment of B-cell activation in all p.P522R-carriers and non-carriers upon BCR stimulation. Measurement of calcium release (‘flux’) after B-cell stimulation with IgM Fabs in pre-GC B cells (CD27-IgG-IgA-) (A) or unswitched memory B cells (CD27+IgG-IgA-) (B) in cohort I. Ionomycin was added to calculate maximum calcium release. Differences between carriers and non-carriers were evaluated by comparing the area under the curve (AUC) of the total Fab stimulation (from stimulation until the moment ionomycin was added, ~ 10 min, flux intensity and duration), the peak of the response after Fab stimulation (the 5 highest points after the Fabs were added to the cells; flux intensity), and after ionomycin was added (to determine the maximum flux). AUC was calculated only for points that were higher than baseline value (unstimulated sample). N = 31 (two samples were lost due to technical failure). No significant differences were observed. Pre-GC; pre-Germinal Center. Fig. S4. Phagocytosis and ROS production in innate immune cell subsets after stimulation with pHRodo™ Green E. coli Bioparticles (FcR/PLCγ2-dependent stimulation). To evaluate the outcome of the phagocytosis assays, three different readouts were used per population: % of cells that were phagocytosing, the average amount of particles phagocytosed per cell, and the ROS production upon phagocytosis. These three readouts were further combined into one value: the normalized ROS. These values are presented for the CD62L+ classical monocyte (cMo) subset (A), intermediate monocytes (iMo) (B), neutrophils (C) CD14- and CD14dim myeloid dendritic cells (mDCs) (D,E), and non-phagocytosing plasmacytoid dendritic cells (pDCs) (F). Lastly, the outcomes for T cells (negative control) are shown (G). Mann-Whitney U test was used to evaluate differences between carriers and non-carriers, but no statistically significant differences were found. N = 14. In two donors, monocytes could not be divided into subsets due to absence of a differentiating antibody in the prepared antibody cocktail, therefore, in panel A and B, only 5 non-carriers and 7 carriers are shown. Dashed lines indicate the background level of ROS (ROS production in negative control population; T cells). All outcomes were corrected for background or baseline activation by subtracting the value of the control (incubated on ice) from the activated (incubated at 37 °C) sample. Negative values (caused by higher background in control samples than activated samples in cell populations that did not perform phagocytosis) were set to 0. Fig. S5. ROS generation in innate immune cell subsets in p.P522R-carriers and non-carriers upon stimulation with PMA (FcR/PLCγ2-independent stimulation). N = 14. In two donors, monocytes could not be divided into subsets due to absence of an antibody in the prepared antibody cocktail, therefore, in panel A-D, only 5 non-carriers and 7 carriers are shown. Dashed lines indicate the background level of ROS (ROS production in negative control population; T cells). All outcomes were corrected for background or baseline activation by subtracting the value of the control (incubated on ice) from the activated (incubated at 37 °C) sample. Table S1. Description of all included families and additional donors. Table S2. Overview of the flow cytometry panels that were used in this study. Table S3. Phenotypic descriptions used to define B-cell subsets stained with EuroFlow PERISCOPE B-cell and plasma cell panel (BIGH) panel by manual analysis. Table S4. Phenotypic descriptions used to define T-cell subsets stained with EuroFlow PERISCOPE CD4 T-cell (TCD4) panel by manual analysis. Table S5. Phenotypic descriptions used to define T-cell and NK-cell subsets stained with the EuroFlow PERISCOPE CD8 cytotoxic T-cell (CYTOX) panel by manual analysis. Table S6. Phenotypic descriptions used to define innate immune cell (sub) sets stained with the EuroFlow PERISCOPE DC-Monocyte panel by manual analysis. Table S7. Polygenic Risk Score and SNP annotation for immune-related SNPs. Table S8. Control and assay tubes measured in the phagocytosis experiment. Table S9. Control and assay tubes measured when detection production of reactive oxygen species (ROS)., ZonMw Health Holland HorstingStuit Foundation, the Hans und Ilse Breuer Foundation and Stichting VUmc Fund H2020 Marie Skłodowska-Curie Actions, Peer reviewed

