Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community

A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO3-.N mg of mixed-liquor volatile suspended solids (MLVSS)(-1) h(-1) to a steady-state value of 0.06 mg of NO3-.N mg of MLVSS-1 h(-1) over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [C-13] methanol to biomark the DNA of the denitrifiers. The extracted [C-13]DNA and [C-12]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [C-13]DNA clone library was closely related to those of the obligate methylotrophs Methylobacillus and Methylophilus in the order Methylophilales of the Betaproteobacteria (96 to 97% sequence identities), while the most abundant clone groups in the [C-12]DNA clone library mostly belonged to the family Saprospiraceae in the Bacteroidetes phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and Methylophilales (probes DEN67 and MET1216, respectively) and the Saprospiraceae clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera Hyphomicrobium and Paracoccus or the Saprospiraceae clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [C-14] methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that Methylophilales bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.

Real-time reverse transcriptase PCR for the endogenous koala retrovirus reveals an association between plasma viral load and neoplastic disease in koalas

Koala retrovirus (KoRV) is a newly described endogenous retrovirus and is unusual in that inserts comprise a full-length replication competent genome. As koalas are known to suffer from an extremely high incidence of leukaemia/lymphoma, the association between this retrovirus and disease in koalas was examined. Using quantitative real-time reverse transcriptase PCR it was demonstrated that KoRV RNA levels in plasma are significantly increased in animals suffering from leukaemia or lymphoma when compared with healthy animals. Increased levels of KoRV were also seen for animals with clinical chlamydiosis. A significant positive association between viral RNA levels and age was also demonstrated. Real-time PCR demonstrated as much as 5 log variation in KoRV proviral DNA levels in genomic DNA extracted from whole blood from different animals. Taken together these data indicate that KoRV is an active endogenous retrovirus and suggests that it may be causally linked to neoplastic disease in koalas.

Zero-non-zero patterned vector error correction modeling for I(2) cointegrated time series with applications in testing PPP and stock market relationships

Vector error-correction models (VECMs) have become increasingly important in their application to financial markets. Standard full-order VECM models assume non-zero entries in all their coefficient matrices. However, applications of VECM models to financial market data have revealed that zero entries are often a necessary part of efficient modelling. In such cases, the use of full-order VECM models may lead to incorrect inferences. Specifically, if indirect causality or Granger non-causality exists among the variables, the use of over-parameterised full-order VECM models may weaken the power of statistical inference. In this paper, it is argued that the zero–non-zero (ZNZ) patterned VECM is a more straightforward and effective means of testing for both indirect causality and Granger non-causality. For a ZNZ patterned VECM framework for time series of integrated order two, we provide a new algorithm to select cointegrating and loading vectors that can contain zero entries. Two case studies are used to demonstrate the usefulness of the algorithm in tests of purchasing power parity and a three-variable system involving the stock market.

Real-time PCR assays for detection of bocavirus in human specimens

The recently discovered human bocavirus (HBoV) is the first member of the family Parpoviridae, genus Bocavirus, to be potentially associated with human disease. Several studies have identified HBoV in respiratory specimens from children with acute respiratory disease, but the full spectrum of clinical disease and the epidemiology of HBoV infection remain unclear. The availability of rapid and reliable molecular diagnostics would therefore aid future studies of this novel virus. To address this, we developed two sensitive and specific real-time TaqMan PCR assays that target the HBoV NS1 and NP-1 genes. Both assays could reproducibly detect 10 copies of a recombinant DNA plasmid containing a partial region of the HBoV genome, with a dynamic range of 8 log units (10(1) to 10(8) copies). Eight blinded clinical specimen extracts positive for HBoV by an independent PCR assay were positive by both real-time assays. Among 1,178 NP swabs collected from hospitalized pneumonia patients in Sa Kaeo Province, Thailand, 53 (4.5%) were reproducibly positive for HBoV by one or both targets. Our data confirm the possible association of HBoV infection with pneumonia and demonstrate the utility of these real-time PCR assays for HBoV detection.

Full-field Fourier-domain optical coherence tomography

Full-field Fourier-domain optical coherence tomography (3F-OCT) is a full-field version of spectraldomain/swept-source optical coherence tomography. A set of two-dimensional Fourier holograms is recorded at discrete wavenumbers spanning the swept-source tuning range. The resultant three-dimensional data cube contains comprehensive information on the three-dimensional morphological layout of the sample that can be reconstructed in software via three-dimensional discrete Fourier-transform. This method of recording of the OCT signal confers signal-to-noise ratio improvement in comparison with "flying-spot" time-domain OCT. The spatial resolution of the 3F-OCT reconstructed image, however, is degraded due to the presence of a phase cross-term, whose origin and effects are addressed in this paper. We present theoretical and experimental study of imaging performance of 3F-OCT, with particular emphasis on elimination of the deleterious effects of the phase cross-term.

