A time-domain probe method for three-dimensional rough surface reconstructions

The task of this paper is to develop a Time-Domain Probe Method for the reconstruction of impenetrable scatterers. The basic idea of the method is to use pulses in the time domain and the time-dependent response of the scatterer to reconstruct its location and shape. The method is based on the basic causality principle of timedependent scattering. The method is independent of the boundary condition and is applicable for limited aperture scattering data. In particular, we discuss the reconstruction of the shape of a rough surface in three dimensions from time-domain measurements of the scattered field. In practise, measurement data is collected where the incident field is given by a pulse. We formulate the time-domain fieeld reconstruction problem equivalently via frequency-domain integral equations or via a retarded boundary integral equation based on results of Bamberger, Ha-Duong, Lubich. In contrast to pure frequency domain methods here we use a time-domain characterization of the unknown shape for its reconstruction. Our paper will describe the Time-Domain Probe Method and relate it to previous frequency-domain approaches on sampling and probe methods by Colton, Kirsch, Ikehata, Potthast, Luke, Sylvester et al. The approach significantly extends recent work of Chandler-Wilde and Lines (2005) and Luke and Potthast (2006) on the timedomain point source method. We provide a complete convergence analysis for the method for the rough surface scattering case and provide numerical simulations and examples.

Accurate analysis of noble gas concentrations in small water samples and its application to fluid inclusions in stalagmites

The concentrations of dissolved noble gases in water are widely used as a climate proxy to determine noble gas temperatures (NGTs); i.e., the temperature of the water when gas exchange last occurred. In this paper we make a step forward to apply this principle to fluid inclusions in stalagmites in order to reconstruct the cave temperature prevailing at the time when the inclusion was formed. We present an analytical protocol that allows us accurately to determine noble gas concentrations and isotope ratios in stalagmites, and which includes a precise manometrical determination of the mass of water liberated from fluid inclusions. Most important for NGT determination is to reduce the amount of noble gases liberated from air inclusions, as they mask the temperature-dependent noble gas signal from the water inclusions. We demonstrate that offline pre-crushing in air to subsequently extract noble gases and water from the samples by heating is appropriate to separate gases released from air and water inclusions. Although a large fraction of recent samples analysed by this technique yields NGTs close to present-day cave temperatures, the interpretation of measured noble gas concentrations in terms of NGTs is not yet feasible using the available least squares fitting models. This is because the noble gas concentrations in stalagmites are not only composed of the two components air and air saturated water (ASW), which these models are able to account for. The observed enrichments in heavy noble gases are interpreted as being due to adsorption during sample preparation in air, whereas the excess in He and Ne is interpreted as an additional noble gas component that is bound in voids in the crystallographic structure of the calcite crystals. As a consequence of our study's findings, NGTs will have to be determined in the future using the concentrations of Ar, Kr and Xe only. This needs to be achieved by further optimizing the sample preparation to minimize atmospheric contamination and to further reduce the amount of noble gases released from air inclusions.

Neuromantic : from semi-manual to semi-automatic reconstruction of neuron morphology

The ability to create accurate geometric models of neuronal morphology is important for understanding the role of shape in information processing. Despite a significant amount of research on automating neuron reconstructions from image stacks obtained via microscopy, in practice most data are still collected manually. This paper describes Neuromantic, an open source system for three dimensional digital tracing of neurites. Neuromantic reconstructions are comparable in quality to those of existing commercial and freeware systems while balancing speed and accuracy of manual reconstruction. The combination of semi-automatic tracing, intuitive editing, and ability of visualizing large image stacks on standard computing platforms provides a versatile tool that can help address the reconstructions availability bottleneck. Practical considerations for reducing the computational time and space requirements of the extended algorithm are also discussed.

