Nuclear instruments and methods in physics research section B : beam interactions with materials and atoms

The impact-induced deposition of Al13 clusters with icosahedral structure on Ni(0 0 1) surface was studied by molecular dynamics (MD) simulation using Finnis–Sinclair potentials. The incident kinetic energy (Ein) ranged from 0.01 to 30 eV per atom. The structural and dynamical properties of Al clusters on Ni surfaces were found to be strongly dependent on the impact energy. At much lower energy, the Al cluster deposited on the surface as a bulk molecule. However, the original icosahedral structure was transformed to the fcc-like one due to the interaction and the structure mismatch between the Al cluster and Ni surface. With increasing the impinging energy, the cluster was deformed severely when it contacted the substrate, and then broken up due to dense collision cascade. The cluster atoms spread on the surface at last. When the impact energy was higher than 11 eV, the defects, such as Al substitutions and Ni ejections, were observed. The simulation indicated that there exists an optimum energy range, which is suitable for Al epitaxial growth in layer by layer. In addition, at higher impinging energy, the atomic exchange between Al and Ni atoms will be favourable to surface alloying.

The evolution and biogeography of the austral horse fly tribe Scionini (Diptera: Tabanidae: Pangoniinae) inferred from multiple mitochondrial and nuclear genes

Phylogenetic relationships within the Tabanidae are largely unknown, despite their considerable medical and ecological importance. The first robust phylogenetic hypothesis for the horse fly tribe Scionini is provided, completing the systematic placement of all tribes in the subfamily Pangoniinae. The Scionini consists of seven mostly southern hemisphere genera distributed in Australia, New Guinea, New Zealand and South America. A 5757. bp alignment of 6 genes, including mitochondrial (COI and COII), ribosomal (28S) and nuclear (AATS and CAD regions 1, 3 and 4) genes, was analysed for 176 taxa using both Bayesian and maximum likelihood approaches. Results indicate the Scionini are strongly monophyletic, with the exclusion of the only northern hemisphere genus Goniops. The South American genera Fidena, Pityocera and Scione were strongly monophyletic, corresponding to current morphology-based classification schemes. The most widespread genus Scaptia was paraphyletic and formed nine strongly supported monophyletic clades, each corresponding to either the current subgenera or several previously synonymised genera that should be formally resurrected. Molecular results also reveal a newly recognised genus endemic to New Zealand, formerly placed within Scaptia. Divergence time estimation was employed to assess the global biogeographical patterns in the Pangoniinae. These analyses demonstrated that the Scionini are a typical Gondwanan group whose diversification was influenced by the fragmentation of that ancient land mass. Furthermore, results indicate that the Scionini most likely originated in Australia and subsequently radiated to New Zealand and South American by both long distance dispersal and vicariance. The phylogenetic framework of the Scionini provided herein will be valuable for taxonomic revisions of the Tabanidae.

Characterisation of candidate nuclear genes for species delineation in the genus Cherax

Understanding the evolutionary history and phylogenetic relationships between rare and common species is necessary for the effective management of rare species. The genus Cherax, a group of freshwater crayfish species, is of interest in this regard as a number of species are rare or have restricted distributions while other species are common and widespread. Here we describe the characterisation of three novel nuclear genes of the haemocyanin superfamily for phylogenetic reconstruction of the genus. All novel markers developed in this study amplified consistently in species from three divergent clades of the genus Cherax. The level of polymorphism found in these markers was consistently higher than that found in other nuclear genes previously used in invertebrate systematics, such as NaK ATP-ase. In combination, these markers will be useful to delineate phylogenetic relationships between rare and common Cherax species.

