DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes.

Despite antibiotic resistance being a matter of growing concern worldwide, the bacterial mechanisms of pathogenesis remain underexplored, restraining our ability to develop new antimicrobials. The rise of high-throughput sequencing technology has made available a massive amount of transcriptomic data that could help elucidate the mechanisms underlying bacterial infection. Here, we introduce the DualSeqDB database, a resource that helps the identification of gene transcriptional changes in both pathogenic bacteria and their natural hosts upon infection. DualSeqDB comprises nearly 300 000 entries from eight different studies, with information on bacterial and host differential gene expression under in vivo and in vitro conditions. Expression data values were calculated entirely from raw data and analyzed through a standardized pipeline to ensure consistency between different studies. It includes information on seven different strains of pathogenic bacteria and a variety of cell types and tissues in Homo sapiens, Mus musculus and Macaca fascicularis at different time points. We envisage that DualSeqDB can help the research community in the systematic characterization of genes involved in host infection and help the development and tailoring of new molecules against infectious diseases. DualSeqDB is freely available at http://www.tartaglialab.com/dualseq.

BacFITBase: a database to assess the relevance of bacterial genes during host infection.

Bacterial infections have been on the rise world-wide in recent years and have a considerable impact on human well-being in terms of attributable deaths and disability-adjusted life years. Yet many mechanisms underlying bacterial pathogenesis are still poorly understood. Here, we introduce the BacFITBase database for the systematic characterization of bacterial proteins relevant for host infection aimed to enable the identification of new antibiotic targets. BacFITBase is manually curated and contains more than 90 000 entries with information on the contribution of individual genes to bacterial fitness under in vivo infection conditions in a range of host species. The data were collected from 15 different studies in which transposon mutagenesis was performed, including top-priority pathogens such as Acinetobacter baumannii and Campylobacter jejuni, for both of which increasing antibiotic resistance has been reported. Overall, BacFITBase includes information on 15 pathogenic bacteria and 5 host vertebrates across 10 different tissues. It is freely available at www.tartaglialab.com/bacfitbase.

HPIPred: Host-pathogen interactome prediction with phenotypic scoring.

Protein-protein interactions (PPIs) are involved in most cellular processes. Unfortunately, current knowledge of host-pathogen interactomes is still very limited. Experimental methods used to detect PPIs have several limitations, including increasing complexity and economic cost in large-scale screenings. Hence, computational methods are commonly used to support experimental data, although they generally suffer from high false-positive rates. To address this issue, we have created HPIPred, a host-pathogen PPI prediction tool based on numerical encoding of physicochemical properties. Unlike other available methods, HPIPred integrates phenotypic data to prioritize biologically meaningful results. We used HPIPred to screen the entire Homo sapiens and Pseudomonas aeruginosa PAO1 proteomes to generate a host-pathogen interactome with 763 interactions displaying a highly connected network topology. Our predictive model can be used to prioritize protein-protein interactions as potential targets for antibacterial drug development. Available at: https://github.com/SysBioUAB/hpi_predictor.

Time-Resolved Transcriptional Profiling of Epithelial Cells Infected by Intracellular Acinetobacter baumannii.

The rise in the number of antibiotic-resistant bacteria has become a serious threat to health, making it important to identify, characterize and optimize new molecules to help us to overcome the infections they cause. It is well known that Acinetobacter baumannii has a significant capacity to evade the actions of antibacterial drugs, leading to its emergence as one of the bacteria responsible for hospital and community-acquired infections. Nonetheless, how this pathogen infects and survives inside the host cell is unclear. In this study, we analyze the time-resolved transcriptional profile changes observed in human epithelial HeLa cells after infection by A. baumannii, demonstrating how it survives in host cells and starts to replicate 4 h post infection. These findings were achieved by sequencing RNA to obtain a set of Differentially Expressed Genes (DEGs) to understand how bacteria alter the host cells' environment for their own benefit. We also determine common features observed in this set of genes and identify the protein-protein networks that reveal highly-interacted proteins. The combination of these findings paves the way for the discovery of new antimicrobial candidates for the treatment of multidrug-resistant bacteria.