Differentiation of neotropical ecosystems by modern soil phytolith assemblages and its implications for palaeoenvironmental and archaeological reconstructions

The interpretation of Neotropical fossil phytolith assemblages for palaeoenvironmental and archaeological reconstructions relies on the development of appropriate modern analogues. We analyzed modern phytolith assemblages from the soils of ten distinctive tropical vegetation communities in eastern lowland Bolivia, ranging from terra firme humid evergreen forest to seasonally-inundated savannah. Results show that broad ecosystems – evergreen tropical forest, semi-deciduous dry tropical forest, and savannah – can be clearly differentiated by examination of their phytolith spectra and the application of Principal Component Analysis (PCA). Differences in phytolith assemblages between particular vegetation communities within each of these ecosystems are more subtle, but can still be identified. Comparison of phytolith assemblages with pollen rain data and stable carbon isotope analyses from the same vegetation plots show that these proxies are not only complementary, but significantly improve taxonomic and ecosystem resolution, and therefore our ability to interpret palaeoenvironmental and archaeological records. Our data underline the utility of phytolith analyses for reconstructing Amazon Holocene vegetation histories and pre-Columbian land use, particularly the high spatial resolution possible with terrestrial soil-based phytolith studies.

Pollen-based biome reconstructions for Latin America at 0, 6000 and 18000 radiocarbon years

The biomisation method is used to reconstruct Latin American vegetation at 6000±500 and 18 000±1000 radiocarbon years before present (14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human impact, methodological artefacts and mechanisms of pollen representivity of the parent vegetation.

Late Pleistocene climate change and the global expansion of anatomically modern humans

The extent to which past climate change has dictated the pattern and timing of the out-of-Africa expansion by anatomically modern humans is currently unclear [Stewart JR, Stringer CB (2012) Science 335:1317–1321]. In particular, the incompleteness of the fossil record makes it difficult to quantify the effect of climate. Here, we take a different approach to this problem; rather than relying on the appearance of fossils or archaeological evidence to determine arrival times in different parts of the world, we use patterns of genetic variation in modern human populations to determine the plausibility of past demographic parameters. We develop a spatially explicit model of the expansion of anatomically modern humans and use climate reconstructions over the past 120 ky based on the Hadley Centre global climate model HadCM3 to quantify the possible effects of climate on human demography. The combinations of demographic parameters compatible with the current genetic makeup of worldwide populations indicate a clear effect of climate on past population densities. Our estimates of this effect, based on population genetics, capture the observed relationship between current climate and population density in modern hunter–gatherers worldwide, providing supporting evidence for the realism of our approach. Furthermore, although we did not use any archaeological and anthropological data to inform the model, the arrival times in different continents predicted by our model are also broadly consistent with the fossil and archaeological records. Our framework provides the most accurate spatiotemporal reconstruction of human demographic history available at present and will allow for a greater integration of genetic and archaeological evidence.

The atmospheric impact of uncertainties in recent Arctic Sea ice reconstructions

There are significant discrepancies between observational datasets of Arctic sea ice concentrations covering the last three decades, which result in differences of over 20% in Arctic summer sea ice extent/area and 5%–10% in winter. Previous modeling studies have shown that idealized sea ice anomalies have the potential for making a substantial impact on climate. In this paper, this theory is further developed by performing a set of simulations using the third Hadley Centre Coupled Atmospheric Model (HadAM3). The model was driven with monthly climatologies of sea ice fractions derived from three of these records to investigate potential implications of sea ice inaccuracies for climate simulations. The standard sea ice climatology from the Met Office provided a control. This study focuses on the effects of actual inaccuracies of concentration retrievals, which vary spatially and are larger in summer than winter. The smaller sea ice discrepancies in winter have a much larger influence on climate than the much greater summer sea ice differences. High sensitivity to sea ice prescription was observed, even though no SST feedbacks were included. Significant effects on surface fields were observed in the Arctic, North Atlantic, and North Pacific. Arctic average surface air temperature anomalies in winter vary by 2.5°C, and locally exceed 12°C. Arctic mean sea level pressure varies by up to 5 mb locally. Anomalies extend to 45°N over North America and Eurasia but not to lower latitudes, and with limited changes in circulation above the boundary layer. No statistically significant impact on climate variability was simulated, in terms of the North Atlantic Oscillation. Results suggest that the uncertainty in summer sea ice prescription is not critical but that winter values require greater accuracy, with the caveats that the influences of ocean–sea ice feedbacks were not included in this study.

