Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data

Motivation: The development of the omics technologies such as transcriptomics, proteomics and metabolomics has made possible the realization of systems biology studies where biological systems are interrogated at different levels of biochemical activity (gene expression, protein activity and/or metabolite concentration). An effective approach to the analysis of these complex datasets is the joined visualization of the disparate biomolecular data on the framework of known biological pathways

Spindle cell carcinoma: Two instances mistaken for vocal polyps

Spindle cell carcinoma is a variant of squamous carcinoma, with behavior that is apparently more aggressive than that of squamous carcinoma and that can produce distant lymphatic metastasis. It was first described by Virchow in 1864 [1], but the origin of the tumor is still not clear. The tumor is biphasic, with an epidermal component and a sarcomatous component involving spindle cells; transition zones between these components can be found [2–5]. In part due to this peculiar and complex nature, the tumor has accumulated various names since it was first described: sarcomatoid tumor, carci- nosarcoma, pleomorphic carcinoma, collision tumor, etc. [2,5,6]

Computational modelling of epithelial cell monolayers during infection with Listeria monocytogenes

Intracellular bacterial infections alter the normal functionality of human host cells and tissues. Infection can also modify the mechanical properties of host cells, altering the mechanical equilibrium of tissues. In order to advance our understanding of host–pathogen interactions, simplified in vitro models are normally used. However, in vitro studies present certain limitations that can be alleviated by the use of computer-based models. As complementary tools these computational models, in conjunction with in vitro experiments, can enhance our understanding of the mechanisms of action underlying infection processes. In this work, we extend our previous computer-based model to simulate infection of epithelial cells with the intracellular bacterial pathogen Listeria monocytogenes. We found that forces generated by host cells play a regulatory role in the mechanobiological response to infection. After infection, in silico cells alter their mechanical properties in order to achieve a new mechanical equilibrium. The model pointed the key role of cell–cell and cell–extracellular matrix interactions in the mechanical competition of bacterial infection. The obtained results provide a more detailed description of cell and tissue responses to infection, and could help inform future studies focused on controlling bacterial dissemination and the outcome of infection processes. © 2022 The Author(s

Investigaciones paleobotánicas en la cuenca central del Duero

El objetivo del trabajo es dar a conocer el estado actual de conocimientos científicos sobre el pasado del paisaje vegetal (Cuaternario final) en los territorios interiores no montanos de la depresión del Duero. Se recogen todos los yacimientos cuyo estudio ya ha concluido así como los que se encuentran en fase de investigación o prospección. Se precisa el tipo de informador en cada caso (polen, carbones, maderas, otros macrorrestos), el rango cronológico conocido hasta el momento así como el grado o proporción de trabajo realizado en cada yacimiento en relación con las previsiones efectuadas. Se aporta una síntesis-resumen de los principales resultados obtenidos hasta el momento y de los aspectos más concluyentes de los mismos en relación con la elaboración de modelos de evolución del paisaje vegetal posteriores al último máximo glacial en la Meseta norte. A nuestro juicio debe destacarse, como uno de los resultados más relevantes, el conocimiento ya afianzado de que los pinares de meseta han sido el elemento más significativo en amplios sectores del sur y este de la cuenca a lo largo de todo o gran parte del Holoceno, circunstancia que contrasta con todas las propuestas de paisaje pretérito (preantrópico) existentes antes de la realización de las prospecciones paleobotánicas

Impacto psicosocial en adultos con dermatitis atópica: estudio cualitativo

Antecedentes y objetivo La dermatitis atópica afecta a la calidad de vida del paciente de muchas maneras. Por tanto, es importante analizar los efectos que la enfermedad produce en la vida del paciente al objeto de definir mejor las necesidades de atención de los pacientes adultos con dermatitis atópica. Pacientes y métodos Se realizaron entrevistas a 14 pacientes adultos con dermatitis atópica. Las entrevistas cualitativas fueron semiestructuradas apoyadas en un guion simple, lo que permitió una entrevista completa y flexible para un mayor nivel de profundidad y riqueza de datos. Resultados Se identificaron 6 esferas afectadas de la vida del paciente con dermatitis atópica: económica, laboral, personal, psicosocial, clínica y relacional. Se destaca que la dermatitis atópica tiene un gran impacto psicosocial en el paciente adulto, ya que altera las relaciones interpersonales, genera rechazo, estigmatización y aislamiento social, limita al paciente en diversas áreas y actividades de su vida cotidiana o altera el sueño, entre otros. Preocupan mucho el aspecto visible, el ciclo picor-rascamiento, la falta de concienciación y desconocimiento de la enfermedad, la ausencia de una solución definitiva entre los tratamientos y los efectos secundarios de algunos de ellos. Conclusiones La calidad de vida de los pacientes con dermatitis atópica se ve afectada negativamente y se hace necesaria una intervención profesional desde un abordaje multidisciplinar holístico que intente mitigar el impacto negativo de la enfermedad. Background and objective: Atopic dermatitis affects a patient''s quality of life in many ways. Analysis of the effects of this disease on the lives of adult patients is therefore important for the purpose of better defining their care needs. Patients and methods: We interviewed 14 adult patients with atopic dermatitis in this qualitative study. The interviews were semistructured according to a simple outline to allow for completeness and flexibility and afford greater depth and richness of information. Results: Atopic dermatitis affected the patients’ lives in 6 spheres of activity: economic, occupational, personal, psychosocial, clinical, and relational. A clear finding was that the disease has a considerable psychosocial effect on adult patients, altering their interpersonal relationships and leading to rejection, stigmatization, and social isolation. It limits the patient in various spheres of life and in activities of daily living, causing sleep alterations among other effects. The patients were very concerned about appearance, the itch–scratch cycle, poor understanding and lack of awareness of their disease, the absence of a definitive treatment, and the adverse effects of some treatments. Conclusions: The quality of life of adults with atopic dermatitis is negatively affected. This disease requires a professional, holistic, multidisciplinary management approach that attempts to mitigate the adverse effects

