bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salt body detection from seismic data via sparse representation
Authors: Ramirez Carlos , Larrazabal German , Gonzalez Gladys 
Published: June 2015

ABSTRACTIn seismic interpretation and seismic data analysis, it is of critical importance to effectively identify certain geologic formations from very large seismic data sets. In particular, the problem of salt characterization from seismic data can lead to important savings in time during the interpretation process if solved efficiently and in an automatic manner. In this work, we present a novel numerical approach that is able to automatically segmenting or identifying salt structures from a post‐stack seismic data set with a minimum intervention from the interpreter. The proposed methodology is based on the recent theory of sparse representation and consists in three major steps: first, a supervised learning assisted by the user which is performed only once, second a segmentation process via unconstrained ℓ1 optimization, and finally a post‐processing step based on signal separation. Furthermore, since the second step only depends upon local information at each time, the whole process greatly benefits from parallel computing platforms. We conduct numerical experiments in a synthetic 3D seismic data set demonstrating the viability of our method. More specifically, we found that the proposed approach matches up to 98.53% with respect to the corresponding 3D velocity model available in advance. Finally, in appendixes A and B, we present a convergence analysis providing theoretical guarantees for the proposed method.
Trade‐offs in parasitism efficiency and brood size mediate parasitoid coexistence, with implications for biological control of the invasive emerald ash borer
Authors: Wang Xiao‐Yi , Jennings David E. , Duan Jian J. 
Published: June 2015

SummaryParasitoids often are selected for use as biological control agents because of their high host specificity, yet such host specificity can result in strong interspecific competition. Few studies have examined whether and how various extrinsic factors (such as parasitism efficiency, i.e. the ability to optimize host‐finding attack rates) influence the outcome of competition between parasitoids, even though they could have profound effects on the implementation of classical biological control programmes.To determine the potential influence of extrinsic competition and coexistence on host suppression efficacy, we compared parasitism by two larval parasitoids (Tetrastichus planipennisiandSpathius galinae) of the invasive emerald ash borer (EAB)Agrilus planipennis, under different host densities, parasitoid densities, host plant sizes and parasitoid–host ratios.Spathius galinaehad significantly higher parasitism efficiency (≈4 times), but significantly lower brood size (>6 times) than that ofT. planipennisi. The attack rates of hosts increased significantly with parasitoid density, whereas host density did not significantly affect multiparasitism. The parasitism rate ofT. planipennision small host logs was significantly higher than that on large logs, while host plant (log) size had no significant impact onS. galinaeparasitism.The multiparasitism rate was rather low regardless of host log size and parasitoid/host density, indicating that intrinsic competition between the two species of parasitoids might seldom occur in the field. The two species of parasitoids could therefore coexist in the same habitat, and any adverse effects on the suppression ofEABpopulations caused by competitive behaviour between the two species of parasitoids would likely be negligible.Synthesis and applications. Our findings suggest that introducing multiple species of parasitic natural enemies could be feasible for management of invasive species, but it is important to examine multiple extrinsic factors simultaneously when evaluating interspecific competition between them. Among these different extrinsic factors, we found that coexistence between parasitoids can be mediated by trade‐offs in their parasitism efficiency and brood sizes. Thus, the differences in life‐history traits of natural enemies could be used to select among biological control agents being considered for releases.
Assessing the efficacy and ecology of biocontrol and biomanipulation for managing invasive pest fish
Authors: Davies Gareth D. , Britton J. Robert 
Published: June 2015

Summary

Management of non‐native species aims to prevent biological invasions using actions including control and containment of the potential invader. Biocontrol and biomanipulation strategies are used frequently to reduce population sizes of non‐native species and reduce their ecological impacts and dispersal rates.

Assessments of the efficacy of biocontrol and biomanipulation actions for managing non‐native pest fish, and the ecological mechanisms involved, were studied here using lentic populations of the invasive fish Pseudorasbora parva. Biocontrol was through release of the indigenous piscivorous fish Perca fluviatilis and biomanipulation through intensive fish removals.