Palaeovegetation in China during the late Quaternary: Biome reconstructions based on a global scheme of plant functional types

Two previous reconstructions of palaeovegetation across the whole of China were performed using a simple classification of plant functional types (PFTs). Now a more explicit, global PFT classification scheme has been developed, and a substantial number of additional pollen records have become available. Here we apply the global scheme of PFTs to a comprehensive set of pollen records available from China to test the applicability of the global scheme of PFTs in China, and to obtain a well-founded reconstruction of changing palaeovegetation patterns. A total of 806 pollen surface samples, 188 mid-Holocene (MH, 6000 14C yr BP) and 50 last glacial maximum (LGM, 18,000 14C yr BP) pollen records were used to reconstruct vegetation patterns in China, based on a new global classification system of PFTs and a standard numerical technique for biome assignment (biomization). The biome reconstruction based on pollen surface samples showed convincing agreement with present potential natural vegetation. Coherent patterns of change in biome distribution between MH, LGM and present are observed. In the MH, cold and cool-temperate evergreen needleleaf forests and mixed forests, temperate deciduous broadleaf forest, and warm-temperate evergreen broadleaf and mixed forest in eastern China were shifted northward by 200–500 km. Cold-deciduous forest in northeastern China was replaced by cold evergreen needleleaf forest while in central northern China, cold-deciduous forest was present at some sites now occupied by temperate grassland and desert. The forest–grassland boundary was 200–300 km west of its present position. Temperate xerophytic shrubland, temperate grassland and desert covered a large area on the Tibetan Plateau, but the area of tundra was reduced. Treeline was 300–500 m higher than present in Tibet. These changes imply generally warmer winters, longer growing seasons and more precipitation during the MH. Westward shifts of the forest–shrubland–grassland and grassland–desert boundaries imply greater moisture availability in the MH, consistent with a stronger summer monsoon. During the LGM, in contrast, cold-deciduous forest, cool-temperate evergreen needleleaf forest, cool mixed forests, warm-temperate evergreen broadleaf and mixed forest in eastern China were displaced to the south by 300–1000 km, while temperate deciduous broadleaf forest, pure warm-temperate evergreen forest, tropical semi-evergreen and evergreen broadleaf forests were restricted or absent from the mainland of southern China, implying colder winters than present. Strong shifts of temperate xerophytic shrubland, temperate grassland and desert to the south and east in northern and western China and on the Tibetan Plateau imply drier conditions than present.

Pollen-based reconstructions of biome distributions for Australia, Southeast Asia and the Pacific (SEAPAC region) at 0,6000 and 18,000 14C yr B.P.

