Integrating differential expression, co-expression and gene network analysis for the identification of common genes associated with tumor angiogenesis deregulation

Angiogenesis is essential for tumor growth and cancer metastasis. Identifying the molecular pathways involved in this process is the first step in the rational design of new therapeutic strategies to improve cancer treatment. In recent years, RNA-seq data analysis has helped to determine the genetic and molecular factors associated with different types of cancer. In this work we performed integrative analysis using RNA-seq data from human umbilical vein endothelial cells (HUVEC) and patients with angiogenesis-dependent diseases to find genes that serve as potential candidates to improve the prognosis of tumor angiogenesis deregulation and understand how this process is orchestrated at the genetic and molecular level. We downloaded four RNA-seq datasets (including cellular models of tumor angiogenesis and ischaemic heart disease) from the Sequence Read Archive. Our integrative analysis includes a first step to determine differentially and co-expressed genes. For this, we used the ExpHunter Suite, an R package that performs differential expression, co-expression and functional analysis of RNA-seq data. We used both differentially and co-expressed genes to explore the human gene interaction network and determine which genes were found in the different datasets that may be key for the angiogenesis deregulation. Finally, we performed drug repositioning analysis to find potential targets related to angiogenesis inhibition...This work was supported by the Spanish Ministry of Science, Innovation and Universities (grant PID2019-105010RB-I00, grant PID2019-108096RB-C21), the Andalusian Government and FEDER (grants UMA18-FEDERJA-102, UMA18-FEDERJA-220, PY20_00257, PY20_00372, RH-0079-2021 and funds from the group PAIDI BIO 267); the Spanish Ministry of Economy and Competitiveness (grant PID2019-108096RB-C21), the Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, ‘‘A way to make Europe"); and the European Union (HORIZON-HLTH-2022-DISEASE-06, Project ID: 101080580) to JAGR. JRP holds a research grant from the Andalusian Government (Fundacion Progreso y Salud) [PI-0075-2017]. BM is awarded of the Ayudas para la formación del profesorado universitario (FPU18/00755, Ministerio de Universidades). The ‘‘CIBER de Enfermedades Raras’’ is an initiative from the ISCIII (Spain). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. Funding for open access charge: Universidad de Málaga / CBU

El profesorado tiene la palabra. Anexo II de "Resolviendo conflictos en el aula". Entrevistas

Las entrevistas que publicamos representan parte de la información recogida por las autoras en el contexto del estudio exploratorio que realizaron sobre los conflictos en el aula y la manera en que el profesorado intenta resolverlos. En este caso se entrevistó a los profesores de los grupos que estudiaron: al maestro de 5º de E. Primaria y a la maestra de 3º de E. Infantil de dos Centros públicos de Córdoba. Por el interés que tienen las opiniones plasmadas en ambas entrevistas para las personas que trabajamos en el campo de la educación, decidimos publicarlas junto al Informe

¿Qué hace el profesorado?. Anexo I de "Resolviendo conflictos en el aula". Registros diarios

A continuación incluimos algunos retazos de los registros diarios que el grupo de investigadoras realizaron durante dos jornadas: en la clase de tercer nivel del 2º Ciclo de infantil de un colegio de clase media y en la clase de 5º curso de Educación Primaria de otro colegio de clase media de Córdoba. El diario se centró exclusivamente en los conflictos que sucedían en cada una de las aulas y la manera en que el profesor/a los afronta

Resolviendo conflictos en el aula

Presentamos un estudio exploratorio sobre los conflictos que se producen en aulas de Infantil y Primaria de dos centros publicas de Córdoba las estrategias que aplican una profesora y un profesor para resolverlos. A través de registros de observación en clase y entrevistas con ambos profesores. Las autoras perfilan un boceto de los sucesos cotidianos en un aula, parecidos a los que suceden en otras muchas, y nos permiten conocer las preocupaciones. problemas, ideas y valores de maestros/as que se esfuer.mn. de diferentes formas, en avanzar en la difícil tarea de educar en la convivencia ¡a pesar de todas las dificultades! Por su interés, incluimos como Anexos parte de los registros diarios realizados y los entrevistas

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae.