Detection of mRNA levels for the estrogen alpha, estrogen beta and androgen nuclear receptor genes in archival breast cancer tissue

Previous studies in our laboratory have shown association of nuclear receptor expression and histological breast cancer grade. To further investigate these findings, it was the objective of this study to determine if expression levels of the estrogen alpha, estrogen beta and androgen nuclear receptor genes varied in different breast cancer grades. RNA extracted from paraffin embedded archival breast tumour tissue was converted into cDNA and cDNA underwent PCR to enable quantitation of mRNA expression. Expression data was normalised against the 18S ribosomal gene multiplex and analysed using ANOVA. Analysis indicated a significant alteration of expression for the androgen receptor in different cancer grades (P=0.014), as well as in tissues that no longer possess estrogen receptor alpha proteins (P=0.025). However, expression of estrogen receptors alpha and beta did not vary significantly with cancer grade (P=0.057 and 0.622, respectively). Also, the expression of estrogen receptor alpha or beta did not change, regardless of the presence of estrogen receptor alpha protein in the tissue (P=0.794 and 0.716, respectively). Post-hoc tests indicate that the expression of the androgen receptor is increased in estrogen receptor negative tissue as well as in grade 2 and grade 3 tumours, compared to control tissue. This increased expression in late stage breast tumours may have implications to the treatment of breast tumours, particularly those lacking expression of other nuclear receptor genes.

Detection of mRNA for nuclear receptor co-activators 1 and 3 in archival breast cancer tissue and surrounding stroma : a tissue expression study

Before the age of 75 years, approximately 10% of women will be diagnosed with breast cancer, one of the most common malignancies and a leading cause of death among women. The objective of this study was to determine if expression of the nuclear receptor coactivators 1 and 3 (NCoA1 and NCoA3) varied in breast cancer grades. RNA was extracted from 25 breast tumours and transcribed into cDNA which underwent semi-quantitative polymerase chain reaction, normalised using 18S. Analysis indicated that an expression change for NCoA1 in cancer grades and estrogen receptor alpha negative tissue (P= 0.028 and 0.001 respectively). NCoA1 expression increased in grade 3 and estrogen receptor alpha negative tumours, compared to controls. NCoA3 showed a similar, but not significant, trend in grade and a non-significant decrease in estrogen receptor alpha negative tissues. Expression of NCoA1 in late stage and estrogen receptor alpha negative breast tumours may have implications to breast cancer treatment, particularly in the area of manipulation of hormone signalling systems in advanced tumours.

Expression of glucocorticoid and progesterone nuclear receptor genes in archival breast cancer tissue.

BACKGROUND: Previous studies in our laboratory have shown associations of specific nuclear receptor gene variants with sporadic breast cancer. In order to investigate these findings further, we conducted the present study to determine whether expression levels of the progesterone and glucocorticoid nuclear receptor genes vary in different breast cancer grades. METHODS: RNA was extracted from paraffin-embedded archival breast tumour tissue and converted into cDNA. Sample cDNA underwent PCR using labelled primers to enable quantitation of mRNA expression. Expression data were normalized against the 18S ribosomal gene multiplex and analyzed using analysis of variance. RESULTS: Analysis of variance indicated a variable level of expression of both genes with regard to breast cancer grade (P = 0.00033 for glucocorticoid receptor and P = 0.023 for progesterone receptor). CONCLUSION: Statistical analysis indicated that expression of the progesterone nuclear receptor is elevated in late grade breast cancer tissue.

The construction of social identity in new nuclear operators : a longitudinal study

Countless studies have stressed the importance of social identity, particularly its role in various organizational outcomes, yet questions remain as to how identities initially develop, shift and change based on the configuration of multiple, pluralistic relationships grounded in an organizational setting. The interactive model of social identity formation has been proposed recently to explain the internalization of shared norms and values – critical in identity formation – has not received empirical examination. We analyzed multiple sources of data from nine nuclear professionals over three years to understand the construction of social identity in new entrants entering an organization. Informed by our data analyses, we found support for the interactive model and that age and level of experience influenced whether they undertook an inductive or deductive route of the group norm and value internalization. This study represents an important contribution to the study of social identity and the process by which identities are formed, particularly under conditions of duress or significant organizational disruption.

Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis

In plants, silencing of mRNA can be transmitted from cell to cell and also over longer distances from roots to shoots. To investigate the long-distance mechanism, WT and mutant shoots were grafted onto roots silenced for an mRNA. We show that three genes involved in a chromatin silencing pathway, NRPD1a encoding RNA polymerase IVa, RNA-dependent RNA polymerase 2 (RDR2), and DICER-like 3 (DCL3), are required for reception of long-distance mRNA silencing in the shoot. A mutant representing a fourth gene in the pathway, argonaute4 (ago4), was also partially compromised in the reception of silencing. This pathway produces 24-nt siRNAs and resulted in decapped RNA, a known substrate for amplification of dsRNA by RDR6. Activation of silencing in grafted shoots depended on RDR6, but no 24-nt siRNAs were detected in mutant rdr6 shoots, indicating that RDR6 also plays a role in initial signal perception. After amplification of decapped transcripts, DCL4 and DCL2 act hierarchically as they do in antiviral resistance to produce 21- and 22-nt siRNAs, respectively, and these guide mRNA degradation. Several dcl genotypes were also tested for their capacity to transmit the mobile silencing signal from the rootstock. dcl1-8 and a dcl2 dcl3 dcl4 triple mutant are compromised in micro-RNA and siRNA biogenesis, respectively, but were unaffected in signal transmission. © 2007 by The National Academy of Sciences of the USA.

Taxonomy and redescription of the Fawn Antechinus, Antechinus bellus (Thomas) (Marsupialia: Dasyuridae)

We provide a taxonomic redescription of the Fawn Antechinus, Antechinus bellus (Thomas). A. bellus is the only member of its genus to occur in Australia’s Northern Territory, where it can be found in savannah woodlands of the Top End. It is perhaps the most distinctive antechinus, and clearly distinguishable from the other 10 extant species of antechinus found in Australia: externally, A. bellus has pale body fur, white feet and large ears; A. bellus skulls have large auditory bullae and narrow interorbital width, while broadening abruptly at the molar row; mitochondrial and nuclear genes clearly dis-tinguish A. bellus from all congeners, phylogenetically positioning the Fawn Antechinus as sister to Queensland’s A. leo Van Dyck, 1980, with which it shares a curled supratragus of the external ear and a similar tropical latitudinal range.

Targeting nuclear factor-kappa B to overcome resistance to chemotherapy

Intrinsic or acquired resistance to chemotherapeutic agents is a common phenomenon and a major challenge in the treatment of cancer patients. Chemoresistance is defined by a complex network of factors including multi-drug resistance proteins, reduced cellular uptake of the drug, enhanced DNA repair, intracellular drug inactivation, and evasion of apoptosis. Pre-clinical models have demonstrated that many chemotherapy drugs, such as platinum-based agents, antracyclines, and taxanes, promote the activation of the NF-κB pathway. NF-κB is a key transcription factor, playing a role in the development and progression of cancer and chemoresistance through the activation of a multitude of mediators including anti-apoptotic genes. Consequently, NF-κB has emerged as a promising anti-cancer target. Here, we describe the role of NF-κB in cancer and in the development of resistance, particularly cisplatin. Additionally, the potential benefits and disadvantages of targeting NF-κB signaling by pharmacological intervention will be addressed.

Jacobian-free Newton-Krylov methods with GPU acceleration for computing nonlinear ship wave patterns

The nonlinear problem of steady free-surface flow past a submerged source is considered as a case study for three-dimensional ship wave problems. Of particular interest is the distinctive wedge-shaped wave pattern that forms on the surface of the fluid. By reformulating the governing equations with a standard boundary-integral method, we derive a system of nonlinear algebraic equations that enforce a singular integro-differential equation at each midpoint on a two-dimensional mesh. Our contribution is to solve the system of equations with a Jacobian-free Newton-Krylov method together with a banded preconditioner that is carefully constructed with entries taken from the Jacobian of the linearised problem. Further, we are able to utilise graphics processing unit acceleration to significantly increase the grid refinement and decrease the run-time of our solutions in comparison to schemes that are presently employed in the literature. Our approach provides opportunities to explore the nonlinear features of three-dimensional ship wave patterns, such as the shape of steep waves close to their limiting configuration, in a manner that has been possible in the two-dimensional analogue for some time.

