ALBERT

Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.

Description: Regional and local patterns in depth to water table, hydrochemistry and peat properties of bogs and their laggs in coastal British Columbia Hydrology and Earth System Sciences, 17, 3421-3435, 2013 Author(s): S. A. Howie and H. J. van Meerveld In restoration planning for damaged raised bogs, the lagg at the bog margin is often not given considerable weight and is sometimes disregarded entirely. However, the lagg is critical for the proper functioning of the bog, as it supports the water mound in the bog. In order to include the lagg in a restoration plan for a raised bog, it is necessary to understand the hydrological characteristics and functions of this rarely studied transition zone. We studied 13 coastal British Columbia (BC) bogs and identified two different gradients in depth to water table, hydrochemistry and peat properties: (1) a local bog expanse–bog margin gradient, and (2) a regional gradient related to climate and proximity to the ocean. Depth to water table generally increased across the transition from bog expanse to bog margin. In the bog expanse, pH was above 4.2 in the Pacific Oceanic wetland region (cooler and wetter climate) and below 4.3 in the Pacific Temperate wetland region (warmer and drier climate). Both pH and pH-corrected electrical conductivity increased significantly across the transition from bog expanse to bog margin, though not in all cases. Na + and Mg 2+ concentrations were generally highest in exposed, oceanic bogs and lower in inland bogs. Ash content in peat samples increased across the bog expanse–bog margin transition, and appears to be a useful abiotic indicator of the location of the bog margin. The observed variation in the hydrological and hydrochemical gradients across the bog expanse–bog margin transition highlights both local and regional diversity of bogs and their associated laggs.

Description: Imperfect scaling in distributions of radar-derived rainfall fields Hydrology and Earth System Sciences Discussions, 10, 11385-11422, 2013 Author(s): M. J. van den Berg, L. Delobbe, and N. E. C. Verhoest Fine scale rainfall observations for modeling exercises are often not available, but rather coarser data derived from a variety of sources are used. Effectively using these data sources in models often requires the probability distribution of the data at the applicable scale. Although numerous models for scaling distributions exist, these are often based on theoretical developments, rather than on data. In this study, we develop a model based on the α-stable distribution of rainfall fields, and tested on 5 min radar data from a Belgian weather radar. We use these data to estimate functions that describe parameters of the distribution over various scales. Moreover, we study how the mean of the distribution and the intermittency change with scale, and validate and design functions to describe the shape parameter of the distribution. This information was combined into an effective model of the distribution. Finally, the model was fitted to data from numerous storms, and the resulting parameters were compared to investigate the change in scaling behavior through time.

Description: Spatially resolved information on karst conduit flow from in-cave dye-tracing Hydrology and Earth System Sciences Discussions, 10, 11311-11335, 2013 Author(s): U. Lauber, W. Ufrecht, and N. Goldscheider Artificial tracers are powerful tools to investigate karst systems. Tracers are commonly injected into sinking streams or dolines, while springs serve as monitoring sites. The obtained flow and transport parameters represent mixed information from the vadose, epiphreatic and phreatic zones, i.e., the aquifer remains a black box. Accessible active caves constitute valuable but underexploited natural laboratories to gain detailed insights into the hydrologic functioning of the aquifer. Two multi-tracer tests in the catchment of a major karst spring (Blautopf, Germany) with injections and monitoring in two associated water caves aimed at obtaining spatially and temporally resolved information on groundwater flow in different compartments of the system. Two tracers were injected in the caves to characterize the hydraulic connections between them and with the spring. Two injections at the land surface, far from the spring, aimed at resolving the aquifer's internal drainage structure. Tracer breakthrough curves were monitored by field fluorimeters in caves and at the spring. Results demonstrate the dendritic drainage structure of the aquifer. It was possible to obtain relevant flow and transport parameters for different sections of this system. The highest mean flow velocities (275 m h −1 ) were observed in the near-spring epiphreatic section (open-channel flow), while velocities in the phreatic zone (pressurized flow) were one order of magnitude lower. Determined conduit water volumes confirm results of water balances and hydrograph analyses. In conclusion, experiments and monitoring in caves can deliver spatially resolved information on karst aquifer heterogeneity and dynamics that cannot be obtained by traditional investigative methods.

Description: On the lack of robustness of hydrologic models regarding water balance simulation – a diagnostic approach on 20 mountainous catchments using three models of increasing complexity Hydrology and Earth System Sciences Discussions, 10, 11337-11383, 2013 Author(s): L. Coron, V. Andréassian, C. Perrin, M. Bourqui, and F. Hendrickx This paper investigates the robustness of rainfall–runoff models when their parameters are transferred in time. More specifically, we studied their ability to simulate water balance on periods with different hydroclimatic characteristics. The testing procedure consisted in a series of parameter transfers between 10-yr periods and the systematic analysis of mean-volume errors. This procedure was applied to three conceptual models of different structural complexity over 20 mountainous catchments in southern France. The results showed that robustness problems are common. Errors on 10-yr-mean flows were significant for all three models and calibration periods, even when the entire record was used for calibration. Various graphical and numerical tools were used to show strong similarities between the shapes of mean flow biases calculated on a 10-yr-long sliding window when various parameter sets are used. Unexpected behavioural similarities were observed between the three models tested, considering their large differences in structural complexity. While the actual causes for robustness problems in these models remain unclear, this work stresses the limited transferability in time of the water balance adjustments made through parameter optimization. Although absolute differences between simulations obtained with different calibrated parameter sets were sometimes substantial, relative differences in simulated mean flows between time periods remained similar regardless of the calibrated parameter sets.

Description: Bayesian networks modelling in support to cross-cutting analysis of water supply and sanitation in developing countries Hydrology and Earth System Sciences, 17, 3397-3419, 2013 Author(s): C. Dondeynaz, J. López Puga, and C. Carmona Moreno Despite the efforts made towards the Millennium Development Goals targets during the last decade, improved access to water supply or basic sanitation still remains unavailable for millions of people across the world. This paper proposes a set of models that use 25 key variables and country profiles from the WatSan4Dev data set involving water supply and sanitation (Dondeynaz et al., 2012). This paper suggests the use of Bayesian network modelling methods because they are more easily adapted to deal with non-normal distributions, and integrate a qualitative approach for data analysis. They also offer the advantage of integrating preliminary knowledge into the probabilistic models. The statistical performance of the proposed models ranges between 20 and 5% error rates, which are very satisfactory taking into account the strong heterogeneity of variables. Probabilistic scenarios run from the models allow an assessment of the relationships between human development, external support, governance aspects, economic activities and water supply and sanitation (WSS) access. According to models proposed in this paper, gaining a strong poverty reduction will require the WSS access to reach 75–76% through: (1) the management of ongoing urbanisation processes to avoid slums development; and (2) the improvement of health care, for instance for children. Improving governance, such as institutional efficiency, capacities to make and apply rules, or control of corruption is positively associated with WSS sustainable development. The first condition for an increment of the HDP (human development and poverty) remains of course an improvement of the economic conditions with higher household incomes. Moreover, a significant country commitment to the environment, associated with civil society freedom of expression constitutes a favourable setting for sustainable WSS services delivery. Intensive agriculture using irrigation practises also appears as a mean for sustainable WSS thanks to multi-uses and complementarities. With a WSS sector organised at national level, irrigation practices can support the structuring and efficiency of the agriculture sector. It may then induce rural development in areas where WSS access often is set back compared to urban areas 1 . External financial support, called Official Development Assistance (ODA CI), plays a role in WSS improvement but comes last in the sensitivity analyses of models. An overall 47% of the Official Development Assistance goes first to poor countries, and is associated to governance aspects: (1) political stability and (2) country commitment to the environment and civil society degree of freedom. These governance aspects constitute a good framework for aid implementation in recipient countries. Modelling is run with the five groups of countries as defined in Dondeynaz et al. (2012). Models for profile 4 (essential external support) and profile 5 (primary material consumption) are specifically detailed and analysed in this paper. For countries in profile 4, fighting against water scarcity and progressing desertification should be the priority. However, for countries in profile 5, efforts should first concentrate on consolidation of political stability while supporting diversification of the economic activities. Nevertheless, for both profiles, reduction of poverty should remain the first priority as previously indicated. 1 JMP statistics, 2004 http://www.wssinfo.org/data-estimates/table/ , last access: 22 July 2013.

Description: Technical Note: A comparison of model and empirical measures of catchment-scale effective energy and mass transfer Hydrology and Earth System Sciences, 17, 3389-3395, 2013 Author(s): C. Rasmussen and E. L. Gallo Recent work suggests that a coupled effective energy and mass transfer (EEMT) term, which includes the energy associated with effective precipitation and primary production, may serve as a robust prediction parameter of critical zone structure and function. However, the models used to estimate EEMT have been solely based on long-term climatological data with little validation using direct empirical measures of energy, water, and carbon balances. Here we compare catchment-scale EEMT estimates generated using two distinct approaches: (1) EEMT modeled using the established methodology based on estimates of monthly effective precipitation and net primary production derived from climatological data, and (2) empirical catchment-scale EEMT estimated using data from 86 catchments of the Model Parameter Estimation Experiment (MOPEX) and MOD17A3 annual net primary production (NPP) product derived from Moderate Resolution Imaging Spectroradiometer (MODIS). Results indicated positive and significant linear correspondence ( R 2 = 0.75; P 〈 0.001) between model and empirical measures with an average root mean square error (RMSE) of 4.86 MJ m −2 yr −1 . Modeled EEMT values were consistently greater than empirical measures of EEMT. Empirical catchment estimates of the energy associated with effective precipitation ( E PPT ) were calculated using a mass balance approach that accounts for water losses to quick surface runoff not accounted for in the climatologically modeled E PPT . Similarly, local controls on primary production such as solar radiation and nutrient limitation were not explicitly included in the climatologically based estimates of energy associated with primary production ( E BIO ), whereas these were captured in the remotely sensed MODIS NPP data. These differences likely explain the greater estimate of modeled EEMT relative to the empirical measures. There was significant positive correlation between catchment aridity and the fraction of EEMT partitioned into E BIO ( F BIO ), with an increase in F BIO as a fraction of the total as aridity increases and percentage of catchment woody plant cover decreases. In summary, the data indicated strong correspondence between model and empirical measures of EEMT with limited bias that agree well with other empirical measures of catchment energy and water partitioning and plant cover.

Description: Analysis of projected changes in the occurrence of heat waves in Hungary Advances in Geosciences, 35, 115-122, 2013 Author(s): R. Pongrácz, J. Bartholy, and E. B. Bartha Heat wave events are important temperature-related hazards due to their impacts on human health. In 2004, a Heat Health Warning System including three levels of heat wave warning was developed on the basis of a retrospective analysis of mortality and meteorological data in Hungary to anticipate heat waves that may result in a large excess of mortality. Projected changes in the frequency of different heat wave warning levels are analysed for the 21st century. For this purpose, outputs of regional climate model PRECIS (Providing REgional Climates for Impacts Studies) are used taking into account three different global emissions scenarios (A2, A1B, B2). The results clearly show an increase in occurrence and length of heat waves with respect to the underlying emissions scenarios and regional climate model used. Moreover, the potential season of heat wave occurrences is projected to be lengthened by two months in 2071–2100 compared to 1961–1990.

Description: Review Article: On the relation between the seismic activity and the Hurst exponent of the geomagnetic field at the time of the 2000 Izu swarm Natural Hazards and Earth System Science, 13, 2189-2194, 2013 Author(s): F. Masci and J. N. Thomas Many papers document the observation of earthquake-related precursory signatures in geomagnetic field data. However, the significance of these findings is ambiguous because the authors did not adequately take into account that these signals could have been generated by other sources, and the seismogenic origin of these signals have not been validated by comparison with independent datasets. Thus, they are not reliable examples of magnetic disturbances induced by the seismic activity. Hayakawa et al. (2004) claim that at the time of the 2000 Izu swarm the Hurst exponent of the Ultra-Low-Frequency (ULF: 0.001–10 Hz) band of the geomagnetic field varied in accord with the energy released by the seismicity. The present paper demonstrates that the behaviour of the Hurst exponent was insufficiently investigated and also misinterpreted by the authors. We clearly show that during the Izu swarm the changes of the Hurst exponent were strongly related to the level of global geomagnetic activity and not to the increase of the local seismic activity.

Description: Forest fire danger rating in complex topography – results from a case study in the Bavarian Alps in autumn 2011 Natural Hazards and Earth System Science, 13, 2157-2167, 2013 Author(s): C. Schunk, C. Wastl, M. Leuchner, C. Schuster, and A. Menzel Forest fire danger rating based on sparse meteorological stations is known to be potentially misleading when assigned to larger areas of complex topography. This case study examines several fire danger indices based on data from two meteorological stations at different elevations during a major drought period. This drought was caused by a persistent high pressure system, inducing a pronounced temperature inversion and its associated thermal belt with much warmer, dryer conditions in intermediate elevations. Thus, a massive drying of fuels, leading to higher fire danger levels, and multiple fire occurrences at mid-slope positions were contrasted by moderate fire danger especially in the valleys. The ability of fire danger indices to resolve this situation was studied based on a comparison with the actual fire danger as determined from expert observations, fire occurrences and fuel moisture measurements. The results revealed that, during temperature inversion, differences in daily cycles of meteorological parameters influence fire danger and that these are not resolved by standard meteorological stations and fire danger indices (calculated on a once-a-day basis). Additional stations in higher locations or high-resolution meteorological models combined with fire danger indices accepting at least hourly input data may allow reasonable fire danger calculations under these circumstances.

