Spud 1.0: generalising and automating the user interfaces of scientific computer models

The interfaces by which users specify the scenarios to be simulated by scientific computer models are frequently primitive, under-documented and ad-hoc text files which make using the model in question difficult and error-prone and significantly increase the development cost of the model. In this paper, we present a model-independent system, Spud, which formalises the specification of model input formats in terms of formal grammars. This is combined with an automated graphical user interface which guides users to create valid model inputs based on the grammar provided, and a generic options reading module, libspud, which minimises the development cost of adding model options. <br><br> Together, this provides a user friendly, well documented, self validating user interface which is applicable to a wide range of scientific models and which minimises the developer input required to maintain and extend the model interface

Gauge links for transverse momentum dependent correlators at tree-level

In this paper we discuss the incorporation of gauge links in hadronic matrix elements that describe the soft hadronic physics in high energy scattering processes. In this description the matrix elements appear in soft correlators and they contain non-local combinations of quark and gluon fields. In our description we go beyond the collinear approach in which case also the dependence on transverse momenta of partons is taken into consideration. The non-locality in the transverse direction leads to a complex gauge link structure for the full process, in which color is entangled, even at tree-level. We show that at tree-level in a 1-parton unintegrated (1PU) situation, in which only the transverse momentum of one of the initial state hadrons is relevant, one can get a factorized expression involving transverse momentum dependent (TMD) distribution functions. We point out problems at the level of two initial state hadrons, even for relatively simple processes such as Drell-Yan scattering.Comment: 25 pages, corrected typos and updated reference

Kinetics of coupled Fe(II)-catalysed ferrihydrite transformation and U(VI) reduction

Antimony is released into the environment in some natural and man-induced processes. [1]. Yet, its impact on the transformation processes of heavy metal-adsorbing minerals remains poorly understood. In acid-mine drainage systems and shooting ranges, the adsorption of antimony by iron oxides such as ferrihydrite can play a major role. The poorly crystalline 2-line ferrihydrite represents one of the most common Fe oxides in these settings and can transform to goethite (,-FeOOH) or hematite (,-Fe2O3) with time [2]. The rate of transformation depends on the pH, temperature, and on the ions and molecules present during the transformation process [3]. This study focuses on the transformation of synthetic ferrihydrite to crystalline iron oxides in the presence of Sb(V). Transformations were carried out for 1-16 days at 70 ºC and at pH 4, 7 and 12, with different concentrations of Sb(V) (0.00, 0.23, 0.75, 2.25 and 6.00 mM Sb). Samples taken from aqueous suspensions were washed, dried, and characterized by X-ray diffraction (XRD) and atomic absorption spectroscopy (AAS). At pH 12, goethite (Sb concentrations up to 3.7 mg Sb/g) is favored and the transformation is completed after one day. Only a concentration of 6 mM Sb retarded the transformation, where even after 8 days only 50 % of the ferrihydrite was transformed into goethite. Transformations at pH 7 led to a mixture of 75 % hematite and 25 % goethite (4.3 mg Sb/g). However, at concentrations of 6 mM Sb, feroxyhyte (!- FeOOH) (9.1 mg Sb/g) was favored instead. At pH 4, hematite (32.3 mg Sb/g) was favored except for concentrations of 6 mM Sb, were again feroxyhyte (141.1 mg Sb/g) occurred. We assume that increased Sb concentrations favor feroxyhyte and indicate the incorporation of Sb into the structure of feroxyhyte. © The Author

Ferric iron geometry and coordination during hydrolysis and ferrihydrite precipitation

Definitive structural characterisation of ferrihydrite has challenged scientists primarily due to its nanosized particles and inherent long-range structural disorder which challenges analytical methodology (and modelling) typically employed to determine the structure of minerals. Here we report on the application of a synchrotron quick-scanning X-ray absorption spectroscopy (XAS) approach, which allows the collection of Extended X-ray Absorption Fine Structure (EXAFS) spectral data to k = 15 Å-1 in < 1 minute, to obtain unparalleled iron Kedge data on the hydrolysis of FeIII(H2O)6 and ferrihydrite precipitation. Modelling of the pre-edge and EXAFS data: 1) supports theoretical studies which have suggested the existence of a monomeric penta-coordinated FeIII hydrolysis species and; 2) corroborates recently proposed structural models of ferrihydrite that contain tetrahedral FeIII. Modelling results indicate that ferrihydrite consists of 15 to 25 % tetrahedral FeIII and suggest that this geometry must be included in any comprehensive structural model of ferrihydrite and, furthermore, should be considered when evaluating the reactivity, stability and other structure-property relationships of this mineral. © The Authors

Homogeneous catalysis under ultra-dilute conditions: TAML/NaClO oxidation of persistent metaldehyde

