Characterising the within-field scale spatial variation of nitrogen in a grassland soil to inform the efficient design of in-situ nitrogen sensor networks for precision agriculture

The use of in-situ sensors capable of real-time monitoring of soil nitrogen (N) may facilitate improvements in agricultural N-use efficiency (NUE) through better fertiliser management. The optimal design of such sensor networks, consisting of clusters of sensors each attached to a data logger, depends upon the spatial variation of soil N and the relative cost of the data loggers and sensors. The primary objective of this study was to demonstrate how in-situ networks of N sensors could be optimally designed to enable the cost-efficient monitoring of soil N within a grassland field (1.9 ha). In the summer of 2014, two nested sampling campaigns (June & July) were undertaken to assess spatial variation in soil amino acids, ammonium (NH4+) and nitrate (NO3−) at a range of scales that represented the within (less than 2 m) and between (greater than 2 m) data logger/sensor cluster variability. Variance at short range (less than 2 m) was found to be dominant for all N forms. Variation at larger scales (greater than 2 m) was not as large but was still considered an important spatial component for all N forms, especially NO3−. The variance components derived from the nested sampling were used to inform the efficient design of theoretical in-situ networks of NH4+ and NO3− sensors based on the costs of a commercially available data logger and ion-selective electrodes (ISEs). Based on the spatial variance observed in the June nested sampling, and given a budget of £5000, the NO3− field mean could be estimated with a 95% confidence interval width of 1.70 μg N g−1 using 2 randomly positioned data loggers each with 5 sensors. Further investigation into “aggregate-scale” (less than 1 cm) spatial variance revealed further large variation at the sub 1-cm scale for all N forms. Sensors, for which the measurement represents an integration over a sensor-soil contact area of diameter less than 1 cm, would be subject to this aggregate-scale variability. As such, local replication at scales less than 1 cm would be needed to maintain the precision of the resulting field mean estimation. Adoption of in-situ sensor networks will depend upon the development of suitable low‐cost sensors, demonstration of the cost-benefit and the construction of a decision support system that utilises the generated data to improve the NUE of fertiliser N management

Upper Arm Compartment Syndrome Secondary to Intramuscular Cocaine and Heroin Injection

Compartment syndrome threatens the viability of a limb. We present a case of upper arm compartment syndrome secondary to an intramuscular injection of cocaine and heroin. Timely diagnosis and surgical intervention avoided extensive muscle necrosis and morbidity. This complication has not been previously reported and highlights a condition which should be considered in intravenous drug abusers presenting with arm pain

Common Era sea-level budgets along the U.S. Atlantic coast

Sea-level budgets account for the contributions of processes driving sea-level change, but are predominantly focused on global-mean sea level and limited to the 20th and 21st centuries. Here we estimate site-specific sea-level budgets along the U.S. Atlantic coast during the Common Era (0-2000 CE) by separating relative sea-level (RSL) records into process-related signals on different spatial scales. Regional-scale, temporally linear processes driven by glacial isostatic adjustment dominate RSL change and exhibit a spatial gradient, with fastest rates of rise in southern New Jersey (1.6 ± 0.02 mm yr-1). Regional and local, temporally non-linear processes, such as ocean/atmosphere dynamics and groundwater withdrawal, contributed between -0.3 and 0.4 mm yr-1 over centennial timescales. The most significant change in the budgets is the increasing influence of the common global signal due to ice melt and thermal expansion since 1800 CE, which became a dominant contributor to RSL with a 20th century rate of 1.3 ± 0.1 mm yr-1

The River Orontes in Syria and Turkey: downstream variation of fluvial archives in different crustal blocks