Description: The Mediterranean Sea system: a review and an introduction to the special issue Ocean Science, 9, 789-803, 2013 Author(s): T. Tanhua, D. Hainbucher, K. Schroeder, V. Cardin, M. Álvarez, and G. Civitarese The Mediterranean Sea is a semi-enclosed sea characterized by high salinities, temperatures and densities. The net evaporation exceeds the precipitation, driving an anti-estuarine circulation through the Strait of Gibraltar, contributing to very low nutrient concentrations. The Mediterranean Sea has an active overturning circulation, one shallow cell that communicates directly with the Atlantic Ocean, and two deep overturning cells, one in each of the two main basins. It is surrounded by populated areas and is thus sensitive to anthropogenic forcing. Several dramatic changes in the oceanographic and biogeochemical conditions have been observed during the past several decades, emphasizing the need to better monitor and understand the changing conditions and their drivers. During 2011 three oceanographic cruises were conducted in a coordinated fashion in order to produce baseline data of important physical and biogeochemical parameters that can be compared to historic data and be used as reference for future observational campaigns. In this article we provide information on the Mediterranean Sea oceanographic situation, and present a short review that will serve as background information for the special issue in Ocean Science on "Physical, chemical and biological oceanography of the Mediterranean Sea". An important contribution of this article is the set of figures showing the large-scale distributions of physical and chemical properties along the full length of the Mediterranean Sea.

Description: Corrigendum to "NEMO on the shelf: assessment of the Iberia–Biscay–Ireland configuration" published in Ocean Sci., 9, 745–771, 2013 Ocean Science, 9, 787-787, 2013 Author(s): C. Maraldi, J. Chanut, B. Levier, N. Ayoub, P. De Mey, G. Reffray, F. Lyard, S. Cailleau, M. Drévillon, E. A. Fanjul, M. G. Sotillo, P. Marsaleix, and the Mercator Research and Development Team No abstract available.

Description: Preface "Landslide hazard and risk assessment at different scales" Natural Hazards and Earth System Science, 13, 2169-2171, 2013 Author(s): P. Reichenbach, A. Günther, and T. Glade

Description: O -GlcNAcylation is an inducible, highly dynamic and reversible post-translational modification, mediated by a unique enzyme named O -linked N -acetyl- d -glucosamine ( O -GlcNAc) transferase (OGT). In response to nutrients, O -GlcNAc levels are differentially regulated on many cellular proteins involved in gene expression, translation, immune reactions, protein degradation, protein–protein interaction, apoptosis and signal transduction. In contrast to eukaryotic cells, little is known about the role of O -GlcNAcylation in the viral life cycle. Here, we show that the overexpression of the OGT reduces the replication efficiency of Kaposi's sarcoma-associated herpesvirus (KSHV) in a dose-dependent manner. In order to investigate the global impact of O -GlcNAcylation in the KSHV life cycle, we systematically analyzed the 85 annotated KSHV-encoded open reading frames for O -GlcNAc modification. For this purpose, an immunoprecipitation (IP) strategy with three different approaches was carried out and the O -GlcNAc signal of the identified proteins was properly controlled for specificity. Out of the 85 KSHV-encoded proteins, 18 proteins were found to be direct targets for O -GlcNAcylation. Selected proteins were further confirmed by mass spectrometry for O -GlcNAc modification. Correlation of the functional annotation and the O -GlcNAc status of KSHV proteins showed that the predominant targets were proteins involved in viral DNA synthesis and replication. These results indicate that O -GlcNAcylation plays a major role in the regulation of KSHV propagation.

Description: Galectins are potent adhesion/growth-regulatory effectors with characteristic expression profiles. Understanding the molecular basis of gene regulation in each case requires detailed information on copy number of genes and sequence(s) of their promoter(s). Our report reveals plasticity in this respect between galectins and species. We here describe occurrence of a two-gene constellation for human galectin (Gal)-7 and define current extent of promoter-sequence divergence. Interestingly, cross-species genome analyses also detected single-copy display. Because the regulatory potential will then be different, extrapolations of expression profiles are precluded between respective species pairs. Gal-4 coding in chromosomal vicinity was found to be confined to one gene, whereas copy-number variation also applied to Gal-9. The example of rat Gal-9 teaches the lesson that the presence of multiple bands in Southern blotting despite a single-copy gene constellation is attributable to two pseudogenes. The documented copy-number variability should thus be taken into consideration when studying regulation of galectin genes, in a species and in comparison between species.

Description: In studying the molecular basis for the potent immune activity of previously described gamma and delta inulin particles and to assist in production of inulin adjuvants under Good Manufacturing Practice, we identified five new inulin isoforms, bringing the total to seven plus the amorphous form. These isoforms comprise the step-wise inulin developmental series amorphous -〉 alpha-1 (AI-1) -〉 alpha-2 (AI-2) -〉 gamma (GI) -〉 delta (DI) -〉 zeta (ZI) -〉 epsilon (EI) -〉 omega (OI) in which each higher isoform can be made either by precipitating dissolved inulin or by direct conversion from its precursor, both cases using regularly increasing temperatures. At higher temperatures, the shorter inulin polymer chains are released from the particle and so the key difference between isoforms is that each higher isoform comprises longer polymer chains than its precursor. An increasing trend of degree of polymerization is confirmed by end-group analysis using 1 H nuclear magnetic resonance spectroscopy. Inulin isoforms were characterized by the critical temperatures of abrupt phase-shifts (solubilizations or precipitations) in water suspensions. Such (aqueous) "melting" or "freezing" points are diagnostic and occur in strikingly periodic steps reflecting quantal increases in noncovalent bonding strength and increments in average polymer lengths. The (dry) melting points as measured by modulated differential scanning calorimetry similarly increase in regular steps. We conclude that the isoforms differ in repeated increments of a precisely repeating structural element. Each isoform has a different spectrum of biological activities and we show the higher inulin isoforms to be more potent alternative complement pathway activators.

Description: The methylotrophic yeast, Pichia pastoris , is an important organism used for the production of therapeutic proteins. Previously, we have reported the glycoengineering of this organism to produce human-like N -linked glycans but up to now no one has addressed engineering the O -linked glycosylation pathway. Typically, O -linked glycans produced by wild-type P. pastoris are linear chains of four to five α-linked mannose residues, which may be capped with β- or phospho-mannose. Previous genetic engineering of the N-linked glycosylation pathway of P. pastoris has eliminated both of these two latter modifications, resulting in O -linked glycans which are linear α-linked mannose structures. Here, we describe a method for the co-expression of an α-1,2-mannosidase, which reduces these glycans to primarily a single O -linked mannose residue. In doing so, we have reduced the potential of these glycans to interact with carbohydrate-binding proteins, such as dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin. Furthermore, the introduction of the enzyme protein- O -linked-mannose β-1,2- N -acetylglucosaminyltransferase 1, resulted in the capping of the single O -linked mannose residues with N -acetylglucosamine. Subsequently, this glycoform was extended into human-like sialylated glycans, similar in structure to α-dystroglycan-type glycoforms. As such, this represents the first example of sialylated O -linked glycans being produced in yeast and extends the utility of the P. pastoris production platform beyond N -linked glycosylated biotherapeutics to include molecules possessing O -linked glycans.

Description: Neurons and other cells require intracellular transport of essential components for viability and function. Previous work has shown that while net amyloid precursor protein (APP) transport is generally anterograde, individual vesicles containing APP move bi-directionally. This discrepancy highlights our poor understanding of the in vivo regulation of APP-vesicle transport. Here, we show that reduction of presenilin (PS) or suppression of gamma-secretase activity substantially increases anterograde and retrograde velocities for APP vesicles. Strikingly, PS deficiency has no effect on an unrelated cargo vesicle class containing synaptotagmin, which is powered by a different kinesin motor. Increased velocities caused by PS or gamma-secretase reduction require functional kinesin-1 and dynein motors. Together, our findings suggest that a normal function of PS is to repress kinesin-1 and dynein motor activity during axonal transport of APP vesicles. Furthermore, our data suggest that axonal transport defects induced by loss of PS-mediated regulatory effects on APP-vesicle motility could be a major cause of neuronal and synaptic defects observed in Alzheimer's Disease (AD) pathogenesis. Thus, perturbations of APP/PS transport could contribute to early neuropathology observed in AD, and highlight a potential novel therapeutic pathway for early intervention, prior to neuronal loss and clinical manifestation of disease.

Description: With age, muscle mass and integrity are progressively lost leaving the elderly frail, weak and unable to independently care for themselves. Defined as sarcopenia, this age-related muscle atrophy appears to be multifactorial but its definite cause is still unknown. Mitochondrial dysfunction has been implicated in this process. Using a novel transgenic mouse model of mitochondrial DNA (mtDNA) double-strand breaks (DSBs) that presents a premature aging-like phenotype, we studied the role of mtDNA damage in muscle wasting. We caused DSBs in mtDNA of adult mice using a ubiquitously expressed mitochondrial-targeted endonuclease, mito- Pst I. We found that a short, transient systemic mtDNA damage led to muscle wasting and a decline in locomotor activity later in life. We found a significant decline in muscle satellite cells, which decreases the muscle's capacity to regenerate and repair during aging. This phenotype was associated with impairment in acetylcholinesterase (AChE) activity and assembly at the neuromuscular junction (NMJ), also associated with muscle aging. Our data suggests that systemic mitochondrial dysfunction plays important roles in age-related muscle wasting by preferentially affecting the myosatellite cell pool.

Description: Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation.

Description: We present a methodology for infrasonic remote sensing of winds in the stratosphere that does not require discrete ground-truth events. Our method uses measured time delays between arrays of sensors to provide group velocities (referred to here as celerities) and then minimizes the difference between observed and predicted celerities by perturbing an initial atmospheric specification. Because we focus on interarray propagation effects, it is not necessary to simulate the full propagation path from source to receiver. This feature allows us to use a relatively simple forward model that is applicable over short-regional distances. By focusing on stratospheric returns, we show that our non-linear inversion scheme converges much better if the starting model contains a strong stratospheric duct. Using the Horizontal Wind Model (HWM)/Mass Spectrometer Incoherent Scatter (MSISE) empirical climatology as a starting model, we demonstrate that the inversion scheme is robust to large uncertainties in backazimuth, but that uncertainties in the measured trace velocity and celerity require the use of prior constraints to ensure suitable convergence. The inversion of synthetic data, using realistic estimates of measurement error, shows that our scheme will nevertheless improve upon a starting model under most scenarios. The inversion scheme is applied to infrasound data recorded from a large event on 2010 December 25, which is presumed to be a bolide, using data from a nine-element infrasound network in Utah. We show that our recorded data require a stronger zonal wind speed in the stratosphere than is present in the HWM profile, and are more consistent with the Ground-to-Space (G2S) profile.

Description: Coda- Q is a stochastic parameter reflecting the heterogeneities of medium that seismic waves travel through. We confirmed that coda- Q would vary with the stress loaded to an elastic medium using numerical simulations of seismic wave propagation. When the stress is loaded, cracks in the crust could either close or newly open. The closure and opening of the cracks are not random but depending on the magnitude and the direction of the stress and the crack aspect ratio. The cracks in the medium after loading stress could be aligned in a specific orientation, and elastic wave velocity field would become anisotropic due to the alignment of specific crack orientations. Elastic wave velocity is in general faster along the direction corresponding with the crack orientation while slower along the perpendicular direction. In the numerical simulation, the effect of anisotropy in elastic wave velocity field due to the selective closure and opening of the cracks is calculated using a 2-D finite difference method assuming elastic wave velocity to be a function of the magnitude of loaded stress. The coda- Q calculated from seismic waves simulated for a model varies when the averaged normal stress changes. Our simulation indicated that the sensitivity of coda- Q –1 , that is the reciprocal of the coda- Q , would be 1.0 10 –2 (1.0 MPa –1 ) against the magnitude of the confining pressure and 1.0 10 –3 (1.0 deg –1 ) against the direction of principal stress. We would like to conclude that coda- Q , a stochastic parameter reflecting heterogeneities of subsurface medium, could become a quantitative state indicator of the stress field of the medium where seismic waves propagate through. Spatiotemporal variation of coda- Q reflects change in the stress field in the crust.

Description: The Chemistry CATT-BRAMS model (CCATT-BRAMS 4.5): a regional atmospheric model system for integrated air quality and weather forecasting and research Geoscientific Model Development, 6, 1389-1405, 2013 Author(s): K. M. Longo, S. R. Freitas, M. Pirre, V. Marécal, L. F. Rodrigues, J. Panetta, M. F. Alonso, N. E. Rosário, D. S. Moreira, M. S. Gácita, J. Arteta, R. Fonseca, R. Stockler, D. M. Katsurayama, A. Fazenda, and M. Bela Coupled Chemistry Aerosol-Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CCATT-BRAMS, version 4.5) is an on-line regional chemical transport model designed for local and regional studies of atmospheric chemistry from the surface to the lower stratosphere suitable both for operational and research purposes. It includes gaseous/aqueous chemistry, photochemistry, scavenging and dry deposition. The CCATT-BRAMS model takes advantage of BRAMS-specific development for the tropics/subtropics as well as the recent availability of preprocessing tools for chemical mechanisms and fast codes for photolysis rates. BRAMS includes state-of-the-art physical parameterizations and dynamic formulations to simulate atmospheric circulations down to the meter. This on-line coupling of meteorology and chemistry allows the system to be used for simultaneous weather and chemical composition forecasts as well as potential feedback between the two. The entire system is made of three preprocessing software tools for user-defined chemical mechanisms, aerosol and trace gas emissions fields and the interpolation of initial and boundary conditions for meteorology and chemistry. In this paper, the model description is provided along with the evaluations performed by using observational data obtained from ground-based stations, instruments aboard aircrafts and retrieval from space remote sensing. The evaluation accounts for model applications at different scales from megacities and the Amazon Basin up to the intercontinental region of the Southern Hemisphere.

