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26 pages, 11 figures, 8 tables.-- This work is distributed under the Creative Commons Attribution 4.0 License, The Global Ocean Data Analysis Project (GLODAP) is a synthesis effort providing regular compilations of surface to bottom ocean biogeochemical bottle data, with an emphasis on seawater inorganic carbon chemistry and related variables determined through chemical analysis of seawater samples. GLODAPv2.2023 is an update of the previous version, GLODAPv2.2022 (Lauvset et al., 2022). The major changes are as follows: data from 23 new cruises were added. In addition, a number of changes were made to the data included in GLODAPv2.2022. GLODAPv2.2023 includes measurements from more than 1.4 million water samples from the global oceans collected on 1108 cruises. The data for the now 13 GLODAP core variables (salinity, oxygen, nitrate, silicate, phosphate, dissolved inorganic carbon, total alkalinity, pH, chlorofluorocarbon-11 (CFC-11), CFC-12, CFC-113, CCl4, and SF6) have undergone extensive quality control with a focus on the systematic evaluation of bias. The data are available in two formats: (i) as submitted by the data originator but converted to World Ocean Circulation Experiment (WOCE) exchange format and (ii) as a merged data product with adjustments applied to minimize bias. For the present annual update, adjustments for the 23 new cruises were derived by comparing those data with the data from the 1085 quality-controlled cruises in the GLODAPv2.2022 data product using crossover analysis. SF6 data from all cruises were evaluated by comparison with CFC-12 data measured on the same cruises. For nutrients and ocean carbon dioxide (CO2), chemistry comparisons to estimates based on empirical algorithms provided additional context for adjustment decisions. The adjustments that we applied are intended to remove potential biases from errors related to measurement, calibration, and data-handling practices without removing known or likely time trends or variations in the variables evaluated. The compiled and adjusted data product is believed to be consistent to better than 0.005 in salinity, 1 % in oxygen, 2 % in nitrate, 2 % in silicate, 2 % in phosphate, 4 µmol kg−1 in dissolved inorganic carbon, 4 µmol kg−1 in total alkalinity, 0.01–0.02 in pH (depending on region), and 5 % in the halogenated transient tracers. The other variables included in the compilation, such as isotopic tracers and discrete CO2 fugacity (fCO2), were not subjected to bias comparison or adjustments, Nico Lange has been funded by EU Horizon 2020 through the EuroSea action (grant no. 862626). Siv K. Lauvset has received internal strategic funding from NORCE Climate. Are Olsen, Nico Lange, and Siv K. Lauvset have received funding from the EU Horizon Europe project OceanICU (grant no. 101083922). Leticia Cotrim da Cunha has been supported by the Prociencia 2022–2024 grant from Universidade do Estado do Rio de Janeiro (UERJ, Brazil) and the PQ2 309708/2021-4 grant from the National Council for Scientific and Technological Development (CNPq, Brazil). Marta Álvarez has been supported by an Instituto Español de Oceanografía (IEO) RADPROF project. Peter J. Brown has received partial funding from the UK Climate Linked Atlantic Sector Science (CLASS) NERC National Capability Long-term Single Centre Science Programme (grant no. NE/R015953/1). Anton Velo and Fiz F. Perez have been supported by the BOCATS2 (grant no. PID2019-104279GB-C21) project funded by MCIN/AEI/10.13039/501100011033 and the Horizon Europe project EuroGO-SHIP (grant no. 101094690). Brendan R. Carter has received funding from the Global Ocean Monitoring and Observing (GOMO) program of the National Oceanic and Atmospheric Administration (NOAA) through contributions (project no. 100007298) via the Cooperative Institute for Climate, Ocean, and Ecosystem Studies (CIOCES) under a NOAA Cooperative Agreement (grant no. NA20OAR4320271; contribution no. 2022–2012). Mario Hoppema has received funding from the EU Horizon 2020 Action SO-CHIC (grant no. 821001). Adam Ulfsbo has been supported by the Swedish Research Council Formas (grant no. 2018-01398). Jens Daniel Müller has received support from the European Union's Horizion 2020 research and innovation program for project 4C (grant no. 821003). Alex Kozyr has been supported by NOAA (grant no. NA19NES4320002; Cooperative Institute for Satellite Earth System Studies – CISESS) at the University of Maryland/ESSIC. Ryan J. Woosley has been supported by NSF grants (grant nos. OCE-1923312 and OCE-2148468). Masao Ishii has been supported by the Environment Research and Technology Development Fund of the Environmental Restoration and Conservation Agency of Japan (grant no. JPMEERF21S20810). GLODAP also acknowledges funding from the Initiative and Networking Fund of the Helmholtz Association through the project “Digital Earth” (grant no. ZT-0025), Peer reviewed

