Parasites that change predator or prey behaviour can have keystone effects on community composition

Parasites play pivotal roles in structuring communities, often via indirect interactions with non-host species. These effects can be density-mediated (through mortality) or trait-mediated (behavioural, physiological and developmental), and may be crucial to population interactions, including biological invasions. For instance, parasitism can alter intraguild predation (IGP) between native and invasive crustaceans, reversing invasion outcomes. Here, we use mathematical models to examine how parasite-induced trait changes influence the population dynamics of hosts that interact via IGP. We show that trait-mediated indirect interactions impart keystone effects, promoting or inhibiting host coexistence. Parasites can thus have strong ecological impacts, even if they have negligible virulence, underscoring the need to consider trait-mediated effects when predicting effects of parasites on community structure in general and biological invasions in particular.

The impact of peer review on the radiotherapy treatment planning process in the treatment of lung cancer

Background:
Advanced radiotherapy techniques permit accurate delivery of radiotherapy to lung tumours. Improved accuracy increases the possibility of radiotherapy field geographic miss of the tumour. One source of error is the accuracy of target volume (TV) delineation by the clinical oncologist. Colleague peer review of all curative intent lung cancer plans has been mandatory in our institution since May 2013. At least 2 clinical oncologists review plans checking treatment paradigm, TV delineated, dose to tumour and dose to critical organs. We report the impact of peer review on the radiotherapy planning process for lung cancer.

Methods:
The radiotherapy treatment plans of all patients receiving radical radiotherapy were presented at weekly peer review meetings after their TVs volumes were provisionally signed off by the treating consultant or post-fellowship registrar. All cases and any resultant change to the treatment plan were recorded in our prospective peer review database. We present the summary of changes agreed following the peer review process for a 6 month period.

Results:
Fifteen peer review sessions, including 46 patients (36 NSCLC, 10 SCLC) were analysed. An average of 3 cases were discussed per meeting (range 1 5). 24% of treatment courses were changed. In 4% there was a complete change in paradigm
of treatment (1 patient proceeded to induction chemotherapy, 1 patient had high dose palliative radiotherapy). In 16% there was a change in TV delineated and in 9% a change in dose (2 dose reductions and 2 alterations to post-operative dose fractionations).

Conclusions:
Consultant led peer review resulted in a change in a component of the treatment plan for 28% of patients that would not otherwise have taken place. Given this impact, consultant led peer review should be considered as an essential component in the radiotherapy planning process for all patients treated with curative radiotherapy.

Ellerman Bombs - Evidence for Magnetic Reconnection in the Lower Solar Atmosphere

The presence of photospheric magnetic reconnection has long been thought to give rise to short and impulsive events, such as Ellerman bombs (EBs) and Type II spicules. In this article, we combine high-resolution, high-cadence observations from the Interferometric BIdimensional Spectrometer and Rapid Oscillations in the Solar Atmosphere instruments at the Dunn Solar Telescope, National Solar Observatory, New Mexico, with co-aligned Solar Dynamics Observatory Atmospheric Imaging Assembly and Hinode Solar Optical Telescope (SOT) data to observe small-scale events situated within an active region. These data are then compared with state-of-the-art numerical simulations of the lower atmosphere made using the MURaM code. It is found that brightenings, in both the observations and the simulations, of the wings of the Hα line profile, interpreted as EBs, are often spatially correlated with increases in the intensity of the Fe I λ6302.5 line core. Bipolar regions inferred from Hinode/SOT magnetic field data show evidence of flux cancellation associated, co-spatially, with these EBs, suggesting that magnetic reconnection could be a driver of these high-energy events. Through the analysis of similar events in the simulated lower atmosphere, we are able to infer that line profiles analogous to the observations occur co-spatially with regions of strong opposite-polarity magnetic flux. These observed events and their simulated counterparts are interpreted as evidence of photospheric magnetic reconnection at scales observable using current observational instrumentation.

