SNP addresses are a pathogen typing method based on whole-genome sequences (WGSs), assigning groups at seven different levels of genetic similarity. Public health surveillance uses it for several gastro-intestinal infections; this work trialled its use in veterinary surveillance for salmonella outbreak detection. Comparisons were made between temporal and spatio-temporal cluster detection models that either defined cases by their SNP address or by phage type, using historical data sets. Clusters of SNP incidents were effectively detected by both methods, but spatio-temporal models consistently detected these clusters earlier than the corresponding temporal models. Unlike phage type, SNP addresses appeared spatially and temporally limited, which facilitated the differentiation of novel, stable, or expanding clusters in spatio-temporal models. Furthermore, these models flagged spatio-temporal clusters containing only two to three cases at first detection, compared with a median of seven cases in phage-type models. The large number of SNP addresses will require automated methods to implement these detection models routinely. Further work is required to explore how temporal changes and different host species may impact the sensitivity and specificity of cluster detection. In conclusion, given validation with more sequencing data, SNP addresses are likely to be a valuable addition to early warning systems in veterinary surveillance.

This study investigated sex differences in Fe status, and associations between Fe status and endurance and musculoskeletal outcomes, in military training. In total, 2277 British Army trainees (581 women) participated. Fe markers and endurance performance (2·4 km run) were measured at the start (week 1) and end (week 13) of training. Whole-body areal body mineral density (aBMD) and markers of bone metabolism were measured at week 1. Injuries during training were recorded. Training decreased Hb in men and women (mean change (–0·1 (95 % CI –0·2, –0·0) and –0·7 (95 % CI –0·9, –0·6) g/dl, both P < 0·001) but more so in women (P < 0·001). Ferritin decreased in men and women (–27 (95 % CI –28, –23) and –5 (95 % CI –8, –1) µg/l, both P ≤ 0·001) but more so in men (P < 0·001). Soluble transferrin receptor increased in men and women (2·9 (95 % CI 2·3, 3·6) and 3·8 (95 % CI 2·7, 4·9) nmol/l, both P < 0·001), with no difference between sexes (P = 0·872). Erythrocyte distribution width increased in men (0·3 (95 % CI 0·2, 0·4)%, P < 0·001) but not in women (0·1 (95 % CI –0·1, 0·2)%, P = 0·956). Mean corpuscular volume decreased in men (–1·5 (95 % CI –1·8, –1·1) fL, P < 0·001) but not in women (0·4 (95 % CI –0·4, 1·3) fL, P = 0·087). Lower ferritin was associated with slower 2·4 km run time (P = 0·018), sustaining a lower limb overuse injury (P = 0·048), lower aBMD (P = 0·021) and higher beta C-telopeptide cross-links of type 1 collagen and procollagen type 1 N-terminal propeptide (both P < 0·001) controlling for sex. Improving Fe stores before training may protect Hb in women and improve endurance and protect against injury.

We present a comparison between the performance of a selection of source finders (SFs) using a new software tool called Hydra. The companion paper, Paper I, introduced the Hydra tool and demonstrated its performance using simulated data. Here we apply Hydra to assess the performance of different source finders by analysing real observational data taken from the Evolutionary Map of the Universe (EMU) Pilot Survey. EMU is a wide-field radio continuum survey whose primary goal is to make a deep ($20\mu$Jy/beam RMS noise), intermediate angular resolution ($15^{\prime\prime}$), 1 GHz survey of the entire sky south of $+30^{\circ}$ declination, and expecting to detect and catalogue up to 40 million sources. With the main EMU survey it is highly desirable to understand the performance of radio image SF software and to identify an approach that optimises source detection capabilities. Hydra has been developed to refine this process, as well as to deliver a range of metrics and source finding data products from multiple SFs. We present the performance of the five SFs tested here in terms of their completeness and reliability statistics, their flux density and source size measurements, and an exploration of case studies to highlight finder-specific limitations.

