The effect of organic carbon content on soil compression characteristics.

We investigated the effect of soil organic carbon (SOC) on the consolidation behaviour of soil from two long term field experiments at Rothamsted; the Broadbalk Wheat Experiment and Hoosfield Spring Barley. These experiments are located on soil with similar particle size distributions, and include treatments with SOC contents ranging from approximately 1-3.5 g/100 g. Soils taken from plots with contrasting SOC contents were compressed and deformed in a triaxial cell and the normal consolidation and critical state lines were determined. We found that the compression index was independent of SOC, but the void ratio at any given effective stress was highly correlated with organic carbon content. By comparison with uniaxial compression data, the apparent influence of SOC on the compression index is likely to be due to its effect on soil hydraulic properties rather than any intrinsic effects of strength. The plastic limit test appears to be a useful and simple test to allow direct comparison of soil physical behaviour and expected soil density.

Age at death and the effect of lead-time bias in patients with colorectal cancer: a 10-year follow-up.

AIM: Studies addressing the benefit of early intervention are prone to lead-time bias, which results in an artificial improvement in cancer-specific mortality. We have previously compared the age at death for patients with colorectal cancer presenting on an emergency or elective basis. In this study, we aimed to repeat the analysis with a minimum follow-up of 10 years. METHOD: A nonscreen-detected cohort of patients presenting with colorectal cancer to three Lanarkshire Hospitals between 2000 and 2006 were entered into a prospective database, with analysis performed on 28 November 2016. The following data were collected: age at death, presentation type (emergency/elective), operative intent (palliative/curative) and Dukes stage. Results are presented as [mean (95% confidence intervals)]. Statistical analysis was undertaken using Student's t-test and multivariate analysis performed using Cox proportional hazard models. RESULTS: One thousand six hundred and thirty-six patients were identified. Elective patients presented younger than emergency patients [67.9 (67.3-68.5) vs 70.9 (69.6-72.2) years; P < 0.0001]. Overall mortality was 71.1% at time of analysis; no difference was seen in the mean age at death between emergency and elective presentation [73.5 (72.4-74.8) vs 73.6 (72.3-74.9) years; P = 0.841]. CONCLUSION: Current early detection strategies to diagnose colorectal cancer may improve cancer-specific survival by increasing lead-time bias. However, in our cohort of symptomatic patients, treatment on an elective or emergency basis does not influence overall survival. These data suggest that in selected patients, particularly where there is comorbidity, it may be reasonable to adopt a more expectant approach to investigate and treat colorectal symptoms.

Cross sectional imaging of truncal and quadriceps muscles relates to different functional outcomes in cancer.

INTRODUCTION: Following the consensus definition of cancer cachexia, more studies are using CT scan analysis of truncal muscles as a marker of muscle wasting. However, how CT-derived body composition relates to function, strength and power in patients with cancer is largely unknown. AIMS: We aimed to describe the relationship between CT truncal (L3) skeletal muscle index (SMI) and MRI quadriceps cross sectional area with lower limb strength, power and measures of complex function. METHODS: Patients undergoing assessment for potentially curative surgery for oesophagogastric or pancreatic cancer were recruited from the regional upper gastrointestinal (UGI) or hepatopancreaticobiliary (HPB) multi-disciplinary team meetings. Maximum Isometric Knee Extensor Strength (IKES) and Maximum Leg Extensor Power (Nottingham Power Rig) (LEP) were used as measures of lower limb performance. Both Sit to Stand (STS) and Timed Up and Go (TUG) were used as measures of global complex muscle function. Muscle SMI was measured from routine CT scans at the level of the third lumbar vertebrae (L3) and MRI scan was used for the assessment of quadriceps muscles. Linear regression analysis was performed for CT SMI or MRI quadriceps as a predictor of each measure of performance. RESULTS: Forty-four patients underwent assessment. Height and weight were significantly related to function in terms of quadriceps power, while only weight was associated with strength (P < 0.001). CT SMI was not related to measures of quadriceps strength or power but had significant association with more complex functional measures (P = 0.006, R2 = 0.234 and 0.0019, R2 = 0.175 for STS and TUG respectively). In comparison, both gross and fat-subtracted measures of quadriceps muscle mass from MRI were significantly correlated with quadriceps strength and power (P < 0.001), but did not show any significant association with complex functional measures. CONCLUSION: CT SMI and MRI quadriceps have been shown to reflect different aspects of functional ability with CT SMI being a marker of global muscle function and MRI quadriceps being specific to quadriceps power and strength. This should therefore be considered when choosing outcome measures for trials or definitions of muscle mass and function.