This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of the American Chemical Society, copyright © American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/jacs.6b11145TAML activators enable homogenous oxidation catalysis where the catalyst and substrate (S) are ultra-dilute (pM–low μM) and the oxidant is very dilute (high nM–low mM). Water contamination by exceptionally persistent micropollutants (MPs), including metaldehyde (Met), provides an ideal space for determining the characteristics and utilitarian limits of this ultradilute catalysis. The low MP concentrations decrease throughout catalysis with S oxidation (kII) and catalyst inactivation (ki) competing for the active catalyst. The percentage of substrate converted (%Cvn) can be increased by discovering methods to increase kII/ki. Here we show that NaClO extends catalyst lifetime to increase the Met turnover number (TON) threefold compared with H2O2, highlighting the importance of oxidant choice as a design tool in TAML systems. Met oxidation studies (pH 7, D2O, 0.01 M phosphate, 25 °C) monitored by 1H NMR spectroscopy show benign acetic acid as the only significant product. Analysis of TAML/NaClO treated Met solutions employing successive identical catalyst doses revealed that the processes can be modeled by the recently published relationship between the initial and final [S] (S0 and S∞, respectively), the initial [catalyst] (FeTot) and kII/ki. Consequently, this study establishes that S is proportional to S0 and that the %Cvn is conserved across all catalyst doses in multicatalyst-dose processes because the rate of the kII process depends on [S] while that of the ki process does not. A general tool for determining the FeTot required to effect a desired %Cvn is presented. Examination of the dependence of TON on kII/ki and FeTot at a fixed S0 indicates that for any TAML process employing FeTot < 1 10-6 M, small catalyst doses are not more efficient than one large dose.T.J.C thanks the Heinz Endowments for funding. NMR instrumentation at CMU was partially supported by NSF (CHE-0130903 and CHE-1039870)

Giving stakeholders a voice in governance: Biodiversity priorities for New Zealand's agriculture

Abstract: Mainstreaming biodiversity across government and society is recognised by international policy as critical to achieving positive conservation outcomes. With ‘participatory governance’ increasingly being applied to achieve collective action in conservation, there are growing calls to critically review such processes to capture their complexity and manage for emergent outcomes. This paper critically reviews a case study, aiming to give a broad range of stakeholders a voice in setting biodiversity priorities for New Zealand's agricultural landscape, in relation to four principles for knowledge co‐production in sustainability: context‐based, pluralistic, goal‐orientated and interactive. Aiming to facilitate an inclusive but rapid participation process, while not overburdening those willing to participate, three pathways for engagement were offered. Stakeholder participants were recruited from public, private and civic sectors involved in managing New Zealand's farmland biodiversity. An initial scoping exercise helped elevate biodiversity groups and management actions distinct to New Zealand's social and environmental context. Online surveys then gave stakeholders, from a diverse range of roles and sectors, a nationwide voice to express their own biodiversity interests and needs; these were reviewed by an advisor panel to reach consensus on final priorities that reflected the biodiversity outcomes that matter most to stakeholders involved in managing New Zealand's agricultural landscape and the management practices they considered most relevant to achieving those outcomes. This knowledge co‐production process delivered multiple gains that would not have been achieved had a more traditional science‐based process been applied, such as wide stakeholder engagement, identification of a tangible starting point, mitigation of bias or conflict risks, enhanced researcher and practitioner capabilities and a shared understanding of the opportunities and challenges for future development. Institutes addressing conservation challenges within local contexts need to: be ‘boundary‐spanning’ to manage cross‐scale influences and enable desired conservation behaviours; plan explicitly for the substantial effort required to overcome existing power hierarchies and facilitate transparent and structured decision processes that deliver social justice; better capture the relational values of nature to more successfully leverage peoples’ connection to nature in conservation policies and practices; and incorporate wider environmental (e.g. biosecurity), social, economic and political considerations. A free Plain Language Summary can be found within the Supporting Information of this article

Squirrelpox virus: assessing prevalence, transmission and environmental degradation

Red squirrels (Sciurus vulgaris) declined in Great Britain and Ireland during the last century, due to habitat loss and the introduction of grey squirrels (Sciurus carolinensis), which competitively exclude the red squirrel and act as a reservoir for squirrelpox virus (SQPV). The disease is generally fatal to red squirrels and their ecological replacement by grey squirrels is up to 25 times faster where the virus is present. We aimed to determine: (1) the seropositivity and prevalence of SQPV DNA in the invasive and native species at a regional scale; (2) possible SQPV transmission routes; and, (3) virus degradation rates under differing environmental conditions. Grey (n = 208) and red (n = 40) squirrel blood and tissues were sampled. Enzyme-linked immunosorbent assay (ELISA) and quantitative real-time polymerase chain reaction (qPCR) techniques established seropositivity and viral DNA presence, respectively. Overall 8% of squirrels sampled (both species combined) had evidence of SQPV DNA in their tissues and 22% were in possession of antibodies. SQPV prevalence in sampled red squirrels was 2.5%. Viral loads were typically low in grey squirrels by comparison to red squirrels. There was a trend for a greater number of positive samples in spring and summer than in winter. Possible transmission routes were identified through the presence of viral DNA in faeces (red squirrels only), urine and ectoparasites (both species). Virus degradation analyses suggested that, after 30 days of exposure to six combinations of environments, there were more intact virus particles in scabs kept in warm (25°C) and dry conditions than in cooler (5 and 15°C) or wet conditions. We conclude that SQPV is present at low prevalence in invasive grey squirrel populations with a lower prevalence in native red squirrels. Virus transmission could occur through urine especially during warm dry summer conditions but, more notably, via ectoparasites, which are shared by both species