1 file, Supplementary material for the article https://doi.org/10.3390/biom10081184, Figure S1: Fermentations of L. brevis.-- Figure S2: Kinetic growth of P. fluorescens.-- Figure S3: Kinetic growth of B. subtilis.-- Figure S4: Economical evaluation of L. plantarum bioproduction costs.-- Figure S5: Economical evaluation of P. fluorescens, B. subtilis and S. epidermidis growth costs.-- Table S1: Composition of culture media.-- Table S2: Kinetic Parameters of L. plantarum cultures on FP media.-- Table S3: Kinetic Parameters of L. plantarum cultures on TP media.-- Table S4: Kinetic parameters of L. brevis cultures on FP media.-- Table S5: Kinetic parameters of L. brevis cultures on TP media.-- Table S6: Productive yields of LAB bioproductions.-- Table S7: Kinetic parameters of P. fluorescens cultures on FP media.-- Table S8: Kinetic parameters of P. fluorescens cultures on TP media.-- Table S9: Kinetic parameters of Phaeobacter sp. cultures on FP media.-- Table S10: Kinetic parameters of Phaeobacter sp. cultures on TP media.-- Table S11: Kinetic parameters of B. subtilis cultures on FP media.-- Table S12: Kinetic parameters of B. subtilis cultures on TP media.-- Table S13: Kinetic parameters of S. epidermidis cultures on FP media.-- Table S14: Kinetic parameters of S. epidermidis cultures on TP media, Peer reviewed

Additional file 1: Fig. S1. CrkL binds through the SH3N domain and with similar affinity to the four isolated PRMs of C3G. Fig. S2. Analysis of CrkL by sedimentation velocity. Fig. S3. ITC analysis of the binding of CrkL to single-PRM mutants of C3G. Fig. S4. Linear concentration dependence of the nucleotide exchange activity of phospho-C3G. Fig. S5. Binding of CrkL fragments and CrkII to C3G. Table S1. Constructs of human C3G in the vector pETEV15b-His-Halo-TEV for expression in E coli. Table S2. Oligonucleotides used to create constructs of C3G and for site directed mutagenesis. Table S3. Constructs of human C3G in the vectors for expression in mammalian cells. Table S4. Constructs of human CrkL and CrkII in the vectors for expression in E coli. Table S5. Oligonucleotides used to create constructs of CrkL and CrkII. Table S6. Oligonucleotides to subclone the abGFP4 nanobody in a modified pET22b vector. Table S7. Parameters of the CrkL/C3G interaction determined by ITC. Table S8. Hydrodynamic parameters of C3G and CrkL. Table S9. Parameters of the CrkL/C3G interaction determined by ITC and sedimentation velocity. Table S10. Parameters of the CrkL binding to single-PRM mutants of C3G determined by ITC. Table S11. Parameters of the binding of CrkL fragments to C3G determined by ITC., Universidad de Salamanca Ministerio de Ciencia e Innovación Consejería de Educación, Junta de Castilla y León Agencia Estatal de Investigación National Institute of Biomedical Imaging and Bioengineering Junta de Castilla y León Consejo Superior de Investigaciones Cientificas (CSIC), Peer reviewed

Additional file 2. Raw data of the figures., Universidad de Salamanca Ministerio de Ciencia e Innovación Consejería de Educación, Junta de Castilla y León Agencia Estatal de Investigación National Institute of Biomedical Imaging and Bioengineering Junta de Castilla y León Consejo Superior de Investigaciones Cientificas (CSIC), Peer reviewed

