Talking of many things : using topical networks to study discussions in social media

This paper outlines a method for studying online activity using both qualitative and quantitative methods: topical network analysis. A topical network refers to "the collection of sites commenting on a particular event or issue, and the links between them" (Highfield, Kirchhoff, & Nicolai, 2011, p. 341). The approach is a complement for the analysis of large datasets enabling the examination and comparison of different discussions as a means of improving our understanding of the uses of social media and other forms of online communication. Developed for an analysis of political blogging, the method also has wider applications for other social media websites such as Twitter.

Protein monoubiquitination and polyubiquitination generate structural diversity to control distinct biological processes

Ubiquitination involves the attachment of ubiquitin (Ub) to lysine residues on substrate proteins or itself, which can result in protein monoubiquitination or polyubiquitination. Polyubiquitination through different lysines (seven) or the N-terminus of Ub can generate different protein-Ub structures. These include monoubiquitinated proteins, polyubiqutinated proteins with homotypic chains through a particular lysine on Ub or mixed polyubiquitin chains generated by polymerization through different Ub lysines. The ability of the ubiquitination pathway to generate different protein-Ub structures provides versatility of this pathway to target proteins to different fates. Protein ubiquitination is catalyzed by Ub-conjugating and Ub-ligase enzymes, with different combinations of these enzymes specifying the type of Ub modification on protein substrates. How Ub-conjugating and Ub-ligase enzymes generate this structural diversity is not clearly understood. In the current review, we discuss mechanisms utilized by the Ub-conjugating and Ub-ligase enzymes to generate structural diversity during protein ubiquitination, with a focus on recent mechanistic insights into protein monoubiquitination and polyubiquitination.

Krüppel-associated box (KRAB)-associated co-repressor (KAP-1) Ser-473 phosphorylation regulates heterochromatin protein 1 (HP1- ) mobilization and DNA repair in heterochromatin

The DNA damage response encompasses a complex series of signaling pathways that function to regulate and facilitate the repair of damaged DNA. Recent studies have shown that the repair of transcriptionally inactive chromatin, named heterochromatin, is dependent upon the phosphorylation of the co-repressor, Krüppel-associated box (KRAB) domain-associated protein (KAP-1), by the ataxia telangiectasia-mutated (ATM) kinase. Co-repressors, such as KAP-1, function to regulate the rigid structure of heterochromatin by recruiting histone-modifying enzymes, such HDAC1/2, SETDB1, and nucleosome-remodeling complexes such as CHD3. Here, we have characterized a phosphorylation site in the HP1-binding domain of KAP-1, Ser-473, which is phosphorylated by the cell cycle checkpoint kinase Chk2. Expression of a nonphosphorylatable S473A mutant conferred cellular sensitivity to DNA-damaging agents and led to defective repair of DNA double-strand breaks in heterochromatin. In addition, cells expressing S473A also displayed defective mobilization of the HP1-β chromodomain protein. The DNA repair defect observed in cells expressing S473A was alleviated by depletion of HP1-β, suggesting that phosphorylation of KAP-1 on Ser-473 promotes the mobilization of HP1-β from heterochromatin and subsequent DNA repair. These results suggest a novel mechanism of KAP-1-mediated chromatin restructuring via Chk2-regulated HP1-β exchange from heterochromatin, promoting DNA repair.

A note on a reaction-diffusion model describing the bone morphogen protein gradient in Drosophila embryonic patterning

In this article, we consider the Eldar model [3] from embryology in which a bone morphogenic protein, a short gastrulation protein, and their compound react and diffuse. We carry out a perturbation analysis in the limit of small diffusivity of the bone morphogenic protein. This analysis establishes conditions under which some elementary results of [3] are valid.

A qualitative study of stakeholder views of the conditions for and outcomes of successful clinical networks

The article informs on a research that analyzes the views of the stakeholders on the conditions required for the effective working on the clinical networks and the outcomes that marks the success of the networks. It is mentioned that clinical networks work to improve the health care access and outcome by undertaking innovations and projects based on local requirements. The factors for the success of clinical networks include building relationships, effective leadership and strategic workplans.