Changes in soil organic matter over 70 years in continuous arable and ley-arable rotations on a sandy loam soil in England.

The sequestration in soil of organic carbon (SOC) derived from atmospheric carbon dioxide (CO2) by replacing arable crops with leys, has been measured over 70 years on a sandy loam soil. The experiment was designed initially to test the effect of leys on the yields of arable crops. A 3-year grazed grass with clover (grass + clover) ley in a 5-year rotation with arable crops increased percentage organic carbon (%OC) in the top 25 cm of the soil from 0.98 to 1.23 in 28 years, but with little further increase during the next 40 years with all-grass leys given fertilizer nitrogen (N). In this second period, OC inputs were balanced by losses, suggesting that about 1.3% OC might be near the equilibrium content for this rotation. Including 3-year lucerne (Medicago sativa) leys had little effect on %OC over 28 years, but after changing to grass + clover leys, %OC increased to 1.24 during the next 40 years. Eight-year leys (all grass with N or grass + clover) in 10-year rotations with arable crops were started in the 1970s, and after three rotations %OC had increased to ca. 1.40 in 2000-2009. Over 70 years, %OC declined from 0.98 to 0.94 in an all-arable rotation with mainly cereals and to 0.82 with more root crops. Applications of 38 t ha-1 farmyard manure (FYM) every fifth year increased %OC by 0.13% by the mid-1960s when applications ceased. Soil treated with FYM still contained 0.10% more OC in 2000-2009. Changes in the amount of OC have been modelled with RothC-26.3 and estimated inputs of C for selected rotations. Little of the OC input during the 70 years has been retained; most was retained in the grazed ley rotation, but 9 t ha-1 only of a total input of 189 t ha-1. In other rotations more than 98% of the total OC input was lost. Despite large losses of C, annual increases in OC of 4‰ are possible on this soil type with the inclusion of grass or grass + clover leys or the application of FYM, but only for a limited period. Such increases in SOC might help to limit increases in atmospheric CO2. HIGHLIGHTS: Can leys sequester significant amounts of atmospheric CO 2 in SOM and contribute to the 4‰ initiative?Changes in the percentage and amount of OC were measured and modelled over 70 years and OC losses estimated.Three-year grass or grass + clover leys increased %OC, but only to an equilibrium level that was then maintained.Despite large losses, sequestering CO 2-C at 4‰ year-1 by growing grass or grass + clover leys is possible.

Dispersing artifacts in FT-STS: a comparison of set point effects across acquisition modes.

Fourier-transform scanning tunnelling spectroscopy (FT-STS), or quasiparticle interference, has become an influential tool for the study of a wide range of important materials in condensed matter physics. However, FT-STS in complex materials is often challenging to interpret, requiring significant theoretical input in many cases, making it crucial to understand potential artifacts of the measurement. Here, we compare the most common modes of acquiring FT-STS data and show through both experiment and simulations that artifact features can arise that depend on how the tip height is stabilized throughout the course of the measurement. The most dramatic effect occurs when a series of dI/dV maps at different energies are acquired with simultaneous constant current feedback; here a feature that disperses in energy appears that is not observed in other measurement modes. Such artifact features are similar to those arising from real physical processes in the sample and are susceptible to misinterpretation.

