Publications

Introducing SimpliPyTEM, a Python library and accompanying GUI that simplifies the post-acquisition evaluation of transmission electron microscopy (TEM) images, helping streamline the workflow. After an imaging session, a folder of image and/or video files, typically containing low contrast and large file size 32-bit images, can be quickly processed via SimpliPyTEM into high-quality, high-contrast.jpg images with suitably sized scale bars. The app can also generate HTML or PDF files containing the processed images for easy viewing and sharing. Additionally, SimpliPyTEM specifically focuses on in situ TEM videos, an emerging field of EM involving the study of dynamic processes whilst imaging. The package allows fast data processing into preview movies, averages, image series, or motion-corrected averages. The accompanying Python library offers many standard image processing methods, all simplified to a single command, plus a module to analyse particle morphology and population. This latter application is particularly useful for life sciences investigations. User-friendly tutorials and clear documentation are included to help guide users through the processing and analysis. We invite the EM community to contribute to and further develop this open-source package.

JTD Keywords: Image processing, computer-assisted, Microscopy, electron, transmission, Mobile applications, Software

The use of broadly neutralizing antibodies against human immunodeficiency virus type 1 (HIV-1) has been shown to be a promising therapeutic modality in the prevention of HIV infection. Understanding the b12-gp120 binding mechanism under physiological conditions may assist the development of more broadly effective antibodies. In this work, the main conformations and interactions between the receptor-binding domain (RBD) of spike glycoprotein gp120 of HIV-1 and the IgG1-b12 mAb are studied. Accelerated molecular dynamics (aMD) and ab initio hybrid molecular dynamics have been combined to determine the most persistent interactions between the most populated conformations of the antibody-antigen complex under physiological conditions. The results show the most persistent receptor-binding mapping in the conformations of the antibody-antigen interface in solution. The binding-free-energy decomposition reveals a small enhancement in the contribution played by the CDR-H3 region to the b12-gp120 interface compared to the crystal structure.

JTD Keywords: antibody, complex, functionals, gp120 envelope glycoprotein, hiv, immunodeficiency-virus, noncovalent interactions, simulations, software integration, Ab initio, Accelerated molecular dynamics, Accelerated molecular-dynamics, Antibodies, Antigens, Binding energy, Binding mechanisms, Computational studies, Crystal structure, Diseases, Free energy, Hiv infection, Human immunodeficiency virus, Molecular dynamics, Neutralizing antibodies, Physiological condition, Physiology, Receptor-binding domains, Therapeutic modality, Viruses

Generating complex, human-like behaviour in a humanoid robot like the iCub requires the integration of a wide range of open source components and a scalable cognitive architecture. Hence, we present the iCub-HRI library which provides convenience wrappers for components related to perception (object recognition, agent tracking, speech recognition, touch detection), object manipulation (basic and complex motor actions) and social interaction (speech synthesis, joint attention) exposed as a C++ library with bindings for Java (allowing to use iCub-HRI within Matlab) and Python. In addition to previously integrated components, the library allows for simple extension to new components and rapid prototyping by adapting to changes in interfaces between components. We also provide a set of modules which make use of the library, such as a high-level knowledge acquisition module and an action recognition module. The proposed architecture has been successfully employed for a complex human-robot interaction scenario involving the acquisition of language capabilities, execution of goal-oriented behaviour and expression of a verbal narrative of the robot's experience in the world. Accompanying this paper is a tutorial which allows a subset of this interaction to be reproduced. The architecture is aimed at researchers familiarising themselves with the iCub ecosystem, as well as expert users, and we expect the library to be widely used in the iCub community.

JTD Keywords: Robotics, iCub Humanoid, YARP, Software architecture, C++, Python, Java, Human-robot interaction

Background: Most stroke survivors continue to experience motor impairments even after hospital discharge. Virtual reality-based techniques have shown potential for rehabilitative training of these motor impairments. Here we assess the impact of at-home VR-based motor training on functional motor recovery, corticospinal excitability and cortical reorganization. Objective: The aim of this study was to identify the effects of home-based VR-based motor rehabilitation on (1) cortical reorganization, (2) corticospinal tract, and (3) functional recovery after stroke in comparison to home-based occupational therapy. Methods: We conducted a parallel-group, controlled trial to compare the effectiveness of domiciliary VR-based therapy with occupational therapy in inducing motor recovery of the upper extremities. A total of 35 participants with chronic stroke underwent 3 weeks of home-based treatment. A group of subjects was trained using a VR-based system for motor rehabilitation, while the control group followed a conventional therapy. Motor function was evaluated at baseline, after the intervention, and at 12-weeks follow-up. In a subgroup of subjects, we used Navigated Brain Stimulation (NBS) procedures to measure the effect of the interventions on corticospinal excitability and cortical reorganization. Results: Results from the system?s recordings and clinical evaluation showed significantly greater functional recovery for the experimental group when compared with the control group (1.53, SD 2.4 in Chedoke Arm and Hand Activity Inventory). However, functional improvements did not reach clinical significance. After the therapy, physiological measures obtained from a subgroup of subjects revealed an increased corticospinal excitability for distal muscles driven by the pathological hemisphere, that is, abductor pollicis brevis. We also observed a displacement of the centroid of the cortical map for each tested muscle in the damaged hemisphere, which strongly correlated with improvements in clinical scales. Conclusions: These findings suggest that, in chronic stages, remote delivery of customized VR-based motor training promotes functional gains that are accompanied by neuroplastic changes. Trial Registration: International Standard Randomized Controlled Trial Number NCT02699398 (Archived by ClinicalTrials.gov at https://clinicaltrials.gov/ct2/show/NCT02699398?term=NCT02699398&rank=1)

JTD Keywords: Stroke, Movement disorder, Recovery of function, neuroplasticity, Transcranial magnetic stimulation, Physical therapy, Hemiparesis, Computer applications software

A new method for obtaining a three-dimensional volumetric reconstruction from a set of views improving the classical Shape from Silhouette method (SFS) is presented. SFS approaches can be easily accelerated through hardware and software techniques but they are very sensible to errors arising during calibration and segmentation processes so they present difficulties when dealing with real images. This paper proposes a new algorithm which uses the information about pixel segmentation uncertainty contained in each view in order to get a reliable 3D reconstruction of the scene. Aggregation of the projected uncertainties permits to classify scene's voxels by means of a decision rule but also makes it possible to create a three-dimensional confidence map of the scene. As a consequence, the regions where more information is needed can be foreseen. Sample reconstructions from real image sets are presented and evaluated.

JTD Keywords: Calibration, Image classification, Image reconstruction, Image segmentation, 3D reconstruction, Calibration process, Decision rule, Hardware technique, Pixel segmentation, Pixel-level certainty measures, Scene voxel classification, Segmentation process, Shape from silhouette method, Software technique, Three-dimensional confidence map, Three-dimensional volumetric reconstruction