HGCA2.0: An RNA-Seq Based Webtool for Gene Coexpression Analysis in Homo sapiens

Genes with similar expression patterns in a set of diverse samples may be considered coexpressed. Human Gene Coexpression Analysis 2.0 (HGCA2.0) is a webtool which studies the global coexpression landscape of human genes. The website is based on the hierarchical clustering of 55,431 Homo sapiens genes based on a large-scale coexpression analysis of 3500 GTEx bulk RNA-Seq samples of healthy individuals, which were selected as the best representative samples of each tissue type. HGCA2.0 presents subclades of coexpressed genes to a gene of interest, and performs various built-in gene term enrichment analyses on the coexpressed genes, including gene ontologies, biological pathways, protein families, and diseases, while also being unique in revealing enriched transcription factors driving coexpression. HGCA2.0 has been successful in identifying not only genes with ubiquitous expression patterns, but also tissue-specific genes. Benchmarking showed that HGCA2.0 belongs to the top performing coexpression webtools, as shown by STRING analysis. HGCA2.0 creates working hypotheses for the discovery of gene partners or common biological processes that can be experimentally validated. It offers a simple and intuitive website design and user interface, as well as an API endpoint

Providing Foot Clearance during Stair Climbing with Tendon-Driven Systems: An Experimental Approach

Tendon-driven soft exosuits have gained much attention in recent years due to their ability to support people with mobility problems during daily life activities. A task that is particularly assisted by such robotic systems, due to its challenging nature, is stair climbing. However, assisting foot clearance during the swing phase of stair climbing with a tendon-driven system that actively supports hip and knee flexion has not been investigated. In the current study, we built a tendon-driven system to experimentally identify the foot clearance, the joint moments, the tendon forces, and the tendon velocities, that the system should provide to lift the foot above a stair-step. We experimented with able-bodied subjects that, while standing still, were instructed to keep their right leg relaxed to mimic muscle weakness. With this experimental approach, we showed how to systematically identify the basic requirements for developing an assistive device. The system provided up to 40.1 Nm at the hip and up to 23.2 Nm at the knee when simultaneously flexing both joints, while not being constrained by any space limitations. When modified to mimic a wearable, portable exosuit, that does not protrude more than 10 cm from the body, the setup provided an average foot clearance of 17 cm with thigh tendon forces up to 455 N and shank tendon forces up to 50 N. Consequently, exosuits that support hip and knee flexion should exploit the low required shank tendon forces and the possibility of simultaneously flexing the hip and knee joints to more efficiently assist foot clearance during stair climbing.Mechanical Engineerin

BRIDE v2: A Validated Collection of Genes Involved in the Mammalian Brain Response to Low-Dose Ionizing Radiation

There is significant interest in the response of the mammalian brain to low-dose ionizing radiation (LDIR), mainly examined by gene or protein expression, with applications in radiation safety on Earth, the atmosphere and outer space. Potential associations of molecular-level responses with sensory or cognitive defects and neurodegenerative diseases are currently under investigation. Previously, we have described a light-weight approach for the storage, analysis and distribution of relevant datasets, with the platform BRIDE. We have re-implemented the platform as BRIDE v2 on the cloud, using the bioinformatics infrastructure ELIXIR. We connected the annotated list of 3174 unique gene records with modern omics resources for downstream computational analysis. BRIDE v2 is a cloud-based platform with capabilities that enable researchers to extract, analyze, visualize as well as export the gene collection. The resource is freely available online at

A Review about the Sustainability of Pit Lakes as a Rehabilitation Factor after Mine Closure

At the end of surface mining activities, the remnant voids are of great concern regarding rehabilitating the final open pits. The investigation of the sustainability of pit lakes in post-mining regions constitutes a challenging research problem. This paper aims to highlight the effectiveness of pit lakes as a rehabilitation factor. In this framework, several cases worldwide and in Greece were examined in detail and evaluated. The results indicate that mine pit lakes must be evaluated as dynamic systems, natural or artificial, which demand rational mine water management to ensure their sustainability. Specifically in Greece, it is of great importance during the transition to the post-lignite era

Smart Traffic Data for the Analysis of Sustainable Travel Modes

We present and validate the image analysis algorithm μ-scope to capture personal mobility devices’ (PMDs) movement characteristics and extract their movement dynamics even when they interact with each other and with pedestrians. Experimental data were used for validation of the proposed algorithm. Data were collected through a large-scale, semicontrolled, real-track experiment at the University of Patras campus. Participants (N = 112) included pedestrians, cyclists, and e-scooter drivers. The experiment was video recorded, and μ-scope was used for trajectory extraction. Some of the participants had installed, beforehand, the Phyphox application in their smartphones. Phyphox accurately measures x-y-z acceleration rates and was used, in our case, as the baseline measurement (i.e., “ground truth”). Statistical comparison between Phyphox and camera-based measurements shows very low difference in most cases. High pedestrian densities were the only case where relatively high root mean square errors were registered. The proposed algorithm can be thus considered capable of producing reliable speed and acceleration estimates. Low-quality conventional smartphone cameras were used in this experiment. As a result, the proposed method can be easily applied to all urban contexts under normal traffic conditions, but eventually not in the case of special or emergency events generating very high pedestrian densities

Smart Traffic Data for the Analysis of Sustainable Travel Modes

We present and validate the image analysis algorithm μ-scope to capture personal mobility devices’ (PMDs) movement characteristics and extract their movement dynamics even when they interact with each other and with pedestrians. Experimental data were used for validation of the proposed algorithm. Data were collected through a large-scale, semicontrolled, real-track experiment at the University of Patras campus. Participants (N = 112) included pedestrians, cyclists, and e-scooter drivers. The experiment was video recorded, and μ-scope was used for trajectory extraction. Some of the participants had installed, beforehand, the Phyphox application in their smartphones. Phyphox accurately measures x-y-z acceleration rates and was used, in our case, as the baseline measurement (i.e., “ground truth”). Statistical comparison between Phyphox and camera-based measurements shows very low difference in most cases. High pedestrian densities were the only case where relatively high root mean square errors were registered. The proposed algorithm can be thus considered capable of producing reliable speed and acceleration estimates. Low-quality conventional smartphone cameras were used in this experiment. As a result, the proposed method can be easily applied to all urban contexts under normal traffic conditions, but eventually not in the case of special or emergency events generating very high pedestrian densities

Dynamic modelling and torque ripple minimization of a lightweight ultra-high transmission ratio harmonic drive

Harmonic drives have been of significant importance in many industrial and high-end applications including robotics, aerospace and manufacturing. Their unique characteristics combine high torque capabilities, high to ultra-high transmission per stage and low backlash performance in compact designs, suited for limited space applications. However, apart from the eminent merits of the technology, this type of gearboxes is associated with complex dynamic performance. Since their operations is associated with high compliance and friction a non – linear behavior is imposed to the system. This is also intensified due to torque ripples which in many cases apart from adding up to the overall complexity of the system, can also interfere with components of similar resonance frequency. In the frame of this paper a novel concept for a low-cost lightweight plastic harmonic drive used in positioning of telecommunication antennas is presented. Due to the tight dynamic specifications of the application (settling time, positioning error etc.) the torque ripple of the transmission was modelled and minimized. Design changes were also incorporated in various features in order to improve the overall dynamic performance