Characteristics of Transverse Waves in Chromospheric Mottles

Using data obtained by the high temporal and spatial resolution Rapid Oscillations in the Solar Atmosphere instrument on the Dunn Solar Telescope, we investigate at an unprecedented level of detail transverse oscillations in chromospheric fine structures near the solar disk center. The oscillations are interpreted in terms of propagating and standing magnetohydrodynamic kink waves. Wave characteristics including the maximum transverse velocity amplitude and the phase speed are measured as a function of distance along the structure's length. Solar magnetoseismology is applied to these measured parameters to obtain diagnostic information on key plasma parameters (e.g., magnetic field, density, temperature, flow speed) of these localized waveguides. The magnetic field strength of the mottle along the ~2 Mm length is found to decrease by a factor of 12, while the local plasma density scale height is ~280 ± 80 km.

Predicting the ecological impacts of a new freshwater invader:Functional responses and prey selectivity of the 'killer shrimp', Dikerogammarus villosus, compared to the native Gammarus pulex

The ability to predict the likely ecological impacts of invasive species in fresh waters is a pressing research requirement. Whilst comparisons of species traits and considerations of invasion history have some efficacy in this respect, we require robust methods that can compare the effects of native and invasive species. Here, we utilise comparative functional responses and prey selectivity experiments to understand and predict the ecological impact of an invader as compared to a native. We compared the predatory functional responses of an emerging invasive species in Europe, the 'killer shrimp', Dikerogammarus villosus, and an analogous native species, Gammarus pulex, towards three representative prey species: Asellus aquaticus, Daphnia magna and Chironomus sp. Furthermore, as ecological impact may be greater for invasive species with more indiscriminate feeding habits, we compared the selectivity for the three prey types between the invasive and native species. In both the presence and absence of experimental habitats, large D. villosus, and those matched for body size with G. pulex, generally showed higher (Type II) functional responses than G. pulex, with the invasive species exhibiting higher maximum feeding rates. Further, D. villosus exhibited significantly more indiscriminate prey selection compared with G. pulex, a trait that became more evident as the invader increased in size. Differences in functional responses and prey selectivity were prey species specific, with higher to lower predicted impacts in the order A. aquaticus, D. magna and Chironomus sp. This is in accord with the impact of this invasive species on macroinvertebrates in the field. We thus provide understanding of the known ecological impact of D. villosus and discuss the utility of the phenomenological use of comparative functional responses and resource use as a tool through which the potential ecological impacts of invasive species may be identified. © 2013 John Wiley & Sons Ltd.

Tracking magnetic bright point motions through the solar atmosphere

High-cadence, multiwavelength observations and simulations are employed for the analysis of solar photospheric magnetic bright points (MBPs) in the quiet Sun. The observations were obtained with the Rapid Oscillations in the Solar Atmosphere (ROSA) imager and the Interferometric Bidimensional Spectrometer at the Dunn Solar Telescope. Our analysis reveals that photospheric MBPs have an average transverse velocity of approximately 1 km s-1, whereas their chromospheric counterparts have a slightly higher average velocity of 1.4 km s-1. Additionally, chromospheric MBPs were found to be around 63 per cent larger than the equivalent photospheric MBPs. These velocity values were compared with the output of numerical simulations generated using the muram code. The simulated results were similar, but slightly elevated, when compared to the observed data. An average velocity of 1.3 km s-1 was found in the simulated G-band images and an average of 1.8 km s-1 seen in the velocity domain at a height of 500 km above the continuum formation layer. Delays in the change of velocities were also analysed. Average delays of ˜4 s between layers of the simulated data set were established and values of ˜29 s observed between G-band and Ca ii K ROSA observations. The delays in the simulations are likely to be the result of oblique granular shock waves, whereas those found in the observations are possibly the result of a semi-rigid flux tube.