Effect of bone morphogenetic protein-4 (BMP-4) on the expression of Sox2, Oct-4 and c-Myc in human periodontal ligament cells during long-term culture

Recent studies demonstrated endogenous expression level of Sox2, Oct-4 and c-Myc is correlated with the pluripotency and successful induction of induced pluripotent stem cells (iPSCs). Periondontal ligament cells (PDLCs)have multi-lineage diferentiation capability and ability to maintain undifferentiated stage, which makes PDLCs a suitable cell source for tissue repair and regeneration. To elucidate the effect of in vitro culture condition on the stemness potential of PDLCs, we explored the cell growth, proliferation, cell cycle, and the expression of Sox2, Oct-4 and c-Myc in PDLCs from passage 1 to 7 with or without the addition of recombinant human BMP4(rhBMP4). Our results revealed that BMP-4 promoted cell growth and proliferation, arrested PDLCs in S phase of cell cycle and upregulated PI value. It was revealed that without the addition of rhBMP4, the expression of Sox2, Oct-4 and c-Myc in PDLCs only maintained nucleus location until passage 3, then lost nucleus location subsequently. The mRNA expression in PDLCs further confirmed that the level of Sox2 and Oct-4 peaked at passage 3, then decreased afterwards, whereas c-Myc maintained consistently upregulation along passages. after the treatment with rhBMP4, the expression of Sox2, Oct-4 and c-Myc in PDLCs maintained nucleus location even at passage 7 and the mRNA expression of Sox2 and Oct-4 significantly upregulated at passage 5 and 7. These results demonstrated that addition of rhBMP-4 in the culture media could improve the current culture condition for PDLCs to maintain in an undifferentiated stage.

Funds of knowledge of sorting and patterning : networks of exchange in a Torres Strait Island community

The purpose of this article is to describe a project with one Torres Strait Islander Community. It provides some insights into parents’ funds of knowledge that are mathematical in nature, such as sorting shells and giving fish. The idea of funds of knowledge is based the premise that people are competent and have knowledge that has been historically and culturally accumulated into a body of knowledge and skills essential for their functioning and well-being. This knowledge is then practised throughout their lives and passed onto the next generation of children. Through using a community research approach, funds of knowledge that can be used to validate the community’s identities as knowledgeable people, can be used as foundations for future learnings for teachers, parents and children in the early years of school. They can be the bridge that joins a community’s funds of knowledge with schools validating that knowledge.

Combinatorial design of key distribution mechanisms for wireless sensor networks

Secure communications in wireless sensor networks operating under adversarial conditions require providing pairwise (symmetric) keys to sensor nodes. In large scale deployment scenarios, there is no prior knowledge of post deployment network configuration since nodes may be randomly scattered over a hostile territory. Thus, shared keys must be distributed before deployment to provide each node a key-chain. For large sensor networks it is infeasible to store a unique key for all other nodes in the key-chain of a sensor node. Consequently, for secure communication either two nodes have a key in common in their key-chains and they have a wireless link between them, or there is a path, called key-path, among these two nodes where each pair of neighboring nodes on this path have a key in common. Length of the key-path is the key factor for efficiency of the design. This paper presents novel deterministic and hybrid approaches based on Combinatorial Design for deciding how many and which keys to assign to each key-chain before the sensor network deployment. In particular, Balanced Incomplete Block Designs (BIBD) and Generalized Quadrangles (GQ) are mapped to obtain efficient key distribution schemes. Performance and security properties of the proposed schemes are studied both analytically and computationally. Comparison to related work shows that the combinatorial approach produces better connectivity with smaller key-chain sizes.

Establishing initial trust in autonomous delay tolerant networks without centralised PKI

A Delay Tolerant Network (DTN) is one where nodes can be highly mobile, with long message delay times forming dynamic and fragmented networks. Traditional centralised network security is difficult to implement in such a network, therefore distributed security solutions are more desirable in DTN implementations. Establishing effective trust in distributed systems with no centralised Public Key Infrastructure (PKI) such as the Pretty Good Privacy (PGP) scheme usually requires human intervention. Our aim is to build and compare different de- centralised trust systems for implementation in autonomous DTN systems. In this paper, we utilise a key distribution model based on the Web of Trust principle, and employ a simple leverage of common friends trust system to establish initial trust in autonomous DTN’s. We compare this system with two other methods of autonomously establishing initial trust by introducing a malicious node and measuring the distribution of malicious and fake keys. Our results show that the new trust system not only mitigates the distribution of fake malicious keys by 40% at the end of the simulation, but it also improved key distribution between nodes. This paper contributes a comparison of three de-centralised trust systems that can be employed in autonomous DTN systems.

