Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections-an Australian perspective

Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realize the full potential of DNA barcoding for plants, and particularly its application to metabarcoding for mixed-species environmental samples, systematic sequencing of reference collections is required using an augmented set of DNA barcode loci, applied according to agreed data generation and analysis standards. The largest and most complete reference collections of plants are held in herbaria. Australia has a globally significant flora that is well sampled and expertly curated by its herbaria, coordinated through the Council of Heads of Australasian Herbaria. There exists a tremendous opportunity to provide a comprehensive and taxonomically robust reference database for plant DNA barcoding applications by undertaking coordinated and systematic sequencing of the entire flora of Australia utilizing existing herbarium material. In this paper, we review the development of DNA barcoding and metabarcoding and consider the requirements for a robust and comprehensive system. We analyzed the current availability of DNA barcode reference data for Australian plants, recommend priority taxa for database inclusion, and highlight future applications of a comprehensive metabarcoding system. We urge that large-scale and coordinated analysis of herbarium collections be undertaken to realize the promise of DNA barcoding and metabarcoding, and propose that the generation and curation of reference data should become a national investment priority

Preliminary analysis of the genetic variability of two natural beds of the Scallop Euvola ziczac (Linnaeus, 1758) in Brazil

Euvola ziczac (formerly Pecten ziczac), a simultaneous hermaphroditic scallop was heavily fished in Brazil between 1972 and 1980. The production peaked in 1980 with 8,800 tons and was followed by the total collapse of the resource. In order to investigate the possible loss of genetic variability of the stock associated to overfishing and self-fertilization, the polymorphism of phosphoglucomutase (PGM) and glucose phosphate isomerase (GPI) was analyzed by electrophoresis of the adductor muscle of scallops from São Francisco (26° 20.583S; 48° 16.507W) and Bom Abrigo (25° 28.735S; 47° 37.621W) beds; the southern and northern extremes of the scallop fishing ground, respectively. Animals from São Francisco showed a strong deficiency of heterozygosity for GPI and PGM. In addition, PGM showed *exclusive alleles for each bed. Such results coupled with other information about the species suggested the following hypothesis: a) the stock was a metapopulation with at least two populations; b) some reproductive isolation might be occurring which might be influenced by conditions of larval transport and by the extremely low densities of scallops; c) presently, the stock seemed to be mostly maintained through self-fertilization; d) São Francisco could constitute a source-area, contributing with larvae and recruits to Bom Abrigo and other areas; e) both beds were suffering a genetic homogenization more evident in São Francisco. Such hypothesis needed to be investigated in order to furnish guidelines for future programs of recovery and management of the resource.info:eu-repo/semantics/publishedVersio

Age, growth, and mortality of Loligo vulgaris wild paralarvae : implications for understanding of the life cycle and longevity

Peer reviewedPreprin

Measuring the patient perspective on latissimus dorsi donor site outcomes following breast reconstruction.

BACKGROUND: There is little evidence about the long-term donor site outcome of latissimus dorsi breast reconstruction and no patient-reported outcome measures designed specifically for the procedure. METHODS: A prospective cohort of breast cancer patients having latissimus dorsi reconstruction after a mastectomy was recruited from 270 hospitals in the United Kingdom. An 18-month follow up questionnaire containing two novel scales was sent to consenting patients. The prevalence of aesthetic and functional morbidity at the donor site was described. The two new scales were refined using the Rasch measurement model and subsequently validated. RESULTS: 1,096 women completed the new scales. 78% of patients reported that no back appearance issues had bothered them "most of the time" or "all of the time" in the past two weeks. The equivalent figure for functional morbidity was 60%. Four items were eliminated following initial psychometric testing. This produced an 8-item Back Appearance scale and an 11-item Back and Shoulder Function scale. Both scales showed adequate fit to the Rasch measurement model. Higher levels of aesthetic and functional bother were observed for completely autologous procedures versus those where latissimus dorsi reconstruction was used to cover an implant (p <0.05). Higher levels of aesthetic bother were observed in women who had suffered a perioperative complication at the donor site (p = 0.003). CONCLUSION: These results can inform patients of the morbidity associated with latissimus dorsi reconstruction. The new scales can be used to compare groups undergoing different variations of the procedure and to monitor individual patients

The participation myth

Policy rhetoric around strategies to and the value of increasing participation in the arts has been well documented internationally over more than a decade. But in the UK, which is the focus for this article, targets to increase participation have been consistently missed and there remains a direct correlation between those taking part in cultural activity and their socio-economic status. The starting point for this article is to examine the barriers to increasing participation in the arts and question the way that such policy has been implemented within the English context, which may have relevance for policy making in other countries. What is demonstrated is that policy implementation is influenced by vested interest of those in receipt of funding and that a narrow range of voices, from a powerful cultural elite, are involved in the decision making in the arts. The article makes a case for widening the range of voices heard in decision making in order to support both artistic practice and public engagement

Climate Influence on Deep Sea Populations

Dynamics of biological processes on the deep-sea floor are traditionally thought to be controlled by vertical sinking of particles from the euphotic zone at a seasonal scale. However, little is known about the influence of lateral particle transport from continental margins to deep-sea ecosystems. To address this question, we report here how the formation of dense shelf waters and their subsequent downslope cascade, a climate induced phenomenon, affects the population of the deep-sea shrimp Aristeus antennatus. We found evidence that strong currents associated with intense cascading events correlates with the disappearance of this species from its fishing grounds, producing a temporary fishery collapse. Despite this initial negative effect, landings increase between 3 and 5 years after these major events, preceded by an increase of juveniles. The transport of particulate organic matter associated with cascading appears to enhance the recruitment of this deep-sea living resource, apparently mitigating the general trend of overexploitation. Because cascade of dense water from continental shelves is a global phenomenon, we anticipate that its influence on deep-sea ecosystems and fisheries worldwide should be larger than previously thought

