Comparative Stem Transcriptome Analysis Reveals Pathways Associated with Drought Tolerance in Maritime Pine Grafts.

The maritime pine (Pinus pinaster Ait.) is a highly valuable Mediterranean conifer. However, recurrent drought events threaten its propagation and conservation. P. pinaster populations exhibit remarkable differences in drought tolerance. To explore these differences, we analyzed stem transcriptional profiles of grafts combining genotypes with contrasting drought responses under well-watered and water-stress regimes. Our analysis underscored that P. pinaster drought tolerance is mainly associated with constitutively expressed genes, which vary based on genotype provenance. However, we identified key genes encoding proteins involved in water stress response, abscisic acid signaling, and growth control including a PHD chromatin regulator, a histone deubiquitinase, the ABI5-binding protein 3, and transcription factors from Myb-related, DOF NAC and LHY families. Additionally, we identified that drought-tolerant rootstock could enhance the drought tolerance of sensitive scions by regulating the accumulation of transcripts involved in carbon mobilization, osmolyte biosynthesis, flavonoid and terpenoid metabolism, and reactive oxygen species scavenging. These included genes encoding galactinol synthase, CBL-interacting serine/threonine protein kinase 5, BEL1-like homeodomain protein, dihydroflavonol 4-reductase, and 1-deoxy-D-xylulose-5-phosphate. Our results revealed several hub genes that could help us to understand the molecular and physiological response to drought of conifers. Based on all the above, grafting with selected drought-tolerant rootstocks is a promising method for propagating elite recalcitrant conifer species, such as P. pinaster.

Cancer characteristics in patients with schizophrenia: a 25-year retrospective analysis.

Schizophrenia is associated with higher cancer-related mortality, perhaps due to delayed diagnosis and limited access to treatment. The study aimed to compare patients diagnosed with cancer with and without schizophrenia to determine whether these groups differ in terms of oncological variables and survival outcomes. This was a retrospective, observational cohort study that included 30.990 patients diagnosed with cancer between 1997 and 2021. We performed univariate and bivariate analyses for the sociodemographic and clinical variables, and constructed Kaplan-Meier survival curves and used the log-rank test to perform the comparisons. All variables were compared for each cancer type. One hundred and sixty-two (0.52 %) patients had a confirmed diagnosis of schizophrenia (ICD-9 criteria). The mean age at diagnosis was significantly lower in the schizophrenia group. A significantly higher proportion of the schizophrenia group was diagnosed with cancer through the emergency department and a lower percentage through scheduled appointments. A smaller percentage of patients in the schizophrenia group received radical treatment for cancer. The mortality rate was higher in the schizophrenia group and median survival was lower. These findings suggest that cancer patients with schizophrenia have worse outcomes than patients without schizophrenia in terms of oncological variables and survival.

The effectiveness, cost-effectiveness and policy processes of regulatory, voluntary and partnership policies to improve food environments: an evidence synthesis.

Background: Dietary factors are among the largest and costliest drivers of chronic diseases in England. As a response, the government implements a range of population interventions to promote healthy diets by targeting food environments. Objectives: This study aimed to conduct a systematic review of the effectiveness, cost-effectiveness and policy process of real-world evaluations of national and state policies on improving food environments, with a focus on whether they were regulatory, voluntary or partnership approaches. Data sources: Fourteen relevant English-language databases were searched in November 2020 for studies published between 2010 and 2020. Methods: Six separate evidence reviews were conducted to assess the evidence of effectiveness, cost-effectiveness and policy processes of policies to improve food environments. Results: A total of 483 primary research evaluations and 14 evidence syntheses were included. The study reveals considerable geographic, methodological and other imbalances across the literature, with, for example, 81% of publications focusing only on 12 countries. The systematic reviews also reveal the effectiveness and cost-effectiveness of reviewed regulatory approaches designed to improve health, consumer behaviour and food environment outcomes while public-private partnerships and voluntary approaches to improve diets via reformulation, advertising and promotion restrictions or other changes to the environment were limited in their effectiveness and cost-effectiveness. The study also revealed key enabling and impeding factors across regulatory, voluntary and public-private partnership approaches. Conclusion: From the available evidence reviewed, this study finds that regulatory approaches appear most effective at improving the food environment, and voluntary agreements and partnerships have limited effectiveness. These findings should be carefully considered in future public health policy development, as should the findings of geographic imbalance in the evidence and inadequate representation of equity dimensions across the policy evaluations. We find that food policies are at times driven by factors other than the evidence and shaped by compromise and pragmatism. Food policy should be first and foremost designed and driven by the evidence of greatest effectiveness to improve food environments for healthier diets. Limitations: This was a complex evidence synthesis due to its scope and some policy evaluations may have been missed as the literature searches did not include specific policy names. The literature was limited to studies published in English from 2010 to 2020, potentially missing studies of interest. Future work: Priorities include the need for guidance for appraising risk of bias and quality of non-clinical studies, for reporting policy characteristics in evaluations, for supporting evaluations of real-world policies equitably across geographic regions, for capturing equity dimensions in policy evaluations, and for guideline development for quality and risk of bias of policy evaluations. Study registration: This study is registered as PROSPERO CRD42020170963. Funding: This award project was funded by the National Institute for Health and Care Research (NIHR) Public Health Research programme (NIHR award ref: NIHR128607) and is published in full in Public Health Research; Vol. 12, No. 8. See the NIHR Funding and Awards website for further award information.