Senegalese sole is an economically important flatfish species in aquaculture and an attractive model to decipher the molecular mechanisms governing the severe transformations occurring during metamorphosis, where retinoic acid seems to play a key role in tissue remodeling. In this study, a robust sole transcriptome was envisaged by reducing the number of assembled libraries (27 out of 111 available), fine-tuning a new automated and reproducible set of workflows for de novo assembling based on several assemblers, and removing low confidence transcripts after mapping onto a sole female genome draft. From a total of 96 resulting assemblies, two "raw" transcriptomes, one containing only Illumina reads and another with Illumina and GS-FLX reads, were selected to provide SOLSEv5.0, the most informative transcriptome with low redundancy and devoid of most single-exon transcripts. It included both Illumina and GS-FLX reads and consisted of 51,348 transcripts of which 22,684 code for 17,429 different proteins described in databases, where 9527 were predicted as complete proteins. SOLSEv5.0 was used as reference for the study of retinoic acid (RA) signalling in sole larvae using drug treatments (DEAB, a RA synthesis blocker, and TTNPB, a RA-receptor agonist) for 24 and 48 h. Differential expression and functional interpretation were facilitated by an updated version of DEGenes Hunter. Acute exposure of both drugs triggered an intense, specific and transient response at 24 h but with hardly observable differences after 48 h at least in the DEAB treatments. Activation of RA signalling by TTNPB specifically increased the expression of genes in pathways related to RA degradation, retinol storage, carotenoid metabolism, homeostatic response and visual cycle, and also modified the expression of transcripts related to morphogenesis and collagen fibril organisation. In contrast, DEAB mainly decreased genes related to retinal production, impairing phototransduction signalling in the retina. A total of 755 transcripts mainly related to lipid metabolism, lipid transport and lipid homeostasis were altered in response to both treatments, indicating non-specific drug responses associated with intestinal absorption. These results indicate that a new assembling and transcript sieving were both necessary to provide a reliable transcriptome to identify the many aspects of RA action during sole development that are of relevance for sole aquaculture

Symbolic Recurrence Analysis of RR Interval to Detect Atrial Fibrillation

Atrial fibrillation (AF) is a sustained cardiac arrhythmia associated with stroke, heart failure, and related health conditions. Though easily diagnosed upon presentation in a clinical setting, the transient and/or intermittent emergence of AF episodes present diagnostic and clinical monitoring challenges that would ideally be met with automated ambulatory monitoring and detection. Current approaches to address these needs, commonly available both in smartphone applications and dedicated technologies, combine electrocardiogram (ECG) sensors with predictive algorithms to detect AF. These methods typically require extensive preprocessing, preliminary signal analysis, and the integration of a wide and complex array of features for the detection of AF events, and are consequently vulnerable to over-fitting. In this paper, we introduce the application of symbolic recurrence quantification analysis (SRQA) for the study of ECG signals and detection of AF events, which requires minimal pre-processing and allows the construction of highly accurate predictive algorithms from relatively few features. In addition, this approach is robust against commonly-encountered signal processing challenges that are expected in ambulatory monitoring contexts, including noisy and non-stationary data. We demonstrate the application of this method to yield a highly accurate predictive algorithm, which at optimal threshold values is 97.9% sensitive, 97.6% specific, and 97.7% accurate in classifying AF signals. To confirm the robust generalizability of this approach, we further evaluated its performance in the implementation of a 10-fold cross-validation paradigm, yielding 97.4% accuracy. In sum, these findings emphasize the robust utility of SRQA for the analysis of ECG signals and detection of AF. To the best of our knowledge, the proposed model is the first to incorporate symbolic analysis for AF beat detection.This research was funded by projects AIM, ref. TEC2016-76465-C2-1-R (AEI/FEDER, UE), e-DIVITA, ref.20509/PDC/18 (Proof of Concept, 2018) and it is the result of the activity performed under the program Groups of Excellence of the Region of Murcia (Spain), the Fundación Séneca, Science and Technology Agency of the region of Murcia project under grant 19884/GERM/15 and ATENTO, ref. 20889/PI/18. All remaining errors are our responsibility

