Pre-trained biomedical language models for clinical NLP in Spanish

This work presents the first large-scale biomedical Spanish language models trained from scratch, using large biomedical corpora consisting of a total of 1.1B tokens and an EHR corpus of 95M tokens. We compared them against general-domain and other domain-specific models for Spanish on three clinical NER tasks. As main results, our models are superior across the NER tasks, rendering them more convenient for clinical NLP applications. Furthermore, our findings indicate that when enough data is available, pre-training from scratch is better than continual pre-training when tested on clinical tasks, raising an exciting research question about which approach is optimal. Our models and fine-tuning scripts are publicly available at HuggingFace and GitHub.This work was funded by the Spanish State Secretariat for Digitalization and Artificial Intelligence (SEDIA) within the framework of the Plan-TLPeer ReviewedPostprint (published version

Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world's oceans

Research articleThe transformation of leucine incorporation into prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world’s oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e. removal of grazers; F treatment) or filtration combined with dilution (i.e. relieving also resource competition; FD treatment). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu-1 and were significantly lower in the filtered and diluted (FD) than in the filtered (F) treatments. Also, changes in bacterial community composition during the incubations, as assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA), were stronger in the FD than in the F treatments, as compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCFs determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus) and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCFs variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts although resulting into relatively low carbon production rates in the oligotrophic ocean.En prensa3,829

Mortality due to non-AIDS-defining cancers among people living with HIV in Spain over 18 years of follow-up

Purpose: Our aim was to describe non-AIDS-defining cancer (NADC) mortality among people living with HIV (PLWH), to compare it with that of the general population, and to assess potential risk factors. Methods: We included antiretroviral-naive PLWH from the multicentre CoRIS cohort (2004-2021). We estimated mortality rates and standardised mortality ratios (SMRs). We used cause-specific Cox models to identify risk factors. Results: Among 17,978 PLWH, NADC caused 21% of all deaths observed during the follow-up. Mortality rate due to NADC was 1.58 (95%CI 1.36, 1.83) × 1000 person-years and lung and liver were the most frequent cancer-related causes of death. PLWH had 79% excess NADC mortality risk compared to the general population with the highest SMR found for Hodgkin lymphoma, anal and liver cancers. The SMRs decreased with age and were the highest in age groups under 50 years. The most important prognostic factor was low CD4 count, followed by smoking, viral hepatitis and HIV transmission through heterosexual contact or injection drug use. Conclusion: Non-AIDS cancers are an important cause of death among PLWH. The excess mortality related to certain malignancies and the association with immunodeficiency, smoking, and coinfections highlights the need for early detection and treatment of cancer in this population.Purpose: Our aim was to describe non-AIDS-defining cancer (NADC) mortality among people living with HIV (PLWH), to compare it with that of the general population, and to assess potential risk factors. Methods: We included antiretroviral-naive PLWH from the multicentre CoRIS cohort (2004-2021). We estimated mortality rates and standardised mortality ratios (SMRs). We used cause-specific Cox models to identify risk factors. Results: Among 17,978 PLWH, NADC caused 21% of all deaths observed during the follow-up. Mortality rate due to NADC was 1.58 (95%CI 1.36, 1.83) × 1000 person-years and lung and liver were the most frequent cancer-related causes of death. PLWH had 79% excess NADC mortality risk compared to the general population with the highest SMR found for Hodgkin lymphoma, anal and liver cancers. The SMRs decreased with age and were the highest in age groups under 50 years. The most important prognostic factor was low CD4 count, followed by smoking, viral hepatitis and HIV transmission through heterosexual contact or injection drug use. Conclusion: Non-AIDS cancers are an important cause of death among PLWH. The excess mortality related to certain malignancies and the association with immunodeficiency, smoking, and coinfections highlights the need for early detection and treatment of cancer in this population.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This research was supported by CIBER -Consorcio Centro de Investigación Biomédica en Red- (CB21/13/00091), Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación and Unión Europea – NextGenerationEU, the Gilead Scholarship Program for Biomedical Research (GLD19_00106) and the ISCIII- Miguel Servet CP19CIII—00002 contract.S

Humoral and cellular immunity to SARS-COV-2 after vaccination with mRNA vaccines in PLWH with discordant immune response. Influence of the vaccine administered