Enemies with benefits: parasitic endoliths protect mussels against heat stress

Positive and negative aspects of species interactions can be context dependant and strongly affected by environmental conditions. We tested the hypothesis that, during periods of intense heat stress, parasitic phototrophic endoliths that fatally degrade mollusc shells can benefit their mussel hosts. Endolithic infestation significantly reduced body temperatures of sun-exposed mussels and, during unusually extreme heat stress, parasitised individuals suffered lower mortality rates than nonparasitised hosts. This beneficial effect was related to the white discolouration caused by the excavation activity of endoliths. Under climate warming, species relationships may be drastically realigned and conditional benefits of phototrophic endolithic parasites may become more important than the costs of infestation

SPIRE - combining SGI-110 with cisplatin and gemcitabine chemotherapy for solid malignancies including bladder cancer: study protocol for a phase Ib/randomised IIa open label clinical trial

Background Urothelial bladder cancer (UBC) accounts for 10,000 new diagnoses and 5000 deaths annually in the UK (Cancer Research UK, http://www.cancerresearchuk.org/health-professional/cancer-statistics/statistics-by-cancer-type/bladder-cancer, Cancer Research UK, Accessed 26 Mar 2018). Cisplatin-based chemotherapy is standard of care therapy for UBC for both palliative first-line treatment of advanced/metastatic disease and radical neoadjuvant treatment of localised muscle invasive bladder cancer. However, cisplatin resistance remains a critical cause of treatment failure and a barrier to therapeutic advance in UBC. Based on supportive pre-clinical data, we hypothesised that DNA methyltransferase inhibition would circumvent cisplatin resistance in UBC and potentially other cancers. Methods The addition of SGI-110 (guadecitabine, a DNA methyltransferase inhibitor) to conventional doublet therapy of gemcitabine and cisplatin (GC) is being tested within the phase Ib/IIa SPIRE clinical trial. SPIRE incorporates an initial, modified rolling six-dose escalation phase Ib design of up to 36 patients with advanced solid tumours followed by a 20-patient open-label randomised controlled dose expansion phase IIa component as neoadjuvant treatment for UBC. Patients are being recruited from UK secondary care sites. The dose escalation phase will determine a recommended phase II dose (RP2D, primary endpoint) of SGI-110, by subcutaneous injection, on days 1–5 for combination with GC at conventional doses (cisplatin 70 mg/m2, IV infusion, day 8; gemcitabine 1000 mg/m2, IV infusion, days 8 and 15) in every 21-day cycle. In the dose expansion phase, patients will be randomised 1:1 to GC with or without SGI-110 at the proposed RP2D. Secondary endpoints will include toxicity profiles, SGI-110 pharmacokinetics and pharmacodynamic biomarkers, and pathological complete response rates in the dose expansion phase. Analyses will not be powered for formal statistical comparisons and descriptive statistics will be used to describe rates of toxicity, efficacy and translational endpoints by treatment arm. Discussion SPIRE will provide evidence for whether SGI-110 in combination with GC chemotherapy is safe and biologically effective prior to future phase II/III trials as a neoadjuvant therapy for UBC and potentially in other cancers treated with GC

Linking learning with governance in networks and clusters: key issues for analysis and policy

In this paper we analyse the relationship between governance and learning in clusters and networks. In particular, we see these two key elements as interdependent, suggesting that, under particular circumstances, such interdependence may drive clusters and networks towards a dynamic development trajectory. A pure ‘governance perspective’ makes the development of any locality dependent on the system of powers which exists within the locality or across the global value chain. In parallel, a pure ‘competence-based approach’ focuses mainly on the capabilities of actors to learn and undertake activities. In contrast, we open the prospects for an interdependent relation that may change the actual competences of actors as well as the governance settings and dynamics in networks and clusters. When supported by public policies, the learning process may have the potential to modify the governance environment. Simultaneously, the learning process is intrinsically influenced by economic power, which may seriously affect the development prospects of clusters and networks. This is why an intertwined consideration of both aspects is necessary to promote specific approaches to learning and to design appropriate policies. In this paper we offer two preliminary case studies to clarify some of these dynamics: the first taken from the computers cluster in Costa Rica and the second from an Italian bio-pharmaceutical firm and its production network. The first case study refers to the software cluster that was created from scratch in Costa Rica thanks to an enlightened government policy in coordination with new local enterprises and an important foreign direct investor; while the second reflects on the ability of an individual company to create a network of relationships with large transnational companies in order to acquire new competences without falling into a subordinate position with respect to its larger partners

Using Machine Learning to Uncover Latent Research Topics in Fishery Models

© 2018 The Author(s). Published with license by Taylor & Francis © 2018, Shaheen Syed and Charlotte Teresa Weber. Modeling has become the most commonly used method in fisheries science, with numerous types of models and approaches available today. The large variety of models and the overwhelming amount of scientific literature published yearly can make it difficult to effectively access and use the output of fisheries modeling publications. In particular, the underlying topic of an article cannot always be detected using keyword searches. As a consequence, identifying the developments and trends within fisheries modeling research can be challenging and time-consuming. This paper utilizes a machine learning algorithm to uncover hidden topics and subtopics from peer-reviewed fisheries modeling publications and identifies temporal trends using 22,236 full-text articles extracted from 13 top-tier fisheries journals from 1990 to 2016. Two modeling topics were discovered: estimation models (a topic that contains the idea of catch, effort, and abundance estimation) and stock assessment models (a topic on the assessment of the current state of a fishery and future projections of fish stock responses and management effects). The underlying modeling subtopics show a change in the research focus of modeling publications over the last 26 years