Numerical investigation of mechanical properties of nanowires : a review

Nanowires (NWs) have attracted intensive researches owing to the broad applications that arise from their remarkable properties. Over the last decade, immense numerical studies have been conducted for the numerical investigation of mechanical properties of NWs. Among these numerical simulations, the molecular dynamics (MD) plays a key role. Herein we present a brief review on the current state of the MD investigation of nanowires. Emphasis will be placed on the FCC metal NWs, especially the Cu NWs. MD investigations of perfect NWs’ mechanical properties under different deformation conditions including tension, compression, torsion and bending are firstly revisited. Following in succession, the studies for defected NWs including the defects of twin boundaries (TBs) and pre-existing defects are discussed. The different deformation mechanism incurred by the presentation of defects is explored and discussed. This review reveals that the numerical simulation is an important tool to investigate the properties of NWs. However, the substantial gaps between the experimental measurements and MD results suggest the urgent need of multi-scale simulation technique.

Control and application of minimally-actuated underwater vehicles

Establishing a persistent presence in the ocean with an Autonomous Underwater Vehicle capable of observing temporal variability of large-scale ocean processes requires a unique sensor platform. In this paper, we examine the utility of Lagrangian profiling floats for such extended deployments. We propose a strategy that utilizes ocean model predictions to facilitate a basic level of autonomy to achieve general control of this minimally-actuated underwater vehicle. We extend experimentally validated techniques for utilising ocean current models to control under-actuated autonomous underwater vehicles by presenting this investigation into the application of these methods on profiling floats. With the appropriate vertical actuation, and utilising spatiotemporal variations in water speed and direction, we show that broad controllability results can be met. First, we apply an A* planner to a local controllability map generated from predictions of ocean currents. This computes a path between start and goal waypoints that has the highest likelihood of successful execution over a given duration. The computed depth plan is generated with a model predictive controller, and selects the depths for the vehicle so that ambient currents guide it toward the goal. Mission constraints are included to simulate and motivate a practical data collection mission. Results are presented in simulation for a mission off the coast of Los Angeles, CA USA, that show surprising results in the ability of a drifting vehicle to maintain a prescribed course and reach a desired location.