Doom and gloom or a time for optimism: Potential aspirants' views about school leadership - now and for the future

Principal recruitment has attracted national and international attention in recent years (eg. Barty et al, 2005 in Australia; Earley et al, 2002 in the UK; Brooking et al, 2003 in New Zealand; Williams, 2003 in Canada). Importantly, Australian research in both state and non-state schools suggests that potential principal aspirants are less enthusiastic than might be expected in their desire to become principals (D’Arbon et al, 2002; Cranston et al, 2004; Lacey, 2002). Given the importance of ensuring we have quality leaders for our schools in the future, the research reported here (which is on-going) examined the views of potential aspirants (primary and secondary deputy principals) from one large government education system in Australia about the principalship and their intentions in seeking promotion (or otherwise) to such positions and the reasons driving these intentions. Data were collected via the Aspiring Principals Questionnaire (APQ) – especially developed for the study – comprising 38 closed items mainly of a Likert-type format, 5 open-ended items linked to particular closed items allowing participants to add their own suggestions/ideas, expand/elaborate on responses; and 4 further more general open-ended items. A number of system-level policy and practice recommendations have been developed from the findings.

Understanding and Managing the Late Time of Ratooning Effect on Cane Yield

Each year growers are faced with the decision of when to harvest individual blocks of sugarcane throughout the harvest season. This decision influences the yield of the current crop and can affect the yield in the following season. Growers must therefore decide which blocks to harvest early and which to harvest later in the harvest season. Usually, the latest harvested cane is the lowest yielding the following year (the �late harvest� effect). Block productivity data from Tully were used to determine the effects of harvest timing on cane yield of the current and subsequent crop. The results are tabulated to provide a ready reference to these time of harvest effects on the current and future crop in either a single year or over the full crop cycle for the Tully district.

The response to and effects of microcomputers in the education sector:the introduction of an innovation in local authority secondary schools

The study addresses the introduction of an innovation of new technology into a bureaucratic profession. The organisational setting is that of local authority secondary schools at a time at which microcomputers were being introduced in both the organisational core (for teaching) and its periphery (school administration). The research studies innovation-adopting organisations within their sectoral context; key actors influencing the innovation are identified at the levels of central government, local government and schools.A review of the literature on new technology and innovation (including educational innovation), and on schools as organisations in a changing environment leads to the development of the conceptual framework of the study using a resource dependency model within a cycle of the acquisition, allocation and utilisation of financial, physical and intangible resources. The research methodology is longitudinal and draws from both positivist and interpretive traditions. lt includes an initial census of the two hundred secondary schools in four local education authorities, a final survey of the same population, and four case studies, using both interview methods and documentation. Two modes of innovation are discerned. In respect of administrative use a rationalising, controlling mode is identified, with local education authorities developing standardised computer-assisted administrative systems for use in schools. In respect of curricular use, in contrast, teachers have been able to maintain an indeterminate occupational knowledge base, derived from an ideology of professionalism in respect of the classroom use of the technology. The mode of innovation in respect of curricular use has been one of learning and enabling. The resourcing policies of central and local government agencies affect the extent of use of the technology for teaching purposes, but the way in which it is used is determined within individual schools, where staff with relevant technical expertise significantly affect the course of the innovation.

A common rule for integration and suppression of luminance contrast across eyes, space, time, and pattern

Visual perception begins by dissecting the retinal image into millions of small patches for local analyses by local receptive fields. However, image structures extend well beyond these receptive fields and so further processes must be involved in sewing the image fragments back together to derive representations of higher order (more global) structures. To investigate the integration process, we also need to understand the opposite process of suppression. To investigate both processes together, we measured triplets of dipper functions for targets and pedestals involving interdigitated stimulus pairs (A, B). Previous work has shown that summation and suppression operate over the full contrast range for the domains of ocularity and space. Here, we extend that work to include orientation and time domains. Temporal stimuli were 15-Hz counter-phase sine-wave gratings, where A and B were the positive and negative phases of the oscillation, respectively. For orientation, we used orthogonally oriented contrast patches (A, B) whose sum was an isotropic difference of Gaussians. Results from all four domains could be understood within a common framework in which summation operates separately within the numerator and denominator of a contrast gain control equation. This simple arrangement of summation and counter-suppression achieves integration of various stimulus attributes without distorting the underlying contrast code.