The latest generation of radio surveys are now producing sky survey images containing many millions of radio sources. In this context it is highly desirable to understand the performance of radio image source finder (SF) software and to identify an approach that optimises source detection capabilities. We have created Hydra to be an extensible multi-SF and cataloguing tool that can be used to compare and evaluate different SFs. Hydra, which currently includes the SFs Aegean, Caesar, ProFound, PyBDSF, and Selavy, provides for the addition of new SFs through containerisation and configuration files. The SF input RMS noise and island parameters are optimised to a 90% ‘percentage real detections’ threshold (calculated from the difference between detections in the real and inverted images), to enable comparison between SFs. Hydra provides completeness and reliability diagnostics through observed-deep ($\mathcal{D}$) and generated-shallow ($\mathcal{S}$) images, as well as other statistics. In addition, it has a visual inspection tool for comparing residual images through various selection filters, such as S/N bins in completeness or reliability. The tool allows the user to easily compare and evaluate different SFs in order to choose their desired SF, or a combination thereof. This paper is part one of a two part series. In this paper we introduce the Hydra software suite and validate its $\mathcal{D/S}$ metrics using simulated data. The companion paper demonstrates the utility of Hydra by comparing the performance of SFs using both simulated and real images.

We report the experimental results of the commissioning phase in the 10 PW laser beamline of the Shanghai Superintense Ultrafast Laser Facility (SULF). The peak power reaches 2.4 PW on target without the last amplifying during the experiment. The laser energy of 72 ± 9 J is directed to a focal spot of approximately 6 μm diameter (full width at half maximum) in 30 fs pulse duration, yielding a focused peak intensity around 2.0 × 1021 W/cm2. The first laser-proton acceleration experiment is performed using plain copper and plastic targets. High-energy proton beams with maximum cut-off energy up to 62.5 MeV are achieved using copper foils at the optimum target thickness of 4 μm via target normal sheath acceleration. For plastic targets of tens of nanometers thick, the proton cut-off energy is approximately 20 MeV, showing ring-like or filamented density distributions. These experimental results reflect the capabilities of the SULF-10 PW beamline, for example, both ultrahigh intensity and relatively good beam contrast. Further optimization for these key parameters is underway, where peak laser intensities of 1022–1023 W/cm2 are anticipated to support various experiments on extreme field physics.

In this era of spatially resolved observations of planet-forming disks with Atacama Large Millimeter Array (ALMA) and large ground-based telescopes such as the Very Large Telescope (VLT), Keck, and Subaru, we still lack statistically relevant information on the quantity and composition of the material that is building the planets, such as the total disk gas mass, the ice content of dust, and the state of water in planetesimals. SPace Infrared telescope for Cosmology and Astrophysics (SPICA) is an infrared space mission concept developed jointly by Japan Aerospace Exploration Agency (JAXA) and European Space Agency (ESA) to address these questions. The key unique capabilities of SPICA that enable this research are (1) the wide spectral coverage $10{-}220\,\mu\mathrm{m}$, (2) the high line detection sensitivity of $(1{-}2) \times 10^{-19}\,\mathrm{W\,m}^{-2}$ with $R \sim 2\,000{-}5\,000$ in the far-IR (SAFARI), and $10^{-20}\,\mathrm{W\,m}^{-2}$ with $R \sim 29\,000$ in the mid-IR (SPICA Mid-infrared Instrument (SMI), spectrally resolving line profiles), (3) the high far-IR continuum sensitivity of 0.45 mJy (SAFARI), and (4) the observing efficiency for point source surveys. This paper details how mid- to far-IR infrared spectra will be unique in measuring the gas masses and water/ice content of disks and how these quantities evolve during the planet-forming period. These observations will clarify the crucial transition when disks exhaust their primordial gas and further planet formation requires secondary gas produced from planetesimals. The high spectral resolution mid-IR is also unique for determining the location of the snowline dividing the rocky and icy mass reservoirs within the disk and how the divide evolves during the build-up of planetary systems. Infrared spectroscopy (mid- to far-IR) of key solid-state bands is crucial for assessing whether extensive radial mixing, which is part of our Solar System history, is a general process occurring in most planetary systems and whether extrasolar planetesimals are similar to our Solar System comets/asteroids. We demonstrate that the SPICA mission concept would allow us to achieve the above ambitious science goals through large surveys of several hundred disks within $\sim\!2.5$ months of observing time.

We study the evolution of unidirectional water waves from a randomly forced input condition with uncorrelated Fourier components. We examine the kurtosis of the linearised free surface as a convenient proxy for the probability of a rogue wave. We repeat the laboratory experiments of Onorato et al. (Phys. Rev. E, vol. 70, 2004, 067302), both experimentally and numerically, and extend the parameter space in our numerical simulations. We consider numerical simulations based on the modified nonlinear Schrödinger equation and the fully nonlinear water wave equations, which are in good agreement. For low steepness, existing analytical models based on the nonlinear Schrödinger equation (NLS) are found to be accurate. For cases which are steep or have very narrow bandwidths, these analytical models over-predict the rate at which excess kurtosis develops. In these steep cases, the kurtosis in both our experiments and numerical simulations peaks before returning to an equilibrium level. Such transient maxima are not predicted by NLS-based analytical models. Above a certain threshold of steepness, the steady-state value of kurtosis is primarily dependent on the spectral bandwidth. We also examine how the average shape of extreme events is modified by nonlinearity over the evolution distance, showing significant asymmetry during the initial evolution, which is greatly reduced once the spectrum has reached equilibrium. The locations of the maxima in asymmetry coincide approximately with the locations of the maxima in kurtosis.