Grassland biodiversity bounces back from long-term nitrogen addition.

The negative effect of increasing atmospheric nitrogen (N) pollution on grassland biodiversity is now incontrovertible. However, the recent introduction of cleaner technologies in the UK has led to reductions in the emissions of nitrogen oxides, with concomitant decreases in N deposition. The degree to which grassland biodiversity can be expected to 'bounce back' in response to these improvements in air quality is uncertain, with a suggestion that long-term chronic N addition may lead to an alternative low biodiversity state. Here we present evidence from the 160-year-old Park Grass Experiment at Rothamsted Research, UK, that shows a positive response of biodiversity to reducing N addition from either atmospheric pollution or fertilizers. The proportion of legumes, species richness and diversity increased across the experiment between 1991 and 2012 as both wet and dry N deposition declined. Plots that stopped receiving inorganic N fertilizer in 1989 recovered much of the diversity that had been lost, especially if limed. There was no evidence that chronic N addition has resulted in an alternative low biodiversity state on the Park Grass plots, except where there has been extreme acidification, although it is likely that the recovery of plant communities has been facilitated by the twice-yearly mowing and removal of biomass. This may also explain why a comparable response of plant communities to reduced N inputs has yet to be observed in the wider landscape.

Long- versus Short-Range Scattering in Doped Epitaxial Graphene.

Tuning the electronic properties of graphene by adatom deposition unavoidably introduces disorder into the system, which directly affects the single-particle excitations and electrodynamics. Using angle-resolved photoemission spectroscopy (ARPES) we trace the evolution of disorder in graphene by thallium adatom deposition and probe its effect on the electronic structure. We show that the signatures of quasiparticle scattering in the photoemission spectral function can be used to identify thallium adatoms, although charged, as efficient short-range scattering centers. Employing a self-energy model for short-range scattering, we are able to extract a δ-like scattering potential δ = -3.2 ± 1 eV. Therefore, isolated charged scattering centers do not necessarily act just as good long-range (Coulomb) scatterers but can also act as efficient short-range (δ-like) scatterers; in the case of thallium, this happens with almost equal contributions from both mechanisms.

Optical microscope and tapered fiber coupling apparatus for a dilution refrigerator.

We have developed a system for tapered fiber measurements of optomechanical resonators inside a dilution refrigerator, which is compatible with both on- and off-chip devices. Our apparatus features full three-dimensional control of the taper-resonator coupling conditions enabling critical coupling, with an overall fiber transmission efficiency of up to 70%. Notably, our design incorporates an optical microscope system consisting of a coherent bundle of 37,000 optical fibers for real-time imaging of the experiment at a resolution of ∼1 µm. We present cryogenic optical and optomechanical measurements of resonators coupled to tapered fibers at temperatures as low as 9 mK.

Sex-linked and autosomal microsatellites provide new insights into island populations of the tammar wallaby.

The emerging availability of microsatellite markers from mammalian sex chromosomes provides opportunities to investigate both male- and female-mediated gene flow in wild populations, identifying patterns not apparent from the analysis of autosomal markers alone. Tammar wallabies (Macropus eugenii), once spread over the southern mainland, have been isolated on several islands off the Western Australian and South Australian coastlines for between 10,000 and 13,000 years. Here, we combine analyses of autosomal, Y-linked and X-linked microsatellite loci to investigate genetic variation in populations of this species on two islands (Kangaroo Island, South Australia and Garden Island, Western Australia). All measures of diversity were higher for the larger Kangaroo Island population, in which genetic variation was lowest at Y-linked markers and highest at autosomal markers (θ=3.291, 1.208 and 0.627 for autosomal, X-linked and Y-linked data, respectively). Greater relatedness among females than males provides evidence for male-biased dispersal in this population, while sex-linked markers identified genetic lineages not apparent from autosomal data alone. Overall genetic diversity in the Garden Island population was low, especially on the Y chromosome where most males shared a common haplotype, and we observed high levels of inbreeding and relatedness among individuals. Our findings highlight the utility of this approach for management actions, such as the selection of animals for translocation or captive breeding, and the ecological insights that may be gained by combining analyses of microsatellite markers on sex chromosomes with those derived from autosomes.

