A method for automatically extracting infectious disease-related primers and probes from the literature

BACKGROUND: Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1) convert each document into a tree of paper sections, (2) detect the candidate sequences using a set of finite state machine-based recognizers, (3) refine problem sequences using a rule-based expert system, and (4) annotate the extracted sequences with their related organism/gene information. RESULTS: We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. CONCLUSIONS: We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch.The present work has been funded, in part, by the European Commission through the ACGT integrated project (FP6-2005-IST-026996) and the ACTION-Grid support action (FP7-ICT-2007-2-224176), the Spanish Ministry of Science and Innovation through the OntoMineBase project (ref. TSI2006-13021-C02-01), the ImGraSec project (ref. TIN2007-61768), FIS/AES PS09/00069 and COMBIOMED-RETICS, and the Comunidad de Madrid, Spain.S

Casual Learn: A Smart Application to Learn History of Art

Producción CientíficaSmart Learning promises the connection between formal and informal learning, but how to offer informal learning tasks related to formal learning is still a challenge. This demonstration paper presents CasualLearn, a smart learning application that bridges formal and informal learning to learn History of Art in the Spanish region of Castile and Leon. CasualLearn uses a dataset of 16,221 contextualized informal learning tasks that were semi-automatically created exploiting Open Data from the Web. CasualLearn offers these tasks to students based on their context: their geolocation, the activity they do and the topics covered in their formal education. A demo application is currently available for Android devices.Junta de Castilla y León (Project VA257P18)Ministerio de Ciencia, Innovación y Universidades (Project TIN2017-85179-C3-2-R)European Commission (Project grant 588438-EPP-1-2017-1-EL-EPPKA2-KA

Functional recovery in patients with schizophrenia: recommendations from a panel of experts

emission and encompasses multiple aspects of the patient's life, making it difficult to settle on a definition and to develop reliable assessment criteria. In this consensus process based on a panel of experts in schizophrenia, we aimed to provide useful insights on functional recovery and its involvement in clinical practice and clinical research. Methods: After a literature review of functional recovery in schizophrenia, a scientific committee of 8 members prepared a 75-item questionnaire, including 6 sections: (I) the concept of functional recovery (9 items), (II) assessment of functional recovery (23 items), (III) factors influencing functional recovery (16 items), (IV) psychosocial interventions and functional recovery (8 items), (V) pharmacological treatment and functional recovery (14 items), and (VI) the perspective of patients and their relatives on functional recovery (5 items). The questionnaire was sent to a panel of 53 experts, who rated each item on a 9-point Liken scale. Consensus was achieved in a 2-round Delphi dynamics, using the median (interquartile range) scores to consider consensus in either agreement (scores 7-9) or disagreement (scores 1-3). Items not achieving consensus in the first round were sent back to the experts for a second consideration. Results: After the two recursive rounds, consensus was achieved in 64 items (85.3%): 61 items (81.3%) in agreement and 3 (4.0%) in disagreement all of them from section II (assessment of functional recovery). Items not reaching consensus were related to the concepts of functional recovery (1 item, 13%), functional assessment (5 items, 6.7%), factors influencing functional recovery (3 items, 4.0%), and psychosocial interventions (2 items, 5.6%). Conclusions: Despite the lack of a well-defined concept of functional recovery, we identified a trend towards a common archetype of the definition and factors associated with functional recovery, as well as its applicability in clinical practice and clinical research.This project was funded by Janssen. The funding body participated in study design and data interpretation

Increased micronuclei and nuclear abnormalities in buccal mucosa and oxidative damage in saliva from patients with chronic and aggressive periodontal diseases

Background and objective Periodontal disease is a chronic bacterial infection characterized by connective tissue breakdown and alveolar bone destruction because of inflammatory and immune response caused by periodontopathogens and long-term release of reactive oxygen species. A high number of reactive oxygen species result in periodontal tissue damage through multiple mechanisms such as lipid peroxidation, protein denaturation and DNA damage. The aim of this study was to evaluate DNA and oxidative damage in subjects with chronic or aggressive periodontitis and healthy controls. Material and methods Buccal mucosa cells and whole saliva were collected from 160 subjects, who were divided into three groups: subjects with chronic periodontitis (CP) (n = 58), subjects with aggressive periodontitis (AgP) (n = 42) and a control group (n = 60). DNA damage was determined by counting micronuclei (MN) and nuclear abnormalities (NAs) in exfoliated cells, including binucleated cells, cells with nuclear buds and karyolitic, karyorrhectic, condensed chromatin and pyknotic cells. The degree of oxidative stress was determined by quantifying 8-hydroxy-2'-deoxyguanosine (8-OHdG) in whole saliva. Results Subjects with CP or AgP presented significantly more ( p < 0.05) MN and NAs and higher levels of 8-OHdG ( p < 0.05) compared with the control group. Conclusion Our results indicate that subjects with periodontitis (CP or AgP) exhibited an increase in the frequency of MN, NAs and 8-OHdG, which is directly related to DNA damage. In addition, a positive correlation exists between oxidative stress produced by periodontitis disease and MN

2020: Archivos in Times of COVID-19

Nota editorial de la revista Archivos de Prevención de riesgos laborales durante la pandemia de Covid-19

Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma.

