Diploptene δ13C values from contemporary thermokarst lake sediments show complex spatial variation

Cryospheric changes in northern high latitudes are linked to significant greenhouse gas flux to the atmosphere, for example, methane that originates from organic matter decomposition in thermokarst lakes. The set of pathways that link methane production in sediments, via oxidation in the lake system, to the flux of residual methane to the atmosphere is complex and exhibits temporal and spatial variation. The isotopic signal of bacterial biomarkers (hopanoids, e.g. diploptene) in sediments has been used to identify contemporary ocean-floor methane seeps and, in the geological record, periods of enhanced methane production (e.g. the PETM). The biomarker approach could potentially be used to assess temporal changes in lake emissions through the Holocene via the sedimentary biomarker record. However, there are no data on the consistency of the signal of isotopic depletion in relation to source or on the amount of noise (unexplained variation) in biomarker values from modern lake sediments. We assessed methane oxidation as represented by the isotopic signal of biomarkers from methane oxidising bacteria (MOB) in multiple surface sediment samples in three distinct areas known to emit varying levels of methane in two shallow Alaskan thermokarst lakes. Diploptene was present and had δ13C values lower than -38g‰ in all sediments analysed, suggesting methane oxidation was widespread. However, there was considerable variation in δ13C values within each area. The most 13C-depleted diploptene was found in an area of high methane ebullition in Ace Lake (diploptene δ13C values between -68.2 and -50.1‰). In contrast, significantly higher diploptene δ13C values (between -42.9 and -38.8g‰) were found in an area of methane ebullition in Smith Lake. δ13C values of diploptene between -56.8 and -46.9g‰ were found in the centre of Smith Lake, where ebullition rates are low but diffusive methane efflux occurs. The small-scale heterogeneity of the samples may reflect patchy distribution of substrate and/or MOB within the sediments. The two ebullition areas differ in age and type of organic carbon substrate, which may affect methane production, transport, and subsequent oxidation. Given the high amount of variation in surface samples, a more extensive calibration of modern sediment properties, within and among lakes, is required before down-core records of hopanoid isotopic signatures are developed. © Author(s) 2016

Raman spectroscopic analysis of the effect of the lichenicolous fungus Xanthoriicola physciae on its lichen host

YesLichenicolous (lichen-dwelling) fungi have been extensively researched taxonomically over many years, and phylogenetically in recent years, but the biology of the relationship between the invading fungus and the lichen host has received limited attention, as has the effects on the chemistry of the host, being difficult to examine in situ. Raman spectroscopy is an established method for the characterization of chemicals in situ, and this technique is applied to a lichenicolous fungus here for the first time. Xanthoriicola physciae occurs in the apothecia of Xanthoria parietina, producing conidia at the hymenium surface. Raman spectroscopy of apothecial sections revealed that parietin and carotenoids were destroyed in infected apothecia. Those compounds protect healthy tissues of the lichen from extreme insolation and their removal may contribute to the deterioration of the apothecia. Scytonemin was also detected, but was most probably derived from associated cyanobacteria. This work shows that Raman spectroscopy has potential for investigating changes in the chemistry of a lichen by an invading lichenicolous fungus.This work was completed while D.L.H. was in receipt of an award from the Ministerio de Economica y Competitividad of Spain (Proyectos CGL 2014-55542-P)

Chirality Correlation within Dirac Eigenvectors from Domain Wall Fermions

In the dilute instanton gas model of the QCD vacuum, one expects a strong spatial correlation between chirality and the maxima of the Dirac eigenvectors with small eigenvalues. Following Horvath, {\it et al.} we examine this question using lattice gauge theory within the quenched approximation. We extend the work of those authors by using weaker coupling, $\beta=6.0$, larger lattices, $16^4$, and an improved fermion formulation, domain wall fermions. In contrast with this earlier work, we find a striking correlation between the magnitude of the chirality density, $|\psi^\dagger(x)\gamma^5\psi(x)|$, and the normal density, $\psi^\dagger(x)\psi(x)$, for the low-lying Dirac eigenvectors.Comment: latex, 25 pages including 12 eps figure