Indirect effects of a fungal entomopathogen, Lecanicillium lecanii (Hypocreales: Clavicipitaceae), on a coffee agroecosystem ant community.

Fungal entomopathogens are widely distributed across natural and managed systems, with numerous host species and likely a wide range of community impacts. While the potential for fungal pathogens to provide biological control has been explored in some detail, less is known about their community interactions. Here we investigate the effects of fungal epizootics of the entomopathogen Lecanicillium lecanii (Zimmerman) on a keystone mutualism between Azteca instabilis (F. Smith), a dominant arboreal ant, and the green coffee scale (Coccus viridis Green), as well as broader impacts on a coffee agroecosystem ant community. We hypothesized that seasonal epizootics cause shifts in the foraging ranges of A. instabilis as the ants adapt to the loss of the resource. We further hypothesized that the magnitude of these shifts depends on the availability of alternate resources located in neighboring shade trees. To test these hypotheses, we induced an epizootic in experimental sites, which were compared with control sites. Surveys of ant activity were undertaken pre- and post-epizootic. We found a decrease in foraging activity of A. instabilis and increase in activity of other ant species in the experimental sites post-epizootic. The decrease in abundance of A. instabilis foragers was greater on plants in which an epizootic was induced than in other plants. This relationship was modified by shade tree density where higher shade tree density was associated with larger decreases in A. intabilis foraging activity in coffee plants. These results demonstrate the potential for fungal entomopathogens to influence the structure and diversity of ecological communities.

A novel oral tracer procedure for measurement of habitual myofibrillar protein synthesis.

RATIONALE: Conventionally, myofibrillar protein synthesis is measured over time periods of hours. In clinical studies, interventions occur over weeks. Functional measures over such periods may be more representative. We aimed to develop a novel method to determine myofibrillar protein fractional synthetic rate (FSR) to estimate habitual rates, while avoiding intravenous tracer infusions. METHODS: Four healthy males were given 100 g water enriched to 70 Atom % with (2)H2O as a single oral bolus. Vastus-lateralis needle biopsies were performed and plasma samples collected, 3-13 days post-dose. (2)H enrichment in body water was measured in plasma using continuous flow isotope ratio mass spectrometry (IRMS). Myofibrillar protein was isolated from muscle biopsies and acid hydrolysed. (2)H enrichment of protein-bound and plasma-free alanine was measured by gas chromatography (GC)/pyrolysis/IRMS. Myofibrillar protein FSR was calculated (% day(-1)). RESULTS: The tracer bolus raised the initial enrichment of body water to 1514 ppm (2)H excess. Water elimination followed a simple exponential. The average elimination half-time was 8.3 days. Plasma alanine, labelled during de novo synthesis, followed the same elimination kinetics as water. The weighted average myofibrillar protein FSR from the four subjects was 1.38 % day(-1) (range, 1.0-1.9 % day(-1) ). CONCLUSIONS: Myofibrillar protein FSR was measured in free-living healthy individuals over 3-13 days. Using a single oral (2)H2O bolus, endogenous labelling of alanine occurred in a predictable manner giving estimates of synthesis comparable with published values. Furthermore, the protocol does not compromise the ability to measure other important metabolic processes such as total energy expenditure.

Age at death of patients with colorectal cancer and the effect of lead-time bias on survival in elective vs emergency surgery.