A combined biocontrol and removal programme was completed in an invaded pond over two reproductive seasons. Almost 10 000 P. parva were removed, with cumulative removal numbers significantly related to their decreased abundance (>60 to <0·1 m−2). Ten adult P. fluviatilis were also released initially and reproduced each season. Analyses revealed P. parva contribution to P. fluviatilis diet was high initially, but decreased as P. parva abundance reduced. Individual contributions of the management actions to declined P. parva abundance were difficult to isolate.

The individual effects of biocontrol and removals on P. parva populations were then tested using a field trial in replicated pond mesocosms over three reproductive seasons. Replicates started with 1500 P. parva. The control (no interventions) revealed no significant temporal changes in P. parva abundances. In the removal treatment, where over 17 000 P. parva were removed per replicate over the trial, abundance declined initially, but increased significantly after each reproductive season as remaining fish compensated through increased reproductive output. In the biocontrol, abundance declined and remained low; analyses revealed P. parva were an important dietary component of larger P. fluviatilis, with predation suppressing compensatory responses.

Synthesis and applications. Biocontrol and removals can significantly reduce abundances of lentic populations of small invasive fishes. Removals provide short‐term population suppression, but high effort is needed to overcome compensatory responses. Biocontrol can provide longer‐term suppression but could invoke unintended ecological consequences via ‘stocking‐up’ food webs. Application of these results to decision‐making frameworks should enable managers to make more objective decisions on risk‐commensurate methodologies for controlling small invasive fishes.
Modelling short‐rotation coppice and tree planting for urban carbon management – a citywide analysis
Authors: McHugh Nicola , Edmondson Jill L. , Gaston Kevin J. , Leake Jonathan R. , O'Sullivan Odhran S. 
Published: June 2015

Summary

The capacity of urban areas to deliver provisioning ecosystem services is commonly overlooked and underutilized. Urban populations have globally increased fivefold since 1950, and they disproportionately consume ecosystem services and contribute to carbon emissions, highlighting the need to increase urban sustainability and reduce environmental impacts of urban dwellers. Here, we investigated the potential for increasing carbon sequestration, and biomass fuel production, by planting trees and short‐rotation coppice (SRC), respectively, in a mid‐sized UK city as a contribution to meeting national commitments to reduce CO2 emissions.

Iterative GIS models were developed using high‐resolution spatial data. The models were applied to patches of public and privately owned urban greenspace suitable for planting trees and SRC, across the 73 km2 area of the city of Leicester. We modelled tree planting with a species mix based on the existing tree populations, and SRC with willow and poplar to calculate biomass production in new trees, and carbon sequestration into harvested biomass over 25 years.

An area of 11 km2 comprising 15% of the city met criteria for tree planting and had the potential over 25 years to sequester 4200 tonnes of carbon above‐ground. Of this area, 5·8 km2 also met criteria for SRC planting and over the same period this could yield 71 800 tonnes of carbon in harvested biomass.

The harvested biomass could supply energy to over 1566 domestic homes or 30 municipal buildings, resulting in avoided carbon emissions of 29 236 tonnes of carbon over 25 years when compared to heating by natural gas. Together with the net carbon sequestration into trees, a total reduction of 33 419 tonnes of carbon in the atmosphere could be achieved in 25 years by combined SRC and tree planting across the city.

Synthesis and applications. We demonstrate that urban greenspaces in a typical UK city are underutilized for provisioning ecosystem services by trees and especially SRC, which has high biomass production potential. For urban greenspace management, we recommend that planting SRC in urban areas can contribute to reducing food–fuel conflicts on agricultural land and produce renewable energy sources close to centres of population and demand.
Long‐term avian community response to housing development at the boundary of US protected areas: effect size increases with time
Authors: Wood Eric M. , Pidgeon Anna M. , Radeloff Volker C. , Helmers David P. , Culbert Patrick D. , Keuler Nicholas S. , Flather Curtis H. 
Published: June 2015

Summary

Biodiversity conservation is a primary function of protected areas. However, protected areas also attract people, and therefore, land use has intensified at the boundaries of these lands globally. In the USA, since the 1970s, housing growth at the boundaries (<1 km) of protected areas has increased at a rate far higher than on more distant private lands. Here, we designed our analyses to address our central hypothesis that increasing housing density in and near protected areas will increasingly alter their avian communities.