Soft tissue defects or pathologies frequently necessitate the use of biomaterials that provide the volume required for subsequent vascularization and tissue formation as autrografts are not always a feasible alternative. Supramolecular hydrogels represent promising candidates because of their 3D structure, which resembles the native extracellular matrix, and their capacity to entrap and sustain living cells. Guanosine-based hydrogels have emerged as prime candidates in recent years since the nucleoside self-assembles into well-ordered structures like G-quadruplexes by coordinating K+ ions and π–π stacking, ultimately forming an extensive nanofibrillar network. However, such compositions were frequently inappropriate for 3D printing due to material spreading and low shape stability over time. Thus, the present work aimed to develop a binary cell-laden hydrogel capable of ensuring cell survival while providing enough stability to ensure scaffold biointegration during soft tissue reconstruction. For that purpose, a binary hydrogel made of guanosine and guanosine 5'-monophosphate was optimized, rat mesenchymal stem cells were entrapped, and the composition was bioprinted. To further increase stability, the printed structure was coated with hyperbranched polyethylenimine. Scanning electron microscopic studies demonstrated an extensive nanofibrillar network, indicating excellent G-quadruplex formation, and rheological analysis confirmed good printing and thixotropic qualities. Additionally, diffusion tests using fluorescein isothiocyanate labeled-dextran (70, 500, and 2000 kDa) showed that nutrients of various molecular weights may diffuse through the hydrogel scaffold. Finally, cells were evenly distributed throughout the printed scaffold, cell survival was 85% after 21 days, and lipid droplet formation was observed after 7 days under adipogenic conditions, indicating successful differentiation and proper cell functioning. To conclude, such hydrogels may enable the 3D bioprinting of customized scaffolds perfectly matching the respective soft tissue defect, thereby potentially improving the outcome of the tissue reconstruction intervention., Peer reviewed

17 Pág., Forest biomass is an essential resource in relation to the green transition and its assessment is key for the sustainable management of forest resources. Here, we present a forest biomass dataset for Europe based on the best available inventory and satellite data, with a higher level of harmonisation and spatial resolution than other existing data. This database provides statistics and maps of the forest area, biomass stock and their share available for wood supply in the year 2020, and statistics on gross and net volume increment in 2010-2020, for 38 European countries. The statistics of most countries are available at a sub-national scale and are derived from National Forest Inventory data, harmonised using common reference definitions and estimation methodology, and updated to a common year using a modelling approach. For those counties without harmonised statistics, data were derived from the State of Europe's Forest 2020 Report at the national scale. The maps are coherent with the statistics and depict the spatial distribution of the forest variables at 100 m resolution., We thank the ENFIN and the NFI organisations and national correspondents of 26 European countries who participated in the data harmonisation study supported by the JRC Specific Contracts n. 13, 17, 18, 19, 20 and 21 for the production of data harmonised for definition and estimation method regarding forest biomass, forest area and biomass not available for wood supply, and forest increment. The study was partly funded by the Framework contract for the provision of forest data and services in support to the European Forest Data Centre, Contract numbers 388432 (2012–2017) & 934340 (2017–2021). The views expressed are purely those of the writers and may in no circumstance be regarded as stating an official position of the European Commission., Peer reviewed

Figure S1. Amino acid global propensity in epitopes. Figure S2. Overall global propensity variation in epitopes. Figure S3. Relative entropy values for the epitopes. Figure S4. Distribution of epitopes by source organism. Figure S5. Tokenization of epitopes with tokens of 4 and 5 residues. Figure S6. Amino acid frequency after tokenization. Table S1: Average relative entropies and p-values for the entropy analysis. Table S2: Tokens obtained through BPE tokenization of the entire dataset., Epitopes are specific regions on an antigen’s surface that the immune system recognizes. Epitopes are usually protein regions on foreign immune-stimulating entities such as viruses and bacteria, and in some cases, endogenous proteins may act as antigens. Identifying epitopes is crucial for accelerating the development of vaccines and immunotherapies. However, mapping epitopes in pathogen proteomes is challenging using conventional methods. Screening artificial neoepitope libraries against antibodies can overcome this issue. Here, we applied conventional sequence analysis and methods inspired in natural language processing to reveal specific sequence patterns in the linear epitopes deposited in the Immune Epitope Database (www.iedb.org) that can serve as building blocks for the design of universal epitope libraries. Our results reveal that amino acid frequency in annotated linear epitopes differs from that in the human proteome. Aromatic residues are overrepresented, while the presence of cysteines is practically null in epitopes. Byte pair encoding tokenization shows high frequencies of tryptophan in tokens of 5, 6, and 7 amino acids, corroborating the findings of the conventional sequence analysis. These results can be applied to reduce the diversity of linear epitope libraries by orders of magnitude., Peer reviewed