Supplementary Figure S1. Flp1 phosphatase changes its subcellular localization under oxidative stress in a phosphorylation-dependent manner. (a) Live-cell images of gar2-mCherry cells also expressing either Flp1-GFP, Flp1-6A-GFP or Flp1-9A-GFP fusion proteins under unperturbed growth conditions or after treatment with 1mM of H2O2 for 1 h. Asterisks indicate Flp1-GFP nucleoplasmic localization. Scale bar, 5 µm. (b) Line scans of Flp1-GFP and Gar2-mCherry fluorescence of the boxed nuclei from de merged images in (a), represented by a white line and spanning 4 µm from the white closed circle. Fluorescence intensity was normalized to the maximum value after background subtraction. (c) Schematic representation of Flp1 showing all nine RxxS putative phosphorylation sites, which are mutated to alanine in the Flp1.9A-GFP mutant. Asterisks indicate the six serine residues that are mutated to alanine in the Flp1.6A-GFP mutant. (d) The graph shows the percentage of nuclei with Flp1-GFP, Flp1.6A-GFP or Flp1.9A-GFP detected in the nucleoplasm both under unperturbed growth conditions and after treatment with 1mM of H2O2 for 1h. Supplementary Figure S2. flp1+ deletion partially rescues sensitivity of Dsty1 strain to chronic presence of H2O2 in a pap1+-dependent manner. Tenfold serial dilution of indicated strains were spotted onto YES-agar plates without or with 0.6 mM H2O2 and incubated at 30ºC during 72 h. Supplementary Figure S3. (a) Expression of stress-responsive genes indicated in unstressed wildtype and ∆flp1 cells. Total RNA from asynchronous cultures of the indicated strains grown at 30 ºC was extracted and reverse transcribed using a mix of oligo(dT) and random hexamers primers. mRNA levels of ctt1+, gpd1+, hsp9+ and pyp2+ genes were measured by qPCR and normalized with ribosomal 18S mRNA. The amount of mRNAs relative to the wild-type was expressed as means SD in triplicate. Asterisks indicate statistical significance (*, P<0.05; t-test unpaired) versus wild-type. (b) Exponentially growing cultures of strains indicated at 30 ºC were treated with 1mM H2O2 for 1 hour. Total RNA was extracted, separated by electrophoresis and rRNAs stained with methylene blue were used as loading control. Northern-blot analysis was used to measure the expression levels of atf1+ in the indicated strains. Full-length blots are shown in Supplementary Fig. S9. Supplementary Figure S4. Flp1-9A-GFP strain, expressing a nonphosphorylatable flp1 mutant unable to exit the nucleolus under oxidative stress conditions, shows altered the transcriptional profile of genes such as atf1+, pcr1+, ctt1+, gpd1+ and srx1+ induced in response to oxidative stress. mRNA levels of the mentioned genes were measured by qPCR from total RNA extracted from wild-type and Flp1-9A-GFP strains growing in YES medium containing 1mM H2O2. Total RNAs were prepared from treated cells at the time points indicated. mRNA levels were normalized with ribosomal 18S mRNA and determined with respect to time 0´ value, which was considered as 1. Data represent the average of two biological replicates. Supplementary Figure S5. Dflp1 cells show greater resistance to moderate oxidative stress conditions. Asynchronous cultures of indicated strains growing at 30ºC in YES were incubated with 0.2 mM of H2O2 during 1 h. Then, cells were stressed with 2 mM (a) or 25 mM (b) H2O2. Cell viability was measured at the time points indicated by plating the appropriate dilution of cells onto YES agar plates. The number of viable cells was measured after 3 days incubation at 30ºC. Viability is expressed as a percentage of the number of colonies obtained before the addition of the first dose of H2O2. Supplementary Figure S6. Protein levels of Pyp2 phosphatase upon oxidative stress induction. Wild-type and ∆flp1cells expressing a Pyp2-Myc fusion protein were grown in YES medium to midlog phase and treated with 1mM H2O2 for the indicated times. Total extracts were resolved by SDSPAGE and analyzed by Western blot. Pyp2 was detected by incubation with anti-Myc antibody. Tubulin was used as loading control. Normalization of quantified Pyp2 is shown in bar diagrams. Experiment was repeated three times (Supplementary information Fig. S11), and a representative experiment is shown. Blot membranes were cut prior antibodies incubation. Supplementary Figure S7. Viability of Dpcr1 and Dflp1 Dpcr1 mutants in response to oxidative stress. (a) Tenfold serial dilution of indicated strains were spotted onto YES-agar plates without or with 0.6 mM and 1mM H2O2 and incubated at 30ºC during 72 h. (b) Asynchronous cultures of indicated strains growing at 30ºC in YES were incubated with 2 mM of H2O2 during 1 h. Cell viability was measured before and after treatment by plating the appropriate dilution of cells onto YES agar plates. The number of viable cells was measured after 3 days incubation at 30ºC. Viability is expressed as a percentage of the number of colonies obtained before the addition of H2O2 (0´). Data represent the average of two biological replicates. Supplementary Figure S8. Full-length gels and blots relating to Figure 2b,c are shown. Supplementary Figure S9. Full-length gel and blot relating to Figure S3b are shown. Supplementary Figure S10. Unprocessed original scans and full-length immunoblots relating to Figure 5a,b are shown. Supplementary Figure S11. Unprocessed original scans and full-length blots relating to Figure S6 are shown. Supplementary Figure S12. Full-length immunoblots relating to Figure 6a are shown. Supplementary Figure S13. Unprocessed original scans and full-length immunoblots relating to Figure 7 are shown., Peer reviewed

LEED and Pt 4f core level of the clean and CO-saturated (111), (645), and (312) Pt surfaces; C 1s and O 1s evolution during CO desorption experiments after surface saturation with 10 L CO at the same surfaces; O 1s α-scans at 90 K after a 0.25 and 10 L CO dose, and at 300 K after 50 L O2 dose; and additional details on the W-model., Peer reviewed

The supporting data contains supporting information (SI.pdf), trained models (*.pth), training configuration (nequip_configuration.yaml) to be used with Nequip code (https://github.com/mir-group/nequip), and minimal working example using the models (minimal_working_example.py). Version v2, Peer reviewed