Description: Influence of microphysical schemes on atmospheric water in the Weather Research and Forecasting model Geoscientific Model Development Discussions, 6, 4563-4601, 2013 Author(s): F. Cossu and K. Hocke This study examines how different microphysical parameterization schemes influence orographically-induced precipitation and the distributions of hydrometeors and water vapour for mid-latitude summer conditions in the Weather Research and Forecasting (WRF) model. A high-resolution two-dimensional idealized simulation is used to assess the differences between the schemes in which a moist air flow is interacting with a bell-shaped 2 km high mountain. Periodic lateral boundary conditions are chosen to recirculate atmospheric water in the domain. It is found that the 13 selected microphysical schemes conserve the water in the model domain. The gain or loss of water is less than 0.81% over a simulation time interval of 61 days. The differences of the microphysical schemes in terms of the distributions of water vapour, hydrometeors and accumulated precipitation are presented and discussed. The Kessler scheme, the only scheme without ice-phase processes, shows final values of cloud liquid water 14 times greater than the other schemes. The differences among the other schemes are not as extreme, but still they differ up to 79% in water vapour, up to 10 times in hydrometeors and up to 64% in accumulated precipitation at the end of the simulation. The microphysical schemes also differ in the surface evaporation rate. The WRF single-moment 3-class scheme has the highest surface evaporation rate compensated by the highest precipitation rate. The different distributions of hydrometeors and water vapour of the microphysical schemes induce differences up to 49 W m −2 in the downwelling shortwave radiation and up to 33 W m −2 in the downwelling longwave radiation.

Description: How do body-wave traveltimes constrain the Earth's radial (1-D) seismic structure? Existing 1-D seismological models underpin 3-D seismic tomography and earthquake location algorithms. It is therefore crucial to assess the quality of such 1-D models, yet quantifying uncertainties in seismological models is challenging and thus often ignored. Ideally, quality assessment should be an integral part of the inverse method. Our aim in this study is twofold: (i) we show how to solve a general Bayesian non-linear inverse problem and quantify model uncertainties, and (ii) we investigate the constraint on spherically symmetric P -wave velocity ( V P ) structure provided by body-wave traveltimes from the EHB bulletin (phases Pn , P , PP and PKP ). Our approach is based on artificial neural networks, which are very common in pattern recognition problems and can be used to approximate an arbitrary function. We use a Mixture Density Network to obtain 1-D marginal posterior probability density functions (pdfs), which provide a quantitative description of our knowledge on the individual Earth parameters. No linearization or model damping is required, which allows us to infer a model which is constrained purely by the data. We present 1-D marginal posterior pdfs for the 22 V P parameters and seven discontinuity depths in our model. P -wave velocities in the inner core, outer core and lower mantle are resolved well, with standard deviations of ~0.2 to 1 per cent with respect to the mean of the posterior pdfs. The maximum likelihoods of V P are in general similar to the corresponding ak135 values, which lie within one or two standard deviations from the posterior means, thus providing an independent validation of ak135 in this part of the radial model. Conversely, the data contain little or no information on P -wave velocity in the D '' layer, the upper mantle and the homogeneous crustal layers. Further, the data do not constrain the depth of the discontinuities in our model. Using additional phases available in the ISC bulletin, such as PcP , PKKP and the converted phases SP and ScP , may enhance the resolvability of these parameters. Finally, we show how the method can be extended to obtain a posterior pdf for a multidimensional model space. This enables us to investigate correlations between model parameters.

Description: We have developed a network optimization method for regional-scale microseismic monitoring networks and applied it to optimize the densification of the existing seismic network in northeastern Switzerland. The new network will build the backbone of a 10-yr study on the neotectonic activity of this area that will help to better constrain the seismic hazard imposed on nuclear power plants and waste repository sites. This task defined the requirements regarding location precision (0.5 km in epicentre and 2 km in source depth) and detection capability [magnitude of completeness M c  = 1.0 ( M L )]. The goal of the optimization was to find the geometry and size of the network that met these requirements. Existing stations in Switzerland, Germany and Austria were considered in the optimization procedure. We based the optimization on the simulated annealing approach proposed by Hardt & Scherbaum, which aims to minimize the volume of the error ellipsoid of the linearized earthquake location problem ( D -criterion). We have extended their algorithm to: calculate traveltimes of seismic body waves using a finite difference ray tracer and the 3-D velocity model of Switzerland, calculate seismic body-wave amplitudes at arbitrary stations assuming the Brune source model and using scaling and attenuation relations recently derived for Switzerland, and estimate the noise level at arbitrary locations within Switzerland using a first-order ambient seismic noise model based on 14 land-use classes defined by the EU-project CORINE and open GIS data. We calculated optimized geometries for networks with 10–35 added stations and tested the stability of the optimization result by repeated runs with changing initial conditions. Further, we estimated the attainable magnitude of completeness ( M c ) for the different sized optimal networks using the Bayesian Magnitude of Completeness (BMC) method introduced by Mignan et al. The algorithm developed in this study is also applicable to smaller optimization problems, for example, small local monitoring networks. Possible applications are volcano monitoring, the surveillance of induced seismicity associated with geotechnical operations and many more. Our algorithm is especially useful to optimize networks in populated areas with heterogeneous noise conditions and if complex velocity structures or existing stations have to be considered.

Description: Fluid injection in and withdrawal from wells are basic procedures in mining activities and deep resources exploitation, such as oil and gas extraction, permeability enhancement for geothermal exploitation and waste fluid disposal. All of these activities have the potential to induce seismicity, as exemplified by the 2006 Basel earthquake ( M L 3.4). Despite several decades of experience, the mechanisms of induced seismicity are not known in detail, which prevents effective risk assessment and/or mitigation. In this study, we provide an interpretation of induced seismicity based on computation of Coulomb stress changes that result from fluid injection/withdrawal at depth, mainly focused on the interpretation of induced seismicity due to stimulation of a geothermal reservoir. Seismicity is, theoretically, more likely where Coulomb stress changes are larger. For modeling purposes, we simulate the thermodynamic evolution of a system after fluid injection/withdrawal. The associated changes in pressure and temperature are subsequently considered as sources of incremental stress changes, which are then converted to Coulomb stress changes on favourably oriented faults, taking into account the background regional stress. Numerical results are applied to the water injection that was performed to create the fractured reservoir at the enhanced-geothermal-system site, Soultz-sous-Forets (France). Our approach describes well the observed seismicity, and provides an explanation for the different behaviors of a system when fluids are injected or withdrawn.

Description: We report on a broad-band high-resolution attenuation model for the North China Craton and surrounding regions based on regional Lg -wave data. Vertical broad-band waveforms recorded at 39 stations from 176 crustal earthquakes are collected to extract the Lg -wave amplitude spectra between 0.05 and 10.0 Hz. We use the dual-station method to generate a preliminary Q Lg model and use it as the initial model. Then, we combine the dual- and single-station data together to jointly invert the Q Lg distribution and Lg source excitation functions. These inversions are conducted independently at individual frequencies without using any a priori assumption about the frequency dependences in Q Lg and source terms. The maximum spatial resolution is approximately 1° x 1° in well-covered areas for frequencies between 0.05 and 2.0 Hz. The Q Lg image is then used to determine the relationship between the attenuation and different geological structures. Results show an average Q 0 (1 Hz Q Lg ) of 374 for the entire North China Craton with an increasing trend from east to west. Average Q 0 values are 337, 361 and 421 for the east, central and west blocks, respectively. For the surrounding regions, the Eastern Tibetan plateau has a very low Q 0 of 188, while the Northeast China Plate and the Tianshan–Xingmeng fold belts are characterized by high Q 0 values of 506 and 424, respectively. We also investigate regional variations of the Lg attenuation in low-frequency band between 0.2 and 1.0 Hz.

Description: We present a systematic study on the influence of pressure (0.1–600 MPa), temperature (750–1200 °C), carbon dioxide fugacity (log f CO 2  = –4.41 to 3.60) and time (2–12 hr) on the chemical and physical properties of carbonate rock. Our experiments aim to reproduce the conditions at the periphery of magma chamber where carbonate host rock is influenced by, but not readily assimilated by, magma. This permits the investigation of the natural conditions at which circulating fluids/gases promote infiltration reactions typical of metasomatic skarns that can involve large volumes of subvolcanic carbonate basements. Results show that, providing that carbon dioxide is retained in the pore space, decarbonation does not proceed at any magmatic pressure and temperature. However, when the carbon dioxide is free to escape, decarbonation can occur rapidly and is not hindered by a low initial porosity or permeability. Together with carbon dioxide and lime, portlandite, a mineral commonly found in voluminous metasomatic skarns, readily forms during carbonate decomposition. Post-experimental analyses highlight that thermal microcracking, a result of the highly anisotropic thermal expansion of calcite, exerts a greater influence on rock physical properties (porosity, ultrasonic wave velocities and elastic moduli) than decarbonation. Our data suggest that this will be especially true at the margins of dykes or magma bodies, where temperatures can reach up to 1200 °C. However, rock compressive strength is significantly reduced by both thermal cracking and decarbonation, explained by the relative weakness of lime + portlandite compared to calcite, and an increase in grain size with increasing temperature. Metasomatic skarns, whose petrogenetic reactions may involve a few tens of cubic kilometres, could therefore represent an important source of volcanic instability.

Description: The scattering of plane SH waves incident on a circular sectorial canyon is considered. An accurate region-matching technique is applied to derive a rigorous series solution. Appropriate wavefunctions are employed to describe antiplane motions. Judicious basis functions, involving Gegenbauer polynomials, are well utilized to correctly capture the singular behaviour in stress fields near the canyon bottom. The enforcement of matching conditions on the auxiliary boundary leads to the determination of unknown coefficients. Plotted results demonstrate the influence of pertinent parameters on surface and subsurface motions. Both steady-state and transient results are included. The solution technique proposed achieves a considerable reduction in the computational effort, facilitating benchmark computations. The derived series solution enriches the limited list of series solutions presently known for canyon problems related to SH -wave scattering.

Description: We present 3-D models of the P- and S -wave velocity distributions in the crust and uppermost mantle beneath Sicily, Calabria (Southern Italy), and surrounding submerged areas, obtained by tomographic inversion of traveltimes of regional body waves phases. Our method combines double-difference tomographic inversion with a post-processing procedure [Weighted Average Model method (WAM)]. This procedure was applied to a set of models consistent with the experimental data. We tested the ability of the WAM procedure to mitigate the uncertainty associated with the arbitrary nature of the many input parameters required for each inversion. The local reliability and resolution of the obtained models have been assessed through: synthetic tests, experimental tests carried out with independent data sets and unconventional tests based on the analysis of the internal consistency of the P - and S -velocity models. The tomographic images provide a detailed sketch of P- and S- wave velocity anomalies. These clearly show the shape of the Sicilian-Maghrebian belt beneath Sicily and Calabrian Arc at different depths. Low V P and Vs bodies are imaged beneath Stromboli and Marsili volcanoes in the southern Tyrrhenian, whereas high and low seismic velocities alternate beneath the Etna giving inferences on the possible depth of the mantle melting feeding the volcano. In the upper crust, the main sedimentary basins and tectonic features are also well imaged. Finally, tomographic cross sections show the trend of the Moho in the study area, where its depth ranges between 35 and 40 km beneath the Sicilian belt and between 15 and 22 km in the southern Tyrrhenian basin and Ionian Sea.

Description: We used two tracks of ALOS PALSAR images to investigate the focal mechanism and slip distribution of the 2011 March 24, M W 6.8 Burma strike-slip earthquake. Three different SAR techniques, namely conventional interferometry, SAR pixel offsets (SPO) and multiple-aperture InSAR (MAI), were employed to obtain the coseismic surface deformation fields along the ~30 km length of the fault rupture. Along-track measurements from SPO and MAI techniques show a high correlation, and were subsequently used to precisely determine the location and extent of the surface fault trace. The best-fitting fault model geometry derived from an iterative inversion technique suggests that the rupture occurred on a near-vertical sinistral strike-slip fault west of the Nam Ma fault with a strike of 70°. A maximum slip of 4.2 m occurs at a depth of 2.5 km, with significant slip constrained only to the upper 10 km of the crust.