Stratospheric airships are promising aircraft, usually designed as a non-rigid airship. As an essential part of the non-rigid airship, the envelope plays a significant role in maintaining its shape and bearing the external force load. Generally, the envelope material of a flexible airship consists of plain-weave fabric, composed of warp and weft fibre yarn. At present, biaxial tensile experiments are the primary method used to study the stress–strain characteristics of such flexible airship materials. In this work, biaxial tensile testing of UN-5100 material was carried out. The strain on the material under unusual stress and the stress ratio were obtained using Digital Image Correlation (DIC) technology. Also, the stress–strain curve was corrected by polynomial fitting. The slope of the stress–strain curve at different points, the Membrane Structures Association of Japan (MSAJ) standard and the Radial Basis Function (RBF) model were compared to identify the stress–strain characteristics of the materials. Some conclusions on the mechanical properties of the flexible airship material can be drawn and will play a significant role in the design of such envelopes.

We present the elements required to construct two devices used in an undergraduate plasma physics laboratory. The materials and construction costs of the sources, the vacuum systems and probe drives and electrical circuits are presented in detail in the text and the first appendix. We also provide the software for probe motion and data acquisition as well as the electrical schematics for key components. Experiments which have been performed are listed and two (resonance cones and whistler waves) are described in greater detail. The machines are flexible and original research is possible.

At present, analysis of diet and bladder cancer (BC) is mostly based on the intake of individual foods. The examination of food combinations provides a scope to deal with the complexity and unpredictability of the diet and aims to overcome the limitations of the study of nutrients and foods in isolation. This article aims to demonstrate the usability of supervised data mining methods to extract the food groups related to BC. In order to derive key food groups associated with BC risk, we applied the data mining technique C5.0 with 10-fold cross-validation in the BLadder cancer Epidemiology and Nutritional Determinants study, including data from eighteen case–control and one nested case–cohort study, compromising 8320 BC cases out of 31 551 participants. Dietary data, on the eleven main food groups of the Eurocode 2 Core classification codebook, and relevant non-diet data (i.e. sex, age and smoking status) were available. Primarily, five key food groups were extracted; in order of importance, beverages (non-milk); grains and grain products; vegetables and vegetable products; fats, oils and their products; meats and meat products were associated with BC risk. Since these food groups are corresponded with previously proposed BC-related dietary factors, data mining seems to be a promising technique in the field of nutritional epidemiology and deserves further examination.

A multi-scale strategy is employed in the paper to investigate the thermo-mechanical properties of 2.5D angle-interlock woven shape memory polymer composites (SMPCs). In the study, the mesoscopic model of 2.5D woven SMPCs and microscopic model of yarns are firstly developed. After that, the themo-viscoelastic constitutive relationship of the yarn is described in the form of hereditary integral and the parameters of relaxation moduli are obtained from nonlinear fitting of Prony series based on the results of finite element method (FEM). Based on the multi-scale models and the constitutive relationship, the effects of warp and weft arranged densities on viscoelastic properties of 2.5D woven SMPCs are studied in detail. Finally, the shape memory behavior along the warp direction in small strain region is also analyzed. The research in the paper lays a foundation for design and application of woven SMPCs in engineering.

The response of soil microbial communities to soil quality changes is a sensitive indicator of soil ecosystem health. The current work investigated soil microbial communities under different fertilization treatments in a 31-year experiment using the phospholipid fatty acid (PLFA) profile method. The experiment consisted of five fertilization treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice (Oryza sativa L.) straw residue and chemical fertilizer (RF), low manure rate and chemical fertilizer (LOM), and high manure rate and chemical fertilizer (HOM). Soil samples were collected from the plough layer and results indicated that the content of PLFAs were increased in all fertilization treatments compared with the control. The iC15:0 fatty acids increased significantly in MF treatment but decreased in RF, LOM and HOM, while aC15:0 fatty acids increased in these three treatments. Principal component (PC) analysis was conducted to determine factors defining soil microbial community structure using the 21 PLFAs detected in all treatments: the first and second PCs explained 89.8% of the total variance. All unsaturated and cyclopropyl PLFAs except C12:0 and C15:0 were highly weighted on the first PC. The first and second PC also explained 87.1% of the total variance among all fertilization treatments. There was no difference in the first and second PC between RF and HOM treatments. The results indicated that long-term combined application of straw residue or organic manure with chemical fertilizer practices improved soil microbial community structure more than the mineral fertilizer treatment in double-cropped paddy fields in Southern China.

