Queen's University Belfast, RCUK Open Access Compliance Report 2014/2015

Queen's University Belfast has submitted its open access compliance report to the RCUK for 2014/2015. Queen's receives an annual open access block grant from RCUK. The funds are made available to support universities in meeting the requirements of the RCUK open access policy, in particular meeting the cost of article processing charges (APC) to make articles open access through the publisher.

Gene-associated markers provide tools for tackling illegal fishing and false eco-certification

Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).

Tools and Environments for Networked Electronic Performance

A collection of software and hardware tools and environments that facilitate collective networked performance between electronic musicians. Tools include 'Chat Monkey', a live chat tool for performance, 'DMA Sequencing', a step sequencer using open sound control messaging and multi nodal control, 'tutti, duet, trio, solo, quartet', an ensemble management environment, and 'Por Larrañaga', a cigar box based electro-acoustic instrument with embedded sensors and controllers. Notable performances: w/BLISS, NCAD, Dublin, 1 March 2015; w/BLISS, NI Science Festival, Belfast, 21 Feb 2015

Carbon Sink Conservation and Global Justice: Benefiting, Free Riding and Non-Compliance

It is often assumed that in order to avoid the most severe consequences of global anthropogenic climate change we have to preserve our existing carbon sinks, such as for instance tropical forests. Global carbon sink conservation raises a host of normative issues, though, since it is debatable who should pay the costs of carbon sink conservation, who has the duty to protect which sinks, and how far the duty to conserve one’s carbon sinks actually extends, especially if it conflicts with other duties one might have. According to some, forested states like Ecuador have a duty to preserve their tropical forests while the rich states of the global North have a duty of fairness to compensate states like Ecuador for the costs they incur. My aim in this paper is to critically analyse this standard line of argument and to criticise its validity both internally (i.e. with regard to its normative conclusion based on its premises) and externally (i.e. with regard to the argument’s underlying assumptions and its lack of contextualisation). As I will argue, the duty to conserve one’s forests is only a particular instantiation of a wider, more general duty to contribute towards global climate justice for which the context in which one operates (e.g. whether other agents are complying with their duties of global climate justice or not) matters significantly.

Effectiveness of a short message reminder in increasing compliance with pediatric cataract treatment:A randomized trial

Objective: Regular follow-up is essential to successful management of childhood cataract. We sought to assess whether a mobile phone short message service (SMS) for parents of children with cataract could improve follow-up adherence and the proportion of procedures performed in timely fashion. Design: Randomized, controlled trial. This trial is registered with ClinicalTrials.gov, NCT01417819. Participants: We included 258 parent-child pairs involved in the Childhood Cataract Program of the Chinese Ministry of Health. Methods: Participants were randomized (1:1) to a mobile phone SMS intervention or standard follow-up appointments. All participants were scheduled to attend <4 follow-up appointments according to the protocol. Parents in the intervention group received SMS automated reminders before scheduled appointments. The control group parents did not receive SMSs or any alternative reminder of scheduled appointments. Regular ocular examinations and analyses were performed by investigators masked to group allocation; however, study participants and the manager in charge of randomization and sending SMSs were not masked. Main Outcome Measures: Number of follow-up appointments attended, additional surgeries, laser treatments, changes in eyeglasses prescription, and occurrence of secondary ocular hypertension. Results: Among parent-child participants, 135 were randomly assigned to the SMS intervention and 123 to standard appointments. Attendance rates for the SMS group (first visit, 97.8%; second, 91.9%; third, 92.6%; fourth, 83%) were significantly higher than those for the control group (first visit, 87.8%; second, 69.9%; third, 56.9%; fourth, 33.3%). The increase in attendance rate for total number of follow-up visits with SMS reminders was 47.2% (relative risk [RR] for attendance, 1.47; 95% confidence interval [CI], 1.16-1.78; P = 0.003). The number needed to remind (NNR) to gain 1 additional visit by 1 child was 3 (95% CI, 1.8-4.2). A total of 247 clinical interventions were carried out in the SMS group and 134 in the control group (RR, 1.68; 95% CI, 1.37-1.99; P = 0.007). The NNR to result in 1 additional clinical intervention was 5 (95% CI, 3.5-6.5). Conclusions: The SMS reminders significantly improved follow-up adherence in pediatric cataract treatment. Using readily available mobile phone resources may be an effective and economic strategy to improve management of childhood cataract in China. Financial Disclosure(s): The authors have no proprietary or commercial interest in any of the materials discussed in this article. © 2012 American Academy of Ophthalmology.

Factors associated with spectacle-wear compliance in school-aged Mexican children.