Background: Data on SARS-CoV-2 mRNA vaccine immunogenicity in people living with human immunodeficiency virus (PLWH) and discordant immune response (DIR) are currently limited. Therefore, we compare the immunogenicity of these vaccines in DIR and immunological responders (IR). Methods: A prospective cohort that enrolled 89 participants. Finally, 22 IR and 24 DIR were analyzed before vaccination (T), one (T) and six months (T) after receiving BNT162b2 or mRNA-1273 vaccine. Additionally, 10 IR and 16 DIR were evaluated after a third dose (T). Anti-S-RBD IgG, neutralizing antibodies (nAb), neutralization activity, and specific memory B cells were quantified. Furthermore, specific CD4 and CD8 responses were determined by intracellular cytokine staining and polyfunctionality indexes (Pindex). Results: At T, all participants developed anti-S-RBD. 100% IR developed nAb compared to 83.3% DIR. Spike-specific B cells were detected in all IR and 21/24 DIR. Memory CD4 T cells responded in 5/9 IR and 7/9 DIR, mainly based on the expression of IFN-γ and TNF-α, with a higher Pindex in DIR. Memory CD8 T cells responded in only four participants in each group. At T, anti-S-RBD and nAb titers were higher in DIR than in IR. In both groups, there was an increase in specific B memory cells, higher in DIR. Six IR and five DIR maintained a specific memory CD4 response. Memory CD8 response was preserved in IR but was lost in DIR. In a multivariate linear regression analysis, receiving mRNA-1273 instead of BNT162b2 played a prominent role in the results. Conclusions: Our data suggest that PLWH with DIR can mount an immune response similar to those with higher CD4, provided they receive the mRNA-1273 vaccine instead of others less immunogenic.In collaboration with the Gilead Biomedical Research Grants Program GLD21_00096. In addition, this work was supported by Instituto de Salud Carlos III, co-financed by the European Regional Development Fund “a way to make Europe” through the Program Miguel Servet to AG-V (CP19/00159), PFIS contract to AS-A (FI21/ 00165) and EM-M (FI19/00304) and programa Rio Hortega to MM-T (CM21/00115). Consejerı́a de Transformación Económica, Industria, Conocimiento y Universidades, Junta de Andalucı́a, grant P20_00906

Empirical leucine-to-carbon conversion factors for estimating heterothrophic bacterial production in surface waters of the world oceans

Comunicación oralBacterial biomass production is a key parameter for evaluating the role of bacterioplankton in ocean carbon cycling. However, bacterial production cannot be directly measured and is typically estimated from the incorporation rates of radiolabelled leucine. The conversion of leucine uptake rates into bacterial carbon production rates requires the use of conversion factors (CFs) which must be empirically determined. Despite the empirical leucine-to-carbon CFs vary widely across environments very little is known about its potential controlling factors. We conducted a set of 10 surface seawater cultures experiments where the growth of the natural bacterial assemblage was promoted by filtration (removal of grazers) or by both filtration and dilution. Sampling stations were located between 30 ºN and 30 ºS, including the Atlantic, Pacific and Indian oceans. CFs varied from 0.13 to 1.47 Kg C mol Leu-1, being higher in the filtrated than in the filtrated and diluted treatment. The abundance of picocyanobacteria explained 60% of the observed variability. Our results further suggest that the composition of bacterioplankton, as assessed by ARISA fingerprinting, may partially explain the observed variation in CFs

Deprescribing tool for STOPPFall (screening tool of older persons prescriptions in older adults with high fall risk) items

Background: Health care professionals are often reluctant to deprescribe fall-risk-increasing drugs (FRIDs). Lack of knowledge and skills form a significant barrier. To support clinicians in the management of FRIDs and to facilitate the deprescribing process, a deprescribing tool was developed by a European expert group for STOPPFall (Screening Tool of Older Persons Prescriptions in older adults with high fall risk) items. Methods: STOPPFall was created using an expert Delphi consensus process in 2019 and in 2020, 24 panellists from EuGMS SIG on Pharmacology and Task and Finish on FRIDs completed deprescribing tool questionnaire. To develop the questionnaire, a Medline literature search was performed. The panellists were asked to indicate for every medication class a possible need for stepwise withdrawal and strategy for withdrawal. They were asked in which situations withdrawal should be performed. Furthermore, panellists were requested to indicate those symptoms patients should be monitored for after deprescribing and a possible need for follow-ups. Results: Practical deprescribing guidance was developed for STOPPFall medication classes. For each medication class, a decision tree algorithm was developed including steps from medication review to symptom monitoring after medication withdrawal. Conclusion: STOPPFall was combined with a practical deprescribing tool designed to optimize medication review. This practical guide can help overcome current reluctance towards deprescribing in clinical practice by providing an up-to-date and straightforward source of expert knowledge