Control of differential-drive mobile robots for soft object deformation.

The aim of this work is a control scheme implementation to deform a nonrigid object in which deformation dynamics are modeled by the finite element method. The deformation of a soft object is highly difficult to model because of its non-linearity, time-dependency, and material-response characteristics. Thus, the control implementation for Differential Drive Mobile Robots (DDMR) to deform an elastic object, is a challenge. The proposed steps to solve it are: Position-control designed over DDMR kinematics. Alignment-control applied for DDMRs orientation. The desired shape of the object is achieved using two contact points as the control nodes. A centralized vision algorithm was employed in each stage to obtain positions. To show the usefulness of the proposed scheme, numerical simulation, and real-time implementation were carried out.

Acute lymphoblastic leukemia/lymphoma of the oral and maxillofacial region.

OBJECTIVE: Our objective was to describe the clinicopathologic and immunohistochemical features of acute lymphoblastic leukemia/lymphoma (ALL/LBL) of the oral and maxillofacial region (OMF). STUDY DESIGN: Cases diagnosed as ALL/LBL of the OMF region were retrieved from the files of 2 Brazilian and 1 Guatemalan oral pathology services from 2005 to 2017. Microscopic and immunohistochemical features of each case were reviewed and fully described, and clinical data were retrieved from the pathology reports. RESULTS: During the period considered, 6 cases were identified. Male patients were the most affected (4:2), with a mean age of 19 years old. The mandible was involved in 2 cases, the maxilla in 2, the cheek mucosa in 1, and the parotid gland in 1. Painful swelling was the most common presentation, and 3 patients also had systemic complaints. Microscopically, tumors revealed solid infiltrations of small to medium-sized immature cells. "Puzzle-like" and "starry-sky" patterns were observed, and "single lane" growth was also identified. Immunohistochemically, 2 cases were diagnosed as T-cell ALL/LBL with the leukocyte common antigen (LCA)+/cCD3+/CD79 a+focal/CD20-/PAX5-/CD99+/CD34-/CD10+/terminal deoxynucleotidyl transferase (TdT)+ phenotype and 4 as B-cell ALL/LBL with the LCA+/CD3-/CD20-/CD79 a+/CD10+/CD34 variable/TdT+ predominant phenotype. The Ki67 index ranged from 80% to 99%. CONCLUSION: OMF ALL/LBL is rare, but its microscopic features and immunohistochemical profiles CD3+or CD79 a+/CD10+/CD34+variable/CD99+/TdT+ contribute to the correct diagnosis.

Caracterización de factores pronósticos en pacientes con linfoma B difuso de células grandes / Characterization of prognostic factors to diagnosis of patients with diffuse large B cell lymphoma

Objetivo: describir los factores pronósticos demográficos, clínicos, hematológicos, inmunohistoquímicos y bioquímicos al diagnóstico de pacientes con linfoma B difuso de células grandes y su asociacióncon la severidad según el Índice Pronóstico Internacional en un Hospital Universitario, 2009-2012. Métodos: se realizó un estudio descriptivo en 40 pacientes con dicho linfoma. Se comparó laconcentración de β2 microglobulina con los factores pronósticos que componen el IPI y otros que nohacen parte; se determinó la asociación entre el IPI e IPI revisado y la concentración de β2 microglobulina,infiltración medular, masa voluminosa y expresión de BCL-2 y Ki-67. La información se analizó en SPSS. Resultados: 40% de los pacientes pertenecían al grupo de riesgo alto según el IPI y 55% al grupocon pronóstico pobre según el IPI revisado; 82.5% expresaron BCL-2 y 61.5% tenían un Ki-67>70%.Se observó asociación entre la β2 microglobulina y el Ann Arbor (p=0.036), la β2 microglobulina y lainfiltración medular (p=0.003), y la β2 microglobulina y el IPI revisado (p=0.037). Conclusiones: es probable que el tiempo transcurrido entre la aparición de los síntomas y eldiagnóstico haya favorecido que los pacientes se presentaran en estados avanzados de la enfermedady como consecuencia, con un pronóstico pobre. Así mismo, el estudio de la infiltración medular, elporcentaje de expresión de Ki-67 y la concentración de β2 microglobulina favorece a la identificaciónde pacientes con un pronóstico adverso. (Acta Med Colomb 2014: 39: 137-147).