Viruses of banana in East Africa

Bananas are one of the world's most important food crops, providing sustenance and income for millions of people in developing countries and supporting large export industries. Viruses are considered major constraints to banana production, germplasm multiplication and exchange, and to genetic improvement of banana through traditional breeding. In Africa, the two most important virus diseases are bunchy top, caused by Banana bunchy top virus (BBTV), and banana streak disease, caused by Banana streak virus (BSV). BBTV is a serious production constraint in a number of countries within/bordering East Africa, such as Burundi, Democratic Republic of Congo, Malawi, Mozambique, Rwanda and Zambia, but is not present in Kenya, Tanzania and Uganda. Additionally, epidemics of banana streak disease are occurring in Kenya and Uganda. The rapidly growing tissue culture (TC) industry within East Africa, aiming to provide planting material to banana farmers, has stimulated discussion about the need for virus indexing to certify planting material as virus-free. Diagnostic methods for BBTV and BSV have been reported and, for BBTV, PCR-based assays are reliable and relatively straightforward. However for BSV, high levels of serological and genetic variability and the presence of endogenous virus sequences within the banana genome complicate diagnosis. Uganda has been shown to contain the greatest diversity in BSV isolates found anywhere in the world. A broad-spectrum diagnostic test for BSV detection, which can discriminate between endogenous and episomal BSV sequences, is a priority. This PhD project aimed to establish diagnostic methods for banana viruses, with a particular focus on the development of novel methods for BSV detection, and to use these diagnostic methods for the detection and characterisation of banana viruses in East Africa. A novel rolling-circle amplification (RCA) method was developed for the detection of BSV. Using samples of Banana streak MY virus (BSMYV) and Banana streak OL virus (BSOLV) from Australia, this method was shown to distinguish between endogenous and episomal BSV sequences in banana plants. The RCA assay was used to screen a collection of 56 banana samples from south-west Uganda for BSV. RCA detected at least five distinct BSV isolates in these samples, including BSOLV and Banana streak GF virus (BSGFV) as well as three BSV isolates (Banana streak Uganda-I, -L and -M virus) for which only partial sequences had been previously reported. These latter three BSV had only been detected using immuno-capture (IC)-PCR and thus were possible endogenous sequences. In addition to its ability to detect BSV, the RCA protocol was also demonstrated to detect other viruses within the family Caulimoviridae, including Sugar cane bacilliform virus, and Cauliflower mosaic virus. Using the novel RCA method, three distinct BSV isolates from both Kenya and Uganda were identified and characterised. The complete genome of these isolates was sequenced and annotated. All six isolates were shown to have a characteristic badnavirus genome organisation with three open reading frames (ORFs) and the large polyprotein encoded by ORF 3 was shown to contain conserved amino acid motifs for movement, aspartic protease, reverse transcriptase and ribonuclease H activities. As well, several sequences important for expression and replication of the virus genome were identified including the conserved tRNAmet primer binding site present in the intergenic region of all badnaviruses. Based on the International Committee on Taxonomy of Viruses (ICTV) guidelines for species demarcation in the genus Badnavirus, these six isolates were proposed as distinct species, and named Banana streak UA virus (BSUAV), Banana streak UI virus (BSUIV), Banana streak UL virus (BSULV), Banana streak UM virus (BSUMV), Banana streak CA virus (BSCAV) and Banana streak IM virus (BSIMV). Using PCR with species-specific primers designed to each isolate, a genotypically diverse collection of 12 virus-free banana cultivars were tested for the presence of endogenous sequences. For five of the BSV no amplification was observed in any cultivar tested, while for BSIMV, four positive samples were identified in cultivars with a B-genome component. During field visits to Kenya, Tanzania and Uganda, 143 samples were collected and assayed for BSV. PCR using nine sets of species-specific primers, and RCA, were compared for BSV detection. For five BSV species with no known endogenous counterpart (namely BSCAV, BSUAV, BSUIV, BSULV and BSUMV), PCR was used to detect 30 infections from the 143 samples. Using RCA, 96.4% of these samples were considered positive, with one additional sample detected using RCA which was not positive using PCR. For these five BSV, PCR and RCA were both useful for identifying infected samples, irrespective of the host cultivar genotype (Musa A- or B-genome components). For four additional BSV with known endogenous counterparts in the M. balbisiana genome (BSOLV, BSGFV, BSMYV and BSIMV), PCR was shown to detect 75 infections from the 143 samples. In 30 samples from cultivars with an A-only genome component there was 96.3% agreement between PCR positive samples and detection using RCA, again demonstrating either PCR or RCA are suitable methods for detection. However, in 45 samples from cultivars with some B-genome component, the level of agreement between PCR positive samples and RCA positive samples was 70.5%. This suggests that, in cultivars with some B-genome component, many infections were detected using PCR which were the result of amplification of endogenous sequences. In these latter cases, RCA or another method which discriminates between endogenous and episomal sequences, such as immuno-capture PCR, is needed to diagnose episomal BSV infection. Field visits were made to Malawi and Rwanda to collect local isolates of BBTV for validation of a PCR-based diagnostic assay. The presence of BBTV in samples of bananas with bunchy top disease was confirmed in 28 out of 39 samples from Malawi and all nine samples collected in Rwanda, using PCR and RCA. For three isolates, one from Malawi and two from Rwanda, the complete nucleotide sequences were determined and shown to have a similar genome organisation to previously published BBTV isolates. The two isolates from Rwanda had at least 98.1% nucleotide sequence identity between each of the six DNA components, while the similarity between isolates from Rwanda and Malawi was between 96.2% and 99.4% depending on the DNA component. At the amino acid level, similarities in the putative proteins encoded by DNA-R, -S, -M, - C and -N were found to range between 98.8% to 100%. In a phylogenetic analysis, the three East African isolates clustered together within the South Pacific subgroup of BBTV isolates. Nucleotide sequence comparison to isolates of BBTV from outside Africa identified India as the possible origin of East African isolates of BBTV.