Afferent specific role of NMDA receptors for the circuit integration of hippocampal neurogliaform cells.

This is the final version of the article. Available from Nature Publishing Group via the DOI in this record.Appropriate integration of GABAergic interneurons into nascent cortical circuits is critical for ensuring normal information processing within the brain. Network and cognitive deficits associated with neurological disorders, such as schizophrenia, that result from NMDA receptor-hypofunction have been mainly attributed to dysfunction of parvalbumin-expressing interneurons that paradoxically express low levels of synaptic NMDA receptors. Here, we reveal that throughout postnatal development, thalamic, and entorhinal cortical inputs onto hippocampal neurogliaform cells are characterized by a large NMDA receptor-mediated component. This NMDA receptor-signaling is prerequisite for developmental programs ultimately responsible for the appropriate long-range AMPAR-mediated recruitment of neurogliaform cells. In contrast, AMPAR-mediated input at local Schaffer-collateral synapses on neurogliaform cells remains normal following NMDA receptor-ablation. These afferent specific deficits potentially impact neurogliaform cell mediated inhibition within the hippocampus and our findings reveal circuit loci implicating this relatively understudied interneuron subtype in the etiology of neurodevelopmental disorders characterized by NMDA receptor-hypofunction.Proper brain function depends on the correct assembly of excitatory and inhibitory neurons into neural circuits. Here the authors show that during early postnatal development in mice, NMDAR signaling via activity of long-range synaptic inputs onto neurogliaform cells is required for their appropriate integration into the hippocampal circuitry.We thank Daniel Abebe for mouse colony maintenance and Kurt Auville for additional assistance with confocal imaging. We thank UNC Vector Core and Ed Boyden, MIT, Cambridge, MA, USA for generously providing AAV9-syn-Chrimson-TdTomato and AAV9-syn-Chronos-GFP. This work was supported by an intramural award to C.J.M. from the Eunice Kennedy–Shriver National Institute of Child Health and Human Development and a Competitive Fellowship Award to J.C.W. from the National Institute of Neurological Disorders and Strok

Optimising cervical spine imaging with digital radiography for the trauma patient

This is the author accepted manuscript. The final version is available from the British Institute of Radiology via the DOI in this recor

Genomic analysis and comparison of two gonorrhoea outbreaks

© 2016 Didelot et al.Gonorrhea is a sexually transmitted disease causing growing concern, with a substantial increase in reported incidence over the past few years in the United Kingdom and rising levels of resistance to a wide range of antibiotics. Understanding its epidemiology is therefore of major biomedical importance, not only on a population scale but also at the level of direct transmission. However, the molecular typing techniques traditionally used for gonorrhea infections do not provide sufficient resolution to investigate such fine-scale patterns. Here we sequenced the genomes of 237 isolates from two local collections of isolates from Sheffield and London, each of which was resolved into a single type using traditional methods. The two data sets were selected to have different epidemiological properties: the Sheffield data were collected over 6 years from a predominantly heterosexual population, whereas the London data were gathered within half a year and strongly associated with men who have sex with men. Based on contact tracing information between individuals in Sheffield, we found that transmission is associated with a median time to most recent common ancestor of 3.4 months, with an upper bound of 8 months, which we used as a criterion to identify likely transmission links in both data sets. In London, we found that transmission happened predominantly between individuals of similar age, sexual orientation, and location and also with the same HIV serostatus, which may reflect serosorting and associated risk behaviors. Comparison of the two data sets suggests that the London epidemic involved about ten times more cases than the Sheffield outbreak. IMPORTANCE: The recent increases in gonorrhea incidence and antibiotic resistance are cause for public health concern. Successful intervention requires a better understanding of transmission patterns, which is not uncovered by traditional molecular epidemiology techniques. Here we studied two outbreaks that took place in Sheffield and London, United Kingdom. We show that whole-genome sequencing provides the resolution to investigate direct gonorrhea transmission between infected individuals. Combining genome sequencing with rich epidemiological information about infected individuals reveals the importance of several transmission routes and risk factors, which can be used to design better control measures