Visual Correspondences for Unsupervised Domain Adaptation on Electron Microscopy Images.

We present an Unsupervised Domain Adaptation strategy to compensate for domain shifts on Electron Microscopy volumes. Our method aggregates visual correspondences-motifs that are visually similar across different acquisitions-to infer changes on the parameters of pretrained models, and enable them to operate on new data. In particular, we examine the annotations of an existing acquisition to determine pivot locations that characterize the reference segmentation, and use a patch matching algorithm to find their candidate visual correspondences in a new volume.

The effects of aging on neuropil structure in mouse somatosensory cortex-A 3D electron microscopy analysis of layer 1.

This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region.

Network Flow Integer Programming to Track Elliptical Cells in Time-Lapse Sequences.

We propose a novel approach to automatically tracking elliptical cell populations in time-lapse image sequences. Given an initial segmentation, we account for partial occlusions and overlaps by generating an over-complete set of competing detection hypotheses. To this end, we fit ellipses to portions of the initial regions and build a hierarchy of ellipses, which are then treated as cell candidates.

Linking genetic and environmental factors in amphibian disease risk.

A central question in evolutionary biology is how interactions between organisms and the environment shape genetic differentiation. The pathogen Batrachochytrium dendrobatidis (Bd) has caused variable population declines in the lowland leopard frog (Lithobates yavapaiensis); thus, disease has potentially shaped, or been shaped by, host genetic diversity. Environmental factors can also influence both amphibian immunity and Bd virulence, confounding our ability to assess the genetic effects on disease dynamics.

Fast part-based classification for instrument detection in minimally invasive surgery.

Automatic visual detection of instruments in minimally invasive surgery (MIS) can significantly augment the procedure experience for operating clinicians. In this paper, we present a novel technique for detecting surgical instruments by constructing a robust and reliable instrument-part detector. While such detectors are typically slow to use, we introduce a novel early stopping scheme for multiclass ensemble classifiers which acts as a cascade and significantly reduces the computational requirements at test time, ultimately allowing it to run at framerate.

Domain adaptation for microscopy imaging.

Electron and light microscopy imaging can now deliver high-quality image stacks of neural structures. However, the amount of human annotation effort required to analyze them remains a major bottleneck. While machine learning algorithms can be used to help automate this process, they require training data, which is time-consuming to obtain manually, especially in image stacks.

Learning structured models for segmentation of 2-D and 3-D imagery.

Efficient and accurate segmentation of cellular structures in microscopic data is an essential task in medical imaging. Many state-of-the-art approaches to image segmentation use structured models whose parameters must be carefully chosen for optimal performance. A popular choice is to learn them using a large-margin framework and more specifically structured support vector machines (SSVM).

Exploiting enclosing membranes and contextual cues for mitochondria segmentation.

In this paper, we improve upon earlier approaches to segmenting mitochondria in Electron Microscopy images by explicitly modeling the double membrane that encloses mitochondria, as well as using features that capture context over an extended neighborhood. We demonstrate that this results in both improved classification accuracy and reduced computational requirements for training.

Supervised feature learning for curvilinear structure segmentation.

We present a novel, fully-discriminative method for curvilinear structure segmentation that simultaneously learns a classifier and the features it relies on. Our approach requires almost no parameter tuning and, in the case of 2D images, removes the requirement for hand-designed features, thus freeing the practitioner from the time-consuming tasks of parameter and feature selection. Our approach relies on the Gradient Boosting framework to learn discriminative convolutional filters in closed form at each stage, and can operate on raw image pixels as well as additional data sources, such as the output of other methods like the Optimally Oriented Flux.

Melting curve analysis for the screening of hepatitis B virus genotypes A, D and F in patients from a general hospital in southern Brazil.

Context: Hepatitis B virus (HBV) can cause fulminant hepatitis, cirrhosis and hepatocellular carcinoma, and is one of the most common causes of acute and chronic liver failure. The genetic variants of HBV can be decisive for the evolution of these diseases as well as for the election of therapy.

Objectives: The aim of this study was to evaluate and standardize an in house methodology based on the analysis of the melting curve polymerase chain reaction (PCR) of real-time (qPCR) to screen for genotypes A, D and F of HBV in patients from a hospital in Rio Grande do Sul, Brazil.