Factors affecting 39K NMR detectability in rat tissue

In this study we have found that NMR detectability of 39K in rat thigh muscle may be substantially higher (up to 100% oftotal tissue potassium) than values previously reported of around 40%. The signal was found to consist of two superimposed components, one broad and one narrow, of approximately equal area. Investigations involving improvements in spectral parameters such as signal-to-noise ratio and baseline roll, together with computer simulations of spectra, show that the quality of the spectra has a major effect on the amount of signal detected, which is largely due to the loss of detectability of the broad signal component. In particular, lower-field spectrometers using conventional probes and detection methods generally have poorer signal-to-noise and worse baseline roll artifacts, which make detection of a broad component of the muscle signal difficult.

Simple rules to contain an invasive species with a complex life cycle and high dispersal capacity

Designing practical rules for controlling invasive species is a challenging task for managers, particularly when species are long-lived, have complex life cycles and high dispersal capacities. Previous findings derived from plant matrix population analyses suggest that effective control of long-lived invaders may be achieved by focusing on killing adult plants. However, the cost-effectiveness of managing different life stages has not been evaluated. We illustrate the benefits of integrating matrix population models with decision theory to undertake this evaluation, using empirical data from the largest infestation of mesquite (Leguminosae: Prosopis spp) within Australia. We include in our model the mesquite life cycle, different dispersal rates and control actions that target individuals at different life stages with varying costs, depending on the intensity of control effort. We then use stochastic dynamic programming to derive cost-effective control strategies that minimize the cost of controlling the core infestation locally below a density threshold and the future cost of control arising from infestation of adjacent areas via seed dispersal. Through sensitivity analysis, we show that four robust management rules guide the allocation of resources between mesquite life stages for this infestation: (i) When there is no seed dispersal, no action is required until density of adults exceeds the control threshold and then only control of adults is needed; (ii) when there is seed dispersal, control strategy is dependent on knowledge of the density of adults and large juveniles (LJ) and broad categories of dispersal rates only; (iii) if density of adults is higher than density of LJ, controlling adults is most cost-effective; (iv) alternatively, if density of LJ is equal or higher than density of adults, management efforts should be spread between adults, large and to a lesser extent small juveniles, but never saplings. Synthesis and applications.In this study, we show that simple rules can be found for managing invasive plants with complex life cycles and high dispersal rates when population models are combined with decision theory. In the case of our mesquite population, focussing effort on controlling adults is not always the most cost-effective way to meet our management objective.

Thinking Critically About Rural Gender Relations: Toward a Rural Masculinity/Male Peer Support Model of Separation/Divorce Sexual Assault

After decades of neglect, a growing number of scholars have turned their attention to issues of crime and criminal justice in the rural context. Despite this improvement, rural crime research is underdeveloped theoretically, and is little informed by critical criminological perspectives. In this article, we introduce the broad tenets of a multi-level theory that links social and economic change to the reinforcement of rural patriarchy and male peer support, and in turn, how they are linked to separation/divorce sexual assault. We begin by addressing a series of misconceptions about what is rural, rural homogeneity and commonly held presumptions about the relationship of rurality, collective efficacy (and related concepts) and crime. We conclude by recommending more focused research, both qualitative and quantitative, to uncover specific link between the rural transformation and violence against women.

Democracy, Crime and Justice. Annals of the American Academy of Political and Social Sciences