Residual stress characterization of single and triple-pass autogenously welded stainless steel pipes

Using neutron diffraction the components of the residual stress field have been determined in the region near a mid-length groove in two identical austenitic stainless pipes in which weld beads had been laid down. One pipe sample had a single pass, and the second a triple pass, autogenous weld deposited around the groove circumference. The results show the effect on the stress field of the additional weld deposited and are compared to the results of Finite Element Modelling. The hoop stress component is found to be generally tensile, and greater in the triple pass weldment than in the single pass weldment. The hoop stresses reach peak values of around 400 MPa in tension. X-ray measurements of the residual stress components on the near inner surface of the pipe weldments are also presented, and show tensile stresses in both pipes, with a higher magnitude in the three-pass weldment

Censoring for loss to follow-up in time-to-event analyses of composite outcomes or in the presence of competing risks

Background: In time-to-event analyses, there is limited guidance on when persons who are lost to follow-up (LTFU) should be censored. Methods: We simulated bias in risk estimates for: (1) a composite event of measured (outcome only observable in a patient encounter) and captured events (outcome observable outside a patient encounter); and a (2) measured or (3) captured event in the presence of a competing event of the other type, under three censoring strategies: (i) censor at the last study encounter; (ii) censor when LTFU definition is met; and (iii) a new, hybrid censoring strategy. We demonstrate the real-world impact of this decision by estimating: (1) time to acquired immune deficiency syndrome (AIDS) diagnosis or death, (2) time to initiation of antiretroviral therapy (ART), and (3) time to death before ART initiation among adults engaged in HIV care. Results: For (1) our hybrid censoring strategy was least biased. In our example, 5-year risk of AIDS or death was overestimated using last-encounter censoring (25%) and under-estimated using LTFU-definition censoring (21%), compared with results from our hybrid approach (24%). Last-encounter censoring was least biased for (2). When estimating 5-year risk of ART initiation, LTFU-definition censoring underestimated risk (80% vs. 85% using last-encounter censoring). LTFU-definition censoring was least biased for (3). When estimating 5-year risk of death before ART initiation, last-encounter censoring overestimated risk (5.2% vs. 4.7% using LTFU-definition censoring). Conclusions: The least biased censoring strategy for time-to-event analyses in the presence of LTFU depends on the event and estimand of interest

Congruent biogeographical disjunctions at a continent-wide scale: Quantifying and clarifying the role of biogeographic barriers in the Australian tropics

AIM: To test whether novel and previously hypothesized biogeogaphic barriers in the Australian Tropics represent significant disjunction points or hard barriers, or both, to the distribution of plants. LOCATION: Australian tropics: Australian Monsoon Tropics and Australian Wet Tropics. METHODS: The presence or absence of 6,861 plant species was scored across 13 putative biogeographic barriers in the Australian Tropics, including two that have not previously been recognised. Randomizations of these data were used to test whether more species showed disjunctions (gaps in distribution) or likely barriers (range limits) at these points than expected by chance. RESULTS: Two novel disjunctions in the Australian Tropics flora are identified in addition to eleven putative barriers previously recognized for animals. Of these, eleven disjunction point (all within the Australian Monsoon Tropics) were found to correspond to range-ending barriers to a significant number of species, while neither of the two disjunctions found within the Australian Wet Tropics limited a significant number of species' ranges. MAIN CONCLUSIONS: Biogeographic barriers present significant distributional limits to native plant species in the Australian Monsoon Tropics but not in the Australian Wet TropicsThe authors would like to thank the ‘Coopers and Cladistics’ systematics discussion group at the ANU for comments on early versions of the manuscript. They would also like to acknowledge the University of Queensland for supporting RDE via a Postgraduate Research Scholarship, and the Australian Research Council for supporting LGC and MDC via Discovery Grants during data collection, analysis and manuscript preparatio

