In & out zooming on time-aware user/tag clusters

The common ground behind most approaches that analyze social tagging systems is addressing the information challenge that emerges from the massive activity of millions of users who interact and share resources and/or metadata online. However, lack of any time-related data in the analysis process implicitly denies much of the dynamic nature of social tagging activity. In this paper we claim that holding a temporal dimension, allows for tracking macroscopic and microscopic users’ interests, detecting emerging trends and recognizing events. To this end, we propose a time-aware co-clustering approach for acquiring semantic and temporal patterns out of the tagging activity. The resulted clusters contain both users and tags of similar patterns over time, and reveal non-obvious or “hidden” relations among users and topics of their common interest. Zoom in & out views serve as visualization methods on different aspects of the clusters’ structure, in order to evaluate the efficiency of the approach.     

From dynamic movement primitives to associative skill memories

In recent years, research on movement primitives has gained increasing popularity. The original goals of movement primitives are based on the desire to have a sufficiently rich and abstract representation for movement generation, which allows for efficient teaching, trial-and-error learning, and generalization of motor skills (Schaal 1999). Thus, motor skills in robots should be acquired in a natural dialog with humans, e.g., by imitation learning and shaping, while skill refinement and generalization should be accomplished autonomously by the robot. Such a scenario resembles the way we teach children and connects to the bigger question of how the human brain accomplishes skill learning. In this paper, we review how a particular computational approach to movement primitives, called dynamic movement primitives, can contribute to learning motor skills. We will address imitation learning, generalization, trial-and-error learning by reinforcement learning, movement recognition, and control based on movement primitives. But we also want to go beyond the standard goals of movement primitives. The stereotypical movement generation with movement primitives entails predicting of sensory events in the environment. Indeed, all the sensory events associated with a movement primitive form an associative skill memory that has the potential of forming a most powerful representation of a complete motor skill.     

An in-depth study of the promises and perils of mining GitHub

With over 10 million git repositories, GitHub is becoming one of the most important sources of software artifacts on the Internet. Researchers mine the information stored in GitHub’s event logs to understand how its users employ the site to collaborate on software, but so far there have been no studies describing the quality and properties of the available GitHub data. We document the results of an empirical study aimed at understanding the characteristics of the repositories and users in GitHub; we see how users take advantage of GitHub’s main features and how their activity is tracked on GitHub and related datasets to point out misalignment between the real and mined data. Our results indicate that while GitHub is a rich source of data on software development, mining GitHub for research purposes should take various potential perils into consideration. For example, we show that the majority of the projects are personal and inactive, and that almost 40 % of all pull requests do not appear as merged even though they were. Also, approximately half of GitHub’s registered users do not have public activity, while the activity of GitHub users in repositories is not always easy to pinpoint. We use our identified perils to see if they can pose validity threats; we review selected papers from the MSR 2014 Mining Challenge and see if there are potential impacts to consider. We provide a set of recommendations for software engineering researchers on how to approach the data in GitHub.     

A Thiolactone Strategy for Straightforward Synthesis of Disulfide‐Linked Side‐Chain‐to‐Tail Cyclic Peptides Featuring an N‐Terminal Modification Handle

The development of straightforward and versatile peptide cyclisation methods is highly desired to meet the demand for more stable peptide‐based drugs. Herein, a new method for the synthesis of side‐chain‐to‐tail cyclic peptides with the simultaneous introduction of an N‐terminal handle, based on the introduction of an N‐terminal thiolactone building block, is described. A primary amine liberates a homocysteine analogue from the thiolactone building block, which further enables cyclisation of the peptide through disulfide‐bond formation with a C‐terminal cysteamine. Postcyclisation modification can be achieved by using small bifunctional amines. Alternatively, the synthesis of lipopeptides is demonstrated through direct thiolactone opening with long‐chain alkyl amines.     

A Multi-Pronged Approach to Adaptive and Context Aware Content Dissemination in VANETs

Content dissemination in Vehicular Ad-hoc Networks (VANETs) has the potential to enable a myriad of applications, ranging from advertising, traffic and emergency warnings to infotainment. This variety in applications and services calls for mechanisms able to optimize content storing, retrieval and forwarding among vehicles, without jeopardizing network resources. Content Centric Networking (CCN), takes advantage of inherent content redundancy in the network in order to decrease the utilization of network resources, improve response time and content availability, coping efficiently with some of the effects of mobility. Floating Content (FC), on the other hand, holds potential to implement efficiently a large amount of vehicular applications thanks to its property of geographic content replication, while Software Defined Networking (SDN), is an attractive solution for the lack of flexibility and dynamic programmability that characterizes current VANET architectures. By implementing a logical centralization of the network, SDN enables dynamic and efficient management of network resources. In this paper, for a few reference scenarios, we illustrate how approaches that combine CCN, FC and SDN enable an innovative adaptive VANET architecture able to efficiently accommodate to intermittent connectivity, fluctuating node density and mobility patterns on one side and application performance and network resources on the other side, aiming to achieve high QoS. For each scenario, we highlight the main open research challenges, and we describe possible solutions to improve content dissemination and reduce replication without affecting content availability.     