We quantified the relationship between abundance and richness of protected‐area avian species of greatest conservation need, land‐cover affiliates (e.g. species associated with natural land cover such as forest breeders) and synanthropes (e.g. species associated with humans) with housing density on the boundary of protected areas and on more distant private lands from 1970 to 2010 in three ecoregions of the USA. We accomplished this using linear mixed‐model analyses, data from the US Census Bureau and 90 routes of the North American Breeding Bird Survey.

Housing density at the boundary of protected areas tended to be strongly negatively related with the abundance and richness of species of greatest conservation need and land‐cover affiliates (upwards of 88% of variance explained) and strongly positively related with synanthropes (upwards of 83% of variance explained). The effect size of these relationships increased in most cases from 1970 to 2010 and was greatest in the densely developed eastern forests. In the more sparsely populated West, we found similar, though weaker, associations.

Housing density on private lands more distant from protected areas had similar, but more muted negative effects.

Synthesis and applications. Our results illustrate that as housing density has increased along the boundary of protected areas, the conservation benefit of these lands has likely diminished. We urge conservation planners to prioritize the purchase of private‐land inholdings in order to maximize the extent of unfragmented natural lands within protected areas. Further, we strongly recommend that land‐use planners implement boundary management strategies to alter the pattern of human access to protected areas, cluster development to concentrate the footprint of rural housing, and establish conservation agreements through local land trusts to buffer protected areas from the effects of development along protected‐area boundaries. To maximize the conservation benefit of protected areas, we suggest that housing development should be restricted within 1 km of their boundaries.
Let there be bioluminescence: development of a biophotonic imaging platform for in situ analyses of oral biofilms in animal models
Authors: Merritt Justin , Senpuku Hidenobu , Kreth Jens 
Published: June 2015

SummaryIn the current study, we describe a novel biophotonic imaging‐based reporter system that is particularly useful for the study of virulence in polymicrobial infections and interspecies interactions within animal models. A suite of luciferase enzymes was compared using three early colonizing species of the human oral flora (Streptococcus mutans, Streptococcus gordonii and Streptococcus sanguinis) to determine the utility of the different reporters for multiplexed imaging studies in vivo. Using the multiplex approach, we were able to track individual species within a dual‐species oral infection model in mice with both temporal and spatial resolution. We also demonstrate how biophotonic imaging of multiplexed luciferase reporters could be adapted for real‐time quantification of bacterial gene expression in situ. By creating an inducible dual‐luciferase expressing reporter strain of S. mutans, we were able to exogenously control and measure expression of nlmAB (encoding the bacteriocin mutacin IV) within mice to assess its importance for the persistence ability of S. mutans in the oral cavity. The imaging system described in the current study circumvents many of the inherent limitations of current animal model systems, which should now make it feasible to test hypotheses that were previously impractical to model.
CaCO3 and SrCO3 bioprecipitation by fungi isolated from calcareous soil
Authors: Li Qianwei , Csetenyi Laszlo , Paton Graeme Iain , Gadd Geoffrey Michael 
Published: June 2015