Predicting invasive species impacts: a community module functional response approach reveals context dependencies

Summary
-Predatory functional responses play integral roles in predator–prey dynamics, and their assessment promises greater understanding and prediction of the predatory impacts of invasive species.
-Other interspecific interactions, however, such as parasitism and higher-order predation, have the potential to modify predator–prey interactions and thus the predictive capability of the comparative functional response approach.
-We used a four-species community module (higher-order predator; focal native or invasive predators; parasites of focal predators; native prey) to compare the predatory functional responses of native Gammarus duebeni celticus and invasive Gammarus pulex amphipods towards three invertebrate prey species (Asellus aquaticus, Simulium spp., Baetis rhodani), thus, quantifying the context dependencies of parasitism and a higher-order fish predator on these functional responses.
-Our functional response experiments demonstrated that the invasive amphipod had a higher predatory impact (lower handling time) on two of three prey species, which reflects patterns of impact observed in the field. The community module also revealed that parasitism had context-dependent influences, for one prey species, with the potential to further reduce the predatory impact of the invasive amphipod or increase the predatory impact of the native amphipod in the presence of a higher-order fish predator.
-Partial consumption of prey was similar for both predators and occurred increasingly in the order A. aquaticus, Simulium spp. and B. rhodani. This was associated with increasing prey densities, but showed no context dependencies with parasitism or higher-order fish predator.
-This study supports the applicability of comparative functional responses as a tool to predict and assess invasive species impacts incorporating multiple context dependencies.

Dynamic properties of bright points in an active region

Context. Bright points (BPs) are small-scale, magnetic features ubiquitous across the solar surface. Previously, we have observed and noted their properties for quiet Sun regions. Here, we determine the dynamic properties of BPs using simultaneous quiet Sun and active region data.

Aims. The aim of this paper is to compare the properties of BPs in both active and quiet Sun regions and to determine any difference in the dynamics and general properties of BPs as a result of the varying magnetic activity within these two regions.

Methods. High spatial and temporal resolution G-band observations of active region AR11372 were obtained with the Rapid Oscillations in the Solar Atmosphere instrument at the Dunn Solar Telescope. Three subfields of varying polarity and magnetic flux density were selected with the aid of magnetograms obtained from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory. Bright points within these subfields were subsequently tracked and analysed.

Results. It is found that BPs within active regions display attenuated velocity distributions with an average horizontal velocity of ~0.6 km s-1, compared to the quiet region which had an average velocity of 0.9 km s-1. Active region BPs are also ~21% larger than quiet region BPs and have longer average lifetimes (~132 s) than their quiet region counterparts (88 s). No preferential flow directions are observed within the active region subfields. The diffusion index (γ) is estimated at ~1.2 for the three regions.

Conclusions. We confirm that the dynamic properties of BPs arise predominately from convective motions. The presence of stronger field strengths within active regions is the likely reason behind the varying properties observed. We believe that larger amounts of magnetic flux will attenuate BP velocities by a combination of restricting motion within the intergranular lanes and by increasing the number of stagnation points produced by inhibited convection. Larger BPs are found in regions of higher magnetic flux density and we believe that lifetimes increase in active regions as the magnetic flux stabilises the BPs.

