Exploiting OpenMP and OpenACC to accelerate a geometric approach to molecular docking in heterogeneous HPC nodes

The Journal of Supercomputing - In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used...     

Verifying data secure flow in AUTOSAR models

This paper presents an approach for enhancing the design phase of AUTOSAR models when security annotations are required. The approach is based on information flow analysis and abstract interpretation. The analysis evaluates the correctness of the model by assessing if the flow of data is secure with respect to causal data dependencies within the model. To find these dependencies an exhaustive search through the model would be required. Abstract interpretation is used as a trade-off between the precision and complexity of the analysis. The approach also provides annotated models without oversizing the set of annotations.     

An effective extension of the applicability of alignment-free biological sequence comparison algorithms with Hadoop

Alignment-free methods are one of the mainstays of biological sequence comparison, i.e., the assessment of how similar two biological sequences are to each other, a fundamental and routine task in computational biology and bioinformatics. They have gained popularity since, even on standard desktop machines, they are faster than methods based on alignments. However, with the advent of Next-Generation Sequencing Technologies, datasets whose size, i.e., number of sequences and their total length, is a challenge to the execution of alignment-free methods on those standard machines are quite common. Here, we propose the first paradigm for the computation of k-mer-based alignment-free methods for Apache Hadoop that extends the problem sizes that can be processed with respect to a standard sequential machine while also granting a good time performance. Technically, as opposed to a standard Hadoop implementation, its effectiveness is achieved thanks to the incremental management of a persistent hash table during the map phase, a task not contemplated by the basic Hadoop functions and that can be useful also in other contexts.     

From risk factors to detection and intervention: a practical proposal for future work on cyberbullying

While there is an increasing flow of media stories reporting cases of cyberbullying, particularly within online social media, research efforts in the academic community are scattered over different topics across the social science and computer science academic disciplines. In this work, we explored research pertaining to cyberbullying, conducted across disciplines. We mainly sought to understand scholarly activity on intelligence techniques for the detection of cyberbullying when it occurs. Our findings suggest that the vast majority of academic contributions on cyberbullying focus on understanding the phenomenon, risk factors, and threats, with the prospect of suggesting possible protection strategies. There is less work on intelligence techniques for the detection of cyberbullying when it occurs, while currently deployed algorithms seem to detect the problem only up to some degree of success. The article summarises the current trends aiming to encourage discussion and research with a new scope; we call for more research tackling the problem by leveraging statistical models and computational mechanisms geared to detect, intervene, and prevent cyberbullying. Coupling intelligence techniques with specific web technology problems can help combat this social menace. We argue that a multidisciplinary approach is needed, with expertise from human–computer interaction, psychology, computer science, and sociology, for current challenges to be addressed and significant progress to be made.     

Energy-optimal collaborative file distribution in wired networks

The impact of the ICT sector in worldwide power consumption is an increasing concern, motivating the research community to devote an important effort to define novel energy efficient networking solutions. Despite file distribution is responsible for a major portion of the current Internet traffic, little effort has been dedicated to address the issue of its energy efficiency so far. Most of the previous literature focuses on optimizing the download time of file distribution schemes (e.g. centralized server-based or distributed peer-to-peer solutions) while it is yet unclear how to optimize file distribution schemes from the point of view of energy consumed. In this paper, we present a general modelling framework to analyze the energy consumption of file distribution systems. First, we show that the general problem of minimizing energy consumption in file distribution is NP-hard. Then, for restricted versions of the problem, we establish theoretical bounds to minimal energy consumption. Furthermore, we define a set of optimal algorithms for a variety of system settings, which exploit the service capabilities of hosts in a P2P fashion. We show that our schemes are capable of reducing at least 50 % of the energy consumed by traditional (yet largely used) centralized distribution schemes even when considering effects such as network congestion and heterogeneous access speed across nodes.     

Ultrastructural characteristics of ovine bone marrow‐derived mesenchymal stromal cells cultured with a silicon stabilized tricalcium phosphate bioceramic

Bioceramics are being used in experimental bone engineering application in association with bone marrow derived mesenchymal stem cells (BM‐MSCs) as a new therapeutic tool, but their effects on the ultrastructure of BM‐MSCs are yet unknown. In this study we report the morphological features of ovine (o)BM‐MSCs cultured with Skelite, a resorbable bioceramic based on silicon stabilized tricalcium phosphate (SiTCP), able to promote the repair of induced bone defect in sheep model. oBM‐MSCs were isolated from the iliac crest, cultured until they reached near‐confluence and incubated with SiTCP. After 48 hr the monolayers were highly damaged and only few cells adhered to the plastic. Thus, SiTCP was removed, and after washing the cells were cultured until they became confluent. Then, they were trypsinizated and processed for transmission electron microscopy (TEM) and RT‐PCR analysis. RT‐PCR displayed that oBM‐MSCs express typical surface marker for MSCs. TEM revealed the presence of electron‐lucent cells and electron‐dense cells, both expressing the CD90 surface antigen. The prominent feature of electron‐lucent cells was the concentration of cytoplasmic organelles around the nucleus as well as large surface blebs containing glycogen or profiles of endoplasmic reticulum. The dark cells had a multilocular appearance by the presence of peripheral vacuoles. Some dark cells contained endocytic vesicles, lysosomes, and glycogen aggregates. oBM‐MSCs showed different types of specialized interconnections. The comparison with ultrastructural features of untreated oBM‐MSCs suggests the light and dark cells are two distinct cell types which were differently affected by SiTCP bioceramic. Skelite cultured ovine BM‐MSCs display electron‐dense and electron‐lucent cells which are differently affected by this bioceramic. This suggests that they could play a different role in bioceramic based therapy.     