SummaryThe urease‐positive fungi Pestalotiopsis sp. and Myrothecium gramineum, isolated from calcareous soil, were examined for their properties of CaCO3 and SrCO3 biomineralization. After incubation in media amended with urea and CaCl2 and/or SrCl2, calcite (CaCO3), strontianite (SrCO3), vaterite in different forms [CaCO3, (CaxSr1−x)CO3] and olekminskite [Sr(Sr,Ca)(CO3)2] were precipitated, and fungal ‘footprints’ were observed on mineral surfaces. The amorphous precipitate mediated by Pestalotiopsis sp. grown with urea and equivalent concentrations of CaCl2 and SrCl2 was identified as hydrated Ca and Sr carbonates by Fourier transform infrared spectroscopy. Liquid media experiments showed M. gramineum possessed the highest Sr2+ removal ability, and ∼ 49% of supplied Sr2+ was removed from solution when grown in media amended with urea and 50 mM SrCl2. Furthermore, this organism could also precipitate 56% of the available Ca2+ and 28% of the Sr2+ in the form of CaCO3, SrCO3 and (CaxSr1−x)CO3 when incubated in urea‐amended media and equivalent CaCl2 and SrCl2 concentrations. This is the first report of biomineralization of olekminskite and coprecipitation of Sr into vaterite mediated by fungi. These findings suggest that urease‐positive fungi could play an important role in the environmental fate, bioremediation or biorecovery of Sr or other metals and radionuclides that form insoluble carbonates.
Unconventional membrane lipid biosynthesis in Xanthomonas campestris
Authors: Aktas Meriyem , Narberhaus Franz 
Published: June 2015

SummaryAll bacteria are surrounded by at least one bilayer membrane mainly composed of phospholipids (PLs). Biosynthesis of the most abundant PLs phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and cardiolipin (CL) is well understood in model bacteria such as Escherichia coli. It recently emerged, however, that the diversity of bacterial membrane lipids is huge and that not yet explored biosynthesis pathways exist, even for the common PLs. A good example is the plant pathogen Xanthomonas campestris pv. campestris. It contains PE, PG and CL as major lipids and small amounts of the N‐methylated PE derivatives monomethyl PE and phosphatidylcholine (PC = trimethylated PE). Xanthomonas campestris uses a repertoire of canonical and non‐canonical enzymes for the synthesis of its membrane lipids. In this minireview, we briefly recapitulate standard pathways and integrate three recently discovered pathways into the overall picture of bacterial membrane biosynthesis.
Acclimation of Emiliania huxleyi (1516) to nutrient limitation involves precise modification of the proteome to scavenge alternative sources of N and P
Authors: McKew Boyd A. , Metodieva Gergana , Raines Christine A. , Metodiev Metodi V. , Geider Richard J. 
Published: June 2015

SummaryLimitation of marine primary production by the availability of nitrogen or phosphorus is common. Emiliania huxleyi, a ubiquitous phytoplankter that plays key roles in primary production, calcium carbonate precipitation and production of dimethyl sulfide, often blooms in mid‐latitude at the beginning of summer when inorganic nutrient concentrations are low. To understand physiological mechanisms that allow such blooms, we examined how the proteome of E. huxleyi (strain 1516) responds to N and P limitation. We observed modest changes in much of the proteome despite large physiological changes (e.g. cellular biomass, C, N and P) associated with nutrient limitation of growth rate. Acclimation to nutrient limitation did however involve significant increases in the abundance of transporters for ammonium and nitrate under N limitation and for phosphate under P limitation. More notable were large increases in proteins involved in the acquisition of organic forms of N and P, including urea and amino acid/polyamine transporters and numerous C‐N hydrolases under N limitation and a large upregulation of alkaline phosphatase under P limitation. This highly targeted reorganization of the proteome towards scavenging organic forms of macronutrients gives unique insight into the molecular mechanisms that underpin how E. huxleyi has found its niche to bloom in surface waters depleted of inorganic nutrients.
Specific global responses to N and Fe nutrition in toxic and non‐toxic Microcystis aeruginosa
Authors: Alexova Ralitza , Dang The Cuong , Fujii Manabu , Raftery Mark J. , Waite T. David , Ferrari Belinda C. , Neilan Brett A. 
Published: June 2015

