Hydrogeological controls on regional-scale indirect nitrous oxide (N2O) emission factors for rivers

Indirect nitrous oxide (N2O) emissions from rivers are currently derived using poorly constrained default IPCC emission factors (EF5r) which yield unreliable flux estimates. Here, we demonstrate how hydrogeological conditions can be used to develop more refined regional-scale EF5r estimates required for compiling accurate national greenhouse gas inventories. Focusing on three UK river catchments with contrasting bedrock and superficial geologies, N2O and nitrate (NO3-) concentrations were analyzed in 651 river water samples collected from 2011 to 2013. Unconfined Cretaceous Chalk bedrock regions yielded the highest median N2O-N concentration (3.0 μg L-1), EF5r (0.00036) and N2O-N flux (10.8 kg ha-1 a-1). Conversely, regions of bedrock confined by glacial deposits yielded significantly lower median N2O-N concentration (0.8 μg L-1), EF5r (0.00016) and N2O-N flux (2.6 kg ha-1 a-1), regardless of bedrock type. Bedrock permeability is an important control in regions where groundwater is unconfined, with a high N2O yield from high permeability Chalk contrasting with significantly lower median N2O-N concentration (0.7 μg L-1), EF5r (0.00020) and N2O-N flux (2.0 kg ha-1 a-1) on lower permeability unconfined Jurassic mudstone. The evidence presented here demonstrates EF5r can be differentiated by hydrogeological conditions and thus provide a valuable proxy for generating improved regional-scale N2O emission estimates

Beyond action-specific simulation: Domain-general motor contributions to perception

Preoccupation with action-specific simulation theory, whereby covert imitation is thought to facilitate action interpretation, has overshadowed evidence that motor structures facilitate perception of numerous visual events extending far beyond others’ actions. In light of these domain-general motor contributions to perception, the case for a special role of motor representation in human action perception may be far weaker than widely believed

Bash2py: A bash to Python translator

Abstract—Shell scripting is the primary way for programmers to interact at a high level with operating systems. For decades bash shell scripts have thus been used to accomplish various tasks. But Bash has a counter-intuitive syntax that is not well understood by modern programmers and is no longer adequately supported, making it now difficult to maintain. Bash also suffers from poor performance, memory leakage problems, and limited functionality which make continued dependence on it problematic. At the request of our industrial partner, we therefore developed a source-to-source translator, bash2py, which converts bash scripts into Python. Bash2py leverages the open source bash code, and the internal parser employed by Bash to parse any bash script. However, bash2py re-implements the variable expansion that occurs in Bash to better generate correct Python code. Bash2py correctly converts most Bash into Python, but does require human intervention to handle constructs that cannot easily be automatically translated. In our experiments on real-world open source bash scripts bash2py successfully translates 90 % of the code. Feedback from our industrial partner confirms the usefulness of bash2py in practice

A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease

Peer reviewedPublisher PD

Implications for therapeutic judging (TJ) of a psychoanalytical approach to the judicial role — Reflections on Robert Burt's contribution

Robert Burt in, “The Yale School of Law and Psychoanalysis, from 1963 Onward”, in this issue, explains and laments a decline in influence of psychoanalytic ideas in legal thinking. He notes “the fundamental similarity that both litigation and psychotherapy involve recollections of past events”, buttressing his argument with eight parallels between the two. In this article we take up Burt's theme, first noting the relationship between therapeutic jurisprudence and psychoanalytic concepts before presenting an outline for a psychoanalytical understanding of the judicial role. We then consider the litigation process from the linked perspectives of therapeutic jurisprudence and psychoanalysis before closing with a reflection on the eight parallels elaborated by Burt

MEG-BIDS, the brain imaging data structure extended to magnetoencephalography.