Learning context cues for synapse segmentation.

We present a new approach for the automated segmentation of synapses in image stacks acquired by electron microscopy (EM) that relies on image features specifically designed to take spatial context into account. These features are used to train a classifier that can effectively learn cues such as the presence of a nearby post-synaptic region. As a result, our algorithm successfully distinguishes synapses from the numerous other organelles that appear within an EM volume, including those whose local textural properties are relatively similar.

[Possible prognostic value of atrial fibrillation and atrial flutter in Brugada syndrome].

Objective: To analyze the specific risk for the variables: type 1 spontaneous pattern, type 1 induced pattern, type 1 pattern with spontaneous variability, syncope, family history of sudden death, atrial fibrillation and atrial flutter with the subsequent development of malignant arrhythmic events.

Methods: Forty-three Brugada patients (90% males; mean age 40.4 years), with a type 1 spontaneous pattern (74.

Learning context cues for synapse segmentation in EM volumes.

We present a new approach for the automated segmentation of excitatory synapses in image stacks acquired by electron microscopy. We rely on a large set of image features specifically designed to take spatial context into account and train a classifier that can effectively utilize cues such as the presence of a nearby post-synaptic region. As a result, our algorithm successfully distinguishes synapses from the numerous other organelles that appear within an EM volume, including those whose local textural properties are relatively similar.

Genotyping of hepatitis B virus in a cohort of patients evaluated in a hospital of Porto Alegre, South of Brazil.

Context: In recent years the hepatitis B virus (HBV) genotyping has been considered a relevant factor in the natural history of the disease.

Objective: To determine hepatitis B virus genotypes and its epidemiological and clinical implications, in a cohort of patients in a hospital in Porto Alegre, South of Brazil.

Methods: Sixty seven patients with HBV chronic infection markers who were being treated at ''Complexo Hospitalar Santa Casa'', in Porto Alegre, RS, Brazil, were evaluated.

Hung out to dry: choice of priority ecoregions for conserving threatened neotropical anurans depends on life-history traits.

Background: In the Neotropics, nearly 35% of amphibian species are threatened by habitat loss, habitat fragmentation, and habitat split; anuran species with different developmental modes respond to habitat disturbance in different ways. This entails broad-scale strategies for conserving biodiversity and advocates for the identification of high conservation-value regions that are significant in a global or continental context and that could underpin more detailed conservation assessments towards such areas.

Methodology/principal Findings: We identified key ecoregion sets for anuran conservation using an algorithm that favors complementarity (beta-diversity) among ecoregions.

Habitat split and the global decline of amphibians.

The worldwide decline in amphibians has been attributed to several causes, especially habitat loss and disease. We identified a further factor, namely "habitat split"-defined as human-induced disconnection between habitats used by different life history stages of a species-which forces forest-associated amphibians with aquatic larvae to make risky breeding migrations between suitable aquatic and terrestrial habitats. In the Brazilian Atlantic Forest, we found that habitat split negatively affects the richness of species with aquatic larvae but not the richness of species with terrestrial development (the latter can complete their life cycle inside forest remnants).

Failure of cilostazol in the prevention of ventricular fibrillation in a patient with Brugada syndrome.

The ECG appearance in Brugada syndrome is caused by failure of the dome of the action potential to develop. Increased activity of the I(to) current in epicardial cells generates a transmural gradient with repolarization dispersion between the epicardium and the endocardium in the right ventricular wall, thus favoring the development of VF by a phase 2 reentry mechanism. The efficacy of cilostazol for the management of these arrhythmias has been reported.

One-year follow-up of transcoronary sinus administration of autologous bone marrow in patients with chronic refractory angina.

Purpose: Based on our preclinic studies with autologous unfractionated bone marrow (AUBM) via coronary sinus with transitory occlusion, a clinic study in patients with chronic refractory angina was designed. The objectives were to evaluate tolerance of the procedure, safety, and feasibility with 1 year follow-up.

Methods And Materials: Clinical study with inclusion and exclusion criteria defined by an Independent Clinical Committee was carried out.