SummaryThe bloom‐forming cyanobacteria species Microcystis aeruginosa includes toxic and non‐toxic (microcystin‐producing) strains. Certain stress conditions stimulate synthesis of microcystin (MCYST) and enhance the binding of the MCYST molecule to proteins. In this quantitative proteomic study, we compared the response of a wild‐type toxic strain PCC 7806, an mcyH− knockout non‐toxic strain, and a naturally occurring non‐toxic strain, PCC 7005, after 8 days in low iron (Fe) and nitrogen (N) starvation in order to assess the benefit of MCYST synthesis in non‐optimal conditions. Fe limitation increased MCYST synthesis and caused an accumulation of phycobilisome proteins and the ferric iron transporter FutA only in the toxic PCC 7806 but not the non‐toxic strains. In N starvation, photosynthetic, C and N metabolism proteins were more abundant in the non‐toxic strains, as were chaperones and proteases. Significant interaction between nutrient availability and toxicity existed for thioredoxin peroxidase and several thioredoxin‐regulated proteins. We propose a competition of MCYST for binding sites in thioredoxin‐regulated proteins during oxidative stress (low Fe) but not in growth‐limiting conditions (low N). This then leads to differences in the regulation of C:N metabolism in toxic and non‐toxic M. aeruginosa in nutrient‐replete and nutrient‐limited conditions.
Endomicrobium proavitum, the first isolate of Endomicrobia class. nov. (phylum Elusimicrobia) – an ultramicrobacterium with an unusual cell cycle that fixes nitrogen with a Group IV nitrogenase
Authors: Zheng Hao , Dietrich Carsten , Radek Renate , Brune Andreas 
Published: June 2015

SummaryThe bacterial tree contains many deep‐rooting clades without any cultured representatives. One such clade is ‘Endomicrobia’, a class‐level lineage in the phylum Elusimicrobia represented so far only by intracellular symbionts of termite gut flagellates. Here, we report the isolation and characterization of the first free‐living member of this clade from sterile‐filtered gut homogenate of defaunated (starch‐fed) Reticulitermes santonensis. Strain Rsa215 is a strictly anaerobic ultramicrobacterium that grows exclusively on glucose, which is fermented to lactate, acetate, hydrogen and CO2. Ultrastructural analysis revealed a Gram‐negative cell envelope and a peculiar cell cycle. The genome contains a single set of nif genes that encode homologues of Group IV nitrogenases, which were so far considered to have functions other than nitrogen fixation. We documented nitrogenase activity and diazotrophic growth by measuring acetylene reduction activity and 15N2 incorporation into cell mass, and demonstrated that transcription of nifH and nitrogenase activity occur only in the absence of ammonium. Based on the ancestral relationship to ‘Candidatus Endomicrobium trichonymphae’ and other obligate endosymbionts, we propose the name ‘Endomicrobium proavitum’ gen. nov., sp. nov. for the first isolate of this lineage and the name ‘Endomicrobia’ class. nov. for the entire clade.
Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle
Authors: Patyshakuliyeva Aleksandrina , Post Harm , Zhou Miaomiao , Jurak Edita , Heck Albert J. R. , Hildén Kristiina S. , Kabel Mirjam A. , Mäkelä Miia R. , Altelaar Maarten A. F. , de Vries Ronald P. 
Published: June 2015

SummaryThe economically important edible basidiomycete mushroom Agaricus bisporus thrives on decaying plant material in forests and grasslands of North America and Europe. It degrades forest litter and contributes to global carbon recycling, depolymerizing (hemi‐)cellulose and lignin in plant biomass. Relatively little is known about how A. bisporus grows in the controlled environment in commercial production facilities and utilizes its substrate. Using transcriptomics and proteomics, we showed that changes in plant biomass degradation by A. bisporus occur throughout its life cycle. Ligninolytic genes were only highly expressed during the spawning stage day 16. In contrast, (hemi‐)cellulolytic genes were highly expressed at the first flush, whereas low expression was observed at the second flush. The essential role for many highly expressed plant biomass degrading genes was supported by exo‐proteome analysis. Our data also support a model of sequential lignocellulose degradation by wood‐decaying fungi proposed in previous studies, concluding that lignin is degraded at the initial stage of growth in compost and is not modified after the spawning stage. The observed differences in gene expression involved in (hemi‐)cellulose degradation between the first and second flushes could partially explain the reduction in the number of mushrooms during the second flush.