We present a significant extension of the Brain Imaging Data Structure (BIDS) to support the specific aspects of magnetoencephalography (MEG) data. MEG measures brain activity with millisecond temporal resolution and unique source imaging capabilities. So far, BIDS was a solution to organise magnetic resonance imaging (MRI) data. The nature and acquisition parameters of MRI and MEG data are strongly dissimilar. Although there is no standard data format for MEG, we propose MEG-BIDS as a principled solution to store, organise, process and share the multidimensional data volumes produced by the modality. The standard also includes well-defined metadata, to facilitate future data harmonisation and sharing efforts. This responds to unmet needs from the multimodal neuroimaging community and paves the way to further integration of other techniques in electrophysiology. MEG-BIDS builds on MRI-BIDS, extending BIDS to a multimodal data structure. We feature several data-analytics software that have adopted MEG-BIDS, and a diverse sample of open MEG-BIDS data resources available to everyone

Influence of Pleistocene glacial deposits on the transport of agricultural nitrate in the river Wensum catchment, UK

Mitigating NO3− pollution requires an understanding of the hydrological processes controlling contaminant mobilisation and transport, particularly in agricultural catchments underlain by Pleistocene glacial deposits. Focusing on the Wensum catchment in East Anglia, UK, precipitation (n = 20), stream water (n = 50), field drainage (n = 22) and groundwater (n = 84) samples collected between February–March 2011 and April–September 2012 were variously analysed for water stable isotopes (δ2HH2O and δ18OH2O), the dual-isotopes of NO3− (δ15NNO3 and δ18ONO3), groundwater residence time indicators (CFCs and SF6) and hydrochemical parameters. The residence time indicators suggested a component of modern (post-1960) groundwater throughout the sequence of glacial deposits that corresponds with the penetration of agricultural NO3−. Denitrification and lower NO3− concentrations (<8 mg L−1) are observed in the glacial tills, compared with higher NO3− concentrations (<90 mg L−1) observed under more oxidising conditions in the glacial sands and gravels. Storm hydrograph separation for two storms in April and September 2012 using two- and three-component mixing models showed a faster response with field drainage (36–38 %) and baseflow (5–37 %) contributing to the total stream discharge in areas of clay loam soils over glacial tills. In these areas, the dual stable isotopes of NO3− (δ15NNO3 = +11.8 ‰ and δ18ONO3 = +7.1 ‰) indicated a denitrified source of nitrogen from field drainage and groundwater. In comparison, a dampened response and a higher percentage of baseflow (29–80 %) was observed in areas of sandy clay loam soils over glacial sands and gravels. In these areas, mean NO3− isotopic signatures (δ15NNO3 = +7.8 ‰ and δ18ONO3 = +5.0 ‰) indicated a source of nitrified NH4+. In conclusion, understanding hydrological processes in catchments underlain by variable glacial deposits can inform nutrient management plans and cultivation practices to reduce the risk of agricultural NO3− contamination

The microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the BISCUIT study

&lt;p&gt;Introduction: Children presenting for the first time with inflammatory bowel disease (IBD) offer a unique opportunity to study aetiological agents before the confounders of treatment. Microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium; Helicobacter and Campylobacter are previously implicated in IBD pathogenesis. We set out to study these and other microaerophilic bacteria in de-novo paediatric IBD.&lt;/p&gt; &lt;p&gt;Patients and Methods: 100 children undergoing colonoscopy were recruited including 44 treatment naïve de-novo IBD patients and 42 with normal colons. Colonic biopsies were subjected to microaerophilic culture with Gram-negative isolates then identified by sequencing. Biopsies were also PCR screened for the specific microaerophilic bacterial groups: Helicobacteraceae, Campylobacteraceae and Sutterella wadsworthensis.&lt;/p&gt; &lt;p&gt;Results: 129 Gram-negative microaerophilic bacterial isolates were identified from 10 genera. The most frequently cultured was S. wadsworthensis (32 distinct isolates). Unusual Campylobacter were isolated from 8 subjects (including 3 C. concisus, 1 C. curvus, 1 C. lari, 1 C. rectus, 3 C. showae). No Helicobacter were cultured. When comparing IBD vs. normal colon control by PCR the prevalence figures were not significantly different (Helicobacter 11% vs. 12%, p = 1.00; Campylobacter 75% vs. 76%, p = 1.00; S. wadsworthensis 82% vs. 71%, p = 0.312).&lt;/p&gt; &lt;p&gt;Conclusions: This study offers a comprehensive overview of the microaerophilic microbiota of the paediatric colon including at IBD onset. Campylobacter appear to be surprisingly common, are not more strongly associated with IBD and can be isolated from around 8% of paediatric colonic biopsies. S. wadsworthensis appears to be a common commensal. Helicobacter species are relatively rare in the paediatric colon.&lt;/p&gt

