Reflections on the Poetic

The texts in this section follow on from a Roundtable discussion at the first CounterText conference, held at Durham University on 18–20 November 2016, on ‘The Poetic’. Aside from the papers and readings, the Roundtable had selected participants framing their outlook on the poetic within the context of what they had been hearing at the conference. Five of those outlooks feature here in revised form, together with another offered subsequently. The keywords listed cite only the themes and writers that feature most centrally, or recurrently, across the six pieces

Improving the effectiveness of age-abundance indicators in the management of fisheries in Queensland, Australia

The development of fishery indicators is a crucial undertaking as it ultimately provides evidence to stakeholders about the status of fished species such as population size and survival rates. In Queensland, as in many other parts of the world, age-abundance indicators (e.g. fish catch rate and/or age composition data) are traditionally used as the evidence basis because they provide information on species life history traits as well as on changes in fishing pressures and population sizes. Often, however, the accuracy of the information from age-abundance indicators can be limited due to missing or biased data. Consequently, improved statistical methods are required to enhance the accuracy, precision and decision-support value of age-abundance indicators

A Cost-Benefit Analysis of Early Childhood Intervention: Evidence from an Experimental Evaluation of the Incredible Years Parenting Program.

A number of researchers and policy makers have recently argued that the most effective way of dealing with long-run disadvantage and the intergenerational transmission of poverty is through early childhood intervention and in particular policies aimed at supporting the family. This study was part of a randomised evaluation of the Incredible Years Program, which is aimed at improving the skills and parenting strategies of parents who have children with conduct problems. The results show that the treatment significantly reduced behavioural problems in young children. Furthermore our detailed cost analysis, when combined with a consideration of the potential long-run benefits associated with the programme, suggest that the long-run rate of return to society from this program is likely to be relatively high.

Rapid Evolutionary Rates and Unique Genomic Signatures Discovered in the First Reference Genome for the Southern Ocean Salp, Salpa thompsoni (Urochordata, Thaliacea)

A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely related urochordate species. Using a multiple-platform, multiple-individual approach, we have produced a 318,767,936-bp genome sequence, covering \u3e50% of the estimated 602 Mb (±173 Mb) genome size for S. thompsoni. Using a nonredundant set of predicted proteins, \u3e50% (16,823) of sequences showed significant homology to known proteins and ∼38% (12,151) of the total protein predictions were associated with Gene Ontology functional information. We have generated 109,958 SNP variant and 9,782 indel predictions for this species, serving as a resource for future phylogenomic and population genetic studies. Comparing the salp genome to available assemblies for four other urochordates, Botryllus schlosseri, Ciona intestinalis, Ciona savignyi and Oikopleura dioica, we found that S. thompsoni shares the previously estimated rapid rates of evolution for these species. High mutation rates are thus independent of genome size, suggesting that rates of evolution \u3e1.5 times that observed for vertebrates are a broad taxonomic characteristic of urochordates. Tests for positive selection implemented in PAML revealed a small number of genes with sites undergoing rapid evolution, including genes involved in ribosome biogenesis and metabolic and immune process that may be reflective of both adaptation to polar, planktonic environments as well as the complex life history of the salps. Finally, we performed an initial survey of small RNAs, revealing the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. Collectively, these resources provide a genomic foundation supporting S. thompsoni as a model species for further examination of the exceptional rates and patterns of genomic evolution shown by urochordates. Additionally, genomic data will allow for the development of molecular indicators of key life history events and processes and afford new understandings and predictions of impacts of climate change on this key species of Antarctic pelagic ecosystems

Limitations from Assumptions in Generative Music Evaluation

The merit of a given piece of music is difficult to evaluate objectively; the merit of a computational system that creates such a piece of music may be even more so. In this article, we propose that there may be limitations resulting from assumptions made in the evaluation of autonomous compositional or creative systems. The article offers a review of computational creativity, evolutionary compositional methods and current methods of evaluating creativity. We propose that there are potential limitations in the discussion and evaluation of generative systems from two standpoints. First, many systems only consider evaluating the final artefact produced by the system whereas computational creativity is defined as a behaviour exhibited by a system. Second, artefacts tend to be evaluated according to recognised human standards. We propose that while this may be a natural assumption, this focus on human-like or human-based preferences could be limiting the potential and generality of future music generating or creative-AI systems

Determination of Dosage Compensation of the Mammalian X Chromosome by RNA-seq is Dependent on Analytical Approach

Background An enduring question surrounding sex chromosome evolution is whether effective hemizygosity in the heterogametic sex leads inevitably to dosage compensation of sex-linked genes, and whether this compensation has been observed in a variety of organisms. Incongruence in the conclusions reached in some recent reports has been attributed to different high-throughput approaches to transcriptome analysis. However, recent reports each utilizing RNA-seq to gauge X-linked gene expression relative to autosomal gene expression also arrived at diametrically opposed conclusions regarding X chromosome dosage compensation in mammals. Results Here we analyze RNA-seq data from X-monosomic female human and mouse tissues, which are uncomplicated by genes that escape X-inactivation, as well as published RNA-seq data to describe relative X expression (RXE). We find that the determination of RXE is highly dependent upon a variety of computational, statistical and biological assumptions underlying RNA-seq analysis. Parameters implemented in short-read mapping programs, choice of reference genome annotation, expression data distribution, tissue source for RNA and RNA-seq library construction method have profound effects on comparing expression levels across chromosomes. Conclusions Our analysis shows that the high number of paralogous gene families on the mammalian X chromosome relative to autosomes contributes to the ambiguity in RXE calculations, RNA-seq analysis that takes into account that single- and multi-copy genes are compensated differently supports the conclusion that, in many somatic tissues, the mammalian X is up-regulated compared to the autosomes

The responses of the four main substitution mechanisms of H in olivine to H2O activity at 1050 °C and 3 GPa

The water solubility in olivine (CH2O) has been investigated at 1050 °C and 3 GPa as a function of water activity (aH2O) at subsolidus conditions in the piston-cylinder apparatus, with aH2O varied using H2O–NaCl fluids. Four sets of experiments were conducted to constrain the effect of aH2O on the four main substitution mechanisms. The experiments were designed to grow olivine in situ and thus achieve global equilibrium (G-type), as opposed to hydroxylating olivine with a pre-existing point-defect structure and impurity content (M-type). Olivine grains from the experiments were analysed with polarised and unpolarised FTIR spectroscopy, and where necessary, the spectra have been deconvoluted to quantify the contribution of each substitution mechanism. Olivine buffered with magnesiowüstite produced absorbance bands at high wavenumbers ranging from 3566 to 3612 cm−1. About 50% of the total absorbance was found parallel to the a-axis, 30% parallel to the b-axis and 20% parallel to the c-axis. The total absorbance and hence water concentration in olivine follows the relationship of CH2O∝aH2O2, indicating that the investigated defect must involve four H atoms substituting for one Si atom (labelled as [Si]). Forsterite buffered with enstatite produced an absorbance band exclusively aligned parallel the c-axis at 3160 cm−1. The band position, polarisation and observed CH2O∝aH2O are consistent with two H substituting for one Mg (labelled as [Mg]). Ti-doped, enstatite-buffered olivine displays absorption bands, and polarisation typical of Ti-clinohumite point defects where two H on the Si-site are charge-balanced by one Ti on a Mg-site (labelled as [Ti]). This is further supported by CH2O∝aH2O and a 1:1 relationship of molar H2O and TiO2 in these experiments. Sc-doped, enstatite-buffered experiments display a main absorption band at 3355 cm−1 with CH2O∝aH2O0.5 and a positive correlation of Sc and H, indicating the coupled substitution of a trivalent cation plus a H for two Mg (labelled as [triv]). Our data demonstrate that extreme care has to be taken when inferences from experiments conducted at aH2O=1 are applied to the mantle, where in most cases, a low aH2O persists. In particular, the higher exponent of the [Si] substitution mechanism means that the contribution of this hydrous defect to total water content will decrease more rapidly with decreasing aH2O than the contributions of the other substitution mechanisms. The experiments confirm previous results that the [Mg] mechanism holds an almost negligible amount of water under nearly all T-P-fO2-fH2O conditions that may be anticipated in nature. However, the small amounts of H2O we find in substituting by this mechanism are similar in the experiments on forsterite doped with either Sc or Ti to those in the undoped forsterite at equivalent aH2O (all buffered by enstatite), confirming the assumption that, thermodynamically, CH2O substituting by each mechanism does not depend on the water concentration that substitutes by other mechanisms.We gratefully acknowledge the Australian Research Council (ARC) support through DP110103134 to JH and HON, and FL130100066 to HON, which partly supported PT during the final stages of this project. RS acknowledges an Australian Postgraduate Award

Satellite observations of mesoscale eddy-induced Ekman pumping

Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 104–132, doi:10.1175/JPO-D-14-0032.1.Three mechanisms for self-induced Ekman pumping in the interiors of mesoscale ocean eddies are investigated. The first arises from the surface stress that occurs because of differences between surface wind and ocean velocities, resulting in Ekman upwelling and downwelling in the cores of anticyclones and cyclones, respectively. The second mechanism arises from the interaction of the surface stress with the surface current vorticity gradient, resulting in dipoles of Ekman upwelling and downwelling. The third mechanism arises from eddy-induced spatial variability of sea surface temperature (SST), which generates a curl of the stress and therefore Ekman pumping in regions of crosswind SST gradients. The spatial structures and relative magnitudes of the three contributions to eddy-induced Ekman pumping are investigated by collocating satellite-based measurements of SST, geostrophic velocity, and surface winds to the interiors of eddies identified from their sea surface height signatures. On average, eddy-induced Ekman pumping velocities approach O(10) cm day−1. SST-induced Ekman pumping is usually secondary to the two current-induced mechanisms for Ekman pumping. Notable exceptions are the midlatitude extensions of western boundary currents and the Antarctic Circumpolar Current, where SST gradients are strong and all three mechanisms for eddy-induced Ekman pumping are comparable in magnitude. Because the polarity of current-induced curl of the surface stress opposes that of the eddy, the associated Ekman pumping attenuates the eddies. The decay time scale of this attenuation is proportional to the vertical scale of the eddy and inversely proportional to the wind speed. For typical values of these parameters, the decay time scale is about 1.3 yr.This work was funded by NASA Grants NNX08AI80G, NNX08AR37G, NNX13AD78G, NNX10AE91G, NNX13AE47G, and NNX10AO98G.2015-07-0

Fragment screening reveals salicylic hydroxamic acid as an inhibitor of <em>Trypanosoma brucei</em> GPI GlcNAc-PI de-N-acetylase

The zinc-metalloenzyme GlcNAc-PI de-N-acetylase is essential for the biosynthesis of mature GPI anchors and has been genetically validated in the bloodstream form of Trypanosoma brucei, which causes African sleeping sickness. We screened a focused library of zinc-binding fragments and identified salicylic hydroxamic acid as a GlcNAc-PI de-N-acetylase inhibitor with high ligand efficiency. This is the first small molecule inhibitor reported for the trypanosome GPI pathway. Investigating the structure activity relationship revealed that hydroxamic acid and 2-OH are essential for potency, and that substitution is tolerated at the 4- and 5-positions