Description: Knowledge of the mantle reflectivity structure is highly dependent on our ability to efficiently extract, and properly interpret, small seismic arrivals. Among the various data types and techniques, long-period SS/PP precursors and high-frequency receiver functions are routinely utilized to increase the confidence of the recovered mantle stratifications at distinct spatial scales. However, low resolution and a complex Fresnel zone are glaring weaknesses of SS precursors, while over-reliance on receiver distribution is a formidable challenge for the analysis of converted waves from oceanic regions. A promising high frequency alternative to receiver functions is P ' P ' precursors, which are capable of resolving mantle structures at vertical and lateral resolution of ~5 and ~200 km, respectively, owing to their spectral content, shallow angle of incidence and near-symmetric Fresnel zones. This study presents a novel processing method for both SS (or PP) and P ' P ' precursors based on deconvolution, stacking, Radon transform and depth migration. A suite of synthetic tests is performed to quantify the fidelity and stability of this method under different data conditions. Our multiresolution survey of the mantle at targeted areas near Nazca-South America subduction zone reveal both olivine and garnet related transitions at depths below 400 km. We attribute a depressed 660 to thermal variations, whereas compositional variations atop the upper-mantle transition zone are needed to explain the diminished or highly complex reflected/scattered signals from the 410 km discontinuity. We also observe prominent P ' P ' reflections within the transition zone, and the anomalous amplitudes near the plate boundary zone indicate a sharp (~10 km thick) transition that likely resonates with the frequency content of P ' P ' precursors. The migration of SS precursors in this study shows no evidence of split 660 reflections, but potential majorite–ilmenite (590–640 km) and ilmenite–perovskite transitions (740–750 km) are identified based on similarly processed high-frequency P ' P ' precursors. Additional findings of severely scattered energy in the lithosphere and distinct lower mantle reflections at ~800 km could be potentially important but require further verifications. Overall, our improved imaging methods and the strong sensitivity of P ' P ' precursors to the existence, depth, sharpness and strength of reflective structures offer significant future promise for the understanding of mantle mineralogy and dynamics.

Description: Time-dependent probabilistic seismic hazard assessment requires a stochastic description of earthquake occurrences. While short-term seismicity models are well-constrained by observations, the recurrences of characteristic on-fault earthquakes are only derived from theoretical considerations, uncertain palaeo-events or proxy data. Despite the involved uncertainties and complexity, simple statistical models for a quasi-period recurrence of on-fault events are implemented in seismic hazard assessments. To test the applicability of statistical models, such as the Brownian relaxation oscillator or the stress release model, we perform a systematic comparison with deterministic simulations based on rate- and state-dependent friction, high-resolution representations of fault systems and quasi-dynamic rupture propagation. For the specific fault network of the Lower Rhine Embayment, Germany, we run both stochastic and deterministic model simulations based on the same fault geometries and stress interactions. Our results indicate that the stochastic simulators are able to reproduce the first-order characteristics of the major earthquakes on isolated faults as well as for coupled faults with moderate stress interactions. However, we find that all tested statistical models fail to reproduce the characteristics of strongly coupled faults, because multisegment rupturing resulting from a spatiotemporally correlated stress field is underestimated in the stochastic simulators. Our results suggest that stochastic models have to be extended by multirupture probability distributions to provide more reliable results.

Description: Stress waves, known as acoustic emissions (AEs), are released by localized inelastic deformation events during the progressive failure of brittle rocks. Although several numerical models have been developed to simulate the deformation and damage processes of rocks, such as non-linear stress–strain behaviour and localization of failure, only a limited number have been capable of providing quantitative information regarding the associated seismicity. Moreover, the majority of these studies have adopted a pseudo-static approach based on elastic strain energy dissipation that completely disregards elastodynamic effects. This paper describes a new AE modelling technique based on the combined finite-discrete element method (FEM/DEM), a numerical tool that simulates material failure by explicitly considering fracture nucleation and propagation in the modelling domain. Given the explicit time integration scheme of the solver, stress wave propagation and the effect of radiated seismic energy can be directly captured. Quasi-dynamic seismic information is extracted from a FEM/DEM model with a newly developed algorithm based on the monitoring of internal variables (e.g. relative displacements and kinetic energy) in proximity to propagating cracks. The AE of a wing crack propagation model based on this algorithm are cross-analysed by traveltime inversion and energy estimation from seismic recordings. Results indicate a good correlation of AE initiation times and locations, and scaling of energies, independently calculated with the two methods. Finally, the modelling technique is validated by simulating a laboratory compression test on a granite sample. The micromechanical parameters of the heterogeneous model are first calibrated to reproduce the macroscopic stress–strain response measured during standard laboratory tests. Subsequently, AE frequency–magnitude statistics, spatial clustering of source locations and the evolution of AE rate are investigated. The distribution of event magnitude tends to decay as power law while the spatial distribution of sources exhibits a fractal character, in agreement with experimental observations. Moreover, the model can capture the decrease of seismic b value associated with the macrorupture of the rock sample and the transition of AE spatial distribution from diffuse, in the pre-peak stage, to strongly localized at the peak and post-peak stages, as reported in a number of published laboratory studies. In future studies, the validated FEM/DEM-AE modelling technique will be used to obtain further insights into the micromechanics of rock failure with potential applications ranging from laboratory-scale microcracking to engineering-scale processes (e.g. excavations within mines, tunnels and caverns, petroleum and geothermal reservoirs) to tectonic earthquakes triggering.

Description: We used strong-motion records from the 2012 May 20 and 29 Emilia-Romagna earthquakes ( M w 6.1 and 5.9, respectively) and four aftershocks with magnitudes ranging between 4.9 and 5.5 to analyse the S -wave spectral amplitude decay with distance and estimate acceleration source functions and site effects. The data set consists of six earthquakes, 44 stations and 248 records with hypocentral distances in the range 10 〈 r  〈 100 km. We rotated the accelerograms to calculate transverse and radial components of the acceleration spectrum. We found non-parametric attenuation functions that describe the spectral amplitude decay of SH and SV waves with distance at 60 different frequencies between 0.1 and 40 Hz. These attenuation functions provide an estimate of the quality factor Q at each frequency analysed. Assuming that geometrical spreading is 1/ r for r  ≤ r x and 1/( r x r ) 0.5 for r  〉 r x with r x  = 60 km and normalizing at 15 km (the recording distance where the attenuation functions start to decay), we find that the average Q for SH waves can be approximated by Q SH  = 82 ± 1 f  1.2±0.02 and by Q SV  = 79 ± 1 f  1.24±0.03 for SV waves in the frequency range 0.10 ≤ f  ≤ 10.7 Hz. At higher frequencies, 11.8 ≤ f  ≤ 40 Hz, the frequency dependence of Q weakens and is approximated by Q SH  = 301 ± 1 f   0.36±0.04 and Q SV  = 384 ± 1 f  0.28±0.04 . These results indicate that the S -wave attenuation is radially isotropic at local distances in the epicentral area. Nevertheless, we used these attenuation parameters separately to correct the radial (with Q SV ) and transverse (with Q SH ) components of the acceleration spectra and to separate source and site effects using a non-parametric spectral inversion scheme. We found that the source function of the main event and the bigger aftershocks show enhanced low frequency radiation between 0.4 and 3.0 Hz. We converted the source functions into far-field source acceleration spectra and interpreted the resulting source spectra in terms of Brune's model. The stress drops obtained range between approximately 0.9 and 2.9 MPa. Although all the recording stations used are located in the Po Plain, the site functions obtained from the spectral inversion show important amplification variability between the sites. We compared these site functions with the average horizontal to vertical spectral ratios calculated for each station, and we found consistent results for most stations.

Description: The sensitivity of global climate to the episodicity of fire aerosol emissions Atmospheric Chemistry and Physics Discussions, 13, 23691-23717, 2013 Author(s): S. K. Clark, D. S. Ward, and N. M. Mahowald One of the major ways in which forest and grass fires have an impact on global climate is through the release of aerosols. Most studies focusing on calculating the radiative forcing and other climate impacts of fire aerosols use monthly mean emissions derived from the Global Fire Emissions Database that captures only the seasonal cycle of fire aerosol emissions. Here we present the results of a sensitivity study that investigates the climate response to the episodicity of the fires, based on the standard approach which releases emissions every day, and contrasts that to the response when fires are represented as intense pulses of emissions that occur only over 1–2 days on a monthly, yearly, or five-yearly basis. Overall we find that in the modified cases with increased levels of episodicity, the all sky direct effect radiative forcing increases, the clear sky direct effect radiative forcing remains relatively constant, and the magnitude of the indirect effect radiative forcing decreases by about 1 W m −2 (from −1.6 to −0.6 W m −2 ). In the long term, we find that an increase in aerosol emission episodicity leads to an asymmetric change in indirect radiative forcing in the Northern Hemisphere compared to the Southern Hemisphere contributes to a slight shift in the annual average position of the intertropical convergence zone (ITCZ). This shift is found to have a mixed effect on the overall performance of the model at predicting precipitation rates in the tropics. Given these results we conclude that future studies that look to assess the present day global climate impacts of fire aerosols should consider the need to accurately represent fire episodicity.

Description: Not all calcite ballast is created equal: differing effects of foraminiferan and coccolith calcite on the formation and sinking of aggregates Biogeosciences Discussions, 10, 14861-14885, 2013 Author(s): K. Schmidt, C. L. De La Rocha, M. Gallinari, and G. Cortese Correlation between particulate organic carbon (POC) and calcium carbonate sinking through the deep ocean has led to the idea that ballast provided by calcium carbonate is important for the export of POC from the surface ocean. While this idea is certainly to some extent true, it is worth considering in more nuance, for example, examining the different effects on the aggregation and sinking of POC of small, non-sinking calcite particles like coccoliths and large, rapidly sinking calcite like planktonic foraminiferan tests. We have done that here in a simple experiment carried out in roller tanks that allow particles to sink continuously without being impeded by container walls. Coccoliths were efficiently incorporated into aggregates that formed during the experiment, increasing their sinking speed compared to similarly sized aggregates lacking added calcite ballast. The foraminiferan tests, which sank as fast as 700 m d −1 , became associated with only very minor amounts of POC. In addition, when they collided with other, larger, foraminferan-less aggregates, they fragmented them into two smaller, more slowly sinking aggregates. While these effects were certainly exaggerated within the confines of the roller tanks, they clearly demonstrate that calcium carbonate ballast is not just calcium carbonate ballast- different forms of calcium carbonate ballast have notably different effects on POC aggregation, sinking, and export.

Description: Laboratory studies of immersion and deposition mode ice nucleation of ozone aged mineral dust particles Atmospheric Chemistry and Physics, 13, 9097-9118, 2013 Author(s): Z. A. Kanji, A. Welti, C. Chou, O. Stetzer, and U. Lohmann Ice nucleation in the atmosphere is central to the understanding the microphysical properties of mixed-phase and cirrus clouds. Ambient conditions such as temperature ( T ) and relative humidity (RH), as well as aerosol properties such as chemical composition and mixing state play an important role in predicting ice formation in the troposphere. Previous field studies have reported the absence of sulfate and organic compounds on mineral dust ice crystal residuals sampled at mountain top stations or aircraft based measurements despite the long-range transport mineral dust is subjected to. We present laboratory studies of ice nucleation for immersion and deposition mode on ozone aged mineral dust particles for 233 〈 T 〈 263 K. Heterogeneous ice nucleation of untreated kaolinite (Ka) and Arizona Test Dust (ATD) particles is compared to corresponding aged particles that are subjected to ozone concentrations of 0.4–4.3 ppmv in a stainless steel aerosol tank. The portable ice nucleation counter (PINC) and immersion chamber combined with the Zurich ice nucleation chamber (IMCA-ZINC) are used to conduct deposition and immersion mode measurements, respectively. Ice active fractions as well as ice active surface site densities ( n s ) are reported and observed to increase as a function of decreasing temperature. We present first results that demonstrate enhancement of the ice nucleation ability of aged mineral dust particles in both the deposition and immersion mode due to ageing. We also present the first results to show a suppression of heterogeneous ice nucleation activity without the condensation of a coating of (in)organic material. In immersion mode, low ozone exposed Ka particles showed enhanced ice activity requiring a median freezing temperature of 1.5 K warmer than that of untreated Ka, whereas high ozone exposed ATD particles showed suppressed ice nucleation requiring a median freezing temperature of 3 K colder than that of untreated ATD. In deposition mode, low exposure Ka had ice active fractions of an order of magnitude higher than untreated Ka, whereas high ozone exposed ATD had ice active fractions up to a factor of 4 lower than untreated ATD. From our results, we derive and present parameterizations in terms of n s ( T ) that can be used in models to predict ice nuclei concentrations based on available aerosol surface area.

Description: Antecedent flow conditions and nitrate concentrations in the Mississippi River Basin Hydrology and Earth System Sciences Discussions, 10, 11451-11484, 2013 Author(s): J. C. Murphy, R. M. Hirsch, and L. A. Sprague The influence of antecedent flow conditions on nitrate concentrations was explored at eight sites in the Mississippi River Basin, USA. Antecedent moisture conditions have been shown to influence nutrient export from small, relatively homogenous basins, but this influence has not been observed at a regional or continental scale. Antecedent flow conditions were quantified as the ratio between the mean daily flow of the previous year and the mean daily flow from the period of record ( Q ratio), and the Q ratio was statistically related to nitrate anomalies (the unexplained variability in nitrate concentration after filtering out season, long-term trend, and contemporaneous flow effects) at each site. Nitrate anomaly and Q ratio were negatively related at three of the four major tributary sites and upstream in the Mississippi River, indicating that when the previous year was drier than average, at these sites, nitrate concentrations were higher than expected. The strength of these relationships increased when data were subdivided by contemporaneous flow conditions. Five of the eight sites had significant negative relationships ( p ≤ 0.05) at high or moderately high contemporaneous flows, suggesting nitrate that accumulates in these basins during a drought is flushed during subsequent storm events. At half of the sites, when flow during the previous year was 50% drier than average, nitrate concentration can be from 9 and 27% higher than nitrate concentrations that follow a year with average daily flow. Conversely, nitrate concentration can be from 8 and 21% lower than expected when the previous year was 50% wetter than average. These relationships between nitrate concentration and Q ratio serve as the basis for future studies that can better define specific hydrologic processes occurring during and after a drought, which influence nitrate concentration, such as the duration or magnitude of low flows, and the timing of low and high flows.