FKBPL: a marker of good prognosis in breast cancer

FK506-binding protein-like (FKBPL) has established roles as an anti-tumor protein, with a therapeutic peptide based on this protein, ALM201, shortly entering phase I/II clinical trials. Here, we evaluated FKBPL's prognostic ability in primary breast cancer tissue, represented on tissue microarrays (TMA) from 3277 women recruited into five independent retrospective studies, using immunohistochemistry (IHC). In a meta-analysis, FKBPL levels were a significant predictor of BCSS; low FKBPL levels indicated poorer breast cancer specific survival (BCSS) (hazard ratio (HR) = 1.30, 95% confidence interval (CI) 1.14-1.49, p < 0.001). The prognostic impact of FKBPL remained significant after adjusting for other known prognostic factors (HR = 1.25, 95% CI 1.07-1.45, p = 0.004). For the sub-groups of 2365 estrogen receptor (ER) positive patients and 1649 tamoxifen treated patients, FKBPL was significantly associated with BCSS (HR = 1.34, 95% CI 1.13-1.58, p < 0.001, and HR = 1.25, 95% CI 1.04-1.49, p = 0.02, respectively). A univariate analysis revealed that FKBPL was also a significant predictor of relapse free interval (RFI) within the ER positive patient group, but it was only borderline significant within the smaller tamoxifen treated patient group (HR = 1.32 95% CI 1.05-1.65, p = 0.02 and HR = 1.23 95% CI 0.99-1.54, p = 0.06, respectively). The data suggests a role for FKBPL as a prognostic factor for BCSS, with the potential to be routinely evaluated within the clinic.

Development of a rapid multiplexed assay for the direct screening of antimicrobial residues in raw milk

Antimicrobial residues found to be present in milk can have both health and economic impacts. For these reasons, the widespread routine testing of milk is required. Due to delays with sample handling and test scheduling, laboratory-based tests are not always suited for making decisions about raw material intake and product release, especially when samples require shipping to a central testing facility. Therefore, rapid on-site screening tests that can produce results within a matter of minutes are required to facilitate rapid intake and product release processes. Such tests must be simple for use by non-technical staff. There is increasing momentum towards the development and implementation of multiplexing tests that can detect a range of important antimicrobial residues simultaneously. A simple in situ multiplexed planar waveguide device that can simultaneously detect chloramphenicol, streptomycin and desfuroylceftiofur in raw dairy milk, without sample preparation, has been developed. Samples are simply mixed with antibody prior to an aliquot being passed through the detection cartridge for 5 min before reading on a field-deployable portable instrument. Multiplexed calibration curves were produced in both buffer and raw milk. Buffer curves, for chloramphenicol, streptomycin and desfuroylceftiofur, showed linear ranges (inhibitory concentration (IC)₂₀–IC₈₀) of 0.1–0.9, 3–129 and 12–26 ng/ml, whilst linear range in milk was 0.13–0.74, 11–376 and 2–12 ng/ml, respectively, thus meeting European legislated concentration requirements for both chloramphenicol and streptomycin, in milk, without the need for any sample preparation. Desfuroylceftiofur-contaminated samples require only simple sample dilution to bring positive samples within the range of quantification. Assay repeatability and reproducibility were lower than 12 coefficient of variation (%CV), whilst blank raw milk samples (n = 9) showed repeatability ranging between 4.2 and 8.1 %CV when measured on all three calibration curves.

Hα and EUV observations of a partial CME

We have obtained H$\alpha$ high spatial and time resolution observations of the upper solar chromosphere and supplemented these with multi-wavelength observations from the Solar Dynamic Observatory (SDO) and the {\it Hinode} ExtremeUltraviolet Imaging Spectrometer (EIS). The H$\alpha$ observations were conducted on 11 February 2012 with the Hydrogen-Alpha Rapid Dynamics Camera (HARDcam) instrument at the National Solar Observatory's Dunn Solar Telescope. Our H$\alpha$ observations found large downflows of chromospheric material returning from coronal heights following a failed prominence eruption. We have detected several large condensations ("blobs") returning to the solar surface at velocities of $\approx$200 km s$^{-1}$ in both H$\alpha$ and several SDO AIA band passes. The average derived size of these "blobs" in H$\alpha$ is 500 by 3000 km$^2$ in the directions perpendicular and parallel to the direction of travel, respectively. A comparison of our "blob" widths to those found from coronal rain, indicate there are additional smaller, unresolved "blobs" in agreement with previous studies and recent numerical simulations. Our observed velocities and decelerations of the "blobs" in both H$\alpha$ and SDO bands are less than those expected for gravitational free-fall and imply additional magnetic or gas pressure impeding the flow. We derived a kinetic energy $\approx$2 orders of magnitude lower for the main eruption than a typical CME, which may explain its partial nature.