A comparison of particle mass spectrometers during the 1999 Atlanta Supersite Project

During the Atlanta Supersite Project, four particle mass spectrometers were operated together for the first time: NOAA's Particle Analysis by Laser Mass Spectrometer (PALMS), University of California at Riverside's Aerosol Time-of-Flight Mass Spectrometer (ATOFMS), University of Delaware's Rapid Single-Particle Mass Spectrometer II (RSMS-II), and Aerodyne's Aerosol Mass Spectrometer (AMS). Although these mass spectrometers are generally classified as similar instruments, they clearly have different characteristics due to their unique designs. One primary difference is related to the volatilization/ionization method: PALMS, ATOFMS, and RSMS-II utilize laser desorption/ionization, whereas particles in the AMS instrument are volatilized by impaction onto a heated surface with the resulting components ionized by electron impact. Thus mass spectral data from the AMS are representative of the ensemble of particles sampled, and those from the laser-based instruments are representative of individual particles. In addition, the AMS instrument cannot analyze refractory material such as soot, sodium chloride, and crustal elements, and some sulfate or water-rich particles may not always be analyzed with every laser-based instrument. A main difference among the laser-based mass spectrometers is that the RSMS-II instrument can obtain size-resolved single particle composition information for particles with aerodynamic diameters as small as 15 nm. The minimum sizes analyzed by ATOFMS and PALMS are 0.2 and about 0.35 μm, respectively, in aerodynamic diameter. Furthermore, PALMS, ATOFMS, and RSMS-II use different laser ionization conditions. Despite these differences the laser-based instruments found similar individual particle classifications, and their relative fractions among comparable sized particles from Atlanta were broadly consistent. Finally, the AMS measurements of the nitrate/sulfate mole ratio were highly correlated with composite measurements (r^2 = 0.93). In contrast, the PALMS nitrate/sulfate ion ratios were only moderately correlated (r^2 ∼ 0.7)

Regional and cellular gene expression changes in human Huntington's disease brain

Huntington's disease (HD) pathology is well understood at a histological level but a comprehensive molecular analysis of the effect of the disease in the human brain has not previously been available. To elucidate the molecular phenotype of HD on a genome-wide scale, we compared mRNA profiles from 44 human HD brains with those from 36 unaffected controls using microarray analysis. Four brain regions were analyzed: caudate nucleus, cerebellum, prefrontal association cortex [Brodmann's area 9 (BA9)] and motor cortex [Brodmann's area 4 (BA4)]. The greatest number and magnitude of differentially expressed mRNAs were detected in the caudate nucleus, followed by motor cortex, then cerebellum. Thus, the molecular phenotype of HD generally parallels established neuropathology. Surprisingly, no mRNA changes were detected in prefrontal association cortex, thereby revealing subtleties of pathology not previously disclosed by histological methods. To establish that the observed changes were not simply the result of cell loss, we examined mRNA levels in laser-capture microdissected neurons from Grade 1 HD caudate compared to control. These analyses confirmed changes in expression seen in tissue homogenates; we thus conclude that mRNA changes are not attributable to cell loss alone. These data from bona fide HD brains comprise an important reference for hypotheses related to HD and other neurodegenerative disease