Poor diet is a leading cause of death, globally, including in the United Kingdom. It also causes many types of illness and is one of the biggest drains on the United Kingdom National Health Service budget. Governments act in various ways to promote healthy diets by improving food environments: these are the physical and social surroundings that influence what and how much people eat. Some actions are regulated by government, for example, to control food production, marketing and promotions. Other actions are led by, or with, food businesses, making voluntary changes to the foods they produce, for example, by reducing salt content; this can be done by businesses alone or in partnership with government (referred to as 'public­private partnerships'). The six reviews of published research look at whether, and how, these actions to improve diets work, and whether they can provide value for money. Most regulations appear to be effective at supporting better diets. However, voluntary changes led by businesses had limited success. There were not many evaluations that assessed the effectiveness of public­private partnerships. Of those that did, partnerships with the food industry had limited effectiveness, resulting in largely unchanged outcomes. When looking at how these actions improve diets, we found that clear leadership, public support for the policy, the use of the best evidence and of local expertise helped with getting actions implemented. Factors that appear to make it harder to implement policy actions include a lack of evidence specific to the context, conflicting beliefs about what works, limited human or financial resources, lack of engagement by key people. Although the findings may help us to think about the ways forward to improve diets, more research is needed to understand whether actions to reduce diet-related ill health work, and provide value for money.

ctDNA dynamics and mechanisms of acquired resistance in patients treated with osimertinib with or without bevacizumab from the randomised phase II ETOP-BOOSTER trial.

BACKGROUND: ETOP 10-16 BOOSTER study was a randomised phase II trial of osimertinib and bevacizumab versus osimertinib in patients with an acquired EGFR T790M mutation. The mechanisms of acquired resistance to osimertinib and bevacizumab have not been described previously. METHODS: Next generation sequencing (Guardant360®) was conducted in serial plasma samples. The association between ctDNA and efficacy outcomes was explored and molecular alterations at progression were described. RESULTS: 136 patients (88% of 155 randomised) had plasma samples at baseline (68 per arm), 110 (71%) at week 9 and 65 (42%) at progression. In a multivariable model for progression-free survival (PFS), the treatment effect was found different by smoking status (interaction p=0.046), with the effect of smoking also different by baseline EGFR T790M (interaction p=0.033), while both TP53 at baseline and tissue EGFR Exon 21 L858R mutation were significantly associated with worse PFS outcome. Smokers (current/former) without baseline EGFR T790M showed a significant improvement in PFS under combination treatment, albeit with small numbers (p=0.015). Week-9 EGFR T790M clearance was associated with improved PFS in the osimertinib arm (p=0.0097). Acquired EGFR C797S mutations were detected in 22% and 13% of patients in the combination and osimertinib arm, respectively. CONCLUSIONS: The differential effect of treatment by smoking was not explained by TP53 mutation or other molecular alterations examined. Molecular mechanisms of acquired resistance were detected but no novel molecular alterations were identified in the combination arm.

Prognostic impact of tumor location and gene expression profile in sporadic desmoid tumor.