Can accreditation help a leopard change its spots? Social accountability and stakeholder engagement in business schools

Purpose: Neo-institutional theory suggests that organisations change occurs when institutional contradictions, caused by exogenous and endogenous dynamics, increase over time to the point where change can no longer be resisted. Human praxis will result, but only when sufficiently powerful interests are motivated to act. This paper aims to examine the role that the accreditation of business schools can play in increasing institutional contradictions and hence fostering organisational change towards stakeholder engagement and engagement with social responsibility and sustainability issues. Numerous accreditations are promulgated within the higher education and business school contexts and a number of these relate to, or have aspects that relate to, ethics, social responsibility and sustainability. Design/methodology/approach: The paper first analyses the take up of accreditations across UK business schools and then uses a case study to illustrate and explore stakeholder engagement and changes related to ethics, social responsibility and sustainability linked to accreditation processes. Findings: Accreditations are found to be an increasingly common interest for UK business schools. Further, a number of these accreditations have evolved to incorporate issues related to ethics, social responsibility and sustainability that may cause institutional contradictions and may, therefore, have the potential to foster organisational change. Accreditation alone, however, is not sufficient and the authors find that sufficiently powerful interests need to be motivated to act and enable human praxis to affect change. Research limitations/implications: This paper draws on previous research that considers the role of accreditation in fostering change that has also been carried out in healthcare organisations, public and professional bodies. Its findings stem from an individual case study and as such further research is required to explore whether these findings can be extended and apply more generally in business schools and universities in different contexts. Practical implications: This paper concludes by recommending that the newly established UK & Ireland Chapter of PRME encourages and supports signatory schools to further embed ethics, social responsibility and sustainability into all aspects of university life in the UK. This also provides an opportunity to engage with the accrediting bodies in order to further support the inclusion of stakeholder engagement and issues related to this agenda in their processes. Originality/value: This paper contributes by introducing accreditation as an institutional pressure that may lead indirectly to organisational change and supports this with new evidence from an illustrative case study. Further, it draws on the role of institutional contradictions and human praxis that engender organisational change. © Emerald Group Publishing Limited.

Editorial

The American Academy of Optometry (AAO) had their annual meeting in San Diego in December 2005 and the BCLA and CLAE were well represented there. The BCLA does have a reasonable number of non-UK based members and hopefully in the future will attract more. This will certainly be beneficial to the society as a whole and may draw more delegates to the BCLA annual conference. To increase awareness of the BCLA at the AAO a special evening seminar was arranged where BCLA president Dr. James Wolffsohn gave his presidential address. Dr. Wolffsohn has given the presidential address in the UK, Ireland, Hong Kong and Japan – making it the most travelled presidential address for the BCLA to date. Aside from the BCLA activity at the AAO there were numerous lectures of interest to all, truly a “something for everyone” meeting. All the sessions were multi-track (often up to 10 things occurring at the same time) and the biggest dilemma was often deciding what to attend and more importantly what you will miss! Nearly 200 new AAO Fellows were inducted at the Gala Dinner from many countries including 3 new fellows from the UK (this year they all just happened to be from Aston University!). It is certainly one of the highlights of the AAO to see fellows from different schools of training from around the world fulfilling the same criteria and being duly rewarded for their commitment to the profession. BCLA members will be aware that 2006 sees the introduction of the new fellowship scheme of the BCLA and by the time you read this the first set of fellowship examinations will have taken place. For more details of the FBCLA scheme see the BCLA web site http://www.bcla.org.uk. Since many of CLAE's editorial panel were at the AAO an informal meeting and dinner was arranged for them where ideas were exchanged about the future of the journal. It is envisaged that the panel will meet twice a year – the next meeting will be at the BCLA conference. The biggest excitement by far was the fact that CLAE is now Medline/PubMed indexed. You may ask why is this significant to CLAE? PubMed is the free web-based service from the US National Library of Medicine. It holds over 15 million biomedical citations and abstracts from the Medline database. Medline is the largest component of PubMed and covers over 4800 journals published in more than 70 countries. The impact of this is that CLAE is starting to attract more submissions as researchers and authors are not worried that their work will not be hidden from other colleagues in the field but rather the work is available to view on the World Wide Web. CLAE is one of a very small number of contact lens journals that is indexed this way. Amongst the other CL journals listed you will note that the International Contact Lens Clinic has now merged with CLAE and the journal CLAO has been renamed Eye and Contact Lenses – making the list of indexed CL journals even smaller than it appears. The on-line submission and reviewing system introduced in 2005 has also made it easier for authors to submit their work and easier for reviewers to check the content. This ease of use has lead to quicker times from submission to publication. Looking back at the articles published in CLAE in 2005 reveals some interesting facts. The majority of the material still tends to be from UK groups related to the field of Optometry, although we hope that in the future we will attract more work from non-UK groups and also from non-Optometric areas such as refractive surgery or anterior eye pathology. Interestingly in 2005 the most downloaded article from CLAE was “Wavefront technology: Past, present and future” by Professor W. Neil Charman, who was also the recipient of the Charles F. Prentice award at the AAO – one of the highest awards honours that the AAO can bestow. Professor Charman was also the keynote speaker at the BCLA's first Pioneer's Day meeting in 2004. In 2006, readers of CLAE will notice more changes, firstly we are moving to 5 issues per year. It is hoped that in the future, depending on increased submissions, a move to 6 issues may be feasible. Secondly, CLAE will aim to have one article per issue that carries CL CET points. You will see in this issue there is an article from Professor Mark Wilcox (who was a keynote speaker at the BCLA conference in 2005). In future articles that carry CET points will be either reviews from BCLA conference keynote speakers, members of the editorial panel or material from other invited persons that will be of interest to the readership of CLAE. Finally, in 2006, you will notice a change to the Editorial Panel, some of the distinguished panel felt that it was good time to step down and new members have been invited to join the remaining panel. The panel represent some of the most eminent names in the fields of contact lenses and/or anterior eye and have varying backgrounds and interests from many of the prominent institutions around the world. One of the tasks that the Editorial Panel undertake is to seek out possible submissions to the journal, either from conferences they attend (posters and papers that they will see and hear) and from their own research teams. However, on behalf of CLAE I would like to extend that invitation to seek original articles to all readers – if you hear a talk and think it could make a suitable publication to CLAE please ask the presenters to submit the work via the on-line submission system. If you found the work interesting then the chances are so will others. CLAE invites submissions that are original research, full length articles, short case reports, full review articles, technical reports and letters to the editor. The on-line submission web page is http://www.ees.elsevier.com/clae/.