The geomorphology and Quaternary history of the River Orontes in western Syria and south-central Turkey have been studied using a combination of methods: field survey, differential GPS, satellite imagery, analysis of sediments to determine provenance, flow direction and fluvial environment, incorporation of evidence from fossils for both palaeoenvironments and biostratigraphy, uranium-series dating of calcrete cement, reconciliation of Palaeolithic archaeological contents, and uplift modelling based on terrace height distribution. The results underline the contrasting nature of different reaches of the Orontes, in part reflecting different crustal blocks, with different histories of landscape evolution. Upstream from Homs the Orontes has a system of calcreted terraces that form a staircase extending to ~200 m above the river. New U-series dating provides an age constraint within the lower part of the sequence that suggests underestimation of terrace ages in previous reviews. This upper valley is separated from another terraced reach, in the Middle Orontes, by a gorge cut through the Late Miocene–Early Pliocene Homs Basalt. The Middle Orontes terraces have long been recognized as a source of mammalian fossils and Palaeolithic artefacts, particularly from Latamneh, near the downstream end of the reach. This terraced section of the valley ends at a fault scarp, marking the edge of the subsiding Ghab Basin (a segment of the Dead Sea Fault Zone), which has been filled to a depth of ~ 1 km by dominantly lacustrine sediments of Pliocene–Quaternary age. Review of the fauna from Latamneh suggests that its age is 1.2–0.9 Ma, significantly older than previously supposed, and commensurate with less uplift in this reach than both the Upper and Lower Orontes. Two localities near the downstream end of the Ghab have provided molluscan and ostracod assemblages that record somewhat saline environments, perhaps caused by desiccation within the former lacustrine basin, although they include fluvial elements. The Ghab is separated from another subsiding and formerly lacustrine depocentre, the Amik Basin of Hatay Province, Turkey, by a second gorge, implicit of uplift, this time cut through Palaeogene limestone. The NE–SW oriented lowermost reach of the Orontes is again terraced, with a third and most dramatic gorge through the northern edge of the Ziyaret Dağı mountains, which are known to have experienced rapid uplift, probably again enhanced by movement on an active fault. Indeed, a conclusion of the research, in which these various reaches are compared, is that the crust in the Hatay region is significantly more dynamic than that further upstream, where uplift has been less rapid and less continuous

Autosis is a Na+,K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia.

A long-standing controversy is whether autophagy is a bona fide cause of mammalian cell death. We used a cell-penetrating autophagy-inducing peptide, Tat-Beclin 1, derived from the autophagy protein Beclin 1, to investigate whether high levels of autophagy result in cell death by autophagy. Here we show that Tat-Beclin 1 induces dose-dependent death that is blocked by pharmacological or genetic inhibition of autophagy, but not of apoptosis or necroptosis. This death, termed "autosis," has unique morphological features, including increased autophagosomes/autolysosomes and nuclear convolution at early stages, and focal swelling of the perinuclear space at late stages. We also observed autotic death in cells during stress conditions, including in a subpopulation of nutrient-starved cells in vitro and in hippocampal neurons of neonatal rats subjected to cerebral hypoxia-ischemia in vivo. A chemical screen of ~5,000 known bioactive compounds revealed that cardiac glycosides, antagonists of Na(+),K(+)-ATPase, inhibit autotic cell death in vitro and in vivo. Furthermore, genetic knockdown of the Na(+),K(+)-ATPase α1 subunit blocks peptide and starvation-induced autosis in vitro. Thus, we have identified a unique form of autophagy-dependent cell death, a Food and Drug Administration-approved class of compounds that inhibit such death, and a crucial role for Na(+),K(+)-ATPase in its regulation. These findings have implications for understanding how cells die during certain stress conditions and how such cell death might be prevented

Physical Separation of Straw Stem Components to Reduce Silica

In this paper, we describe ongoing efforts to solve challenges to using straw for bioenergy and bioproducts. Among these, silica in straw forms a low-melting eutectic with potassium, causing slag deposits, and chlorides cause corrosion beneath the deposits. Straw consists principally of stems, leaves, sheaths, nodes, awns, and chaff. Leaves and sheaths are higher in silica, while chaff, leaves and nodes are the primary source of fines. Our approach to reducing silica is to selectively harvest the straw stems using an in-field physical separation, leaving the remaining components in the field to build soil organic matter and contribute soil nutrients

