Bioinformatics approaches applied to the discovery of antifungal peptides

Antifungal peptides (AFPs) comprise a group of substances with a broad spectrum of activities and complex action mechanisms. They develop in nature via an evolutionary process resulting from the interactions between hosts and pathogens. The AFP database is experimentally verified and curated from research articles, patents, and public databases. In this review, we compile information about the primary databases and bioinformatics tools that have been used in the discovery of AFPs during the last 15 years. We focus on the classification and prediction of AFPs using different physicochemical properties, such as polarity, hydrophobicity, hydrophilicity, mass, acidic, basic, and isoelectric indices, and other structural properties. Another method for discovering AFPs is the implementation of a peptidomic approach and bioinformatics filtering, which gave rise to a new family of peptides that exhibit a broad spectrum of antimicrobial activity against Candida albicans with low hemolytic effects. The application of machine intelligence in the sphere of biological sciences has led to the development of automated tools. The progress made in this area has also paved the way for producing new drugs more quickly and effectively. However, we also identified that further advancements are still needed to complete the AFP libraries

Molecular Diagnosis of Invasive Aspergillosis

Invasive aspergillosis (IA) is a disease that is difficult to manage and is associated with a significantly high morbidity and mortality, caused by different species of the genus Aspergillus, and closely related to immunocompromised patients; thus, it is important to understand the distribution and molecular epidemiology of the species causing this disease. Even though Aspergillus fumigatus sensu stricto is the most common species that cause IA, in recent years, there has been an increase in the number of species in the different sections which makes the diagnosis of this invasive fungal disease a great challenge. Conventional tests for the diagnosis of IA present limitations in sensitivity and specificity, while molecular tests have the potential to improve diagnosis by offering a more sensitive and rapid identification, but they are not yet standardized for reliable use in clinic. Nevertheless, there are some tests for the presumptive diagnosis of aspergillosis which, although are not specific for the identification of species, have been decisive in the case of IA. Among these are the Galactomannan test (GM), the Beta-D-glucan assay and volatile organic compounds (VOCs) testing. In this chapter, the recent advances and challenges in the molecular diagnosis of IA are revised

Usefulness of a multiplex PCR for the rapid identification of Candida glabrata species complex in Mexican clinical isolates

Candida glabrata complex includes three species identified through molecular biology methods: C. glabrata sensu stricto, C. nivariensis and C. bracarensis. In Mexico, the phenotypic methods are still used in the diagnosis; therefore, the presence of C. nivariensis and C. bracarensis among clinical isolates is still unknown. The aim of this study was to evaluate the utility of a multiplex PCR for the identification of the C. glabrata species complex. DNA samples from 92 clinical isolates that were previously identified through phenotypic characteristics as C. glabrata were amplified by four oligonucleotides (UNI-5.8S, GLA-f, BRA-f, and NIV-f) that generate amplicons of 397, 293 and 223-bp corresponding to C. glabrata sensu stricto, C. nivariensis, and C. bracarensis, respectively. The amplicon sequences were used to perform a phylogenetic analysis through the Maximum Likelihood method (MEGA6), including strains and reference sequences of species belonging to C. glabrata complex. In addition, recombination and linkage disequilibrium were estimated (DnaSP version 5.0) for C. glabrata sensu stricto isolates. Eighty-eight isolates generated a 397-bp fragment and only in one isolate a 223-bp amplicon was observed. In the phylogenetic tree, the sequences of 397-bp were grouped with C. glabrata reference sequences, and the sequence of 223-bp was grouped with C. bracarensis reference sequences, corroborating the PCR identification. The number of recombination events for the isolates of C. glabrata sensu stricto was zero, suggesting a clonal population structure. Three isolates that did not amplify any of the expected fragments were identified as Saccharomyces cerevisiae through the sequencing of the D1/D2 domain region within the 28S rDNA gene. The multiplex PCR is a fast, cost-effective and reliable tool that can be used in clinical laboratories to identify C. glabrata complex species