Aim  This paper documents reconstructions of the vegetation patterns in Australia, Southeast Asia and the Pacific (SEAPAC region) in the mid-Holocene and at the last glacial maximum (LGM). Methods  Vegetation patterns were reconstructed from pollen data using an objective biomization scheme based on plant functional types. The biomization scheme was first tested using 535 modern pollen samples from 377 sites, and then applied unchanged to fossil pollen samples dating to 6000 ± 500 or 18,000 ± 1000 14C yr bp. Results  1. Tests using surface pollen sample sites showed that the biomization scheme is capable of reproducing the modern broad-scale patterns of vegetation distribution. The north–south gradient in temperature, reflected in transitions from cool evergreen needleleaf forest in the extreme south through temperate rain forest or wet sclerophyll forest (WSFW) and into tropical forests, is well reconstructed. The transitions from xerophytic through sclerophyll woodlands and open forests to closed-canopy forests, which reflect the gradient in plant available moisture from the continental interior towards the coast, are reconstructed with less geographical precision but nevertheless the broad-scale pattern emerges. 2. Differences between the modern and mid-Holocene vegetation patterns in mainland Australia are comparatively small and reflect changes in moisture availability rather than temperature. In south-eastern Australia some sites show a shift towards more moisture-stressed vegetation in the mid-Holocene with xerophytic woods/scrub and temperate sclerophyll woodland and shrubland at sites characterized today by WSFW or warm-temperate rain forest (WTRF). However, sites in the Snowy Mountains, on the Southern Tablelands and east of the Great Dividing Range have more moisture-demanding vegetation in the mid-Holocene than today. South-western Australia was slightly drier than today. The single site in north-western Australia also shows conditions drier than today in the mid-Holocene. Changes in the tropics are also comparatively small, but the presence of WTRF and tropical deciduous broadleaf forest and woodland in the mid-Holocene, in sites occupied today by cool-temperate rain forest, indicate warmer conditions. 3. Expansion of xerophytic vegetation in the south and tropical deciduous broadleaf forest and woodland in the north indicate drier conditions across mainland Australia at the LGM. None of these changes are informative about the degree of cooling. However the evidence from the tropics, showing lowering of the treeline and forest belts, indicates that conditions were between 1 and 9 °C (depending on elevation) colder. The encroachment of tropical deciduous broadleaf forest and woodland into lowland evergreen broadleaf forest implies greater aridity. Main conclusions  This study provides the first continental-scale reconstruction of mid-Holocene and LGM vegetation patterns from Australia, Southeast Asia and the Pacific (SEAPAC region) using an objective biomization scheme. These data will provide a benchmark for evaluation of palaeoclimate simulations within the framework of the Palaeoclimate Modelling Intercomparison Project.

Pollen-based reconstructions of Japanese biomes at 0, 6000 and 18,000 14C yr bp

A biomization method, which objectively assigns individual pollen assemblages to biomes ( Prentice et al., 1996 ), was tested using modern pollen data from Japan and applied to fossil pollen data to reconstruct palaeovegetation patterns 6000 and 18,000 14C yr bp Biomization started with the assignment of 135 pollen taxa to plant functional types (PFTs), and nine possible biomes were defined by specific combinations of PFTs. Biomes were correctly assigned to 54% of the 94 modern sites. Incorrect assignments occur near the altitudinal limits of individual biomes, where pollen transport from lower altitudes blurs the local pollen signals or continuous changes in species composition characterizes the range limits of biomes. As a result, the reconstructed changes in the altitudinal limits of biomes at 6000 and 18,000 14C yr bp are likely to be conservative estimates of the actual changes. The biome distribution at 6000 14C yr bp was rather similar to today, suggesting that changes in the bioclimate of Japan have been small since the mid-Holocene. At 18,000 14C yr bp the Japanese lowlands were covered by taiga and cool mixed forests. The southward expansion of these forests and the absence of broadleaved evergreen/warm mixed forests reflect a pronounced year-round cooling.

Pollen-based biome reconstructions for China at 0 and 6000 years

Biomization provides an objective and robust method of assigning pollen spectra to biomes so that pollen data can be mapped and compared directly with the output of biomgeographic models. We have tested the applicability of this procedure, originally developed for Europe, to assign modern surface samples from China to biomes. The procedure successfully delineated the major vegetation types of China. When the same procedure was applied to fossil pollen samples for 6000 years ago, the reconstructions showed systematic differences from present, consistent with previous interpretations of vegetation changes since the mid-Holocene. In eastern China, the forest zones were systematically shifted northwards, such that cool mixed forests displaced taiga in northeastern China, while broad-leaved evergreen forest extended c. 300 km and temperate deciduous forestc. 500–600 km beyond their present northern limits. In northwestern China, the area of desert and steppe vegetation was reduced compared to present. On the Tibetan Plateau, forest vegetation extended to higher elevations than today and the area of tundra was reduced. These shifts in biome distributions imply significant changes in climate since 6000 years ago that can be interpreted qualitatively as a response to orbital forcing and its secondary effects on the Asian monsoon.