Description: Tidally induced velocity variations of the Beardmore Glacier, Antarctica, and their representation in satellite measurements of ice velocity The Cryosphere, 7, 1375-1384, 2013 Author(s): O. J. Marsh, W. Rack, D. Floricioiu, N. R. Golledge, and W. Lawson Ocean tides close to the grounding line of outlet glaciers around Antarctica have been shown to directly influence ice velocity, both linearly and non-linearly. These fluctuations can be significant and have the potential to affect satellite measurements of ice discharge, which assume displacement between satellite passes to be consistent and representative of annual means. Satellite observations of horizontal velocity variation in the grounding zone are also contaminated by vertical tidal effects, the importance of which is highlighted here in speckle tracking measurements. Eight TerraSAR-X scenes from the grounding zone of the Beardmore Glacier are analysed in conjunction with GPS measurements to determine short-term and decadal trends in ice velocity. Diurnal tides produce horizontal velocity fluctuations of 〉50% on the ice shelf, recorded in the GPS data 4 km downstream of the grounding line. This variability decreases rapidly to 〈5% only 15 km upstream of the grounding line. Daily fluctuations are smoothed to 〈1% in the 11-day repeat pass TerraSAR-X imagery, but fortnightly variations over this period are still visible and show that satellite-velocity measurements can be affected by tides over longer periods. The measured tidal displacement observed in radar look direction over floating ice also allows the grounding line to be identified, using differential speckle tracking where phase information cannot be easily unwrapped.

Description: A new data set of soil mineralogy for dust-cycle modeling Atmospheric Chemistry and Physics Discussions, 13, 23943-23993, 2013 Author(s): E. Journet, Y. Balkanski, and S. P. Harrison The mineralogy of airborne dust affects the impact of dust particles on direct and indirect radiative forcing, on atmospheric chemistry and on biogeochemical cycling. It is determined partly by the mineralogy of the dust-source regions and partly by size-dependent fractionation during erosion and transport. Here we present a data set that characterizes the clay and silt sized fractions of global soil units in terms of the abundance of 12 minerals that are important for dust-climate interactions: quartz, feldspars, illite, smectite, kaolinite, chlorite, vermiculite, mica, calcite, gypsum, hematite and goethite. The basic mineralogical information is derived from the literature, and is then expanded following explicit rules, in order to characterize as many soil units as possible. We present three alternative realisations of the mineralogical maps that account for the uncertainties in the mineralogical data. We examine the implications of the new database for calculations of the single scattering albedo of airborne dust and thus for dust radiative forcing.

Description: Calibration of the passive cavity aerosol spectrometer probe for airborne determination of the size distribution Atmospheric Measurement Techniques, 6, 2349-2358, 2013 Author(s): Y. Cai, J. R. Snider, and P. Wechsler This work describes calibration methods for the particle sizing and particle concentration systems of the passive cavity aerosol spectrometer probe (PCASP). Laboratory calibrations conducted over six years, in support of the deployment of a PCASP on a cloud physics research aircraft, are analyzed. Instead of using the many calibration sizes recommended by the PCASP manufacturer, a relationship between particle diameter and scattered light intensity is established using three sizes of mobility-selected polystyrene latex particles, one for each amplifier gain stage. In addition, studies of two factors influencing the PCASP's determination of the particle size distribution – amplifier baseline and particle shape – are conducted. It is shown that the PCASP-derived size distribution is sensitive to adjustments of the sizing system's baseline voltage, and that for aggregates of spheres, a PCASP-derived particle size and a sphere-equivalent particle size agree within uncertainty dictated by the PCASP's sizing resolution. Robust determinations of aerosol concentration, and size distribution, also require calibration of the PCASP's aerosol flowrate sensor. Sensor calibrations, calibration drift, and the sensor's non-linear response are documented.

Description: Contribution of snow and glacier melt to discharge for highly glacierised catchments in Norway Hydrology and Earth System Sciences Discussions, 10, 11485-11517, 2013 Author(s): M. Engelhardt, T. V. Schuler, and L. M. Andreassen Glacierised catchments significantly alter the streamflow regime due to snow and glacier meltwater contribution to discharge. In this study, we modelled the mass balance and discharge rates for three highly glacierised catchments (〉50% glacier cover) in western Norway over the period 1961–2012. The spatial pattern of the catchments follows a gradient in climate continentality from west to east. The model uses gridded temperature and precipitation values from seNorge ( http://senorge.no ) as input which are available at a daily resolution. It accounts for accumulation of snow, transformation of snow to firn and ice, evaporation and melt. The model was calibrated for each catchment based on measurements of seasonal glacier mass-balances and daily discharge rates. For validation, daily melt rates were compared with measurements from sonic rangers located in the ablation zones of two of the glaciers and an uncertainty analysis was performed for the third catchment. The discharge contributions from snowmelt, glacier melt and rain were analysed with respect to spatial variations and temporal evolution. The model simulations reveal an increase of the relative contribution from glacier melt for the three catchments from less than 10% in the early 1990s to 15–30% in the late 2000s. The decline in precipitation by 10–20% in the same period was therefore overcompensated resulting in an increase of the annual discharge by 5–20%. Annual discharge sums and annual glacier melt are strongest correlated with annual and winter precipitation at the most maritime glacier and, with increased climate continentality, variations in both glacier melt contribution and annual discharge are becoming stronger correlated with variations in summer temperatures.

Description: The tension between the meaning of causality in science and law or public policy is well-known; however, defendants in product liability cases or industries that might be affected by a government regulation may try to convince the factfinder to require evidence of a causal relationship that meets the standards of science. From the perspective of public health, however, people may be exposed unnecessarily to a health risk during the time period between the establishment of reasonably strong evidence of a causal relationship and the overwhelming evidence required for scientific causality. The Bayesian paradigm enables one to update information from epidemiologic studies as they accumulate, providing estimates of the probability that the relative risk of a particular harm from exposure exceeds a threshold value, e.g. 2.0 or 4.0 that is sufficient to meet the preponderance of the evidence standard or to support a health initiative. In order to diminish the role of the initial prior distribution, which may be quite subjective, the first case-control study or an analysis of adverse event and case reports is used to determine two prior distributions. One is the most favourable to the defendant, or industry that might be regulated, which is consistent with the previous data. The other is centred on or near the estimated relative risk from the first study. The method is applied to the studies that linked aspirin use to Reye syndrome and demonstrates that the evidence of a causal association was sufficiently strong in 1982, when the Food and Drug Administration first proposed that the public be warned of the risk, to support the regulation. Thus, lives would have been saved had the warning been given at the end of 1982 rather than in early 1985.

Description: In law, inferences of causation are sometimes made through a structured process in which multiple participants play various roles, and make decisions concerning various logical components of the overall inference (such as legal rules, policy objectives, presumptions, evidence, burdens of proof and findings of fact). This article illustrates such a process using empirical research into compensation decisions in the USA for injuries allegedly caused by vaccinations. Empirical research into actual legal processes is essential, in order to discover how various players approach their sub-tasks of decision-making. It also provides insights for areas outside of law, such as non-monotonic logic, cognitive science, sociology and artificial intelligence.

Description: Situations of causal factual uncertainty are relatively common in law. The problems and difficulties regarding ‘factual causation’ in law point to the need of ‘evidence’ and ‘proof’ models that are adequate and capable to accommodate the tests and methodologies used to explain and demonstrate it in a legal context. Given the configuration of the situations of causal factual uncertainty and the available ‘evidence’ and ‘proof’ models, I argue that it is justified to use an ‘argumentative-narrative’ model for ‘proving causation’ in law. However, considering that each model of ‘evidence’ and ‘proof’ reveals a different kind of ‘rationality’ that can still be viewed in different ways, I also argue that we must try to match the perspective we have on the ‘rationality’ behind the chosen model of ‘evidence’ and ‘proof’ with the ‘rationality’ underlying ‘causation’ in law.

Description: At least in some cases, the values confronted in legal decision-making appear to be incommensurable. Some legal theorists resist incommensurability because they fear that this presents an overwhelming obstacle to rational decision-making. By offering a close analysis of proportionality and, more particularly, measures of proportional value satisfaction, I show that this fear is unfounded. Comparative measures of proportional value satisfaction do not require the values to be commensurable. However, assuming incommensurability presents us with the problem of public significance in the proportional satisfaction of values. When two values are commensurable, this public significance is provided by the mediating effects of the overarching third value that provides the common measure of the values. However, when this common measure is removed, then the public significance of value satisfaction must be otherwise achieved. This is why I propose an equal proportional value satisfaction as the most appropriate proportionality maximand. Under equal proportional value satisfaction, the proportional satisfaction of any one value has significance for each and every other value. This kind of public significance is interpersonal rather than impersonal (or second-personal rather than third-personal). The article then shows that the legal process that is most appropriate to equal proportionality is a process that implements defeasible legal rules.

Description: In order to allocate the risk between parties in legal adjudication, we use evidentiary techniques with the main device among them being the standard of proof (SoP). The traditional view holds the grade of probability to be the parameter that shifts when moving to different standards. However, as soon as we dig slightly deeper, an incoherent picture is being revealed. In this article, I challenge the accepted view and try to show that it faces insurmountable problems concerning the rationality, the grammatical consistency and the impact of the SoP for the acceptability of verdicts. At the end of the article, I shortly discuss the theory of epistemological contextualism and propose a framework that allows rational distinctions to be drawn between different standards of proof. In the second part of this project (forthcoming), I will defend a contextualist view according to which shifting parameter is not the grade of (aleatory) probability, but instead the Set of Epistemic Defeaters in play.

Description: Beyond multifractional Brownian motion: new stochastic models for geophysical modelling Nonlinear Processes in Geophysics, 20, 643-655, 2013 Author(s): J. Lévy Véhel Multifractional Brownian motion (mBm) has proved to be a useful tool in various areas of geophysical modelling. Although a versatile model, mBm is of course not always an adequate one. We present in this work several other stochastic processes which could potentially be useful in geophysics. The first alternative type is that of self-regulating processes : these are models where the local regularity is a function of the amplitude, in contrast to mBm where it is tuned exogenously. We demonstrate the relevance of such models for digital elevation maps and for temperature records. We also briefly describe two other types of alternative processes, which are the counterparts of mBm and of self-regulating processes when the intensity of local jumps is considered in lieu of local regularity: multistable processes allow one to prescribe the local intensity of jumps in space/time, while this intensity is governed by the amplitude for self-stabilizing processes .

Description: Decadal trends in the Antarctic sea ice extent ultimately controlled by ice-ocean feedback The Cryosphere Discussions, 7, 4585-4632, 2013 Author(s): H. Goosse and V. Zunz The large natural variability of the Antarctic sea ice is a key characteristic of the system that might be responsible for the small positive trend in sea ice extent observed since 1979. In order to gain insight in the processes responsible for this variability, we have analysed in a control simulation performed with a coupled climate model a strong positive ice-ocean feedback that amplifies sea ice variations. When sea ice concentration increases in a region, in particular close to the ice edge, the mixed layer depth tends to decrease. This can be caused by a net inflow of ice and thus of freshwater that stabilizes the water column. Another stabilizing mechanism at interannual time scales that appears more widespread in our simulation is associated with the downward salt transport due to the seasonal cycle of ice formation: brine is released in winter when ice is formed and mixed over a deep layer while the freshwater flux caused by ice melting is included in a shallow layer, resulting in a net vertical transport of salt. Because of this stronger stratification due to the presence of sea ice, more heat is stored at depth in the ocean and the vertical oceanic heat flux is reduced, which contributes to maintain a higher ice extent. This positive feedback is not associated with a particular spatial pattern. Consequently, the spatial distribution of the trend in ice concentration is largely imposed by the wind changes that can provide the initial perturbation. A positive freshwater flux could alternatively be the initial trigger but the amplitude of the final response of the sea ice extent is finally set up by the amplification related to ice-ocean feedback. Initial conditions have also an influence as the chance to have a large increase in ice extent is higher if starting from a state characterized by a low value.

Description: Growth of sulphuric acid nanoparticles under wet and dry conditions Atmospheric Chemistry and Physics Discussions, 13, 24087-24125, 2013 Author(s): L. Škrabalová, D. Brus, T. Anttila, V. Ždímal, and H. Lihavainen New particle formation, which greatly influences the number concentrations and size distributions of an atmospheric aerosol, is often followed by a rapid growth of freshly formed particles. The initial growth of a newly formed aerosol is the crucial process determining the fraction of nucleated particles growing into cloud condensation nuclei sizes, which have a significant influence on climate. In this study, we report the laboratory observations of the growth of nanoparticles produced by nucleation of H 2 SO 4 and water in a laminar flow tube at temperatures of 283, 293 and 303 K, under dry (a relative humidity of 1%) and wet conditions (relative humidity of 30%) and residence times of 30, 45, 60 and 90 s. The initial H 2 SO 4 concentration spans the range from 2 × 10 8 to 1.4 × 10 10 molecule cm −3 and the calculated wall losses of H 2 SO 4 were assumed to be diffusion limited. The detected particle number concentrations, measured by the Ultrafine Condensation Particle Counter (UCPC) and Differential Mobility Particle Sizer (DMPS), were found to depend strongly on the residence time. Hygroscopic particle growth, presented by growth factors, was found to be in good agreement with the previously reported studies. The experimental growth rates ranged from 20 nm h −1 to 890 nm h −1 at RH 1% and from 7 nm h −1 to 980 nm h −1 at RH 30% and were found to increase significantly with the increasing concentration of H 2 SO 4 . Increases in the nucleation temperature had a slight enhancing effect on the growth rates under dry conditions. The influence of relative humidity on growth was not consistent – at lower H 2 SO 4 concentrations, the growth rates were higher under dry conditions while at H 2 SO 4 concentrations greater than 1×10 9 molecule cm −3 the growth rates were higher under wet conditions. The growth rates show only a weak dependence on the residence time. The experimental observations were compared with predictions made using a numerical model, which investigates the growth of particles with three different extents of neutralization by the ammonia NH 3 : (1) pure H 2 SO 4 – H 2 O particles (2) particles formed by ammonium bisulphate, (NH 4 )HSO 4 (3) particles formed by ammonium sulphate, (NH 4 ) 2 SO 4 . The highest growth rates were found for ammonium sulphate particles. Since the model accounting for the initial H 2 SO 4 concentration predicted the experimental growth rates correctly, our results suggest that the commonly presumed diffusional wall losses of H 2 SO 4 are not so significant. We therefore assume that there are not only losses of H 2 SO 4 on the wall but also a flux of H 2 SO 4 molecules from the wall into the flow tube, the effect being more profound under dry conditions and at higher temperatures of the tube wall. Based on a comparison with the atmospheric observations, our results indicate that sulphuric acid alone can not explain the growth rates of particles formed in the atmosphere.