Effectiveness of Title-Search vs. Full-Text Search in the Web

Search engines sometimes apply the search on the full text of documents or web-pages; but sometimes they can apply the search on selected parts of the documents only, e.g. their titles. Full-text search may consume a lot of computing resources and time. It may be possible to save resources by applying the search on the titles of documents only, assuming that a title of a document provides a concise representation of its content. We tested this assumption using Google search engine. We ran search queries that have been defined by users, distinguishing between two types of queries/users: queries of users who are familiar with the area of the search, and queries of users who are not familiar with the area of the search. We found that searches which use titles provide similar and sometimes even (slightly) better results compared to searches which use the full-text. These results hold for both types of queries/users. Moreover, we found an advantage in title-search when searching in unfamiliar areas because the general terms used in queries in unfamiliar areas match better with general terms which tend to be used in document titles.

Full-vectorial modeling of femtosecond pulses for laser inscription of photonic structures

During the last decade, microfabrication of photonic devices by means of intense femtosecond (fs) laser pulses has emerged as a novel technology. A common requirement for the production of these devices is that the refractive index modification pitch size should be smaller than the inscribing wavelength. This can be achieved by making use of the nonlinear propagation of intense fs laser pulses. Nonlinear propagation of intense fs laser pulses is an extremely complicated phenomenon featuring complex multiscale spatiotemporal dynamics of the laser pulses. We have utilized a principal approach based on finite difference time domain (FDTD) modeling of the full set of Maxwell's equations coupled to the conventional Drude model for generated plasma. Nonlinear effects are included, such as self-phase modulation and multiphoton absorption. Such an approach resolves most problems related to the inscription of subwavelength structures, when the paraxial approximation is not applicable to correctly describe the creation of and scattering on the structures. In a representative simulation of the inscription process, the signature of degenerate four wave mixing has been found. © 2012 Optical Society of America.