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs

Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs is a crucial problem in computational biology and includes the subtask of predicting the location of known TFBS motifs in a given DNA sequence. It has previously been shown that, when scoring matches to known TFBS motifs, interdependencies between positions within a motif should be taken into account. However, this remains a challenging task owing to the fact that sequences similar to those of known TFBSs can occur by chance with a relatively high frequency. Here we present a new method for matching sequences to TFBS motifs based on intuitionistic fuzzy sets (IFS) theory, an approach that has been shown to be particularly appropriate for tackling problems that embody a high degree of uncertainty. Results: We propose SCintuit, a new scoring method for measuring sequence-motif affinity based on IFS theory. Unlike existing methods that consider dependencies between positions, SCintuit is designed to prevent overestimation of less conserved positions of TFBSs. For a given pair of bases, SCintuit is computed not only as a function of their combined probability of occurrence, but also taking into account the individual importance of each single base at its corresponding position. We used SCintuit to identify known TFBSs in DNA sequences. Our method provides excellent results when dealing with both synthetic and real data, outperforming the sensitivity and the specificity of two existing methods in all the experiments we performed. Conclusions: The results show that SCintuit improves the prediction quality for TFs of the existing approaches without compromising sensitivity. In addition, we show how SCintuit can be successfully applied to real research problems. In this study the reliability of the IFS theory for motif discovery tasks is proven

Predictive Value of Carcinoembryonic Antigen in Symptomatic Patients without Colorectal Cancer: A Post-Hoc Analysis within the COLONPREDICT Cohort

We aimed to assess the risk of cancer in patients with abdominal symptoms after a complete colonoscopy without colorectal cancer (CRC), according to the carcinoembryonic antigen (CEA) concentration, as well as its diagnostic accuracy. For this purpose, we performed a post-hoc analysis within a cohort of 1431 patients from the COLONPREDICT study, prospectively designed to assess the fecal immunochemical test accuracy in detecting CRC. Over 36.5 +/- 8.4 months, cancer was detected in 115 (8%) patients. Patients with CEA values higher than 3 ng/mL revealed an increased risk of cancer (HR 2.0, 95% CI 1.3-3.1), CRC (HR 4.4, 95% CI 1.1-17.7) and non-gastrointestinal cancer (HR 1.7, 95% CI 1.0-2.8). A new malignancy was detected in 51 (3.6%) patients during the first year and three variables were independently associated: anemia (OR 2.8, 95% CI 1.3-5.8), rectal bleeding (OR 0.3, 95% CI 0.1-0.7) and CEA level >3 ng/mL (OR 3.4, 95% CI 1.7-7.1). However, CEA was increased only in 31.8% (95% CI, 16.4-52.7%) and 50% (95% CI, 25.4-74.6%) of patients with and without anemia, respectively, who would be diagnosed with cancer during the first year of follow-up. On the basis of this information, CEA should not be used to assist in the triage of patients presenting with lower bowel symptoms who have recently been ruled out a CRC

Efficacy of extended infusion of beta-lactam antibiotics for the treatment of febrile neutropenia in haematologic patients: protocol for a randomised, multicentre, open-label, superiority clinical trial (BEATLE)