PURPOSE: Prognostic biomarkers remain necessary in sporadic desmoid tumor (DT) because the clinical course is unpredictable. DT location along with gene expression between thoracic and abdominal wall locations was analyzed. METHOD: Sporadic DT patients (GEIS Registry) diagnosed between 1982 and 2018 who underwent upfront surgery were enrolled retrospectively in this study. The primary endpoint was relapse-free survival (RFS). Additionally, the gene expression profile was analyzed in DT localized in the thoracic or abdominal wall, harboring the most frequent CTNNB1 T41A mutation. RESULTS: From a total of 454 DT patients, 197 patients with sporadic DT were selected. The median age was 38.2 years (1.8-89.1) with a male/female distribution of 33.5/66.5. Most of them harbored the CTNNB1 T41A mutation (71.6 %), followed by S45F (17.8 %) and S45P (4.1 %). A significant worse median RFS was associated with males (p = 0.019), tumor size ≥ 6 cm (p = 0.001), extra-abdominal DT location (p < 0.001) and the presence of CTNNB1 S45F mutation (p = 0.013). In the multivariate analysis, extra-abdominal DT location, CTNNB1 S45F mutation and tumor size were independent prognostic biomarkers for worse RFS. DTs harboring the CTNNB1 T41A mutation showed overexpression of DUSP1, SOCS1, EGR1, FOS, LIF, MYC, SGK1, SLC2A3, and IER3, and underexpression of BMP4, PMS2, HOXA9, and WISP1 in thoracic versus abdominal wall locations. CONCLUSION: Sporadic DT location exhibits a different prognosis in terms of RFS favoring the abdominal wall compared to extra-abdominal sites. A differential gene expression profile under the same CTNNB1 T41A mutation is observed in the abdominal wall versus the thoracic wall, mainly affecting the Wnt/ß-catenin, TGFß, IFN, and TNF pathways.

Maritime Pine Rootstock Genotype Modulates Gene Expression Associated with Stress Tolerance in Grafted Stems.

Climate change-induced hazards, such as drought, threaten forest resilience, particularly in vulnerable regions such as the Mediterranean Basin. Maritime pine (Pinus pinaster Aiton), a model species in Western Europe, plays a crucial role in the Mediterranean forest due to its genetic diversity and ecological plasticity. This study characterizes transcriptional profiles of scion and rootstock stems of four P. pinaster graft combinations grown under well-watered conditions. Our grafting scheme combined drought-sensitive and drought-tolerant genotypes for scions (GAL1056: drought-sensitive scion; and Oria6: drought-tolerant scion) and rootstocks (R1S: drought-sensitive rootstock; and R18T: drought-tolerant rootstock). Transcriptomic analysis revealed expression patterns shaped by genotype provenance and graft combination. The accumulation of differentially expressed genes (DEGs) encoding proteins, involved in defense mechanisms and pathogen recognition, was higher in drought-sensitive scion stems and also increased when grafted onto drought-sensitive rootstocks. DEGs involved in drought tolerance mechanisms were identified in drought-tolerant genotypes as well as in drought-sensitive scions grafted onto drought-tolerant rootstocks, suggesting their establishment prior to drought. These mechanisms were associated with ABA metabolism and signaling. They were also involved in the activation of the ROS-scavenging pathways, which included the regulation of flavonoid and terpenoid metabolisms. Our results reveal DEGs potentially associated with the conifer response to drought and point out differences in drought tolerance strategies. These findings suggest genetic trade-offs between pine growth and defense, which could be relevant in selecting more drought-tolerant Pinus pinaster trees.

Advanced non-squamous NSCLC with no actionable oncogenic driver in Spain: a cross-sectional descriptive analysis of data from the Thoracic Tumor Registry.

BACKGROUND: Non-small cell lung cancer (NSCLC) accounts for the vast majority of all diagnosed lung cancers. According to their histology, most NSCLCs are considered non-squamous cell carcinoma (NSCC), and up to 85% of the latter may lack either one of the two main actionable oncogenic drivers (i.e., EGFR mutations and ALK rearrangements). OBJECTIVE: Our analysis aimed to describe the clinical and epidemiological characteristics of Spanish patients suffering from NSCC with no actionable oncogenic driver in daily clinical practice. DESIGN: A retrospective, cross-sectional, descriptive analysis. METHODS: We analyzed the records of all Spanish patients with advanced NSCC diagnosed between January 2011 and January 2020 and included in the Spanish Thoracic Tumor Registry database. We evaluated the presence of metastasis and molecular profiling at the time of diagnosis and treatments received. We also assessed overall survival (OS) and progression-free survival (PFS) according to first-line treatment. RESULTS: One thousand seven hundred ninety-seven Spanish patients with NSCC were included. They were mainly men (73.2%), smokers (current [44.4%] and former [44.4%]) and presented adenocarcinoma histology (97.6%). Most patients had at least one comorbidity (80.4%) and one metastatic site (96.8%), and a non-negligible number of those tested were PD-L1 positive (35.2%). Notably, the presence of liver metastasis indicated a shorter median OS and PFS than metastasis in other locations (p < 0.001). Chemotherapy was more often prescribed than immunotherapy as first-, second-, and third-line treatment in that period. In first-line, the OS rates were similar in patients receiving either regimen, but PFS rates significantly better in patients treated with immunotherapy (p = 0.026). Also, a high number of patients did not reach second- and third-line treatment, suggesting the failure of current early diagnostic measures and therapies. CONCLUSIONS: This analysis of the most lethal tumor in Spain could highlight the strengths and the weaknesses of its clinical management and set the ground for further advances and research.