A MAC protocol for low-rate UWB wireless sensor networks using directional antennas

Ultra-wideband (UWB) is a key solution for wireless connectivity, characterized by ultralow power consumption and a good degree of robustness to interference and multipath fading. Evidence of its significance, is its recent use in the IEEE 802.15.4a standard. UWB technology with joint consideration of directional antennas can benefit when compared to classical omni-directional antennas from the energy conservation viewpoint, which is of fundamental concern when it comes to wireless sensor networks (WSNs). However, exploiting directionality requires new approach in the design of a medium access control (MAC) protocol to be applied. In this work, idle nodes continuously rotate their receiving beams over 360° until a predefined preamble trailer is detected. The resulting scheme is a directional ultra-wideband MAC protocol, named DU-MAC, which deals effectively with the problem of deafness and the problem of determination of neighbors’ location. Simulation-based studies will demonstrate the effectiveness of the proposed protocol in many critical parameters, such as throughput and network lifetime.     

Evidence of a role for plant proteases in the degradation of herbage proteins in the rumen of grazing cattle

Protein breakdown in the rumen is generally regarded as a two-stage process in which proteases produced by rumen microorganisms cleave plant protein into peptides and amino acids. However, many of the fiber-degrading cellulolytic species in the rumen are not in fact proteolytic, and the proteolytic activity of the entire rumen microbial population is only moderate when compared to the gastric and pancreatic secretions in the abomasum. Moreover, plant cell walls remain largely intact after initial chewing (particularly in cattle), presenting a physical barrier that must be breached prior to their effective colonization. The present study considers the hypothesis that the plant enzymes are at least partly responsible for herbage protein degradation in grazing ruminants. Ryegrass, red clover, white clover, and bird's-foot trefoil were incubated in the presence and absence of rumen microorganisms. The production of volatile fatty acids indicated the level of microbial activity, whereas the relative disappearance of the large subunit of ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco LSU) indicated proteolytic activity. In all incubations, the relative abundance of the Rubisco LSU decreased as the incubation progressed. When rumen microorganisms were absent, low molecular weight peptides (below 20 kDa) accumulated as the incubation progressed. This accumulation was not observed in the presence of rumen microorganisms. Therefore we suggest that the intrinsic plant proteases contribute to the initial stages of proteolysis of grazed herbage.     

Radiation dose optimisation and risk estimation to patients and staff during hysterosalpingography

Hysterosalpingography (HSG) is an efficient radiological examination for the evaluation of the female reproductive tract. However, it involves unavoidable irradiation to the ovaries of women in childbearing age. Therefore, radiation dose optimisation is required in order to reduce the probability of the associated risks. This study attempts to: measure patient and staff doses, estimate the effective dose and radiation risk for HSG using digital fluoroscopic images. Thirty-seven patients with infertility were examined using two digital X-ray machines. Thermoluminescence dosimeters (TLD) were used to measure entrance surface dose (ESD) for patients and staff during the procedure. The mean ESD and thyroid surface dose of the patient were 3.60 and 0.17 mGy, respectively, while the mean ESD for the staff was 0.18 mGy per procedure. The patient overall risk for cancer and hereditary effects is 24 x 10(-6), while the risk for the staff is negligible. HSG with fluoroscopic technique demonstrate improved dose characteristics, compared to the conventional radiographic-based technique, reducing the surface dose by a factor of 3, without compromising the diagnostic findings.     

Anti-Inflammatory and Anti-Fibrotic Effect of Immortalized Mesenchymal-Stem-Cell-Derived Conditioned Medium on Human Lung Myofibroblasts and Epithelial Cells

Idiopathic pulmonary fibrosis (IPF) is caused by progressive lung tissue impairment due to extended chronic fibrosis, and it has no known effective treatment. The use of conditioned media (CM) from an immortalized human adipose mesenchymal stem cell line could be a promising therapeutic strategy, as it can reduce both fibrotic and inflammatory responses. We aimed to investigate the anti-inflammatory and anti-fibrotic effect of CM on human pulmonary subepithelial myofibroblasts (hPSM) and on A549 pulmonary epithelial cells, treated with pro-inflammatory or pro-fibrotic mediators. CM inhibited the proinflammatory cytokine-induced mRNA and protein production of various chemokines in both hPSMs and A549 cells. It also downregulated the mRNA expression of IL-1α, but upregulated IL-1β and IL-6 mRNA production in both cell types. CM downregulated the pro-fibrotic-induced mRNA expression of collagen Type III and the migration rate of hPSMs, but upregulated fibronectin mRNA production and the total protein collagen secretion. CM’s direct effect on the chemotaxis and cell recruitment of immune-associated cells, and its indirect effect on fibrosis through the significant decrease in the migration capacity of hPSMs, makes it a plausible candidate for further development towards a therapeutic treatment for IPF.     

An Arduino based automatic pressure evaluation system to quantify growth of non-model anaerobes in culture

Measuring the growth rate of non-model anaerobic microbes typically requires the use of time-consuming and often destructive manual measurements. Here, an Arduino based automatic pressure evaluation system (A-APES) was developed to automatically measure the rate of fermentation gas production as a proxy for microbial growth in anaerobic systems. The A-APES system measures accumulated gas pressure in sealed cultures accurately at high-resolution, while venting the system at programmed intervals to prevent over pressurization. The utility of A-APES is demonstrated in this study by quantifying the growth rate and phases of a biomass-degrading anaerobic gut fungus, which cannot be otherwise measured via conventional techniques due to its association with particulate substrates. Given the utility of the A-APES approach, we provide a complete construction guide to fabricate the device, which is three times less expensive compared to existing commercial alternatives.