Convergence of chiral effective field theory

We formulate the expansion for the mass of the nucleon as a function of pion mass within chiral perturbation theory using a number of different ultra-violet regularisation schemes; including dimensional regularisation and various finite-ranged regulators. Leading and next-to-leading order non-analytic contributions are included through the standard one-loop Feynman graphs. In addition to the physical nucleon mass, the expansion is constrained by recent, extremely accurate, lattice QCD data obtained with two flavors of dynamical quarks. The extent to which different regulators can describe the chiral expansion is examined, while varying the range of quark mass over which the expansions are matched. Renormalised chiral expansion parameters are recovered from each regularisation prescription and compared. We find that the finite-range regulators produce consistent, model-independent results over a wide range of quark mass sufficient to solve the chiral extrapolation problem in lattice QCD.Comment: 13 pages, 13 figures; To appear in Progress in Particle and Nuclear Physics; presented at Erice School on Quarks in Hadrons and Nuclei, September 200

When to Censor?

Loss to follow-up is an endemic feature of time-to-event analyses that precludes observation of the event of interest. To our knowledge, in typical cohort studies with encounters occurring at regular or irregular intervals, there is no consensus on how to handle person-time between participants’ last study encounter and the point at which they meet a definition of loss to follow-up. We demonstrate, using simulation and an example, that when the event of interest is captured outside of a study encounter (e.g., in a registry), person-time should be censored when the study-defined criterion for loss to follow-up is met (e.g., 1 year after last encounter), rather than at the last study encounter. Conversely, when the event of interest must be measured within the context of a study encounter (e.g., a biomarker value), person-time should be censored at the last study encounter. An inappropriate censoring scheme has the potential to result in substantial bias that may not be easily corrected

Quenched Lattice QCD with Domain Wall Fermions and the Chiral Limit

Quenched QCD simulations on three volumes, $8^3 \times$, $12^3 \times$ and $16^3 \times 32$ and three couplings, $\beta=5.7$, 5.85 and 6.0 using domain wall fermions provide a consistent picture of quenched QCD. We demonstrate that the small induced effects of chiral symmetry breaking inherent in this formulation can be described by a residual mass (\mres) whose size decreases as the separation between the domain walls ($L_s$) is increased. However, at stronger couplings much larger values of $L_s$ are required to achieve a given physical value of \mres. For $\beta=6.0$ and $L_s=16$, we find \mres/m_s=0.033(3), while for $\beta=5.7$, and $L_s=48$, \mres/m_s=0.074(5), where $m_s$ is the strange quark mass. These values are significantly smaller than those obtained from a more naive determination in our earlier studies. Important effects of topological near zero modes which should afflict an accurate quenched calculation are easily visible in both the chiral condensate and the pion propagator. These effects can be controlled by working at an appropriately large volume. A non-linear behavior of $m_\pi^2$ in the limit of small quark mass suggests the presence of additional infrared subtlety in the quenched approximation. Good scaling is seen both in masses and in $f_\pi$ over our entire range, with inverse lattice spacing varying between 1 and 2 GeV.Comment: 91 pages, 34 figure

Topology and chiral symmetry breaking in SU(N) gauge theories

We study the low-lying eigenmodes of the lattice overlap Dirac operator for SU(N) gauge theories with N=2,3,4 and 5 colours. We define a fermionic topological charge from the zero-modes of this operator and show that, as N grows, any disagreement with the topological charge obtained by cooling the fields, becomes rapidly less likely. By examining the fields where there is a disagreement, we are able to show that the Dirac operator does not resolve instantons below a critical size of about rho = 2.5 a, but resolves the larger, more physical instantons. We investigate the local chirality of the near-zero modes and how it changes as we go to larger N. We observe that the local chirality of these modes, which is prominent for SU(2) and SU(3), becomes rapidly weaker for larger N and is consistent with disappearing entirely in the limit of N -> infinity. We find that this is not due to the observed disappearance of small instantons at larger N.Comment: 41 pages, 12 figures, RevTe