MotilityJ: An open-source tool for the classification and segmentation of bacteria on motility images.

BACKGROUND AND OBJECTIVES: Infectious diseases produced by antimicrobial resistant microorganisms are a major threat to human, and animal health worldwide. This problem is increased by the virulence and spread of these bacteria. Surface motility has been regarded as a pathogenicity element because it is essential for many biological functions, but also for disease spreading; hence, investigations on the motility behaviour of bacteria are crucial to understand chemotaxis, biofilm formation and virulence in general. To identify a motile strain in the laboratory, the bacterial spread area is observed on media solidified with agar. Up to now, the task of measuring bacteria spread was a manual, and, therefore, tedious and time-consuming task. The aim of this work is the development of a set of tools for bacteria segmentation in motility images. METHODS: In this work, we address the problem of measuring bacteria spread on motility images by creating an automatic pipeline based on deep learning models. Such a pipeline consists of a classification model to determine whether the bacteria has spread to cover completely the Petri dish, and a segmentation model to determine the spread of those bacteria that do not fully cover the Petri dishes. In order to annotate enough images to train our deep learning models, a semi-automatic annotation procedure is presented. RESULTS: The classification model of our pipeline achieved a F1-score of 99.85%, and the segmentation model achieved a Dice coefficient of 95.66%. In addition, the segmentation model produces results that are indistinguishable, and in many cases preferred, from those produced manually by experts. Finally, we facilitate the dissemination of our pipeline with the development of MotilityJ, an open-source and user-friendly application for measuring bacteria spread on motility images. CONCLUSIONS: In this work, we have developed an algorithm and trained several models for measuring bacteria spread on motility images. Thanks to this work, the analysis of motility images will be faster and more reliable. The developed tools will help to advance our understanding of the behaviour and virulence of bacteria.

CLoDSA: a tool for augmentation in classification, localization, detection, semantic segmentation and instance segmentation tasks.

BACKGROUND: Deep learning techniques have been successfully applied to bioimaging problems; however, these methods are highly data demanding. An approach to deal with the lack of data and avoid overfitting is the application of data augmentation, a technique that generates new training samples from the original dataset by applying different kinds of transformations. Several tools exist to apply data augmentation in the context of image classification, but it does not exist a similar tool for the problems of localization, detection, semantic segmentation or instance segmentation that works not only with 2 dimensional images but also with multi-dimensional images (such as stacks or videos). RESULTS: In this paper, we present a generic strategy that can be applied to automatically augment a dataset of images, or multi-dimensional images, devoted to classification, localization, detection, semantic segmentation or instance segmentation. The augmentation method presented in this paper has been implemented in the open-source package CLoDSA. To prove the benefits of using CLoDSA, we have employed this library to improve the accuracy of models for Malaria parasite classification, stomata detection, and automatic segmentation of neural structures. CONCLUSIONS: CLoDSA is the first, at least up to the best of our knowledge, image augmentation library for object classification, localization, detection, semantic segmentation, and instance segmentation that works not only with 2 dimensional images but also with multi-dimensional images.

Resolution of disseminated fusariosis in a child with acute leukemia treated with combined antifungal therapy: a case report.

BACKGROUND: Fusarium spp. is being isolated with increasing frequency as a pathogen in oncohematologic patients. Caspofungin and amphotericin B have been reported to have synergistic activity against Fusarium spp. CASE PRESENTATION: We herein report a case of disseminated fusariosis diagnosed by chest CT scan and positive blood cultures to Fusarium spp. Because the patient's clinical condition deteriorated, CRP levels increased, and blood cultures continued to yield Fusarium spp. despite liposomal amphotericin B monotherapy up to 5 mg/kg daily, treatment with caspofungin was added. Within 2 weeks of onset of combined antifungal therapy, the chest CT scan demonstrated a progressive resolution of the pulmonary lesions. Upon discontinuation of intravenous antifungals, the patient received suppressive therapy with oral voriconazole. Three months later, a chest CT scan showed no abnormalities. Twenty-five months after discontinuation of all antifungal therapy, the patient remains in complete remission of her neoplastic disease with no signs of clinical activity of the Fusarium infection. CONCLUSION: This is the first description of successful treatment of disseminated fusariosis in a pediatric patient with acute lymphoblastic leukemia with caspofungin and amphotericin B followed by oral suppressive therapy with voriconazole.

Respuesta mantenida al tratamiento con anticuerpos anti-CD20 (rituximab) en un caso de anemia hemolítica autoinmune asociada a artritis reumatoide / Efficacy of therapy with anti-CD20 antibody (rituximab)in a patient with autoimmune hemolytic anemia associated with rheumatoid arthritis

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Complicaciones a corto plazo del aborto / Shrot Term complications of abortion

Se realiza una revisión de 5 469 interrupciones de embarazo realizadas en el hospital docente ginecológico "América Arias", por el método de dilatación y curetaje. Se ofrecen las complicaciones inmediatas y mediatas en relación con edad de la paciente, abortos previos, paridad, tiempo de gestación, calificación del operador. Se relacionan también las diferentes complicaciones (AU)

Epidemiología del aborto. Estudio preliminar / Epidemiology of abortion. Preliminary study

Se realiza un estudio sobre la epidemiología del aborto en 800 pacientes en los municipios de Centro Habana y Habana Vieja que solicitaron la interrupción del embarazo en el hospital docente ginecobstétrico "América Arias", mediante la utilización de una encuesta, elaborada a tal efecto. Se ofrecen los resultados preliminares en diez cuadros, donde se relacionana: edad, escolaridad, ocupación, estado civil, percápita familiar, paridad, abortos anteriores provocados, conocimiento de métodos anticonceptivos, causa del no uso de anticonceptivos, y motivo del aborto. Todo esto comparado con la literatura mundial (AU)