In this work, a sequential covalent co-immobilization of graphene oxide (GO) and hyaluronic acid (HA) is performed to obtain a biocompatible wear-resistant nanocoating on the surface of the biomedical grade Cobalt-Chrome (CoCr) alloy. Nanocoated CoCr surfaces were characterized by Raman spectroscopy and electrochemical impedance spectroscopy (EIS) in 3 g/L HA electrolyte. Tribocorrosion tests of the nanocoated CoCr surfaces were carried out in a pin on flat tribometer. The biological response of covalently HA/GO biofunctionalized CoCr surfaces with and without wear-corrosion processes was studied through the analysis of the proteome of macrophages. Raman spectra revealed characteristic bands of GO and HA on the functionalized CoCr surfaces. The electrochemical response by EIS showed a stable and protective behavior over 23 days in the simulated biological environment. HA/GO covalently immobilized on CoCr alloy is able to protect the surface and reduce the wear volume released under tribocorrosion tests. Unsupervised classification analysis of the macrophage proteome via Hierarchical clustering and Principal Component Analysis (PCA) revealed that the covalent functionalization on CoCr enhances the macrophage biocompatibility in vitro. On the other hand, disruption of the HA/GO nanocoating by tribocorrosion processes induced a macrophage proteome which was differently clustered and was distantly located in the PCA space. In addition, tribocorrosion induced an increase in the percentage of upregulated and downregulated proteins in the macrophage proteome, revealing that disruption of the covalent nanocoating impacts the macrophage proteome. Although macrophage inflammation induced by tribocorrosion of HA/GO/CoCr surfaces is observed, it is ameliorated by the covalently grafting of HA, which provides immunomodulation by eliciting downregulations in characteristic pro-inflammatory signaling involved in inflammation and aseptic loosening of CoCr joint arthroplasties. Covalent HA/GO nanocoating on CoCr provides potential applications for in vivo joint prostheses led a reduced metal-induced inflammation and degradation by wear-corrosion in vivo., Proteome Dataset: Macrophage Proteomic Analysis of Covalent Immobilization of Hyaluronic Acid and Graphene Oxide on CoCr Alloy in a Tribocorrosive Environment, Peer reviewed

The dataset includes: Microstructure profiles collected with a MSS Sea&Sun profiler during the three intensive samplings of the cruise (I01, I02, I03), Ocean currents measured with a bottom moored RD Instruments acoustic Doppler profiler (ADCP, 300Khz) for the duration of the cruise, Acoustic backscatter from a ship-borne echosounder Simrad EK80 for the frequencies 18, 38, 70, 120 and 200 KHz and the three intensive samplings of the cruise (I01, I02, I03), European anchovy (Engraulis encrasicolus) egg counts from plankton hauls samplings, This dataset includes data collected during the cruise REMEDIOS-TL in the Ría de Pontevedra (NW Iberia) at station P2 (42.357°N, 8.773°W) from 29 June to 18 July 2018 onboard of the Research Vessel Ramón Margalef belonging to the Spanish Institude of Oceanography. The archived data are described in a manuscript entitled "Intense upper ocean mixing due to large aggregations of spawning fish" by Fernández Castro et al. published in Nature Geoscience: Fernández Castro, B., Peña, M., Nogueira, E. et al. Intense upper ocean mixing due to large aggregations of spawning fish. Nat. Geosci. 15, 287–292 (2022). https://doi.org/10.1038/s41561-022-00916-3. The manuscript presents evidence that night-time aggregations of anchovies produce intense ocean turbulence and mixing. All the data needed to support the conclusions of the article are included in this dataset, The REMEDIOS project is funded by the Spanish Ministry of Economy and Innovation under the research project REMEDIOS (CTM2016-75451-C2-1-R), acoustic_backscatter_EK80_REMEDIOS_TL_I01.nc.-- acoustic_backscatter_EK80_REMEDIOS_TL_I02.nc.-- acoustic_backscatter_EK80_REMEDIOS_TL_I03.nc.-- bottom_moored_ADCP_REMEDIOS_TL.nc.-- egg_counts.xls.-- MSS_microstructure_REMEDIOS_TL_I01.nc.-- MSS_microstructure_REMEDIOS_TL_I02.nc.-- MSS_microstructure_REMEDIOS_TL_I03.nc, Peer reviewed