The mammalian target of rapamycin (mTOR) has been shown to be involved in lipopolysaccharide (LPS)-induced immune responses in many mammal cells. Here, we suggest that the mTOR pathway is involved in the intestinal inflammatory responses evoked by LPS treatment in chicken embryos. The intestinal tissue from Specific pathogen free chick embryos was cultured in the presence of LPS for 2 h. Secretory immunoglobulin A (sIgA) concentrations, messenger RNA (mRNA) expression of cytokines, and protein levels of nuclear factor-κB (NF-κB), mitogen-activated protein kinase (MAPK), mTOR and p70 ribosomal S6 kinase (p70S6K) were determined. The results showed that LPS treatment increased sIgA concentrations in a dose-dependent manner. The mRNA levels of interleukine (IL)-6, IL-8, IL-10, tumor necrosis factor-α and Toll-like receptor (TLR) 4 were upregulated by LPS treatment (P<0.05). Lipopolysaccharide increased the phosphorylation of Jun N-terminal kinase (JNK), p38 MAPK and NF-κB (P<0.05) while decreasing the phosphorylation level of mTOR (P<0.05). Supplementation of leucine at doses of 10, 20 and 40 mM dose-dependently decreased sIgA production. Leucine supplementation at 40 mM restored the phosphorylation level of mTOR and p70S6K while suppressing the phosphorylation levels of NF-κB (P<0.05) and partially down-regulating the phosphorylation of p38 MAPK and JNK. The transcription of IL-6 was significantly decreased by leucine supplementation. These results suggested that leucine could alleviate LPS-induced inflammatory responses by down-regulating NF-κB signaling pathway and evoking mTOR/p70S6K signaling pathway, which may involve in the regulation of the intestinal immune system in chicken embryos.

Honeybee foraging can transfer exogenous genes from genetically modified (GM) oilseed rape (Brassica napus L.) to closely related plants, which not only induces potential ecological risks but also contaminates non-GM seeds or honey products with GM ingredients. These events may lead to international trade disputes. Chinese honeybees (Apis cerana cerana Fabricius) and a herbicide (glufosinate)-resistant GM strain of B. napus (Z7B10) were studied to examine the effects of honeybee short-range foraging on oilseed rape gene flow and honey ingredients. Results showed variable frequencies of gene flow between GM and non-GM oilseed rape cultivars, with the highest frequency under nylon net isolation with artificially stocked honeybees, the lowest frequency under nylon net isolation alone, and an intermediate frequency under natural pollination, suggesting the important role of honeybee foraging in gene flow frequency. Additionally, GM pollen grains were found in honey collected from honeybees foraging on both GM and non-GM oilseed rape cultivars. The phosphinothricin acetyltransferase protein was also detected in both unbroken pollen-containing and pollen-free honey by protein testing strips, suggesting that honeybee foraging on GM oilseed rape could lead to contamination with GM ingredients. Overall, the results provide a direct scientific basis for the ecological risk assessment and safety management of GM oilseed rape.

An outbreak of gastroenteritis affected 453 attendees (attack rate 28·5%) of six separate events held at a hotel in Singapore. Active case detection, case-control studies, hygiene inspections and microbial analysis of food, environmental and stool samples were conducted to determine the aetiology of the outbreak and the modes of transmission. The only commonality was the food, crockery and cutlery provided and/or handled by the hotel's Chinese banquet kitchen. Stool specimens from 34 cases and 15 food handlers were positive for norovirus genogroup II. The putative index case was one of eight norovirus-positive food handlers who had worked while they were symptomatic. Several food samples and remnants tested positive for Escherichia coli or high faecal coliforms, aerobic plate counts and/or total coliforms, indicating poor food hygiene. This large common-source outbreak of norovirus gastroenteritis was caused by the consumption of contaminated food and/or contact with contaminated crockery or cutlery provided or handled by the hotel's Chinese banquet kitchen.