Vaccinated COVID-19 Index Cases Are Less Likely to Transmit SARS-CoV-2 to Their Household Contacts: A Cohort Study.

The aim of this study was to evaluate the impact of index case vaccination on SARS-CoV-2 transmission to household contacts. In our epidemiological cohort study (May 2022-November 2023), we surveyed registered index case vaccination status and test results for contacts (testing on day 0, and on day 7 for negative contacts) and calculated the secondary attack rate (SAR), i.e., newly infected contacts/susceptible included contacts. The association of the independent variable, index case COVID-19 vaccination (yes/no), with household contact infection was determined using the adjusted odds ratio (aOR) and its 95% confidence interval (CI). We recorded 181 index cases and 314 contacts, of whom 250 agreed to participate; 16 contacts were excluded upon testing positive on day 0. Of the 234 included contacts, 49.1% were women, and the mean (SD) age was 51.9 (19.8) years. The overall SAR of 37.2% (87/234) was lower in the contacts of both vaccinated index cases (34.9% vs. 63.2%; p = 0.014) and index cases with a previous SARS-CoV-2 infection history (27.0% vs. 46.3%; p = 0.002). Index case vaccination showed a protective effect against infection for their household contacts (aOR = 0.21; 95% CI: 0.07, 0.67). The household SAR was high when the Omicron variant circulated. Vaccinated index cases were less likely to transmit SARS-CoV-2 to their contacts.

Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition.

The Ocean microbiome has a crucial role in Earth's biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2-3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome.

Exploring long-term breast cancer survivors' care trajectories using dynamic time warping-based unsupervised clustering.

OBJECTIVES: Long-term breast cancer survivors (BCS) constitute a complex group of patients, whose number is estimated to continue rising, such that, a dedicated long-term clinical follow-up is necessary. MATERIALS AND METHODS: A dynamic time warping-based unsupervised clustering methodology is presented in this article for the identification of temporal patterns in the care trajectories of 6214 female BCS of a large longitudinal retrospective cohort of Spain. The extracted care-transition patterns are graphically represented using directed network diagrams with aggregated patient and time information. A control group consisting of 12 412 females without breast cancer is also used for comparison. RESULTS: The use of radiology and hospital admission are explored as patterns of special interest. In the generated networks, a more intense and complex use of certain healthcare services (eg, radiology, outpatient care, hospital admission) is shown and quantified for the BCS. Higher mortality rates and numbers of comorbidities are observed in various transitions and compared with non-breast cancer. It is also demonstrated how a wealth of patient and time information can be revealed from individual service transitions. DISCUSSION: The presented methodology permits the identification and descriptive visualization of temporal patterns of the usage of healthcare services by the BCS, that otherwise would remain hidden in the trajectories. CONCLUSION: The results could provide the basis for better understanding the BCS' circulation through the health system, with a view to more efficiently predicting their forthcoming needs and thus designing more effective personalized survivorship care plans.

Effect of comorbidity and multimorbidity on adherence to follow-up recommendations among long-term breast cancer survivors.

OBJECTIVES: To study the impact of comorbidities, multimorbidity, and multimorbidity clusters on adherence to recommended follow-up guidelines among long-term breast cancer survivors. STUDY DESIGN: Retrospective cohort study based on 2078 women diagnosed with breast cancer from 2000 to 2006 and followed up from 2012 to 2016. MAIN OUTCOME MEASURES: Adherence to breast cancer follow-up recommendations (annual medical visit and imaging) was determined. Comorbidities were classified as acute/chronic. Multimorbidity was defined as the presence of two or more chronic comorbidities aside from breast cancer. Five multimorbidity clusters were considered. Multivariate logistic regression models were fitted to determine the relationship between adherence to recommendations and the presence of comorbidities and multimorbidity, considering both sociodemographic and clinical characteristics. RESULTS: Overall adherence to recommendations was 79.5 %. Adherence was lower among long-term breast cancer survivors with no comorbidities (75.8 %). Among multimorbidity clusters, adherence was highest in the anxiety and fractures cluster (84.3 %) and was lowest in the musculoskeletal and cardiovascular cluster (76.4 %). In adjusted multivariate models, multimorbidity was associated with higher levels of adherence (OR = 1.52 95 %CI 1.16-1.99), and adherence was highest in the metabolic and degenerative cluster (OR = 2.2 95 %CI 1.4-3.5). CONCLUSION: Adherence to follow-up recommendations was higher among long-term breast cancer survivors with multimorbidity than among those without. Adherence also differed by multimorbidity cluster. These results suggest suboptimal adherence to the current follow-up recommendations in certain groups, suggesting the need to adapt clinical practice guidelines to reflect patients' comorbidities and different characteristics.