Description: There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.

Description: We believe that undergraduate biology students must acquire a foundational background in computing including how to formulate a computational problem; develop an algorithmic solution; implement their solution in software and then test, document and use their code to explore biological phenomena. Moreover, by learning these skills in the first year, students acquire a powerful tool set that they can use and build on throughout their studies. To address this need, we have developed a first-year undergraduate course that teaches students the foundations of computational thinking and programming in the context of problems in biology. This article describes the structure and content of the course and summarizes assessment data on both affective and learning outcomes.

Description: Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.

Description: Experimental quantification of contact freezing in an electrodynamic balance Atmospheric Measurement Techniques, 6, 2373-2382, 2013 Author(s): N. Hoffmann, A. Kiselev, D. Rzesanke, D. Duft, and T. Leisner Heterogeneous nucleation of ice in a supercooled water droplet induced by external contact with a dry aerosol particle has long been known to be more effective than freezing induced by the same nucleus immersed in the droplet. However, the experimental quantification of contact freezing is challenging. Here we report an experimental method to determine the temperature-dependent ice nucleation probability of size-selected aerosol particles. The method is based on the suspension of supercooled charged water droplets in a laminar flow of air containing aerosol particles as contact freezing nuclei. The rate of droplet–particle collisions is calculated numerically with account for Coulomb attraction, drag force and induced dipole interaction between charged droplet and aerosol particles. The calculation is verified by direct counting of aerosol particles collected by a levitated droplet. By repeating the experiment on individual droplets for a sufficient number of times, we are able to reproduce the statistical freezing behavior of a large ensemble of supercooled droplets and measure the average rate of freezing events. The freezing rate is equal to the product of the droplet–particle collision rate and the probability of freezing on a single contact, the latter being a function of temperature, size and composition of the contact ice nuclei. Based on these observations, we show that for the types of particles investigated so far, contact freezing is the dominating freezing mechanism on the timescale of our experiment.

Description: The aim of this paper is to study the relations between the Hausdorff dimensions of k -quasilines and the theory of extremal quasiconformal mappings. We show that there is an open and dense subset (Strebel points) of the universal Teichmüller space T (H) such that, for every [ f ] in the set, the Hausdorff dimension of the k -quasiline determined by [ f ] is strictly less than 1 + k 2 . We also show that there are some points [ f ] != [id] outside the open and dense set in the universal Teichmüller space such that the Hausdorff dimension of the quasiline determined by [ f ] is 1. Moreover, some results on the Hausdorff dimensions of the quasilines varying in the asymptotic Teichmüller space are also obtained.

Description: Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

Description: A new uniqueness result for a general n th order differential equation is obtained. We show that some previous results follow immediately from our theorem.

Description: Consider a discrete uniformly elliptic divergence form equation on the d ≥3 dimensional lattice Z d with random coefficients. In Conlon and Spencer [ Trans. Amer. Math. Soc. , http://www.math.lsa.umich.edu/~conlon/paper/hom10.pdf ], rate of convergence results in homogenization and estimates on the difference between the averaged Green's function and the homogenized Green's function for random environments which satisfy a Poincaré inequality were obtained. Here, these results are extended to certain environments in which correlations can have arbitrarily small power law decay. These environments are simply related via a convolution to environments which do satisfy a Poincaré inequality.

Description: In this paper, we prove that, for any a , M N with ( a , M ) = 1, there are infinitely many Carmichael numbers m such that m a mod M .

Description: We give a topological analogue for openness of a criterion for flatness that originates with Auslander. Over a normal base of dimension n , failure of openness is detected by a vertical component in the n th fibred power of the morphism.

Description: Investigated are regular maps from real algebraic varieties into real Fermat varieties. It is proved that under some natural assumptions, all such maps are null homotopic.

Description: Let ( M , g ) be a complete non-compact Riemannian manifold. We consider operators of the form g + V , where g is the non-negative Laplacian associated with the metric g , and V a locally integrable function. Let be a Riemannian covering, with Laplacian g and potential . If the operator + V is non-negative on ( M , g ), then the operator is non-negative on . In this note, we show that the converse statement is true provided that is a co-amenable subgroup of 1 ( M ).

Description: Peak interpolation is concerned with a foundational kind of mathematical task: building functions in a fixed algebra A , which have prescribed values or behaviour on a fixed closed subset (or on several disjoint subsets). In this paper, we do the same but now A is an algebra of operators on a Hilbert space. We briefly survey this noncommutative peak interpolation , which we have studied with coauthors in a long series of papers, and whose basic theory now appears to be approaching its culmination. This programme developed from, and is based partly on, theorems of Hay and Read whose proofs were spectacular, but therefore inaccessible to an uncommitted reader. We give short proofs of these results, using recent progress in noncommutative peak interpolation, and conversely give examples of the use of these theorems in peak interpolation. For example, we prove a useful new noncommutative peak interpolation theorem.

Description: We show how a parameterized family of maps of the spine of a manifold can be used to construct a family of homeomorphisms of the ambient manifold which have the inverse limits of the spine maps as global attractors. We describe applications to unimodal families of interval maps, to rotation sets, and to the standard family of circle maps.

Description: For every prime p , we give infinitely many examples of torsors under abelian varieties over Q that are locally trivial but not divisible by p in the Weil–Châtelet group. We also give an example of a locally trivial torsor under an elliptic curve over Q that is not divisible by 4 in the Weil–Châtelet group. This gives a negative answer to a question of Cassels.

Description: We show that at least of the zeros of the Riemann zeta-function are simple, assuming the Riemann hypothesis. This was previously established by Conrey, Ghosh and Gonek [ Proc. London Math. Soc. 76 (1998) 497–522] under the additional assumption of the generalized Lindelöf hypothesis. We are able to remove this hypothesis by careful use of the generalized Vaughan identity.

Description: We construct an infinite family of hyperbolic, homologically thin knots that are not quasi-alternating. To establish the latter, we argue that the branched double-cover of each knot in the family does not bound a negative-definite 4-manifold with trivial first homology and bounded second Betti number. This fact depends in turn on information from the correction terms in Heegaard Floer homology, which we establish by way of a relationship to, and calculation of, the Turaev torsion.

Description: We observe that E -resultant of a very ample rank 2 vector bundle E on a real projective curve (with no real points) is nonnegative when restricted to the space of real sections. Moreover, we show that if E has a section vanishing at exactly two points and the degree d of E satisfies d ( d – 6) ≥ 4( g – 1), then this polynomial cannot be written as a sum of squares.

Description: Let G be one of the Ricci-flat holonomy groups SU( n ), Sp( n ), Spin(7) or G 2 , and M a compact manifold of dimension 2 n , 4 n , 8 or 7, respectively. We prove that the natural map from the moduli space of torsion-free G -structures on M to the moduli space of Ricci-flat metrics is open, and that the image is a smooth manifold. For the exceptional cases G = Spin(7) and G 2 , we extend the result to asymptotically cylindrical manifolds.

Description: We improve the results of Booker and Krishnamurthy ( Compos. Math. 147 (2011) 669–715) by allowing restricted sets of poles among the unramified twists. This allows for a clean statement of the GL(2) converse theorem which includes all cases of Eisenstein series.

Description: δ 18 O water isotope in the i LOVECLIM model (version 1.0) – Part 1: Implementation and verification Geoscientific Model Development, 6, 1481-1491, 2013 Author(s): D. M. Roche A new 18 O stable water isotope scheme is developed for three components of the i LOVECLIM coupled climate model: atmospheric, oceanic and land surface. The equations required to reproduce the fractionation of stable water isotopes in the simplified atmospheric model ECBilt are developed consistently with the moisture scheme. Simplifications in the processes are made to account for the simplified vertical structure including only one moist layer. Implementation of these equations together with a passive tracer scheme for the ocean and a equilibrium fractionation scheme for the land surface leads to the closure of the (isotopic-) water budget in our climate system. Following the implementation, verification of the existence of usual δ 18 O to climatic relationships are performed for the Rayleigh distillation, the Dansgaard relationship and the δ 18 O –salinity relationship. Advantages and caveats of the approach taken are outlined. The isotopic fields simulated are shown to reproduce most expected oxygen-18–climate relationships with the notable exception of the isotopic composition in Antarctica.

Description: Contribution of directly connected and isolated impervious areas to urban drainage network hydrographs Hydrology and Earth System Sciences, 17, 3473-3483, 2013 Author(s): Y. Seo, N.-J. Choi, and A. R. Schmidt This paper addresses the mass balance error observed in runoff hydrographs in urban watersheds by introducing assumptions regarding the contribution of infiltrated rainfall from pervious areas and isolated impervious area (IIA) to the runoff hydrograph. Rainfall infiltrating into pervious areas has been assumed not to contribute to the runoff hydrograph until Hortonian excess rainfall occurs. However, mass balance analysis in an urban watershed indicates that rainfall infiltrated to pervious areas can contribute directly to the runoff hydrograph, thereby offering an explanation for the long hydrograph tail commonly observed in runoff from urban storm sewers. In this study, a hydrologic analysis based on the width function is introduced, with two types of width functions obtained from both pervious and impervious areas, respectively. The width function can be regarded as the direct interpretation of the network response. These two width functions are derived to obtain distinct response functions for directly connected impervious areas (DCIA), IIA, and pervious areas. The results show significant improvement in the estimation of runoff hydrographs and suggest the need to consider the flow contribution from pervious areas to the runoff hydrograph. It also implies that additional contribution from flow paths through joints and cracks in sewer pipes needs to be taken into account to improve the estimation of runoff hydrographs in urban catchments.

Description: Let G be a solvable subgroup of the automorphism group Aut( X ) of a compact Kähler manifold X of complex dimension n , and let N ( G ) be the normal subgroup of G consisting of elements with null entropy. Let us denote by G * the image of G under the natural map from Aut( X ) to GL( V , R ), where V is the Dolbeault cohomology group H 1, 1 ( X , R ). Assume that the Zariski closure of G * in GL( V C ) is connected. The main aim of this paper is to show that, when the rank r ( G ) of the quotient group G / N ( G ) is equal to n – 1 and the identity component of Aut( X ) is trivial, then the normal subgroup N ( G ) of G is finite. This affirmatively answers a question in Invent. Math. posed by D.-Q. Zhang.

Description: δ 18 O water isotope in the i LOVECLIM model (version 1.0) – Part 3: A palaeo-perspective based on present-day data–model comparison for oxygen stable isotopes in carbonates Geoscientific Model Development, 6, 1505-1516, 2013 Author(s): T. Caley and D. M. Roche Oxygen stable isotopes (δ 18 O) are among the most useful tools in palaeoclimatology/palaeoceanography. Simulation of oxygen stable isotopes allows testing how the past variability of these isotopes in water can be interpreted. By modelling the proxy directly in the model, the results can also be directly compared with the data. Water isotopes have been implemented in the global three-dimensional model of intermediate complexity i LOVECLIM, allowing fully coupled atmosphere–ocean simulations. In this study, we present the validation of the model results for present-day climate against the global database for oxygen stable isotopes in carbonates. The limitation of the model together with the processes operating in the natural environment reveal the complexity of use the continental calcite-δ 18 O signal of speleothems for a global quantitative data–model comparison exercise. On the contrary, the reconstructed surface ocean calcite-δ 18 O signal in i LOVECLIM does show a very good agreement with the late Holocene database (foraminifers) at the global and regional scales. Our results indicate that temperature and the isotopic composition of the seawater are the main control on the fossil-δ 18 O signal recorded in foraminifer shells when all species are grouped together. Depth habitat, seasonality and other ecological effects play a more significant role when individual species are considered. We argue that a data–model comparison for surface ocean calcite δ 18 O in past climates, such as the Last Glacial Maximum (≈ 21 000 yr), could constitute an interesting tool for mapping the potential shifts of the frontal systems and circulation changes throughout time. Similarly, the potential changes in intermediate oceanic circulation systems in the past could be documented by a data (benthic foraminifers)-model comparison exercise whereas future investigations are necessary in order to quantitatively compare the results with data for the deep ocean.

Description: Phenology as a strategy for carbon optimality: a global model Biogeosciences Discussions, 10, 15107-15152, 2013 Author(s): S. Caldararu, D. W. Purves, and P. I. Palmer Phenology is essential to our understanding of biogeochemical cycles and the climate system. We develop a global mechanistic model of leaf phenology based on the hypothesis that phenology is a strategy for optimal carbon gain at the canopy level so that trees adjust leaf gains and losses in response to environmental factors such as light, temperature and soil moisture, to achieve maximum carbon assimilation. We fit this model to five years of satellite observations of leaf area index (LAI) using a Bayesian fitting algorithm. We show that our model is able to reproduce phenological patterns for all vegetation types and use it to explore variations in growing season length and the climate factors that limit leaf growth for different biomes. Phenology in wet tropical areas is limited by leaf age physiological constraints while at higher latitude leaf seasonality is limited by low temperature and light availability. Leaf growth in grassland regions is limited by water availability but often in combination with other factors. This model will advance the current understanding of phenology for ecosystem carbon models and our ability to predict future phenological behaviour.

Description: Bias correction can modify climate model-simulated precipitation changes without adverse affect on the ensemble mean Hydrology and Earth System Sciences Discussions, 10, 11585-11611, 2013 Author(s): E. P. Maurer and D. W. Pierce When applied to remove climate model biases in precipitation, quantile mapping can in some settings modify the simulated trends. This has important implications when the precipitation will be used to drive an impacts model that is sensitive to changes in precipitation. We use daily precipitation output from 12 general circulation models (GCMs) over the conterminous United States interpolated to a common 1° grid, and gridded observations aggregated to the same scale, to compare precipitation differences before and after quantile mapping bias correction. The change in seasonal mean (winter, DJF, and summer, JJA) precipitation between different 30-yr historical periods is compared to examine (1) the consensus among GCMs as to whether the bias correction tends to amplify or diminish their simulated precipitation trends, and (2) whether the modification of the change in precipitation tends to improve or degrade the correspondence to observed changes in precipitation for the same periods. In some cases, for a particular GCM, the trend modification can be as large as the original simulated change, though the areas where this occurs varies among GCMs so the ensemble median shows smaller trend modification. In specific locations and seasons the trend modification by quantile mapping improves correspondence with observed trends, and in others it degrades it. In the majority of the domain the ensemble median is for little effect on the correspondence of simulated precipitation trends with observed. This highlights the need to use an ensemble of GCMs rather than relying on a small number of models to estimate impacts.

Description: Linking ICT and society in early warning and adaptation to hydrological extremes in mountains Natural Hazards and Earth System Science, 13, 2253-2270, 2013 Author(s): C. de Jong The assessment of the societal impact of hydrological extremes is particularly important in mountain regions, since mountains can be considered both as the generators and victims of extreme events. ICT can provide a powerful tool for transmitting hydro-meteorological information to predict, prepare and adapt to such events. However, in remote regions, such as mountains, the poles, deserts and islands, preventive and adaptive measures are often restricted by data availability and lack and/or incoherence of data networks. This paper distinguishes between early warning of floods and droughts, emphasising the latter in particular in mountains and explores the possibilities of enhancing the role of society in data collection, the identification, activation and application of stakeholder knowledge and transferral of data from gauged to ungauged catchments.

Description: The dihedral angle formed at junctions between two plagioclase grains and a grain of augite is only very rarely in textural equilibrium in gabbros from kilometre-scale crustal layered intrusions. The median of a population of these disequilibrium angles, cpp , varies systematically within a single layered intrusion, remaining constant over large stretches of stratigraphy with significant increases and decreases associated with the addition or reduction respectively of the number of phases on the liquidus of the bulk magma. The stepwise changes in cpp are present in the Upper Zone of the Bushveld Complex, the Megacyclic Unit I of the Sept Iles Intrusion, and the Layered Series of the Skaergaard intrusion. The plagioclase-bearing cumulates of Rum have a bimodal distribution of cpp , dependent on whether the cumulus assemblage includes clinopyroxene. The presence of the stepwise changes is independent of the order of arrival of cumulus phases and of the composition of either the cumulus phases or the inferred composition of the interstitial liquid. The only parameter that behaves in an exactly analogous manner to cpp is the rate of change in enthalpy with temperature ( H / T ) during crystallization. Both H / T and cpp increase with the addition of a liquidus phase, and decrease with the removal of a liquidus phase. The replacement of one phase by another has little effect on H / T and no discernible effect on cpp . An increase of H / T results in an increase in the fraction of the total enthalpy budget that is the latent heat of crystallization (the fractional latent heat). It also increases the mass crystallized in each incremental temperature drop (the crystal productivity). These increases of both fractional latent heat and crystal productivity are likely to cause an increase in the time taken to form three-grain junctions in the mush via thermal buffering of a thickened mushy layer. We suggest these are the underlying causes of stepwise increases in cpp . Stepwise changes in the geometry of three-grain junctions in fully solidified gabbros thus provide a clear microstructural marker for the progress of fractionation down the liquid line of descent in layered intrusions.

Description: High-resolution sampling in monogenetic fields has the potential to reveal fine-scale heterogeneity of the mantle, a feature that may be overwhelmed by larger fluxes of magma, or missed by under-sampling. The Quaternary Auckland Volcanic Field (AVF) in northern New Zealand is a basaltic field of 51 small-volume volcanic centres, and is one of the best-sampled examples of a monogenetic volcanic field. We present data for 12 centres in the volcanic field. These show the large compositional variations between volcanoes as well as through single eruptive sequences. Whole-rock compositions range from subalkaline basalt in the larger centres, through alkali basalt to nephelinite in the smallest centres. Fractional crystallization has had a limited effect in many of the centres, but high-pressure clinopyroxene crystallization may have occurred in others. Three end-members are observed in Pb isotope space, indicating that distinct mantle source components are involved in the petrogenesis of the magmas. Whole-rock multi-element patterns show that the larger centres have prominent positive Sr anomalies and lack K anomalies, whereas the smaller centres have prominent negative K anomalies and lack Sr anomalies. The melting parameters and compositions of the sources involved are modelled using trace element ratios and multi-element patterns, and three components are characterized: (1) fertile peridotite with a Pb-isotope composition similar to Pacific mid-ocean ridge basalt; (2) eclogite domains with a HIMU-like isotope composition dispersed within the fertile peridotite; (3) slightly depleted subduction-metasomatized peridotitic lithospheric mantle (containing c . 3% subduction fluids). Modelling shows that melting in the AVF begins in garnet-bearing fertile asthenosphere (with preferential melting of eclogite domains) and that melts are variably diluted by melts of the lithospheric source. The U–Th isotope compositions of the end-members in the AVF show 230 Th excess [( 230 Th/ 232 Th) ratios of 1·11–1·38], with the samples of lower ( 230 Th/ 232 Th) exhibiting higher ( 238 U/ 232 Th), which we attribute to the dilution effect of the melts from the lithospheric mantle source. Modelling reveals a correlation between melting in the asthenosphere, the degree of melting and incorporation of the metasomatized lithospheric mantle source, and the resultant size of the volcanic centre. This suggests that the scale of the eruption may essentially be controlled by asthenospheric mantle dynamics.

Description: The origin of mafic and ultramafic sills exhibiting different whole-rock compositional profiles (e.g. I-, C-, D-, M- and S-shaped profiles) remains controversial. We have addressed this issue by revisiting three ~100 m thick Siberian dolerite sills (Vavukansky, Kuz’movsky and Vilyuysky) that display remarkable internal differentiation. The Vavukansky sill has an M-shaped profile with prominent basal and top reversals showing inward increases in whole-rock MgO, Mg-number [100Mg/(Mg + Fe)] and normative An content [100An/(An + Ab)], followed by the Layered and Upper Border Series with inward decreases in these indices. The Kuz’movsky and Vilyuysky sills both show S-shaped profiles similar to the Vavukansky sill, but lack a top reversal. These whole-rock M- and S-shaped profiles are accompanied by similar profiles in mineral compositions. Plagioclase and, to a lesser extent, olivine show systematic inward increases in An content and Mg-number, respectively, across basal and top reversals. These compositional trends are followed by inward decreases in these ratios in the interiors of the Vavukansky and Kuz’movsky sills. Currently accepted models attribute whole-rock M- and S-shaped compositional profiles to crystal settling, compositional convection or compaction operating in closed systems. Our observations challenge these traditional interpretations because variations in mineral compositions observed in marginal reversals cannot result from closed-system fractionation. We suggest instead that initially the sills evolved as open systems that were slowly inflated by magmas that became gradually more primitive with time. The inflation was accompanied by in situ crystallization that preserved the preceding fractionation history of the injected magmas by forming basal and top reversals with minerals becoming more primitive inwards. This process culminated with rapid inflation of the sills to their current size owing to a major influx of primitive magma. Subsequently, magma flow through the sills ceased and they evolved as closed systems by fractional crystallization. This resulted in the Layered and Upper Border Series with minerals becoming more evolved inwards. This model can be extended to explain other compositional profiles and petrological features in mafic and ultramafic sills.

Description: The genomes of related species contain valuable information on the history of the considered taxa. Great apes in particular exhibit variation of evolutionary patterns along their genomes. However, the great ape data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms. Previous methods for genome-scale analysis are restricted to very few individuals or cannot disentangle the contribution of mutation rates and fixation biases. This represents a limitation both for the understanding of these forces as well as for the detection of regions affected by selection. Here, we present a new model designed to estimate mutation rates and fixation biases from genetic variation within and between species. We relax the assumption of instantaneous substitutions, modeling substitutions as mutational events followed by a gradual fixation. Hence, we straightforwardly account for shared ancestral polymorphisms and incomplete lineage sorting. We analyze genome-wide synonymous site alignments of human, chimpanzee, and two orangutan species. From each taxon, we include data from several individuals. We estimate mutation rates and GC-biased gene conversion intensity. We find that both mutation rates and biased gene conversion vary with GC content. We also find lineage-specific differences, with weaker fixation biases in orangutan species, suggesting a reduced historical effective population size. Finally, our results are consistent with directional selection acting on coding sequences in relation to exonic splicing enhancers.

Description: A plume-in-grid approach to characterize air quality impacts of aircraft emissions at the Hartsfield–Jackson Atlanta International Airport Atmospheric Chemistry and Physics, 13, 9285-9302, 2013 Author(s): J. Rissman, S. Arunachalam, M. Woody, J. J. West, T. BenDor, and F. S. Binkowski This study examined the impacts of aircraft emissions during the landing and takeoff cycle on PM 2.5 concentrations during the months of June and July 2002 at the Hartsfield–Jackson Atlanta International Airport. Primary and secondary pollutants were modeled using the Advanced Modeling System for Transport, Emissions, Reactions, and Deposition of Atmospheric Matter (AMSTERDAM). AMSTERDAM is a modified version of the Community Multiscale Air Quality (CMAQ) model that incorporates a plume-in-grid process to simulate emissions sources of interest at a finer scale than can be achieved using CMAQ's model grid. Three fundamental issues were investigated: the effects of aircraft on PM 2.5 concentrations throughout northern Georgia, the differences resulting from use of AMSTERDAM's plume-in-grid process rather than a traditional CMAQ simulation, and the concentrations observed in aircraft plumes at subgrid scales. Comparison of model results with an air quality monitor located in the vicinity of the airport found that normalized mean bias ranges from −77.5% to 6.2% and normalized mean error ranges from 40.4% to 77.5%, varying by species. Aircraft influence average PM 2.5 concentrations by up to 0.232 μg m −3 near the airport and by 0.001–0.007 μg m −3 throughout the Atlanta metro area. The plume-in-grid process increases concentrations of secondary PM pollutants by 0.005–0.020 μg m −3 (compared to the traditional grid-based treatment) but reduces the concentration of non-reactive primary PM pollutants by up to 0.010 μg m −3 , with changes concentrated near the airport. Examination of subgrid-scale results indicates that median aircraft contribution to grid cells is higher than median puff concentration in the airport's grid cell and outside of a 20 km × 20 km square area centered on the airport, while in a 12 km × 12 km square ring centered on the airport, puffs have median concentrations over an order of magnitude higher than aircraft contribution to the grid cells. Maximum puff impacts are seen within the 12 km × 12 km ring, not in the airport's own grid cell, while maximum grid cell impacts occur within the airport's grid cell. Twenty-one (21)% of all aircraft-related puffs from the Atlanta airport have at least 0.1 μg m −3 PM 2.5 concentrations. Near the airport, median daily puff concentrations vary between 0.017 and 0.134 μg m −3 (0.05 and 0.35 μg m −3 at ground level), while maximum daily puff concentrations vary between 6.1 and 42.1 μg m −3 (7.5 and 42.1 μg m −3 at ground level) during the 2-month period. In contrast, median daily aircraft contribution to grid concentrations varies between 0.015 and 0.091 μg m −3 (0.09 and 0.40 μg m −3 at ground level), while the maximum varies between 0.75 and 2.55 μg m −3 (0.75 and 2.0 μg m −3 at ground level). Future researchers may consider using a plume-in-grid process, such as the one used here, to understand the impacts of aircraft emissions at other airports, for proposed future airports, for airport expansion projects under various future scenarios, and for other national-scale studies specifically when the maximum impacts at fine scales are of interest.

Description: Corrigendum to "Atmospheric column-averaged mole fractions of carbon dioxide at 53 aircraft measurement sites" published in Atmos. Chem. Phys. 13, 5265–5275, 2013 Atmospheric Chemistry and Physics, 13, 9213-9216, 2013 Author(s): Y. Miyamoto, M. Inoue, I. Morino, O. Uchino, T. Yokota, T. Machida, Y. Sawa, H. Matsueda, C. Sweeney, P. P. Tans, A. E. Andrews, S. C. Biraud, and P. K. Patra No abstract available.