Application of Bayesian statistics to estimate nitrous oxide emission factors of the nitrogen fertilisers in UK grasslands

Trapezoidal integration by linear interpolation of data points is by far the most commonly used method of cumulative flux calculations of nitrous oxide (N2O) in studies that use flux chambers; however, this method is incapable of providing accurate uncertainty estimates. A Bayesian approach was used to calculate N2O emission factors (EFs) and their associated uncertainties from flux chamber measurements made after the application of nitrogen fertilisers, in the form of ammonium nitrate (AN), urea (Ur) and urea treated with Agrotain® urease inhibitor (UI) at four grassland sites in the UK. The comparison between the cumulative fluxes estimated using the Bayesian and linear interpolation methods were broadly similar (R2=0.79); however, the Bayesian method was capable of providing realistic uncertainties when a limited number of data points is available. The study reports mean EF values (and 95% confidence intervals) of 0.60 ± 0.63, 0.29 ± 0.22 and 0.26 ± 0.17% of applied N emitted as N2O for the AN, Ur and UI treatments, respectively. There was no significant difference between N2O emissions from the Ur and UI treatments. In the case of the automatic chamber data collected at one site in this study, the data did not fit the log-normal model, implying that more complex models may be needed, particularly for measurement data with high temporal resolutioninfo:eu-repo/semantics/publishedVersio

Vortex dynamics for two-dimensional XY models

Two-dimensional XY models with resistively shunted junction (RSJ) dynamics and time dependent Ginzburg-Landau (TDGL) dynamics are simulated and it is verified that the vortex response is well described by the Minnhagen phenomenology for both types of dynamics. Evidence is presented supporting that the dynamical critical exponent $z$ in the low-temperature phase is given by the scaling prediction (expressed in terms of the Coulomb gas temperature $T^{CG}$ and the vortex renormalization given by the dielectric constant $\tilde\epsilon$) $z=1/\tilde{\epsilon}T^{CG}-2\geq 2$ both for RSJ and TDGL and that the nonlinear IV exponent a is given by a=z+1 in the low-temperature phase. The results are discussed and compared with the results of other recent papers and the importance of the boundary conditions is emphasized.Comment: 21 pages including 15 figures, final versio

Hydromorphological, hydraulic and ecological effects of restored wood: findings and reflections from an academic partnership approach

This is the peer reviewed version of the following article: Pinto, C. , Ing, R. , Browning, B. , Delboni, V. , Wilson, H. , Martyn, D. and Harvey, G. L. (2019), Hydromorphological, hydraulic and ecological effects of restored wood: findings and reflections from an academic partnership approach. Water and Environment Journal. doi:10.1111/wej.12457, which has been published in final form at https://doi.org/10.1111/wej.12457. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions© 2019 CIWEM Large wood (re)introduction can deliver multiple benefits in river restoration, but there is a dearth of the detailed and longer-term post-project monitoring and evaluation required for improving best practice. We present findings from an academic partnership approach to post-project evaluation, based on successive MSc research projects on restored large wood in the Loddon catchment, UK. Field and modelling data reveal: (i) key differences in large wood features between restored and natural reaches; (ii) increased hydraulic retention and changes to mesohabitats associated with large wood; (iii) differences in macroinvertebrate community composition around large wood but a lack of site-level effects; (iv) interactions between macrophytes and large wood that may be specific to restored reaches; (v) a need for further field and modelling studies to inform the accurate representation of large wood in hydraulic models. Some key challenges in partnership working are identified to aid planning and effectiveness of future collaborations

Detection of long repeat expansions from PCR-free whole-genome sequence data

Identifying large expansions of short tandem repeats (STRs) such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step towards integrating WGS into precision medicine. We have developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3,001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2,786/2,789, 95% CI [0.997, 1.00]) of the wild type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples where every sample had one of eight different pathogenic repeat expansions including those associated with fragile X syndrome, Friedreich's ataxia and Huntington's disease and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions. The software is licensed under GPL v3.0 and the source code is freely available on GitHub