Multimorbidity Patterns and Their Association with Social Determinants, Mental and Physical Health during the COVID-19 Pandemic

Background: The challenge posed by multimorbidity makes it necessary to look at new forms of prevention, a fact that has become heightened in the context of the pandemic. We designed a questionnaire to detect multimorbidity patterns in people over 50 and to associate these patterns with mental and physical health, COVID-19, and possible social inequalities. Methods: This was an observational study conducted through a telephone interview. The sample size was 1592 individuals with multimorbidity. We use Latent Class Analysis to detect patterns and SF-12 scale to measure mental and physical quality-of-life health. We introduced the two dimensions of health and other social determinants in a multinomial regression model. Results: We obtained a model with five patterns (entropy = 0.727): ‘Relative Healthy’, ‘Cardiometabolic’, ‘Musculoskeletal’, ‘Musculoskeletal and Mental’, and ‘Complex Multimorbidity’. We found some differences in mental and physical health among patterns and COVID-19 diagnoses, and some social determinants were significant in the multinomial regression. Conclusions: We identified that prevention requires the location of certain inequalities associated with the multimorbidity patterns and how physical and mental health have been affected not only by the patterns but also by COVID-19. These findings may be critical in future interventions by health services and governments17 página

Clinical and pathological characteristics of peripheral T-cell lymphomas in a Spanish population: a retrospective study

We investigated the clinicopathological features and prognostic factors of patients with peripheral T-cell lymphoma (PTCL) in 13 sites across Spain. Relevant clinical antecedents, CD30 expression and staining pattern, prognostic indices using the International Prognostic Index and the Intergruppo Italiano Linfomi system, treatments, and clinical outcomes were examined. A sizeable proportion of 175 patients had a history of immune-related disorders (autoimmune 16%, viral infections 17%, chemo/radiotherapy-treated carcinomas 19%). The median progression-free survival (PFS) and overall survival (OS) were 7·9 and 15·8 months, respectively. Prognostic indices influenced PFS and OS, with a higher number of adverse factors resulting in shorter survival (P 15% of cells were positive in anaplastic lymphoma kinase-positive and -negative anaplastic large-cell lymphoma and extranodal natural killer PTCL groups. We observed PTCL distribution across subtypes based on haematopathological re-evaluation. Poor prognosis, effect of specific prognostic indices, relevance of histopathological sub-classification, and response level to first-line treatment on outcomes were confirmed. Immune disorders amongst patients require further examination involving genetic studies and identification of associated immunosuppressive factors.This study was sponsored by Takeda

Predictive Power of the "Trigger Tool" for the detection of adverse events in general surgery: a multicenter observational validation study

Background In spite of the global implementation of standardized surgical safety checklists and evidence-based practices, general surgery remains associated with a high residual risk of preventable perioperative complications and adverse events. This study was designed to validate the hypothesis that a new “Trigger Tool” represents a sensitive predictor of adverse events in general surgery. Methods An observational multicenter validation study was performed among 31 hospitals in Spain. The previously described “Trigger Tool” based on 40 specific triggers was applied to validate the predictive power of predicting adverse events in the perioperative care of surgical patients. A prediction model was used by means of a binary logistic regression analysis. Results The prevalence of adverse events among a total of 1,132 surgical cases included in this study was 31.53%. The “Trigger Tool” had a sensitivity and specificity of 86.27% and 79.55% respectively for predicting these adverse events. A total of 12 selected triggers of overall 40 triggers were identified for optimizing the predictive power of the “Trigger Tool”. Conclusions The “Trigger Tool” has a high predictive capacity for predicting adverse events in surgical procedures. We recommend a revision of the original 40 triggers to 12 selected triggers to optimize the predictive power of this tool, which will have to be validated in future studies