(A) Above: Sequence motif enriched in C. elegans HE cluster HMT promoters, relative to other HMTs promoters. Below: previously reported EFL-2 binding motif. (B) Binding of the C. elegans Retinoblastoma orthologue LIN-35 upstream of the TSS of the HE cluster, other HMT genes, and random genes; p-values from Wilcoxon test. (C) Enrichment for transcription factor binding, from ENCODE ChIP-seq experiments, upstream of human HMT genes. Odds ratios and p-value derived from Fisher’s exact test. (D) Boxplots show median total HMT or NNMT expression percentile drawn from 1,000 iterations of pan-cancer sampling of tumours with wild-type RB1 or potentially deleterious RB1 mutations; p-value derived from t test. (E) Total HMT expression in small cell lung cancer cell lines from the CCLE with wild-type RB1 or deleterious RB1 mutations; p-value derived from t test. (F) Estimated E2F1 activity vs. total HMT expression (both corrected for confounders) in breast cancer primary tumours from the TCGA. (G) Potential architectures of the GRN linking RB1, NNMT, and HMTs. (H) Linear model t-values explaining total HMT and NNMT expression for RB1 mutation status as the sole explanatory variable or jointly considered with NNMT/HMT expression respectively; p-value derived from t test. Underlying data for all panels can be found in https://zenodo.org/record/8383542. CCLE, Cancer Cell Line Encyclopedia; GRN, gene regulatory network; HMT, histone methyltransferase; NNMT, nicotinamide N-methyltransferase; Rb, Retinoblastoma; TCGA, The Cancer Genome Atlas; TSS, transcription start site., Peer reviewed

Individual HMT levels in Rb-mutant tumours in TCGA., Peer reviewed

The N-terminal tails of eukaryotic histones are frequently posttranslationally modified. The role of these modifications in transcriptional regulation is well-documented. However, the extent to which the enzymatic processes of histone posttranslational modification might affect metabolic regulation is less clear. Here, we investigated how histone methylation might affect metabolism using metabolomics, proteomics, and RNA-seq data from cancer cell lines, primary tumour samples and healthy tissue samples. In cancer, the expression of histone methyltransferases (HMTs) was inversely correlated to the activity of NNMT, an enzyme previously characterised as a methyl sink that disposes of excess methyl groups carried by the universal methyl donor S-adenosyl methionine (SAM or AdoMet). In healthy tissues, histone methylation was inversely correlated to the levels of an alternative methyl sink, PEMT. These associations affected the levels of multiple histone marks on chromatin genome-wide but had no detectable impact on transcriptional regulation. We show that HMTs with a variety of different associations to transcription are co-regulated by the Retinoblastoma (Rb) tumour suppressor in human cells. Rb-mutant cancers show increased total HMT activity and down-regulation of NNMT. Together, our results suggest that the total activity of HMTs affects SAM metabolism, independent of transcriptional regulation., Peer reviewed

1 file, The Cape Verde Frontal Zone (CVFZ) is a highly dynamic region located in the southern boundary of the Canary Current Eastern Boundary Upwelling Ecosystem. Due to the interaction of the Cape Verde Front with the Mauritanian coastal upwelling, the area features large vertical and horizontal export fluxes of organic matter. Full-depth profiles were recorded during FLUXES I cruise, with four consecutive transects defining a box embracing the giant filament of Cape Blanc and the Cape Verde front. Fifteen levels were sampled in medium and long stations (down to 4000 dbar) and 10 levels in short stations (down to 2000 dbar) where inorganic nutrients (NO3, NO2, Si(OH)4 and PO4), dissolved organic carbon/total dissolved nitrogen (DOC/TDN), and suspended particulate organic carbon and nitrogen (POC and PON) were sampled. Micromolar concentrations of nutrient salts were determined simultaneously by segmented flow analysis in an Alliance Futura autoanalyser. The determination of suspended POC and PON was carried out by high temperature catalytic oxidation at 900 °C in a Perkin Elmer 2400 elemental analyser. DOC and TDN were analysed by high temperature catalytic oxidation at 680 °C with a Shimadzu TOC-V analyser connected in line with a TNM1 measuring unit. Alongside with water samples conductivity, temperature and depth (CTD; SeaBird SBE911 plus), and dissolved oxygen (SeaBird SBE43), fluorescence of chlorophyll (SeaPoint SCF), and turbidity (SeaPoint STM) were measured. CTD conductivity was calibrated with water samples taken from the rosette and analysed on board with a Guildline 8410-A Portasal salinometer. Samples for dissolved oxygen (O2) determination were analysed on board by the Winkler potentiometric method. The chlorophyll (Chl) fluorescence sensor was calibrated with water samples taken at 4 depths in the photic layer which were estimated fluorometrically by means of a Turner Designs bench fluorometer 10-AU, Horizon 2020 (H2020), grant/award no. 817806: Sustainable management of mesopelagic resources; Ministerio de Ciencia e Innovación (MICINN), grant/award no. CTM2015-69392-C3: Constraining organic carbon fluxes in an eastern boundary upwelling ecosystem (NW Africa): the role of non-sinking carbon in the context of the biological pump; Ministerio de Ciencia e Innovación (MICINN), grant/award no. PID2019-109084RB-C21: Biogeochemical impact of mesoscale and sub-mesoscale processes along the life history of cyclonic and anticyclonic eddies: plankton variability and productivity, Peer reviewed