As a growing number of nations embark on a path to democracy, criminologists have become increasingly interested and engaged in the challenges, concerns, and questions connecting democracy with both crime and criminal justice. Rising levels of violence and street crime, white collar crime and corruption both in countries where democracy is securely in place and where it is struggling, have fuelled a deepening skepticism as to the capacity of democracy to deliver on its promise of security and justice for all citizens. What role does crime and criminal justice play in the future of democracy and for democratic political development on a global level? The editors of this special volume of The Annals realized the importance of collecting research from a broad spectrum of countries and covering a range of problems that affect citizens, politicians, and criminal justice officials. The articles here represent a solid balance between mature democracies like the U.S. and U.K. as well as emerging democracies around the globe – specifically in Latin America, Africa and Eastern Europe. They are based on large and small cross-national samples, regional comparisons, and case studies. Each contribution addresses a seminal question for the future of democratic political development across the globe. What is the role of criminal justice in the process of building democracy and instilling confidence in its institutions? Is there a role for unions in democratizing police forces? What is the impact of widespread disenfranchisement of felons on democratic citizenship and the life of democratic institutions? Under what circumstances do mature democracies adopt punitive sentencing regimes? Addressing sensitive topics such as relations between police and the Muslim communities of Western Europe in the wake of terrorist attacks, this volume also sheds light on the effects of terrorism on mature democracies under increasing pressure to provide security for their citizens. By taking a broad vantage point, this collection of research delves into complex topics such as the relationship between the process of democratization and violent crime waves; the impact of rising crime rates on newly established as well as secure democracies; how crime may endanger the transition to democracy; and how existing practices of criminal justice in mature democracies affect their core values and institutions. The collection of these insightful articles not only begins to fill a gap in criminological research but also addresses issues of critical interest to political scientists as well as other social and behavioral scientists and scholars. Taking a fresh approach to the intersection of crime, criminal justice, and democracy, this volume of The Annals is a must-read for criminologists and political scientists and provides a solid foundation for further interdisciplinary research.

Legal Institutions and Collective Memories

In recent decades the debate among scholars, lawyers, politicians and others about how societies deal with their past has been constant and intensive. 'Legal Institutions and Collective Memories' situates the processes of transitional justice at the intersection between legal procedures and the production of collective and shared meanings of the past. Building upon the work of Maurice Halbwachs, this collection of essays emphasises the extended role and active involvement of contemporary law and legal institutions in public discourse about the past, and explores their impact on the shape that collective memories take in the course of time. The authors uncover a complex pattern of searching for truth, negotiating the past and cultivating the art of forgetting. Their contributions explore the ambiguous and intricate links between the production of justice, truth and memory. The essays cover a broad range of legal institutions, countries and topics. These include transitional trials as 'monumental spectacles' as well as constitutional courts, and the restitution of property rights in Central and Eastern Europe and Australia. The authors explore the biographies of victims and how their voices were repressed, as in the case of Korean Comfort Women. They explore the role of law and legal institutions in linking individual and collective memories in the transitional period through processes of lustration, and they analyse divided memories about the past and their impact on future reconciliation in South Africa. The collection offers a genuinely comparative approach, allied to cutting-edge theory.

Criminology: A Sociological Introduction

This sociological introduction provides a much-needed textbook for an increasingly popular area of study. Written by a team of authors with a broad range of teaching and individual expertise, it covers almost every module offered in UK criminological courses and will be valuable to students of criminology worldwide. It covers: - key traditions in criminology, their critical assessment and more recent developments; - new ways of thinking about crime and control, including crime and emotions, drugs and alcohol, from a public health perspective; - different dimensions of the problem of crime and misconduct, including crime and sexuality, crimes against the environment, crime and human rights and organizational deviance; - key debates in criminological theory; - the criminal justice system; - new areas such as the globalization of crime, and crime in cyberspace. Specially designed to be user-friendly, each chapter contains boxed material on current controversies, key thinkers and examples of crime and criminal justice around the world with statistical tables, maps, summaries, critical thinking questions, annotated references and a glossary of key terms, as well as further reading sections and additional resource information as weblinks.

A proposed validation framework for expert elicited Bayesian Networks

The popularity of Bayesian Network modelling of complex domains using expert elicitation has raised questions of how one might validate such a model given that no objective dataset exists for the model. Past attempts at delineating a set of tests for establishing confidence in an entirely expert-elicited model have focused on single types of validity stemming from individual sources of uncertainty within the model. This paper seeks to extend the frameworks proposed by earlier researchers by drawing upon other disciplines where measuring latent variables is also an issue. We demonstrate that even in cases where no data exist at all there is a broad range of validity tests that can be used to establish confidence in the validity of a Bayesian Belief Network.