International session at the BCLA conference

Full text: It seems a long time ago now since we were at the BCLA conference. The excellent FIFA World Cup in Brazil kept us occupied over the summer as well as Formula 1, Wimbledon, Tour de France, Commonwealth Games and of course exam paper marking! The BCLA conference this year was held in Birmingham at the International Convention Centre which again proved to be a great venue. The number of attendees overall was up on previous years, and at a record high of 1500 people. Amongst the highlights at this year's annual conference was the live surgery link where Professor Sunil Shah demonstrated the differences in technique between traditional phacoemulsification cataract surgery and femtosecond assisted phacoemulsification cataract surgery. Dr. Raquel Gil Cazorla, a research optometrist at Aston University, assisted in the procedure including calibrating the femtosecond laser. Another highlight for me was the session that I chaired, which was the international session organised by IACLE (International Association of CL Educators). There was a talk by Mirjam van Tilborg about dry eye prevalence in the Netherlands and how it was managed by medical general practitioners (GPs) or optometrists. It was interesting to know that there are only 2 schools of optometry there and currently under 1000 registered optometrists there. It also seems that GPs were more likely to blame CL as the cause for dry eye whereas optometrists who had a fuller range of tests were better at solving the issue. The next part of the session included the presentation of 5 selected posters from around the world. The posters were also displayed in the main poster area but were selected to be presented here as they had international relevance. The posters were: 1. Motivators and Barriers for Contact Lens Recommendation and Wear by Nilesh Thite (India) 2. Contact lens hygiene among Saudi wearers by Dr. Ali Masmaly (Saudi) 3. Trends of contact lens prescribing and patterns of contact lens practice in Jordan by Dr. Mera Haddad (Jordan) 4. Contact Lens Behaviour in Greece by Dr. Dimitra Makrynioti (Greece) 5. How practitioners inform ametropes about the benefits of contact lenses and overcome the potential barriers: an Italian survey, by Dr. Fabrizio Zeri (Italy) It was interesting to learn about CL practice in different parts, for example the CL wearing population ration in Saudi Arabia is around 1:2 Male:Female (similar to other parts of the world) and although the sale of CL is restricted to registered practitioners there are many unregistered outlets, like clothing stores, that flout the rules. In Jordan some older practitioners will still advise patients to use tap water or even saliva! But thankfully the newer generation of practitioners have been educated not to advise this. In Greece one of the concerns was that some practitioners may advise patients to use disposable lenses for longer than they should and again it seems to be the practitioners with inadequate education that would do this. In India it was found that cost was one barrier to using contact lenses but also some practitioners felt that they shouldn’t offer CLs due to cost too. In Italy sensitive eyes and CL care and maintenance were the barriers to CL wear but the motivators were vision and comfort and aesthetics. Finally the international session ended with the IACLE travel award and educator awards presented by IACLE president Shehzad Naroo and BCLA President Andrew Yorke. The travel award went to Wang Ling, Jinling Institute of Technology, Nanjing, China. There were 3 regional Contact Lens Educator of the Year Awards sponsored by Coopervision and presented by Dr. J.C. Aragorn of Coopervision. 1. Asia Pacific Region – Dr. Rajeswari Mahadevan of Sankara Nethralaya Medical Research Foundation, Chennai, India 2. Americas Region – Dr. Sergio Garcia of University of La Salle, Bogotá and the University Santo Tomás, Bucaramanga, Colombia 3. Europe/Africa – Middle East Region: Dr. Eef van der Worp, affiliated with the University of Maastricht, the Netherlands The posters above were just a small selection of those displayed at this year's BCLA conference. If you missed the BCLA conference then you can see the abstracts for all posters and talks in a virtual issue of CLAE very soon. The poster competition was kindly sponsored by Elsevier. The poster winner this year was: Joan Gispets – Corneal and Anterior Chamber Parameters in Keratoconus The 3 runners up were: Debby Yeung – Scleral Lens Central Corneal Clearance Assessment with Biomicroscopy Sarah L. Smith – Subjective Grading of Lid Margin Staining Heiko Pult – Impact of Soft Contact Lenses on Lid Parallel Conjunctival Folds My final two highlights are a little more personal. Firstly, I was awarded Honorary Life Fellowship of the BCLA for my work with the Journal, and I would like to thank the BCLA, Elsevier, the editorial board of CLAE, the reviewers and the authors for their support of my role. My final highlight from the BCLA conference this year was the final presentation of the conference – the BCLA Gold Medal award. The recipient this year was Professor Philip Morgan with his talk ‘Changing the world with contact lenses’. Phil was the person who advised me to go to my first BCLA conference in 1994 (funnily he didn’t attend himself as he was busy getting married!) and now 20 years later he was being honoured with the accolade of being the BCLA Gold Medallist. The date of his BCLA medal addressed was shared with his father's birthday so a double celebration for Phil. Well done to outgoing BCLA President Andy Yorke and his team at the BCLA (including Nick Rumney, Cheryl Donnelly, Sarah Greenwood and Amir Khan) on an excellent conference. And finally welcome to new President Susan Bowers. Copyright © 2014 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported.