Transcriptome analysis of a parasitic clade V nematode:comparative analysis of potential molecular anthelmintic targets in Cylicostephanus goldi

Clade V nematodes comprise several parasitic species that include the cyathostomins, primary helminth pathogens of horses. Next generation transcriptome datasets are available for eight parasitic clade V nematodes, although no equine parasites are included in this group. Here, we report next generation transcriptome sequencing analysis for the common cyathostomin species, Cylicostephanus goldi. A cDNA library was generated from RNA extracted from 17 C. goldi male and female adult parasites. Following sequencing using a 454 GS FLX pyrosequencer, a total of 475,215 sequencing reads were generated, which were assembled into 26,910 contigs. Using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, 27% of the transcriptome was annotated. Further in-depth analysis was carried out by comparing the C. goldi dataset with the next generation transcriptomes and genomes of other clade V nematodes, with the Oesophagostomum dentatum transcriptome and the Haemonchus contortus genome showing the highest levels of sequence identity with the cyathostomin dataset (45%). The C. goldi transcriptome was mined for genes associated with anthelmintic mode of action and/or resistance. Sequences encoding proteins previously associated with the three major anthelmintic classes used in horses were identified, with the exception of the P-glycoprotein group. Targeted resequencing of the glutamate gated chloride channel α4 subunit (glc-3), one of the primary targets of the macrocyclic lactone anthelmintics, was performed for several cyathostomin species. We believe this study reports the first transcriptome dataset for an equine helminth parasite, providing the opportunity for in-depth analysis of these important parasites at the molecular level. Sequences encoding enzymes involved in key processes and genes associated with levamisole/pyrantel and macrocyclic lactone resistance, in particular the glutamate gated chloride channels, were identified. This novel data will inform cyathostomin biology and anthelmintic resistance studies in future.

Dietary fat and breast cancer mortality: a systematic review and meta-analysis

Background: The influence of dietary fat upon breast cancer mortality remains largely understudied despite extensive investigation into its influence upon breast cancer risk 

Objective: To conduct meta-analyses of studies to clarify the association between dietary fat and breast cancer mortality Design: MEDLINE and EMBASE were searched for relevant articles published up to March 2012. Risk of all-cause or breast cancer specific death was evaluated by combining multivariable adjusted estimates comparing highest versus lowest categories of intake; and per 20 gram increase in intake of total and/or saturated fat (g/day) using random-effects meta-analyses. 

Results: Fifteen prospective cohort studies investigating total fat and/or saturated fat intake (g/day) and breast cancer mortality were included. There was no difference in risk of breast cancer specific death (n = 6; HR = 1.14; 95% CI: 0.86, 1.52; P = 0.34) or all cause death (n = 4; HR = 1.73; 95% CI: 0.82, 3.6; P = 0.15) for women in the highest versus lowest category of total fat intake. Breast cancer specific death (n = 5; HR = 1.63; 95% CI: 1.19, 2.24; p <0.01) was higher for women in the highest versus lowest category of saturated fat intake. 

Conclusions: These meta-analyses have shown that saturated fat intake negatively impacts upon breast cancer survival.

Inland shell midden site-formation:Investigation into a late Pleistocene to early Holocene midden from Trang An, Northern Vietnam

Over the course of the past two decades there has been growing research interest in the site formation processes of shell middens. This stands along-side and is being used to inform cultural, dietary and palaeo-environmental reconstructions. Just as midden site formation processes have turned out to be many and varied, however, the kinds of shell-bearing sites that past human communities created are likely to have been no less diverse. Subsuming such sites under a single category - shell middens - normalises that variation and may lead to the misinterpretation of site function. The greater part of research in this field also continues to focus on coastal shell middens; comparatively little attention has been paid to middens containing freshwater and especially terrestrial molluscs from hinterland locations. As a result, much of the current understanding about shell-midden sites carries a spatial as well as a functional bias. This paper hopes to contribute towards discussion on both fronts. It presents a detailed examination of the formation processes that went into the creation of a land snail-dominated late- to post-glacial midden from northern Vietnam, and considers the role that it may have played in the early settlement of this area. The data presented comes from ongoing archaeological excavations at Hang Boi, a cave located in the sub-coastal karstic uplands of Trang An park, in the Vietnamese Province of Ninh Binh. (C) 2010 Elsevier Ltd and INQUA. All rights reserved.

'Regina v John Terry': The Discursive Construction of an Alleged Racist Event

This article explores the conformation in discourse of a verbal exchange and its subsequent mediatised and legal ramifications. The event concerns an allegedly racist insult directed by high profile English professional footballer John Terry towards another player, Anton Ferdinand, during a televised match in October 2011. The substance of Terry’s utterance, which included the noun phrase ‘fucking black cunt’, was found by a Chief Magistrate not to be a racist insult, although the fact that these actual words were framed within the utterance was not in dispute. The upshot of this ruling was that Terry was acquitted of a racially aggravated public order offence. A subsequent investigation by the regulatory commission of the English Football Association (FA) ruled, almost a year after the event, that Terry was guilty of racially abusing Ferdinand. Terry was banned for four matches and fined £220,000.

It is our contention that this event, played out in legal rulings, social media and print and broadcast media, constitutes a complex web of linguistic structures and strategies in discourse, and as such lends itself well to analysis with a broad range of tools from pragmatics, discourse analysis and cognitive linguistics. Amongst other things, such an analysis can help explain the seemingly anomalous - even contradictory - position adopted in the legal ruling with regard to the speech act status of ‘fucking black cunt’; namely, that the racist content of the utterance was not contested but that the speaker was found not to have issued a racist insult. Over its course, the article addresses this broader issue by making reference to the systemic-functional interpersonal function of language, particularly to the concepts of modality, polarity and modalisation. It also draws on models of verbal irony from linguistic pragmatics, notably from the theory of irony as echoic mention (c.f. Sperber and Wilson, 1981; Wilson and Sperber, 1992). Furthermore, the article makes use of the cognitive-linguistic framework, Text World Theory (c.f. Gavins, 2007; Werth, 1999) to examine the discourse positions occupied by key actors and adapts, from cognitive poetics, the theory of mind-modelling (c.f. Stockwell, 2009) to explore the conceptual means through which these actors discursively negotiate the event.

It is argued that the pragmatic and cognitive strategies that frame the entire incident go a long way towards mitigating the impact of so ostensibly stark an act of racial abuse. Moreover, it is suggested here that the reconciliation of Terry’s action was a result of the confluence of strategies of discourse with relations of power as embodied by the media, the law and perceptions of nationhood embraced by contemporary football culture. It is further proposed that the outcome of this episode, where the FA was put in the spotlight, and where both the conflict and its key antagonists were ‘intranational’, was strongly impelled by the institution of English football and its governing body both to reproduce and maintain social, cultural and ethnic cohesion and to avoid any sense that the event featured a discernable ‘out-group’.

Radiative rates for E1, E2, M1, and M2 transitions in the Br-like ions Sr IV, Y V, Zr VI, Nb VII, and Mo VIII

Energies and lifetimes are reported for the lowest 375 levels of five Br-like ions, namely SrIV, YV, ZrVI, NbVII, and MoVIII, mostly belonging to the 4s²4p⁵, 4s²4p⁴4ℓ, 4s4p⁶, 4s²4p⁴5ℓ, 4s²4p³4d², 4s4p⁵4ℓ, and 4s4p⁵5ℓ configurations. Extensive configuration interaction has been included and the general-purpose relativistic atomic structure package (grasp) has been adopted for the calculations. Additionally, radiative rates are listed among these levels for all E1, E2, M1, and M2 transitions. From a comparison with the measurements, the majority of our energy levels are assessed to be accurate to better than 2%, although discrepancies between theory and experiment for a few are up to 6%. An accuracy assessment of the calculated radiative rates (and lifetimes) is more difficult, because no prior results exist for these ions.

The effect of ionization on the populations of excited levels of C IV and C V in tokamak edge plasmas

The main populating and depopulating mechanisms of the excited energy levels of ions in plasmas with densities <10²³-10²⁴ m^-3 are electron collisional excitation from the ion's ground state and radiative decay, respectively, with the majority of the electron population being in the ground state of the ionization stage. Electron collisional ionization is predominately expected to take place from one ground state to that of the next higher ionization stage. However, the question arises as to whether, in some cases, ionization can also affect the excited level populations. This would apply particularly to those cases involving transient events such as impurity influxes in a laboratory plasma. An analysis of the importance of ionization in populating the excited levels of ions in plasmas typical of those found in the edge of tokamaks is undertaken for the C IV and C V ionization stages. The emphasis is on those energy levels giving rise to transitions of most use for diagnostic purposes (n ≤ 5). Carbon is chosen since it is an important contaminant of JET plasmas; it was the dominant low Z impurity before the installation of the ITER-like wall and is still present in the plasma after its installation. Direct electron collisional ionization both from and to excited levels is considered. Distorted-wave flexible atomic code calculations are performed to generate the required ionization cross sections, due to a lack of atomic data in the literature. Employing these data, ionization from excited level populations is not found to be significant in comparison with radiative decay. However, for some energy levels, ionization terminating in the excited level has an effect in the steady-state of the order of the measurement errors (±10%). During transient events, ionization to excited levels will be of more importance and must be taken into account in the calculation of excited level populations. More accurate atomic data, including possible resonance contributions to the cross sections, would tend to increase further the importance of these effects. 

Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Ti XXI, v XXII, Cr XXIII and Mn XXIV

We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in He-like Ti XXI, V XXII, Cr XXIII and Mn XXIV. grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Additionally, theoretical lifetimes are listed for all the 49 levels of the above four ions. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 10 ^7.5K. Comparisons are made with similar data obtained using the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, in particular for forbidden transitions, are also discussed. Finally, discrepancies between the present results for effective collision strengths with the darc code and earlier semi-relativistic R-matrix data are noted over a wide range of electron temperatures for many transitions in all ions. 

Early-type stars observed in the ESO UVES Paranal Observatory Project - V. Time-variable interstellar absorption

The structure and properties of the diffuse interstellar medium (ISM) on small scales, sub-au to 1 pc, are poorly understood. We compare interstellar absorption-lines, observed towards a selection of O- and B-type stars at two or more epochs, to search for variations over time caused by the transverse motion of each star combined with changes in the structure in the foreground ISM. Two sets of data were used: 83 VLT- UVES spectra with approximately 6 yr between epochs and 21 McDonald observatory 2.7m telescope echelle spectra with 6 - 20 yr between epochs, over a range of scales from 0 - 360 au. The interstellar absorption-lines observed at the two epochs were subtracted and searched for any residuals due to changes in the foreground ISM. Of the 104 sightlines investigated with typically five or more components in Na I D, possible temporal variation was identified in five UVES spectra (six components), in Ca II, Ca I and/or Na I absorption-lines. The variations detected range from 7\% to a factor of 3.6 in column density. No variation was found in any other interstellar species. Most sightlines show no variation, with 3{\sigma} upper limits to changes of the order 0.1 - 0.3 dex in Ca II and Na I. These variations observed imply that fine-scale structure is present in the ISM, but at the resolution available in this study, is not very common at visible wavelengths. A determination of the electron densities and lower limits to the total number density of a sample of the sightlines implies that there is no striking difference between these parameters in sightlines with, and sightlines without, varying components.

Massive stars exploding in a He-rich circumstellar medium - V. Observations of the slow-evolving SN Ibn OGLE-2012-SN-006

We present optical observations of the peculiar Type Ibn supernova (SN Ibn) OGLE-2012-SN-006, discovered and monitored by the Optical Gravitational Lensing Experiment-IV survey, and spectroscopically followed by Public ESO Spectroscopic Survey of Transient Objects (PESSTO) at late phases. Stringent pre-discovery limits constrain the explosion epoch with fair precision to JD = 245 6203.8 +/- 4.0. The rise time to the I-band light-curve maximum is about two weeks. The object reaches the peak absolute magnitude M-I = -19.65 +/- 0.19 on JD = 245 6218.1 +/- 1.8. After maximum, the light curve declines for about 25 d with a rate of 4 mag (100 d)(-1). The symmetric I-band peak resembles that of canonical Type Ib/c supernovae (SNe), whereas SNe Ibn usually exhibit asymmetric and narrower early-time light curves. Since 25 d past maximum, the light curve flattens with a decline rate slower than that of the Co-56-Fe-56 decay, although at very late phases it steepens to approach that rate. However, other observables suggest that the match with the Co-56 decay rate is a mere coincidence, and the radioactive decay is not the main mechanism powering the light curve of OGLE-2012-SN-006. An early-time spectrum is dominated by a blue continuum, with only a marginal evidence for the presence of He I lines marking this SN type. This spectrum shows broad absorptions bluewards than 5000 angstrom, likely O II lines, which are similar to spectral features observed in superluminous SNe at early epochs. The object has been spectroscopically monitored by PESSTO from 90 to 180 d after peak, and these spectra show the typical features observed in a number of SN 2006jc-like events, including a blue spectral energy distribution and prominent and narrow (v(FWHM) approximate to 1900 km s(-1)) He I emission lines. This suggests that the ejecta are interacting with He-rich circumstellar material. The detection of broad (10(4) km s(-1)) O I and Ca II features likely produced in the SN ejecta (including the [OI] lambda lambda 6300,6364 doublet in the latest spectra) lends support to the interpretation of OGLE-2012-SN-006 as a core-collapse event.

Musicking (beyond makers, listeners; impact of recognizing this category)

A specialist entry into the SAGE Encyclopedia on 'musicking'