Background: Febrile neutropaenia (FN) is a very common complication in patients with haematological malignancies and is associated with considerable morbidity and mortality. Broad-spectrum antipseudomonal beta-lactam antibiotics (BLA) are routinely used for the treatment of cancer patients with FN. However, the clinical efficacy of BLA may be diminished in these patients because they present with pathophysiological variations that compromise the pharmacokinetic (PK) parameters of these antibiotics. Optimised administration of BLA in prolonged infusions has demonstrated better clinical outcomes in critically ill patients. However, there is a paucity of data on the usefulness of this strategy in patients with FN. The aim of this study is to test the hypothesis that the administration of BLA would be clinically more effective by extended infusion (EI) than by intermittent infusion (II) in haematological patients with FN. Methods: A randomised, multicentre, open-label, superiority clinical trial will be performed. Patients with haematological malignancies undergoing chemotherapy or haematopoietic stem-cell transplant and who have FN and receive empirical antibiotic therapy with cefepime, piperacillin-tazobactam or meropenem will be randomised (1:1) to receive the antibiotic by EI (during half the time of the dosing interval) in the study group, or by II (30 min) in the control group. The primary endpoint will be clinical efficacy, defined as defervescence without modifying the antibiotic treatment administered within the first 5 days of therapy. The primary endpoint will be analysed in the intention-to-treat population. The secondary endpoints will be pharmacokinetic/pharmacodynamic (PK/PD) target achievement, bacteraemia clearance, decrease in C-reactive protein, overall (30-day) case-fatality rate, adverse events and development of a population PK model of the BLA studied. Discussion: Data on the usefulness of BLA administration in patients with FN are scant. Only three clinical studies addressing this issue have been published thus far, with contradictory results. Moreover, these studies had some methodological flaws that limit the interpretation of their findings. If this randomised, multicentre, phase IV, open-label, superiority clinical trial validates the hypothesis that the administration of BLA is clinically more effective by EI than by II in haematological patients with FN, then the daily routine management of these high-risk patients could be changed to improve their outcomes

Retrospective cohort study: Risk of gastrointestinal cancer in a symptomatic cohort after a complete colonoscopy: Role of faecal immunochemical test

BACKGROUND: Faecal immunochemical test (FIT) has been recommended to assess symptomatic patients for colorectal cancer (CRC) detection. Nevertheless, some conditions could theoretically favour blood originating in proximal areas of the gastrointestinal tract passing through the colon unmetabolized. A positive FIT result could be related to other gastrointestinal cancers (GIC). AIM: To assess the risk of GIC detection and related death in FIT-positive symptomatic patients (threshold 10 µg Hb/g faeces) without CRC. METHODS: Post hoc cohort analysis performed within two prospective diagnostic test studies evaluating the diagnostic accuracy of different FIT analytical systems for CRC and significant colonic lesion detection. Ambulatory patients with gastrointestinal symptoms referred consecutively for colonoscopy from primary and secondary healthcare, underwent a quantitative FIT before undergoing a complete colonoscopy. Patients without CRC were divided into two groups (positive and negative FIT) using the threshold of 10 µg Hb/g of faeces and data from follow-up were retrieved from electronic medical records of the public hospitals involved in the research. We determined the cumulative risk of GIC, CRC and upper GIC. Hazard rate (HR) was calculated adjusted by age, sex and presence of significant colonic lesion. RESULTS: We included 2709 patients without CRC and a complete baseline colonoscopy, 730 (26.9%) with FIT = 10 µgr Hb/gr. During a mean time of 45.5 ± 20.0 mo, a GIC was detected in 57 (2.1%) patients: An upper GIC in 35 (1.3%) and a CRC in 14 (0.5%). Thirty-six patients (1.3%) died due to GIC: 22 (0.8%) due to an upper GIC and 9 (0.3%) due to CRC. FIT-positive subjects showed a higher CRC risk (HR 3.8, 95%CI: 1.2-11.9) with no differences in GIC (HR 1.5, 95%CI: 0.8-2.7) or upper GIC risk (HR 1.0, 95%CI: 0.5-2.2). Patients with a positive FIT had only an increased risk of CRC-related death (HR 10.8, 95%CI: 2.1-57.1) and GIC-related death (HR 2.2, 95%CI: 1.1-4.3), with no differences in upper GIC-related death (HR 1.4, 95%CI: 0.6-3.3). An upper GIC was detected in 22 (0.8%) patients during the first year. Two variables were independently associated: anaemia (OR 5.6, 95%CI: 2.2-13.9) and age = 70 years (OR 2.7, 95%CI: 1.1-7.0). CONCLUSION: Symptomatic patients without CRC have a moderate risk increase in upper GIC, regardless of the FIT result. Patients with a positive FIT have an increased risk of post-colonoscopy CRC

Sudden Cardiac Death and Copy Number Variants: What Do We Know after 10 Years of Genetic Analysis?

Over the last ten years, analysis of copy number variants has increasingly been applied to the study of arrhythmogenic pathologies associated with sudden death, mainly due to significant advances in the field of massive genetic sequencing. Nevertheless, few published reports have focused on the prevalence of copy number variants associated with sudden cardiac death. As a result, the frequency of these genetic alterations in arrhythmogenic diseases as well as their genetic interpretation and clinical translation has not been established. This review summarizes the current available data concerning copy number variants in sudden cardiac death-related diseases