The Fukushima nuclear power plant disaster and percetions of health risk communication : a case study

This case study was conducted to explore the perceptions of health risk messages sent by the Japanese Government following the Fukushima nuclear power plant disaster. The content of health risk messages from the Japanese Government and the Japanese national broadcaster (NHK) were analysed and semi-structured interviews were conducted with a sample of Tokyo residents. Initially, participants trusted these messages but as the crisis unfolded they became sceptical about the messages. Participants felt the messages did not communicate health risk information effectively because the messages were; not supported by evidence, inconsistent, delayed and changed over time. Despite widespread access to the internet, social media and mobile telephones, most participants relied on television news for information about the health risks. The Japanese Government urgently needs to re-build trust by engaging the community in the planning and development phases of health risk communication strategies.

Ship Motion Control : Course Keeping and Roll Stabilisation Using Rudder and Fins

Motion control systems have a significant impact on the performance of ships and marine structures allowing them to perform tasks in severe sea states and during long periods of time. Ships are designed to operate with adequate reliability and economy, and in order to achieve this, it is essential to control the motion. For each type of ship and operation performed (transit, landing a helicopter, fishing, deploying and recovering loads, etc.), there are not only desired motion settings, but also limits on the acceptable (undesired) motion induced by the environment. The task of a ship motion control system is therefore to act on the ship so it follows the desired motion as closely as possible. This book provides an introduction to the field of ship motion control by studying the control system designs for course-keeping autopilots with rudder roll stabilisation and integrated rudder-fin roll stabilisation. These particular designs provide a good overview of the difficulties encountered by designers of ship motion control systems and, therefore, serve well as an example driven introduction to the field. The idea of combining the control design of autopilots with that of fin roll stabilisers, and the idea of using rudder induced roll motion as a sole source of roll stabilisation seems to have emerged in the late 1960s. Since that time, these control designs have been the subject of continuous and ongoing research. This ongoing interest is a consequence of the significant bearing that the control strategy has on the performance and the issues associated with control system design. The challenges of these designs lie in devising a control strategy to address the following issues: underactuation, disturbance rejection with a non minimum phase system, input and output constraints, model uncertainty, and large unmeasured stochastic disturbances. To date, the majority of the work reported in the literature has focused strongly on some of the design issues whereas the remaining issues have been addressed using ad hoc approaches. This has provided an additional motivation for revisiting these control designs and looking at the benefits of applying a contemporary design framework, which can potentially address the majority of the design issues.

Ship roll damping control

The technical feasibility of roll motion control devices has been amply demonstrated for over 100 years. Performance, however, can still fall short of expectations because of difficulties associated with control system designs, which have proven to be far from trivial due to fundamental performance limitations and large variations of the spectral characteristics of wave-induced roll motion. This tutorial paper presents an account of the development of various ship roll motion control systems together with the challenges associated with their design. It discusses the assessment of performance and the applicability of different mathematical models, and it surveys the control methods that have been implemented and validated with full scale experiments. The paper also presents an outlook on what are believed to be potential areas of research within this topic.

Constrained predictive control of ship fin stabilizers to prevent dynamic stall

In moderate to high sea states, the effectiveness of ship fin stabilizers can severely deteriorate due to nonlinear effects arising from unsteady hydrodynamic characteristics of the fins: dynamic stall. These nonlinear effects take the form of a hysteresis, and they become very significant when the effective angle of attack of the fins exceeds a certain threshold angle. Dynamic stall can result in a complete loss of control action depending on how much the fins exceed the threshold angle. When this is detected, it is common to reduce the gain of the controller that commands the fins. This approach is cautious and tends to reduce performance when the conditions leading to dynamic stall disappear. An alternative approach for preventing the effects while keeping high performance, consists of estimating the effective angle of attack and set a conservative constraint on it as part of the control objectives. In this paper, we investigate the latter approach, and propose the use of a model predictive control (MPC) to prevent the development of these nonlinear effects by considering constraints on both the mechanical angle of the fins and the effective angle of attack.