Background: Serrated adenocarcinoma (SAC) is a recently recognized colorectal cancer (CRC) subtype accounting for 7.5–8.7 % of CRCs. It has been shown that SAC has a worse prognosis and different histological and molecular features compared to conventional carcinoma (CC) but, to date, there is no study analysing its methylome profile. Results: The methylation status of 450,000 CpG sites using the Infinium Human Methylation 450 BeadChip array was investigated in 103 colorectal specimens, including 39 SACs and 34 matched CCs, from Spanish and Finnish patients. Microarray data showed a higher representation of morphogenesis-, neurogenesis-, cytoskeleton- and vesicle transport-related functions and also significant differential methylation of 15 genes, including the iodothyronine deiodinase DIO3 and the forkhead family transcription factor FOXD2 genes which were validated at the CpG, mRNA and protein level using pyrosequencing, methylation-specific PCR, quantitative polymerase chain reaction (qPCR) and immunohistochemistry. A quantification study of the methylation status of CpG sequences in FOXD2 demonstrated a novel region controlling gene expression. Moreover, differences in these markers were also evident when comparing SAC with CRC showing molecular and histological features of high-level microsatellite instability. Conclusions: This methylome study demonstrates distinct epigenetic regulation patterns in SAC which are consistent to previous expression profile studies and that DIO3 and FOXD2 might be molecular targets for a specific histologyoriented treatment of CRC.post-print2306 K

Orchestrating ubiquitous learning situations about Cultural Heritage with Casual Learn mobile application

Producción CientíficaCultural Heritage learners can highly benefit from ubiquitous learning approaches that connect in-classroom activities with active on-site learning opportunities. However, teachers face the problem that the current landscape of technological support for learning Cultural Heritage mostly consists of mobile applications for informal contexts, completely decoupled from curricular activities. This paper presents the results of an exploratory-sequential mixed-methods study that focuses on the feasibility, for non-technical expert teachers, of repurposing an existing mobile application in formal Cultural Heritage ubiquitous learning situations. Such feasibility is explored from the perspective of the orchestration metaphor. More specifically, we used the “5+3 aspects orchestration framework” to understand the orchestration challenges of four ubiquitous learning situations about Cultural Heritage carried out in two secondary schools. These situations involved five teachers and 139 students who used a mobile application called Casual Learn for several weeks. The results of the study suggest that, after a brief training, teachers can design, enact, and orchestrate ubiquitous learning situations that involve both in-classroom and out-classroom activities. The teachers were able to transfer to the students most of the orchestration load of out-classroom activities. The results also showed that the flow of learning artifacts and information between in- and out-classroom activities is a critical issue that needs to be addressed by developers of ubiquitous learning technological solutions.Junta de Castilla y Leon - Fondo Europeo de Desarrollo Regional (project VA257P18)Agencia Estatal de Investigación - Fondo Europeo de Desarrollo Regional (project TIN2017-85179-C3-2-R

Método para la detección y determinación de carga viral del virus del papiloma humano

Número de publicación: 2 357 821 Número de solicitud: 200930425Un par de cebadores degenerados capaces de amplificar un fragmento del gen L1 de varios genotipos del virus del papiloma humano (VPH) y un método de detección y de cuantificación de la carga viral del VPH en muestras biológicas aisladas, que comprende: la extracción de ADN de una muestra biológica aislada, poner en contacto la muestra con una mezcla de reacción que contiene al menos un fluorocromo y los cebadores degenerados de la invención, amplificar un fragmento del gen L1 del VPH, medir la fluorescencia obtenida en el paso de amplificación y comparar el valor de fluorescencia obtenido con una secuencia control.Universidad Politécnica de CartagenaFundación para la Formación e Investigación Sanitarias de la Región de Murci

The Spanish version of the reflective functioning questionnaire: Validity data in the general population and individuals with personality disorders.