Description: Genetic control of male or female gonad development displays between different groups of organisms a remarkable diversity of "master sex-determining genes" at the top of the genetic hierarchies, whereas downstream components surprisingly appear to be evolutionarily more conserved. Without much further studies, conservation of sequence has been equalized to conservation of function. We have used the medaka fish to investigate the generality of this paradigm. In medaka, the master male sex-determining gene is dmrt1bY , a highly conserved downstream regulator of sex determination in vertebrates. To understand its function in orchestrating the complex gene regulatory network, we have identified targets genes and regulated pathways of Dmrt1bY. Monitoring gene expression and interactions by transgenic fluorescent reporter fish lines, in vivo tissue-chromatin immunoprecipitation and in vitro gene regulation assays revealed concordance but also major discrepancies between mammals and medaka, notably amongst spatial, temporal expression patterns and regulations of the canonical Hedgehog and R-spondin/Wnt/Follistatin signaling pathways. Examination of Foxl2 protein distribution in the medaka ovary defined a new subpopulation of theca cells, where ovarian-type aromatase transcriptional regulation appears to be independent of Foxl2. In summary, these data show that the regulation of the downstream regulatory network of sex determination is less conserved than previously thought.

Description: Timing of sea ice retreat can alter phytoplankton community structure in the western Arctic Ocean Biogeosciences Discussions, 10, 15153-15180, 2013 Author(s): given_name prefix surname suffix, A. Fujiwara, T. Hirawake, K. Suzuki, I. Imai, and S.-I. Saitoh This study assesses the response of phytoplankton assemblages to recent climate change, especially with regard to the shrinking of sea ice in the northern Chukchi Sea of the western Arctic Ocean. Distribution patterns of phytoplankton groups in the late summers of 2008–2010 were analyzed based on HPLC pigment signatures and, the following four major algal groups were inferred via multiple regression and cluster analyses: prasinophytes, diatoms, haptophytes and dinoflagellates. A remarkable interannual difference in the distribution pattern of the groups was found in the northern basin area. Haptophytes dominated and dispersed widely in warm surface waters in 2008, whereas prasinophytes dominated in cold water in 2009 and 2010. A difference in the onset date of sea ice retreat was evident among years – the sea ice retreat in 2008 was 1–2 months earlier than in 2009 and 2010. The spatial distribution of early sea ice retreat matched the areas in which a shift in algal community composition was observed. Steel-Dwass's multiple comparison tests were used to assess the physical, chemical and biological parameters of the four clusters. We found a statistically significant difference in temperature between the haptophyte-dominated cluster and the other clusters, suggesting that the change in the phytoplankton communities was related to the earlier sea ice retreat in 2008 and the corollary increase in sea surface temperatures. Longer periods of open water during the summer, which are expected in the future, may affect food webs and biogeochemical cycles in the western Arctic due to shifts in phytoplankton community structure.

Description: Can we determine what controls the spatio-temporal distribution of d-excess and 17 O-excess in precipitation using the LMDZ general circulation model? Climate of the Past, 9, 2173-2193, 2013 Author(s): C. Risi, A. Landais, R. Winkler, and F. Vimeux Combined measurements of the H 2 18 O and HDO isotopic ratios in precipitation, leading to second-order parameter D-excess, have provided additional constraints on past climates compared to the H 2 18 O isotopic ratio alone. More recently, measurements of H 2 17 O have led to another second-order parameter: 17 O-excess. Recent studies suggest that 17 O-excess in polar ice may provide information on evaporative conditions at the moisture source. However, the processes controlling the spatio-temporal distribution of 17 O-excess are still far from being fully understood. We use the isotopic general circulation model (GCM) LMDZ to better understand what controls d-excess and 17 O-excess in precipitation at present-day (PD) and during the last glacial maximum (LGM). The simulation of D-excess and 17 O-excess is evaluated against measurements in meteoric water, water vapor and polar ice cores. A set of sensitivity tests and diagnostics are used to quantify the relative effects of evaporative conditions (sea surface temperature and relative humidity), Rayleigh distillation, mixing between vapors from different origins, precipitation re-evaporation and supersaturation during condensation at low temperature. In LMDZ, simulations suggest that in the tropics convective processes and rain re-evaporation are important controls on precipitation D-excess and 17 O-excess. In higher latitudes, the effect of distillation, mixing between vapors from different origins and supersaturation are the most important controls. For example, the lower d-excess and 17 O-excess at LGM simulated at LGM are mainly due to the supersaturation effect. The effect of supersaturation is however very sensitive to a parameter whose tuning would require more measurements and laboratory experiments. Evaporative conditions had previously been suggested to be key controlling factors of d-excess and 17 O-excess, but LMDZ underestimates their role. More generally, some shortcomings in the simulation of 17 O-excess by LMDZ suggest that general circulation models are not yet the perfect tool to quantify with confidence all processes controlling 17 O-excess.

Description: Similarity estimators for irregular and age uncertain time series Climate of the Past Discussions, 9, 5299-5346, 2013 Author(s): K. Rehfeld and J. Kurths Paleoclimate time series are often irregularly sampled and age uncertain, which is an important technical challenge to overcome for successful reconstruction of past climate variability and dynamics. Visual comparison and interpolation-based linear correlation approaches have been used to infer dependencies from such proxy time series. While the first is subjective, not measurable and not suitable for the comparison of many datasets at a time, the latter introduces interpolation bias, and both face difficulties if the underlying dependencies are nonlinear. In this paper we investigate similarity estimators that could be suitable for the quantitative investigation of dependencies in irregular and age uncertain time series. We compare the Gaussian-kernel based cross correlation (gXCF, Rehfeld et al., 2011) and mutual information (gMI, Rehfeld et al., 2013) against their interpolation-based counterparts and the new event synchronization function (ESF). We test the efficiency of the methods in estimating coupling strength and coupling lag numerically, using ensembles of synthetic stalagmites with short, autocorrelated, linear and nonlinearly coupled proxy time series, and in the application to real stalagmite time series. In the linear test case coupling strength increases are identified consistently for all estimators, while in the nonlinear test case the correlation-based approaches fail. The lag at which the time series are coupled is identified correctly as the maximum of the similarity functions in around 60–55% (in the linear case) to 53–42% (for the nonlinear processes) of the cases when the dating of the synthetic stalagmite is perfectly precise. If the age uncertainty increases beyond 5% of the time series length, however, the true coupling lag is not identified more often than the others for which the similarity function was estimated. Age uncertainty contributes up to half of the uncertainty in the similarity estimation process. Time series irregularity contributes less, particularly for the adapted Gaussian-kernel based estimators and the event synchronization function. The introduced link strength concept summarizes the hypothesis test results and balances the individual strengths of the estimators: while gXCF is particularly suitable for short and irregular time series, gMI and the ESF can identify nonlinear dependencies. ESF could, in particular, be suitable to study extreme event dynamics in paleoclimate records. Programs to analyze paleoclimatic time series for significant dependencies are included in a freely available software toolbox.

Description: Assimilating water column and satellite data for marine export production estimation Geoscientific Model Development, 6, 1575-1590, 2013 Author(s): X. Yao and R. Schlitzer Recent advances in satellite retrieval methodology now allow for estimation of particular organic carbon (POC) concentration in ocean surface waters directly from satellite-based optical data. Because of the good coverage, these data reveal small-scale spatial and temporal concentration gradients and document the evolution of surface water POC as well as the underlying driving biogeochemical processes throughout the seasons. Water column nutrient data also reveal biogeochemical activity. However, because of the scarcity of data, the deduction of temporal changes of particle production and export is not possible in most parts of the ocean. Here we present first results from a new study combining both data streams, thereby exploiting the high spatio-temporal resolution of surface POC concentrations from satellite optical sensors with water column nutrient data having sparser coverage but providing information throughout the entire water column. We use a medium-resolution global model with steady-state 3-D circulation that has been optimized by fitting to a large number of hydrographic parameters and tracers, including CFCs and natural radiocarbon. Production and export of POC is allowed to vary monthly, and the magnitudes of the monthly export fluxes are determined by fitting the model to satellite POC data as well as water column nutrient data using the adjoint method. Two cases have been investigated: (1) the production rate of POC is set to be proportional to export production (EP) and the seasonal changes are assumed sinusoidal (meridionally varying amplitude and phase), and (2) the POC production rate is linked to primary production rates (literature). Both cases were run with the same initial state and model settings, and show total cost function decreases of 12 and 95%, respectively. The POC misfit term alone decreased by 75 and 99.8%. The integrated annual global POC exports of the two cases are 9.9 and 12.3 Gt C yr −1 , respectively. Overall, the remaining POC and phosphate misfits of both solutions are considered too large, and the difference fields still exhibit significant systematic geographical patterns. This indicates that the present model runs are too simplistic and do not fully explain the data. Further, more refined model setups are needed.

Description: Simplified PRBMs of spatial compliant multi-beam modules for planar motion Mechanical Sciences, 4, 311-318, 2013 Author(s): G. Hao PRBMs (pseudo-rigid-body models) have been becoming important engineering technologies/methods in the field of compliant mechanisms to simplify the design and analysis through the use of the knowledge body of rigid-body mechanisms coupling with springs. This article addresses the PRBMs of spatial multi-beam modules for planar motion, which are composed of three or more symmetrical wire/slender beams parallel to each other where the planar twisting DOF (degree of freedom) is assumed to be very small for specific applications/loading conditions. Simplified PRBMs are firstly proposed through replacing each beam in spatial multi-beam module with a rigid-body link plus two identical spherical joints at its two ends. The characteristics factor, bending stiffness and twisting stiffness for the spherical joint are determined. Load-displacement equations are then derived for a class of spatial multi-beam modules and general spatial multi-beam modules using the virtual work principle and kinematic relationships. Finally, nonlinear FEA (finite element analysis) is employed with comparisons with the PRBMs. The present PRBMs have shown the ability to predict the primary nonlinear constraint characteristics such as load-stiffening effect, cross-axis coupling in the two primary translational directions and buckling load.

Description: We present measurements of higher order clustering of galaxies in the latest release of the Canada–France–Hawaii Telescope Legacy Survey (CFHTLS)-Wide. We construct a series of volume-limited sample of galaxies containing more than one million galaxies over the redshift range 0.2 〈  z  〈 1 in the four independent fields of the CFHTLS-Wide. Using a counts-in-cells technique we measure the variance ${\bar{\xi }}_2$ and the hierarchical moments $S_{n}= {{\bar{\xi }}_n / {\bar{\xi }}_2^{n-1}}$ (3 ≤  n  ≤ 5) as a function of redshift and angular scale. We find that the measured field-to-field scatter in our estimators is in excellent agreement with analytical predictions. At small scales, corresponding to the highly non-linear regime, we find tentative evidence at the 1 level that the hierarchical moments increase with redshift. At large scales, corresponding to the weakly non-linear regime, our measurements are marginally consistent with perturbation theory predictions for standard cold dark matter cosmology using a simple linear bias. The predictions of perturbation theory tend to slightly overestimate our measurements, which may be a signature of non-linear bias.

Description: We estimate cosmic microwave background (CMB) polarization power spectra and temperature–polarization cross-spectra, from the 9-year data of the Wilkinson Microwave Anisotropy Probe ( WMAP ). Foreground cleaning is implemented using minimum variance linear combinations of the coefficients of needlet decompositions of sky maps for all WMAP channels, to produce maps for CMB temperature anisotropies ( T -mode) and polarization ( E and B -modes), for nine different years of observation. The final power spectra are computed from averages of all possible cross-year power spectra obtained using foreground-cleaned maps for the different years. Our analysis technique yields a measurement of the EE spectrum that is in excellent agreement with theoretical expectations from the current cosmological model. By comparison, the publicly available WMAP EE power spectrum is higher on average (and significantly higher than the predicted EE spectrum from the current best fit) at scales larger than about a degree, an excess that is not confirmed by our analysis. Our TE and TB measurements are in good agreement overall with the WMAP ones and are compatible with the theoretical expectations, although a few data points are off by a few standard deviations, and yield a reduced 2 somewhat above expectation. As predicted for a standard cosmological model with low tensor-to-scalar ratio, the EB and BB power spectra obtained in our analysis are compatible with zero.

Description: We present optical integral field unit observations of two gas pillars surrounding the Galactic young massive star cluster NGC 3603. The high S/N and spectral resolution of these data have allowed us to accurately quantify the Hα, [N ii ] and [S ii ] emission line shapes, and we find a mixture of broad (FWHM ~ 70–100 km s –1 ) and narrow (〈50 km s –1 ) components. The broad components are found close to the edges of both pillars, suggesting that they originate in turbulent mixing layers (TMLs) driven by the effect of the star cluster wind. Both pillars exhibit surprisingly high ionized gas densities of 〉10 000 cm –3 . In one pillar we found that these high densities are only found in the narrow component, implying that they must originate from deeper within the pillar than the broad component. From this, together with our kinematical data, we conclude that the narrow component traces a photoevaporation flow, and that the TML forms at the interface with the hot wind. On the pillar surfaces, we find a consistent offset in radial velocity between the narrow (brighter) components of Hα and [N ii ] of ~5–8 km s –1 , for which we were unable to find a satisfactory explanation. We urge the theoretical community to simulate mechanical and radiative cloud interactions in more detail to address the many unanswered questions raised by this study.