PURPOSE: To study the prevalence and determinants of compliance with spectacle wear among school-age children in Oaxaca, Mexico, who were provided spectacles free of charge. METHODS: A cohort of 493 children aged 5 to 18 years chosen by random cluster sampling from primary and secondary schools in Oaxaca, Mexico, all of whom had received free spectacles through a local program, underwent unannounced, direct examination to determine compliance with spectacle wear within 18 months after initial provision of spectacles. Potential determinants of spectacle wear including age, gender, urban versus rural residence, presenting visual acuity, refractive error, and time since dispensing of the spectacles were examined in univariate and multivariate regression models. Children not currently wearing their spectacles were asked to select the reason from a list of possibilities, and reasons for noncompliance were analyzed within different demographic groups. RESULTS: Among this sample of children with a mean age of 10.4 +/- 2.6 years, the majority (74.5%) of whom were myopic (spherical equivalent [SE] < or = -0.50 D), 13.4% (66/493) were wearing their spectacles at the time of examination. An additional 34% (169/493) had the spectacles with them but were not wearing them. In regression models, the odds of spectacle wear were significantly higher among younger (OR = 1.19 per year of age; 95% CI, 1.05-1.33) rural (OR = 10.6; 95% CI, 5.3-21.0) children and those with myopia < or = -1.25 D (OR = 3.97; 95% CI, 1.98-7.94). The oldest children and children in urban-suburban areas were significantly more likely to list concerns about the appearance of the glasses or about being teased than were younger, rurally resident children. CONCLUSIONS: Compliance with spectacle wear may be very low, even when spectacles are provided free of charge, particularly among older, urban children, who have been shown in many populations to have the highest prevalence of myopia. As screening programs for refractive error become increasingly common throughout the world, new strategies are needed to improve compliance if program resources are to be maximized.

Compliance with follow-up after cataract surgery in rural China.

PURPOSE:

To evaluate reasons for non-compliance with post-cataract surgical follow-up in rural China, and assess the impact of incentives on improving compliance.

METHODS:

Patients having undergone cataract surgery more than 3 months previously at cataract surgery training hospitals in Guangdong were invited by telephone and advertisements to a hospital-based study examination, with compensation for travel costs (US$7). Information on prior post-surgical follow up was collected by questionnaire at the hospital or by telephone. Logistic regression was used to assess predictors of post-operative attendance with or without compensation.

RESULTS:

Among 518 eligible patients, 426 (82.2%) underwent interviews and 342 (66.0%) attended the compensated study examination. Ninety nine participants (23.2%) reported previously returning for uncompensated follow-up ≥ 3 months post-operatively, and 225 (52.8%) had returned for any prior post-operative examination. Uncompensated follow-up at ≥ 3 months was associated with higher income (P = 0.037), and recalling instruction by a doctor to follow-up (P = 0.001), while age, gender, travel cost, and post-operative satisfaction and vision were not associated. Younger (P = 0.002) patients and those reporting being instructed to follow up (P = 0.008) were more likely to return for the compensated research examination. Among all interviewed subjects, only 170 (39.9%) reported knowing they were to return to hospital.

CONCLUSIONS:

Modest compensation, advertisements and telephone contact can increase medium-term follow-up rates after cataract surgery by three-fold. Better communication of specific targets for follow-up may improve follow-up compliance.

A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities

Seafloor massive sulfide (SMS) mining will likely occur at hydrothermal systems in the near future. Alongside their mineral wealth, SMS deposits also have considerable biological value. Active SMS deposits host endemic hydrothermal vent communities, whilst inactive deposits support communities of deep water corals and other suspension feeders. Mining activities are expected to remove all large organisms and suitable habitat in the immediate area, making vent endemic organisms particularly at risk from habitat loss and localised extinction. As part of environmental management strategies designed to mitigate the effects of mining, areas of seabed need to be protected to preserve biodiversity that is lost at the mine site and to preserve communities that support connectivity among populations of vent animals in the surrounding region. These "set-aside" areas need to be biologically similar to the mine site and be suitably connected, mostly by transport of larvae, to neighbouring sites to ensure exchange of genetic material among remaining populations. Establishing suitable set-asides can be a formidable task for environmental managers, however the application of genetic approaches can aid set-aside identification, suitability assessment and monitoring. There are many genetic tools available, including analysis of mitochondrial DNA (mtDNA) sequences (e.g. COI or other suitable mtDNA genes) and appropriate nuclear DNA markers (e.g. microsatellites, single nucleotide polymorphisms), environmental DNA (eDNA) techniques and microbial metagenomics. When used in concert with traditional biological survey techniques, these tools can help to identify species, assess the genetic connectivity among populations and assess the diversity of communities. How these techniques can be applied to set-aside decision making is discussed and recommendations are made for the genetic characteristics of set-aside sites. A checklist for environmental regulators forms a guide to aid decision making on the suitability of set-aside design and assessment using genetic tools. This non-technical primer document represents the views of participants in the VentBase 2014 workshop.

Does Basel Compliance Matter for Bank Performance?

The global financial crisis underscored the importance of regulation and supervision to a well-functioning banking system that efficiently channels financial resources into investment. In this paper, we contribute to the ongoing policy debate by assessing whether compliance with international regulatory standards and protocols enhances bank operating efficiency. We focus specifically on the adoption of international capital standards and the Basel Core Principles for Effective Bank Supervision (BCP). The relationship between bank efficiency and regulatory compliance is investigated using the Simar and Wilson (2007. J. Econ. 136 (1), 31) double bootstrapping approach on an international sample of publicly listed banks. Our results indicate that overall BCP compliance, or indeed compliance with any of its individual chapters,has no association with bank efficiency.

Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.