Objective: to describe demographic, clinical, hematological, and immunohistochemical and biochemical prognostic factors to the diagnosis of patients with diffuse large B cell lymphoma and itsassociation with the severity according to the International Prognostic Index in a University Hospital,2009-2012. Methods: a descriptive study was conducted in 40 patients with this lymphoma. β2 microglobulinconcentration was compared with prognostic factors that compose the IPI and others which are not part of it; the association between IPI and revised IPI and β2 microglobulin concentration, bone marrow infiltration, bulky mass and expression of BCL -2 and Ki p-67 was determined. Data was analyzed in SPSS. Results: 40% of the patients were in the high risk group according to IPI and 55% to the group with poor prognosis according to the revised IPI; 82.5% expressed BCL-2 and 61.5% had a Ki-67 > 70%. Association between β2 microglobulin and Ann Arbor (p = 0.036), the β2 microglobulin and bone marrow infiltration (p = 0.003), and β2 microglobulin and revised IPI (p = 0.037) was observed. Conclusions: it is likely that the time between onset of symptoms and diagnosis has favored tha patients presented in advanced stages of the disease and as a result, with a poor prognosis. Likewise, the study of bone marrow infiltration, the percentage of Ki-67 expression and the concentration of β2 microglobulin favors the identification of patients with an adverse prognosis. (Acta Med Colomb 2014: 39: 137-147).

Consenso médico de biopsia por aspiración con aguja fina de tiroides. reporte de citología tiroidea basado en el sistema de bethesda / Medical consensus of fine-needle aspiration biopsy of the thyroid. bethesda system for reporting thyroid cytopathology

En este artículo se presenta un consenso médico basado en el sistema de Bethesda del Instituto Nacionalde Cáncer (Estados Unidos) para el uso de la biopsia por aspiración con aguja fina en el manejo de nódulos tiroideos, realizado en conjunto con patólogos, radiólogos, endocrinólogos y otras especialidades médicas de Colombia, España, Chile, Venezuela, Estados Unidos y Panamá. En este trabajo se describen las indicaciones de la biopsia por aspiración con aguja fina de tiroides, requisitos previos, entrenamiento, acreditación, técnicas, terminología diagnóstica, pruebas complementarias y opciones de tratamiento. El objetivo del actual artículo es presentar ante la comunidad médica la clasificación de los reportes citológicos, el reporte de ecografía que propone usar el sistema de datos y el reporte de imágenes tiroideas (TIRADS, del inglés The Thyroid Imaging Reporting and Data System), el uso de la medición de tiroglobulina en biopsia por aspiración con aguja fina y técnicas de citología líquida;...

This article presents a medical consensus based on the Bethesda system of the National Cancer Institute (USA) for the use of fine needle aspiration biopsy in the management of thyroid nodules. This consensus was performed in conjunction with pathologists, radiologists, endocrinologists, and other medical specialties of Colombia, Spain, Chile, Venezuela, United States, and Panama. In this work was described the indications for fine needle aspiration biopsy of thyroid, prerequisites, training, accreditation, techniques, diagnostic terminology, additional tests and treatment options. The aim of this article is present to the medical community the classification of cytological report, ultrasound report using the data system, and the thyroid imaging reporting and data system (TIRADS); as well as, the use of thyroglobulin measurement in fine needle aspiration biopsy, and liquid-based cytology techniques...