A reliable real-time transport protocol for control systems over wireless networks

Deploying networked control systems (NCSs) over wireless networks is becoming more and more popular. However, the widely-used transport layer protocols, Transmission Control Protocol (TCP) and User Datagram Protocol (UDP), are not designed for real-time applications. Therefore, they may not be suitable for many NCS application scenarios because of their limitations on reliability and/or delay performance, which real-control systems concern. Considering a typical type of NCSs with periodic and sporadic real-time traffic, this paper proposes a highly reliable transport layer protocol featuring a packet loss-sensitive retransmission mechanism and a prioritized transmission mechanism. The packet loss-sensitive retransmission mechanism is designed to improve the reliability of all traffic flows. And the prioritized transmission mechanism offers differentiated services for periodic and sporadic flows. Simulation results show that the proposed protocol has better reliability than UDP and improved delay performance than TCP over wireless networks, particularly when channel errors and congestions occur.

Efficient route update and maintenance processes for multipath routing in large-scale industrial wireless sensor networks

Reliable communications is one of the major concerns in wireless sensor networks (WSNs). Multipath routing is an effective way to improve communication reliability in WSNs. However, most of existing multipath routing protocols for sensor networks are reactive and require dynamic route discovery. If there are many sensor nodes from a source to a destination, the route discovery process will create a long end-to-end transmission delay, which causes difficulties in some time-critical applications. To overcome this difficulty, the efficient route update and maintenance processes are proposed in this paper. It aims to limit the amount of routing overhead with two-tier routing architecture and introduce the combination of piggyback and trigger update to replace the periodic update process, which is the main source of unnecessary routing overhead. Simulations are carried out to demonstrate the effectiveness of the proposed processes in improvement of total amount of routing overhead over existing popular routing protocols.

Key Management in Wireless Sensor Networks

This chapter presents a comparative survey of recent key management (key distribution, discovery, establishment and update) solutions for wireless sensor networks. We consider both distributed and hierarchical sensor network architectures where unicast, multicast and broadcast types of communication take place. Probabilistic, deterministic and hybrid key management solutions are presented, and we determine a set of metrics to quantify their security properties and resource usage such as processing, storage and communication overheads. We provide a taxonomy of solutions, and identify trade-offs in these schemes to conclude that there is no one-size-fits-all solution.

Polycaprolactone-based scaffold plus recombinant human bone morphogenic protein rhBMP-2) in a sheep thoracic spine fusion model

Adolescent idiopathic scoliosis is a complex three dimensional deformity affecting 2-3% of the general population. The resulting spinal deformity consists of coronal curvature, hypokyphosis of the thoracic spine and vertebral rotation in the axial plane with posterior elements turned into the curve concavity. The potential for curve progression is heightened during the adolescent growth spurt. Success of scoliosis deformity correction depends on solid bony fusion between adjacent vertebrae after the intervertebral (IV) discs have been surgically cleared and the disc spaces filled with graft material. Recently a bioactive and resorbable scaffold fabricated from medical grade polycaprolactone has been developed for bone regeneration at load bearing sites. Combined with rhBMP-2, this has been shown to be successful in acting as a bone graft substitute in a porcine lumbar interbody fusion model when compared to autologous bone graft alone. The study aimed to establish a large animal thoracic spine interbody fusion model, develop spine biodegradable scaffolds (PCL) in combination with biologics (rhBMP-2) and to establish a platform for research into spine tissue engineering constructs. Preliminary results demonstrate higher grades of radiologically evident bony fusion across all levels when comparing fusion scores between the 3 and 6 month postop groups at the PCL CaP coated scaffold level, which is observed to be a similar grade to autograft, while no fusion is seen at the scaffold only level. Results to date suggest that the combination of rhBMP-2 and scaffold engineering actively promotes bone formation, laying the basis of a viable tissue engineered constructs.