Rapid detection of health-care-associated bloodstream infection in critical care using multipathogen real-time polymerase chain reaction technology: a diagnostic accuracy study and systematic review

Background: There is growing interest in the potential utility of real-time polymerase chain reaction (PCR) in diagnosing bloodstream infection by detecting pathogen deoxyribonucleic acid (DNA) in blood samples within a few hours. SeptiFast (Roche Diagnostics GmBH, Mannheim, Germany) is a multipathogen probe-based system targeting ribosomal DNA sequences of bacteria and fungi. It detects and identifies the commonest pathogens causing bloodstream infection. As background to this study, we report a systematic review of Phase III diagnostic accuracy studies of SeptiFast, which reveals uncertainty about its likely clinical utility based on widespread evidence of deficiencies in study design and reporting with a high risk of bias. 

Objective: Determine the accuracy of SeptiFast real-time PCR for the detection of health-care-associated bloodstream infection, against standard microbiological culture. 

Design: Prospective multicentre Phase III clinical diagnostic accuracy study using the standards for the reporting of diagnostic accuracy studies criteria. 

Setting: Critical care departments within NHS hospitals in the north-west of England. 

Participants: Adult patients requiring blood culture (BC) when developing new signs of systemic inflammation. 

Main outcome measures: SeptiFast real-time PCR results at species/genus level compared with microbiological culture in association with independent adjudication of infection. Metrics of diagnostic accuracy were derived including sensitivity, specificity, likelihood ratios and predictive values, with their 95% confidence intervals (CIs). Latent class analysis was used to explore the diagnostic performance of culture as a reference standard. 

Results: Of 1006 new patient episodes of systemic inflammation in 853 patients, 922 (92%) met the inclusion criteria and provided sufficient information for analysis. Index test assay failure occurred on 69 (7%) occasions. Adult patients had been exposed to a median of 8 days (interquartile range 4–16 days) of hospital care, had high levels of organ support activities and recent antibiotic exposure. SeptiFast real-time PCR, when compared with culture-proven bloodstream infection at species/genus level, had better specificity (85.8%, 95% CI 83.3% to 88.1%) than sensitivity (50%, 95% CI 39.1% to 60.8%). When compared with pooled diagnostic metrics derived from our systematic review, our clinical study revealed lower test accuracy of SeptiFast real-time PCR, mainly as a result of low diagnostic sensitivity. There was a low prevalence of BC-proven pathogens in these patients (9.2%, 95% CI 7.4% to 11.2%) such that the post-test probabilities of both a positive (26.3%, 95% CI 19.8% to 33.7%) and a negative SeptiFast test (5.6%, 95% CI 4.1% to 7.4%) indicate the potential limitations of this technology in the diagnosis of bloodstream infection. However, latent class analysis indicates that BC has a low sensitivity, questioning its relevance as a reference test in this setting. Using this analysis approach, the sensitivity of the SeptiFast test was low but also appeared significantly better than BC. Blood samples identified as positive by either culture or SeptiFast real-time PCR were associated with a high probability (> 95%) of infection, indicating higher diagnostic rule-in utility than was apparent using conventional analyses of diagnostic accuracy. 

Conclusion: SeptiFast real-time PCR on blood samples may have rapid rule-in utility for the diagnosis of health-care-associated bloodstream infection but the lack of sensitivity is a significant limiting factor. Innovations aimed at improved diagnostic sensitivity of real-time PCR in this setting are urgently required. Future work recommendations include technology developments to improve the efficiency of pathogen DNA extraction and the capacity to detect a much broader range of pathogens and drug resistance genes and the application of new statistical approaches able to more reliably assess test performance in situation where the reference standard (e.g. blood culture in the setting of high antimicrobial use) is prone to error.