Evaluación de la estabilidad de parámetros hematológicos en muestras pediátricas bajo diferentes condiciones de almacenamiento determinados en un analizador Sysmex XN / Stability of hematological parameters in pediatric samples under different storage conditions using the Sysmex XN analyser / Avaliação de estabilidade de parâmetros hematológicos em amostras pediátricas sob diferentes condições de armazenamento determinados em um analisador Sysmex XN

Resumen Conocer la estabilidad de las muestras biológicas es esencial para obtener resultados confiables en el laboratorio de análisis clínicos. La Norma IRAM-ISO 15189:2023 establece que cada laboratorio debe estandarizar las condiciones de almacenamiento de las muestras. El objetivo de este trabajo fue determinar el tiempo y la temperatura óptimos para conservar muestras sanguíneas para la determinación de parámetros hematológicos en un analizador Sysmex XN 1000. Se procesaron muestras de sangre entera conservadas hasta 48 horas a temperatura ambiente y hasta 72 horas en heladera. De acuerdo a los resultados, para la determinación del hemograma, las muestras almacenadas a temperatura ambiente deben procesarse dentro de las 6-8 horas posextracción; los parámetros limitantes son aquellos influenciados por cambios en el volumen eritrocitario. En las muestras conservadas en heladera el análisis puede retrasarse hasta 48 horas y el recuento de plaquetas es el parámetro menos estable.

Abstract Knowing sample stability is essential to obtain reliable results in the clinical laboratory. The IRAM-ISO 15189:2023 Standard establishes that each laboratory must standardise the storage conditions of biological samples. This study was conducted to investigate the stability of haematological parameters using a Sysmex XN 1000 in samples stored for up to 48-72 hours at different temperatures. According to these results, the hematologic analytes should be processed in this laboratory within 6-8 hours after extraction if they are stored at room temperature. The limiting parameters are those influenced by changes in the erythrocyte volume. If storage is in a refrigerator, the analysis can be delayed up to 48 hours, being platelet count the limiting parameter.

Resumo Conhecer a estabilidade das amostras biológicas é essencial para obter resultados confiáveis no laboratório de exames clínicas. A Norma IRAM-ISO 15189:2023 estabelece que cada laboratório deve padronizar as condições de armazenamento das amostras. O objetivo deste trabalho foi determinar o tempo e a temperatura ideais para preservar amostras de sangue para a determinação de parâmetros hematológicos em um analisador em um Sysmex XN 1000. Para isso, foram processadas amostras de sangue total armazenadas por até 48 horas em temperatura ambiente e por até 72 horas em geladeira. De acordo com os resultados obtidos, para a determinação do hemograma, as amostras armazenadas em temperatura ambiente devem ser processadas dentro de 6-8 horas após a extração, sendo os parâmetros limitantes aqueles influenciados por alterações no volume eritrocitário. Nas amostras armazenadas em geladeira, a análise pode demorar até 48 horas, sendo a contagem de plaquetas o parâmetro menos estável.

SEOM-GEIS clinical guideline for gastrointestinal stromal tumors (2022)

Gastrointestinal stromal tumor (GIST) is the most common malignant neoplasm of mesenchymal origin, and a paradigmatic model for a successful rational development of targeted therapies in cancer. The introduction of tyrosine kinase inhibitors with activity against KIT/PDGFRA in both localized and advanced stages has remarkably improved the survival in a disease formerly deemed resistant to all systemic therapies. These guidelines are elaborated by the conjoint effort of the Spanish Society of Medical Oncology (SEOM) and the Spanish Sarcoma Research Group (GEIS) and provide a multidisciplinary and updated consensus for the diagnosis and treatment of GIST patients. We strongly encourage that the managing of these patients should be performed within multidisciplinary teams in reference centers (AU)