Introduction Mentalization or reflective functioning (RF) is the capacity to interpret oneself or the others in terms of internal mental states. Its failures have been linked to several mental disorders and interventions improving RF have a therapeutic effect. Mentalizing capacity of the parents influences the children’s attachment. The Reflective Functioning Questionnaire (RFQ-8) is a widely used tool for the assessment of RF. No instrument is available to assess general RF in Spanish-speaking samples. The aim of this study is to develop a Spanish version of the RFQ-8 and to evaluate its reliability and validity in the general population and in individuals with personality disorders. Methods 602 non-clinical and 41 personality disordered participants completed a Spanish translation of the RFQ and a battery of self-reported questionnaires assessing several RF related constructs (alexithymia, perspective taking, identity diffusion and mindfulness), psychopathology (general and specific) and interpersonal problems. Temporal stability was tested in a non-clinical sub-sample of 113 participants. Results Exploratory and confirmatory factor analyses suggested a one-factor structure in the Spanish version of the RFQ-8. RFQ-8 understood as a single scale was tested, with low scorings reflecting genuine mentalizing, and high scorings uncertainty. The questionnaire showed good internal consistence in both samples and moderate temporal stability in non-clinical sample. RFQ correlated significantly with identity diffusion, alexithymia, and general psychopathology in both samples; and with mindfulness, perspective taking, and interpersonal problems in clinical sample. Mean values of the scale were significantly higher in the clinical group. Discussion This study provides evidence that the Spanish version of the RFQ-8, understood as a single scale, has an adequate reliability and validity assessing failures in reflective functioning (i.e., hypomentalization) in general population and personality disorders.The study received a Health Strategic Action fund from the Carlos III Health Institute of the Spanish Ministry of Science and Innovation. ID PI16/02058. https://www.isciii.es/QueHacemos/Financiacion/solicitudes/Paginas/default.aspx No researcher have received money from the fund. This kind of public funds are managed by public institutes (in this case BIOEF) that ensure this money is only used for some of the material resources necessary to carry out the investigation. https://www.bioef.org/es/ The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

The Hydropathy Index of the HCDR3 Region of the B-Cell Receptor Identifies Two Subgroups of IGHV-Mutated Chronic Lymphocytic Leukemia Patients With Distinct Outcome

© 2021 Rodríguez-Caballero, Fuentes Herrero, Oliva Ariza, Criado, Alcoceba, Prieto, Pérez Caro, García-Montero, González Díaz, Forconi, Sarmento-Ribeiro, Almeida and Orfao.The HCDR3 sequences of the B-cell receptor (BCR) undergo constraints in length, amino acid use, and charge during maturation of B-cell precursors and after antigen encounter, leading to BCR and antibodies with high affinity to specific antigens. Chronic lymphocytic leukemia consists of an expansion of B-cells with a mixed immature and “antigen-experienced” phenotype, with either a mutated (M-CLL) or unmutated (U-CLL) tumor BCR, associated with distinct patient outcomes. Here, we investigated the hydropathy index of the BCR of 138 CLL patients and its association with the IGHV mutational status and patient outcome. Overall, two clearly distinct subgroups of M-CLL patients emerged, based on a neutral (mean hydropathy index of -0.1) vs. negatively charged BCR (mean hydropathy index of -1.1) with molecular features closer to those of B-cell precursors and peripheral/mature B-cells, respectively. Despite that M-CLL with neutral HCDR3 did not show traits associated with a mature B-cell repertoire, important differences in IGHV gene usage of tumor cells and patient outcome were observed in this subgroup of patients once compared to both U-CLL and M-CLL with negatively charged HCDR3 sequences. Compared to M-CLL with negatively charged HCDR3 sequences, M-CLL with neutral HCDR3 sequences showed predominance of men, more advanced stages of the disease, and a greater frequency of genetic alterations—e.g., del(17p)—together with a higher rate of disease progression and shorter time to therapy (TTT), independently of other prognostic factors. Our data suggest that the hydropathy index of the HCDR3 sequences of CLL cells allows the identification of a subgroup of M-CLL with intermediate prognostic features between U-CLL and the more favorable subgroup of M-CLL with a negatively charged BCR.This work was supported by the following grants: FS/37-2017, from the Fundación Memoria D. Samuel Solórzano, Universidad de Salamanca; FIS PI17/00399-FEDER, from the Fondo de Investigación Sanitaria of Instituto de Salud Carlos III, Madrid, Spain; 0639_IDIAL_NET_3_E, from cooperative network EPINTERREG V A España Portugal (POCTEP); and ECRIN-M3, Accelerator Award Full, Cancer Research UK, Fundación Cientıfíca de la Asociación Española Contra el Cáncer (AECC), Fondazione AIRC per la Ricerca sul Cancro.