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

On-line Clustering Method for Takagi-Sugeno Fuzzy Models Identification

[EN] This paper presents a method for Takagi-Sugeno fuzzy modeling. This method updates on line both the structure and the parameters of the model by combining a new on line clustering algorithm with least squares techniques. The proposed clustering algorithm, that generates clusters that are used to form the fuzzy rule antecedents, is used for model structure identification. The update of consequent parameters is achieved by least squares estimators.[ES] En este trabajo se presenta un método de obtención de modelos borrosos Takagi-Sugeno. Este método actualiza en línea tanto la estructura como los parámetros del modelo mediante la combinación de un nuevo algoritmo de agrupamiento en línea con técnicas de mínimos cuadrados. El algoritmo de agrupamiento propuesto se utiliza para la identificación de la estructura del modelo borroso, generando las clases de las cuales se obtienen los antecedentes de las reglas. La actualización de los parámetros del consecuente se logra mediante estimadores de mínimos cuadrados.Este trabajo ha sido parcialmente financiado por el proyecto MES 6.111 del Ministerio de Educación Superior de Cuba.Martínez, B.; Herrera, F.; Fernández, J.; Marichal, E. (2008). Método de Agrupamiento en Línea para la Identificación de Modelos Borrosos Takagi-Sugeno. Revista Iberoamericana de Automática e Informática industrial. 5(3):63-69. http://hdl.handle.net/10251/145485OJS63695

Necesidades de intervención integral para el desarrollo del distrito del Carmen en el marco de un CDI distrital según el Plan GAM 2013-2030

Proyecto de investigación (Código: 5402-1801-0509) Instituto Tecnológico de Costa Rica. Escuela de Ingeniería en Computación; Campus Tecnológico Local San José. Escuela de Arquitectura y Urbanismo, 2017La presente propuesta pretende identificar necesidades de intervención interdisciplinaria para la promoción del crecimiento y desarrollo en el distrito El Carmen a partir del modelo de Centralidades Densas Integrales (CDI) propuesto en el Plan GAM 2013-2030, y que articule el aporte que puedan hacer para este distrito, dos de las carreras que se imparten en el Centro Académico de San José: Ingeniería en Computación, y Arquitectura y Urbanismo. Luego de 32 años sin lograr ser actualizado y de ocho años de esfuerzos infructuosos para su actualización (2004-2012), el Plan de la Gran Área Metropolitana, denominado Plan GAM 2013-2030, fue aprobado el 30 de abril del 2014. Esto gracias a que el Instituto Tecnológico de Costa Rica tomó la Secretaría del Plan Nacional de Desarrollo Urbano. [D31062] El distrito del Carmen, en el Centro de la ciudad de San José, es el área de acción directa del Centro Académico de San José (ITCR); pero a pesar de contar con las mejores condiciones urbanas en cuanto a infraestructuras, servicios, accesibilidad y espacios públicos; el distrito ha perdido en 50 años el 70% de la población. Esto ha presentado un proceso de decaimiento de la actividad residencial y ha reducido las posibilidades de desarrollo económico a mediana y pequeña escala, dependiendo altamente de la actividad institucional de la zona. A esta problemática se añade el impacto de las dinámicas de alta carga vehicular, un alto porcentaje de estacionamientos públicos y privados, su integración modal y limitadas condiciones de movilidad. La metodología empleada para el desarrollo del trabajo abarca mecanismos tales como mapeos, revisión bibliográfica y un profundo análisis de los temas abordados en cada objetivo

Kerion Celsi: A report of two cases due to Microsporum gypseum and Trichophyton tonsurans

Tinea capitis is a scalp fungal infection involving the hair. Inflammatory cases are usually caused by zoophilic and geophilic species of the genus Microsporum and Trichophyton, and are almost always seen in children. The most effective treatments are with Griseofulvin, itraconazole and terbinafine. We report two cases in children 5 and 7 years old, in which Microsporum gypseum and Trichophyton tonsurans were isolated

Uncommon Clinical Presentations of Sporotrichosis: A Two-Case Report

Sporotrichosis is a subcutaneous endemic mycosis caused by species of the Sporothrix schenckii complex. The most common clinical form of the disease is lymphocutaneous, while the fixed cutaneous and disseminated cutaneous forms are rare. Moreover, it is more prevalent in immunocompetent individuals. In this study, we present two cases of sporotrichosis with uncommon clinical forms: fixed cutaneous (Case 1) and disseminated cutaneous (Case 2). Both cases were diagnosed in immunocompetent males from endemic regions in Mexico, who had at least 1 year of evolution without improvement in response to prior nonspecific treatments. The diagnosis of sporotrichosis caused by S. schenckii sensu stricto was established through the isolation of the pathogen and its identification through the amplification of a 331 bp fragment of the gene encoding calmodulin. In both cases, improvement was observed after treatment with potassium iodide. Cases 1 and 2 illustrate the rarity of these clinical forms in individuals residing in endemic areas; hence, it is important to ensure a high index of clinical suspicion for the diagnosis of mycosis, as the differential diagnoses vary widely