AIM: Colorectal cancer survival depends on stage at presentation, and current strategies aim for improvements through early detection. Previous studies have demonstrated improved survival from diagnosis but not increased life expectancy. While lead-time bias may account for variations in known prognostic indicators and also influence screening programmes, only age at death provides a true representation of the effectiveness of an intervention. We aimed to compare age at death for patients with colorectal cancer presenting on an emergency or elective basis. METHOD: Patients presenting with colorectal cancer (2000-2006) were entered into a prospective database (analysis 1 December 2008). Fields included age at death, emergency/elective presentation, palliative/curative intent and disease stage. RESULTS: One thousand six hundred and fifty patients (922 men) were identified. Elective patients presented younger than emergency patients (67.9 vs 70.6 years; P < 0.005). Dukes B patients presented older than Dukes D (P = 0.02). Mortality was 41% at time of analysis; no difference was seen in mean age at death between emergency and elective presentation (72.8 vs 72.0 years; P = 0.379) or palliative and curative intent (72.0 vs 72.5 years; P = 0.604). CONCLUSION: Colorectal cancer is common in a population where actuarial life expectancy is limited. Current colorectal cancer early detection strategies may improve cancer-specific survival by increasing lead-time bias but do not influence overall life expectancy.

Modeling flow in collecting lymphatic vessels: one-dimensional flow through a series of contractile elements.

The lymphatic system comprises a series of elements, lymphangions, separated by valves and possessed of active, contractile walls to pump interstitial fluid from its collection in the terminal lymphatics back to the main circulation. Despite its importance, there is a dearth of information on the fluid dynamics of the lymphatic system. In this article, we describe linked experimental and computational work aimed at elucidating the biomechanical properties of the individual lymphangions. We measure the static and dynamic mechanical properties of excised bovine collecting lymphatics and develop a one-dimensional computational model of the coupled fluid flow/wall motion. The computational model is able to reproduce the pumping behavior of the real vessel using a simple contraction function producing fast contraction pulses traveling in the retrograde direction to the flow.

A novel, helminth-derived immunostimulant enhances human recall responses to hepatitis C virus and tetanus toxoid and is dependent on CD56+ cells for its action.

We have described previously an immunostimulant derived from Onchocerca volvulus, the helminth parasite that causes onchocerciasis. Recombinant O. volvulus activation-associated secreted protein-1 (rOv-ASP-1) was a potent adjuvant for antibody and cellular responses to protein, polypeptide and small peptide antigens. Our aims were to determine whether rOv-ASP-1 is immunostimulatory for human peripheral blood mononuclear cells (PBMC) and, if so, whether it could augment cellular responses against human pathogen antigens in vitro. Cytokines from rOv-ASP-1-stimulated human PBMC were measured by a fluorescence activated cell sorter-based multiplex assay. Recall responses of normal healthy donor (NHD) and chronic hepatitis C virus (c-HCV)-infected patient PBMC to tetanus toxoid (TT) or HCV core (HCVco) antigen, respectively, were measured by interferon-gamma enzyme-linked immunospot assays. Interferon-gamma was the predominant cytokine induced by rOv-ASP-1. 77.3% of NHD anti-TT and 88.9% of c-HCV anti-HCVco responses were enhanced by rOv-ASP-1. The immunostimulant effect was dependent upon contact between CD56+ and CD56- fractions of PBMC. We have described a helminth-derived protein that can act as an immunostimulant for human recall responses in vitro to TT and, perhaps more importantly, HCV antigens in patients with chronic HCV infection. Our longer-term goal would be to boost anti-viral responses in chronic infections such as HCV.

Missed opportunities for the detection of abdominal aortic aneurysms.

OBJECTIVE: To determine whether patients attending as emergencies with ruptured AAA could have been detected opportunistically prior to rupture. DESIGN: Retrospective analysis. METHODS: The notes of patients attending hospital with ruptured abdominal aortic aneurysms to four City and DGH hospital in the West of Scotland were examined for previous assessments or investigations with the potential to discover an AAA. RESULTS: In this series 77% of patients were not previously known to have and AAA. Of these patients 76% had been reviewed in hospital during the preceding 5 years on a combined total of 355 occasions. 56% of patients had been seen in hospital during the year preceding rupture on a total of 80 occasions, only undergoing 17 abdominal examinations. CONCLUSION: Clinical examination is not frequently considered in routine practice as a screening tool for AAA but patients who subsequently go on to attend as an emergency ruptured AAA are likely to have consulted medical staff during the preceding years. A large number of patients have missed a prior opportunity for detection.