Paralog re-emergence: a novel, historically contingent mechanism in the evolution of antimicrobial resistance

Evolution of resistance to drugs and pesticides poses a serious threat to human health and agricultural production. CYP51 encodes the target site of azole fungicides, widely used clinically and in agriculture. Azole resistance can evolve due to point mutations or overexpression of CYP51, and previous studies have shown that fungicide-resistant alleles have arisen by de novo mutation. Paralogs CYP51A and CYP51B are found in filamentous ascomycetes, but CYP51A has been lost from multiple lineages. Here, we show that in the barley pathogen Rhynchosporium commune, re-emergence of CYP51A constitutes a novel mechanism for the evolution of resistance to azoles. Pyrosequencing analysis of historical barley leaf samples from a unique long-term experiment from 1892 to 2008 indicates that the majority of the R. commune population lacked CYP51A until 1985, after which the frequency of CYP51A rapidly increased. Functional analysis demonstrates that CYP51A retains the same substrate as CYP51B, but with different transcriptional regulation. Phylogenetic analyses show that the origin of CYP51A far predates azole use, and newly sequenced Rhynchosporium genomes show CYP51A persisting in the R. commune lineage rather than being regained by horizontal gene transfer; therefore, CYP51A re-emergence provides an example of adaptation to novel compounds by selection from standing genetic variation.

The importance of accurate wind resource assessment for evaluating the economic viability of small wind turbines

The techno-economic performance of a small wind turbine is very sensitive to the available wind resource. However, due to financial and practical constraints installers rely on low resolution wind speed databases to assess a potential site. This study investigates whether the two site assessment tools currently used in the UK, NOABL or the Energy Saving Trust wind speed estimator, are accurate enough to estimate the techno-economic performance of a small wind turbine. Both the tools tend to overestimate the wind speed, with a mean error of 23% and 18% for the NOABL and Energy Saving Trust tool respectively. A techno-economic assessment of 33 small wind turbines at each site has shown that these errors can have a significant impact on the estimated load factor of an installation. Consequently, site/turbine combinations which are not economically viable can be predicted to be viable. Furthermore, both models tend to underestimate the wind resource at relatively high wind speed sites, this can lead to missed opportunities as economically viable turbine/site combinations are predicted to be non-viable. These results show that a better understanding of the local wind resource is a required to make small wind turbines a viable technology in the UK.

Implication of methodological uncertainties for mid-Holocene sea surface temperature reconstructions

We present and examine a multi-sensor global compilation of mid-Holocene (MH) sea surface temperatures (SST), based on Mg/Ca and alkenone palaeothermometry and reconstructions obtained using planktonic foraminifera and organic-walled dinoflagellate cyst census counts. We assess the uncertainties originating from using different methodologies and evaluate the potential of MH SST reconstructions as a benchmark for climate-model simulations. The comparison between different analytical approaches (time frame, baseline climate) shows the choice of time window for the MH has a negligible effect on the reconstructed SST pattern, but the choice of baseline climate affects both the magnitude and spatial pattern of the reconstructed SSTs. Comparison of the SST reconstructions made using different sensors shows significant discrepancies at a regional scale, with uncertainties often exceeding the reconstructed SST anomaly. Apparent patterns in SST may largely be a reflection of the use of different sensors in different regions. Overall, the uncertainties associated with the SST reconstructions are generally larger than the MH anomalies. Thus, the SST data currently available cannot serve as a target for benchmarking model simulations. Further evaluations of potential subsurface and/or seasonal artifacts that may contribute to obscure the MH SST reconstructions are urgently needed to provide reliable benchmarks for model evaluations.

Accurate delay analysis in prioritised wireless sensor networks for generalized packet arrival

This letter presents an accurate delay analysis in prioritised wireless sensor networks (WSN). The analysis is an enhancement of the existing analysis proposed by Choobkar and Dilmaghani, which is only applicable to the case where the lower priority nodes always have packets to send in the empty slots of the higher priority node. The proposed analysis is applicable for any pattern of packet arrival, which includes the general case where the lower priority nodes may or may not have packets to send in the empty slots of the higher priority nodes. Evaluation of both analyses showed that the proposed delay analysis has better accuracy over the full range of loads and provides an excellent match to simulation results.