Development of a toughened DGEBS/DDS system toward improved thermal and mechanical properties by the addition of a tetrafunctional epoxy resin and a novel thermoplastic

It was the object of the present article to discuss the effect of the addition of a tetrafunctional resin, namely, tetraglycidyl‐4,4′‐diaminodiphenylmethane (TGDDM), and of a novel 40:60 polyethersulfone:polyetherethersulfone (PES:PEES) copolymer on a blend constituted by a difunctional resin, diglycidyl ether of bisphenol S (DGEBS), and an aromatic ammine, 4,4′‐diaminodiphenylsulfone (4,4′DDS). The formulated blends were fully characterized in terms of the morphology and the viscoelastic and mechanical properties. The modification by the tetrafunctional resin was proved to be a useful means to improve the glass transition temperature and, therefore, to widen the range of the working temperature. The addition of the novel copolymer resulted in a marked increase in toughness without negatively affecting the thermal and elastic properties of the blend. TEM analysis, despite the high amount of thermoplastic used, showed a homogeneous morphology that would lead to the conclusion of the existence of a full‐IPN network. Moisture‐uptake experiments were conducted both on the blend and on the resins on their own. It was shown that the combination of the difunctional resin with the tetrafunctional led to a decrease of the percent of the water absorbed. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 268–273, 2003     

A mixed-integer linear programming approach to the optimization of event-bus schedules: a scheduling application in the tourism sector

This paper deals with “The Enchanted Journey,” which is a daily event tour booked by Bollywood-film fans. During the tour, the participants visit original sites of famous Bollywood films at various locations in Switzerland; moreover, the tour includes stops for lunch and shopping. Each day, up to five buses operate the tour. For operational reasons, however, two or more buses cannot stay at the same location simultaneously. Further operative constraints include time windows for all activities and precedence constraints between some activities. The planning problem is how to compute a feasible schedule for each bus. We implement a two-step hierarchical approach. In the first step, we minimize the total waiting time; in the second step, we minimize the total travel time of all buses. We present a basic formulation of this problem as a mixed-integer linear program. We enhance this basic formulation by symmetry-breaking constraints, which reduces the search space without loss of generality. We report on computational results obtained with the Gurobi Solver. Our numerical results show that all relevant problem instances can be solved using the basic formulation within reasonable CPU time, and that the symmetry-breaking constraints reduce that CPU time considerably.     

Potential Anti-Metastatic Role of the Novel miR-CT3 in Tumor Angiogenesis and Osteosarcoma Invasion

Osteosarcoma (OS) is the most common primary bone tumor mainly occurring in young adults and derived from primitive bone-forming mesenchyme. OS develops in an intricate tumor microenvironment (TME) where cellular function regulated by microRNAs (miRNAs) may affect communication between OS cells and the surrounding TME. Therefore, miRNAs are considered potential therapeutic targets in cancer and one of the goals of research is to accurately define a specific signature of a miRNAs, which could reflect the phenotype of a particular tumor, such as OS. Through NGS approach, we previously found a specific molecular profile of miRNAs in OS and discovered 8 novel miRNAs. Among these, we deepen our knowledge on the fifth candidate renamed now miR-CT3. MiR-CT3 expression was low in OS cells when compared with human primary osteoblasts and healthy bone. Through TargetScan, VEGF-A was predicted as a potential biological target of miR-CT3 and luciferase assay confirmed it. We showed that enforced expression of miR-CT3 in two OS cell lines, SAOS-2 and MG-63, reduced expression of VEGF-A mRNA and protein, inhibiting tumor angiogenesis. Enforced expression of miR-CT3 also reduced OS cell migration and invasion as confirmed by soft agar colony formation assay. Interestingly, we found that miR-CT3 behaves inducing the activation of p38 MAP kinase pathway and modulating the epithelial-mesenchymal transition (EMT) proteins, in particular reducing Vimentin expression. Overall, our study highlights the novel role of miR-CT3 in regulating tumor angiogenesis and progression in OS cells, linking also to the modulation of EMT proteins.     

Quinagolide Treatment Reduces Invasive and Angiogenic Properties of Endometrial Mesenchymal Stromal Cells

Endometrial mesenchymal stromal cells (E-MSCs) extensively contribute to the establishment and progression of endometrial ectopic lesions through formation of the stromal vascular tissue, and support to its growth and vascularization. As E-MSCs lack oestrogen receptors, endometriosis eradication cannot be achieved by hormone-based pharmacological approaches. Quinagolide is a non-ergot-derived dopamine receptor 2 agonist reported to display therapeutic effects in in vivo models of endometriosis. In the present study, we isolated E-MSCs from eutopic endometrial tissue and from ovarian and peritoneal endometriotic lesions, and we tested the effect of quinagolide on their proliferation and matrix invasion ability. Moreover, the effect of quinagolide on E-MSC endothelial differentiation was assessed in an endothelial co-culture model of angiogenesis. E-MSC lines expressed dopamine receptor 2, with higher expression in ectopic than eutopic ones. Quinagolide inhibited the invasive properties of E-MSCs, but not their proliferation, and limited their endothelial differentiation. The abrogation of the observed effects by spiperone, a dopamine receptor antagonist, confirmed specific dopamine receptor activation. At variance, no involvement of VEGFR2 inhibition was observed. Moreover, dopamine receptor 2 activation led to downregulation of AKT and its phosphorylation. Of interest, several effects were more prominent on ectopic E-MSCs with respect to eutopic lines. Together with the reported effects on endometrial and endothelial cells, the observed inhibition of E-MSCs may increase the rationale for quinagolide in endometriosis treatment.