Monocyte-derived dendritic cell function in chronic hepatitis C is impaired at physiological numbers of dendritic cells.

Monocyte-derived dendritic cells (MoDCs) are a promising cellular adjuvant for effector immune responses against tumours and chronic viral infections, including hepatitis C virus (HCV). If autologous DC therapeutic approaches are to be applied in persistent HCV infections in patients, it is important to have an unambiguous understanding of the functional status of the cell type used, namely MoDCs from patients with chronic hepatitis C (CHC) infection. Because of conflicting published reports of either impaired or normal MoDC function in CHC infection, we re-examined the ability of MoDCs from CHC and normal healthy donors (NHD) to mature to an inflammatory stimulus [tumour necrosis factor (TNF)-alpha] and their subsequent functional capabilities. Expression of maturation-associated phenotypic markers [human leucocyte antigen (HLA)-DR, CD83, CD86, CD40], allostimulatory capacity in mixed lymphocyte reactions (MLRs) and CD40-ligand-induced cytokine and chemokine generation were compared in CHC- versus NHD-MoDCs. TNF-alpha-stimulated CHC-MoDCs up-regulated phenotypic markers, but to significantly lower levels than NHD-MoDCs. At physiological ratios of DCs to T cells, CHC-MoDCs were less allostimulatory than NHD-MoDCs, but not when DC numbers were substantially increased. CHC- and NHD-MoDCs generated equivalent amounts of cytokines [TNF-alpha, interleukin (IL)-1beta, IL-6, IL-12p70, IL-15, IL-10] and chemokines [interferon-inducible protein (IP)-10, macrophage inflammatory protein (MIP)-1alpha, regulated upon activation, normal T expressed and secreted (RANTES)] after CD40 ligation. Because the functional defect was not apparent at high MoDC : T cell ratios, autologous MoDC therapy with sufficiently high numbers of DCs could, in theory, overcome any impairment of MoDC function in CHC.

Imaging and clinical characteristics of temporal bone meningioma.

BACKGROUND AND PURPOSE: Imaging characteristics of temporal bone meningioma have not been previously reported in the literature. CT and MR imaging findings in 13 cases of temporal bone meningioma are reviewed to define specific imaging features. METHODS: A retrospective review of our institutional case archive revealed 13 cases of histologically confirmed temporal bone meningioma. CT and MR imaging studies were reviewed to characterize mass location, vector of spread, bone changes, enhancement characteristics, and intracranial patterns of involvement. Clinical presenting signs and symptoms were correlated with imaging findings. RESULTS: Thirteen temporal bone meningiomas were reviewed in 8 women and 5 men, aged 18-65 years. Meningiomas were stratified into 3 groups on the basis of location and tumor vector of spread. There were 6 tegmen tympani, 5 jugular foramen (JF), and 2 internal auditory canal (IAC) meningiomas. Tegmen tympani and JF meningiomas were characterized by spread to the middle ear cavity. IAC meningiomas, by contrast, spread to the cochlea and vestibule. Hearing loss was the most common clinical presenting feature in all cases of temporal bone meningioma (10/13). The presence of tumor adjacent to the ossicles strongly correlated with conductive hearing loss (7/9). CONCLUSION: Meningioma involving the temporal bone is rare. Three subgroups of meningioma exist in this location: tegmen tympani, JF, and IAC meningioma. Tegmen tympani and JF meningiomas spread to the middle ear cavity. IAC meningiomas spread to intralabyrinthine structures. Conductive hearing loss is commonly seen in these patients and can be surgically correctable.