Engaging undergraduate nursing students in face-to-face tutorials

Chronic nursing shortages have placed increasing pressure on many nursing schools to recruit greater numbers of students with the consequence of larger class sizes. Larger class sizes have the potential to lead to student disengagement. This paper describes a case study that examined the strategies used by a group of nursing lecturers to engage students and to overcome passivity in a Bachelor of Nursing programme. A non-participant observer attended 20 tutorials to observe five academics deliver four tutorials each. Academics were interviewed both individually and as a group following the completion of all tutorial observations. All observations, field notes, interviews and focus groups were coded separately and major themes identified. From this analysis two broad categories emerged: getting students involved; and engagement as a struggle. Academics used a wide variety of techniques to interest and involve students. Additionally, academics desired an equal relationship with students. They believed that both they and the students had some power to influence the dynamics of tutorials and that neither party had ultimate power. The findings of this study serve to re-emphasise past literature which suggests that to engage students, the academics must also engage.

Clusterin is a critical downstream mediator of stress-induced YB-1 transactivation in prostate cancer

Clusterin is a stress-activated, cytoprotective chaperone that confers broad-spectrum treatment resistance in cancer. However, the molecular mechanisms mediating CLU transcription following anticancer treatment stress remain incompletely defined. We report that Y-box binding protein-1 (YB-1) directly binds to CLU promoter regions to transcriptionally regulate clusterin expression. In response to endoplasmic reticulum stress inducers, including paclitaxel, YB-1 is translocated to the nucleus to transactivate clusterin. Furthermore, higher levels of activated YB-1 and clusterin are seen in taxane-resistant, compared with parental, prostate cancer cells. Knockdown of either YB-1 or clusterin sensitized prostate cancer cells to paclitaxel, whereas their overexpression increased resistance to taxane. Clusterin overexpression rescued cells from increased paclitaxel-induced apoptosis following YB-1 knockdown; in contrast, however, YB-1 overexpression did not rescue cells from increased paclitaxel-induced apoptosis following clusterin knockdown. Collectively, these data indicate that YB-1 transactivation of clusterin in response to stress is a critical mediator of paclitaxel resistance in prostate cancer. Mol Cancer Res; 9(12); 1755–66.

Amphiphilic silicone archtectures via anaerobic thiol - ene chemistry

Despite broad application, few silicone-based surfactants of known structure or, therefore, surfactancy have been prepared because of an absence of selective routes and instability of silicones to acid and base. Herein the synthesis of a library of explicit silicone-poly(ethylene glycol) (PEG) materials is reported. Pure silicone fragments were generated by the B(C(6)F(5))(3)-catalyzed condensation of alkoxysilanes and vinyl-functionalized hydrosilanes. The resulting pure products were coupled to thiol-terminated PEG materials using photogenerated radicals under anaerobic conditions.

Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species.

Mastering the canonical loop of serine protease inhibitors : enhancing potency by optimising the internal hydrogen bond network

Background Canonical serine protease inhibitors commonly bind to their targets through a rigid loop stabilised by an internal hydrogen bond network and disulfide bond(s). The smallest of these is sunflower trypsin inhibitor (SFTI-1), a potent and broad-range protease inhibitor. Recently, we re-engineered the contact β-sheet of SFTI-1 to produce a selective inhibitor of kallikrein-related peptidase 4 (KLK4), a protease associated with prostate cancer progression. However, modifications in the binding loop to achieve specificity may compromise structural rigidity and prevent re-engineered inhibitors from reaching optimal binding affinity. Methodology/Principal Findings In this study, the effect of amino acid substitutions on the internal hydrogen bonding network of SFTI were investigated using an in silico screen of inhibitor variants in complex with KLK4 or trypsin. Substitutions favouring internal hydrogen bond formation directly correlated with increased potency of inhibition in vitro. This produced a second generation inhibitor (SFTI-FCQR Asn14) which displayed both a 125-fold increased capacity to inhibit KLK4 (Ki = 0.0386±0.0060 nM) and enhanced selectivity over off-target serine proteases. Further, SFTI-FCQR Asn14 was stable in cell culture and bioavailable in mice when administered by intraperitoneal perfusion. Conclusion/Significance These findings highlight the importance of conserving structural rigidity of the binding loop in addition to optimising protease/inhibitor contacts when re-engineering canonical serine protease inhibitors.