bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non‐homogeneity of variance components from spatially nested sampling of the soil
Authors: Lark R. M. , Corstanje R. 
Published: April 2009

SummarySpatially nested sampling and the associated nested analysis of variance by spatial scale is a well‐established methodology for the exploratory investigation of soil variation over multiple, disparate scales. The variance components that can be estimated this way can be accumulated to approximate the variogram. This allows us to identify the important scales of variation, and the general form of the spatial dependence, in order to plan more detailed sampling by design‐based or model‐based methods. Implicit in the standard analyses of nested sample data is the assumption of homogeneity in the variance, i.e. that all variations from sub‐station means at some scale represent a random variable of uniform variance. If this assumption fails then the comparable assumption of stationarity in the variance, which is an important assumption in geostatistics, will also be implausible. However, data from nested sampling may be analysed with a linear mixed model in which the variance components are parameters which can be estimated by residual maximum likelihood (REML). Within this framework it is possible to propose an alternative variance parameterization in which the variance depends on some auxiliary variable, and so is not generally homogeneous. In this paper we demonstrate this approach, using data from nested sampling of chemical and biogeochemical soil properties across a region in central England, and use land use as our auxiliary variable to model non‐homogeneous variance components. We show how the REML analysis allows us to make inferences about the need for a non‐homogeneous model. Variances of soil pH and cation exchange capacity at different scales differ between these land uses, but a homogeneous variance model is preferable to such non‐homogeneous models for the variance of soil urease activity at standard concentrations of urea.
Lax‐Wendroff and Nyström methods for seismic modelling
Authors: Chen Jing‐Bo 
Published: April 2009

ABSTRACTLax‐Wendroff and Nyström methods are numerical algorithms of temporal approximations for solving differential equations. These methods provide efficient algorithms for high‐accuracy seismic modeling. In the context of spatial pseudospectral discretizations, I explore these two kinds of methods in a comparative way. Their stability and dispersion relation are discussed in detail. Comparison between the fourth‐order Lax‐Wendroff method and a fourth‐order Nyström method shows that the Nyström method has smaller stability limit but has a better dispersion relation, which is closer to the sixth‐order Lax‐Wendroff method. The structure‐preserving property of these methods is also revealed. The Lax‐Wendroff methods are a second‐order symplectic algorithm, which is independent of the order of the methods. This result is useful for understanding the error growth of Lax‐Wendroff methods. Numerical experiments based on the scalar wave equation are performed to test the presented schemes and demonstrate the advantages of the symplectic methods over the nonsymplectic ones.
Treatment of conflicting dips in the 3D common‐reflection‐surface stack
Authors: Müller Nils‐Alexander 
Published: April 2009

ABSTRACTThe 3D common‐reflection‐surface stack is a tool to simulate zero‐offset sections from the prestack data. In conventional implementations conflicting dip situations, i.e., the contribution of more than one stacking operator per output location, are not taken into account. This leads to stacked sections with fragmentary events and to incomplete sets of stacking parameters. Subsequent applications based on the results of the common‐reflection‐surface stack and its attributes will show deteriorated quality.In this paper, I present a modified workflow for the handling of the conflicting dip problem in context of the 3D common‐reflection‐surface stack. The strategy utilizes the path‐summation technique to obtain an improved input for the conflicting dip search in the zero‐offset domain. The actual detection is done by means of an adapted peak detection algorithm. For each detected event consistent sets of attributes are obtained by a newly introduced search step.Two 3D real data applications show the applicability of the proposed technique. The strategy proves to resolve most of the conflicting dip situations even for poor signal‐to‐noise ratio. With only moderate additional computational cost the presented method provides superior results compared to the conventional 3D common‐reflection‐surface stack.
Indirect effects of soil moisture reverse soil C sequestration responses of a spring wheat agroecosystem to elevated CO2
Authors: MARHAN SVEN , KANDELER ELLEN , REIN STEFANIE , FANGMEIER ANDREAS , NIKLAUS PASCAL A. 
Published: April 2009

AbstractIncreased plant productivity under elevated atmospheric CO2 concentrations might increase soil carbon (C) inputs and storage, which would constitute an important negative feedback on the ongoing atmospheric CO2 rise. However, elevated CO2 often also leads to increased soil moisture, which could accelerate the decomposition of soil organic matter, thus counteracting the positive effects via C cycling. We investigated soil C sequestration responses to 5 years of elevated CO2 treatment in a temperate spring wheat agroecosystem. The application of 13C‐depleted CO2 to the elevated CO2 plots enabled us to partition soil C into recently fixed C (Cnew) and pre‐experimental C (Cold) by 13C/12C mass balance. Gross C inputs to soils associated with Cnew accumulation and the decomposition of Cold were then simulated using the Rothamsted C model ‘RothC.’ We also ran simulations with a modified RothC version that was driven directly by measured soil moisture and temperature data instead of the original water balance equation that required potential evaporation and precipitation as input. The model accurately reproduced the measured Cnew in bulk soil and microbial biomass C. Assuming equal soil moisture in both ambient and elevated CO2, simulation results indicated that elevated CO2 soils accumulated an extra ∼40–50 g C m−2 relative to ambient CO2 soils over the 5 year treatment period. However, when accounting for the increased soil moisture under elevated CO2 that we observed, a faster decomposition of Cold resulted; this extra C loss under elevated CO2 resulted in a negative net effect on total soil C of ∼30 g C m−2 relative to ambient conditions. The present study therefore demonstrates that positive effects of elevated CO2 on soil C due to extra soil C inputs can be more than compensated by negative effects of elevated CO2 via the hydrological cycle.
Scale and uncertainty in modeled soil organic carbon stock changes for US croplands using a process‐based model
Authors: OGLE STEPHEN M. , BREIDT F. JAY , EASTER MARK , WILLIAMS STEVE , KILLIAN KENDRICK , PAUSTIAN KEITH 
Published: April 2009

AbstractProcess‐based model analyses are often used to estimate changes in soil organic carbon (SOC), particularly at regional to continental scales. However, uncertainties are rarely evaluated, and so it is difficult to determine how much confidence can be placed in the results. Our objective was to quantify uncertainties across multiple scales in a process‐based model analysis, and provide 95% confidence intervals for the estimates. Specifically, we used the Century ecosystem model to estimate changes in SOC stocks for US croplands during the 1990s, addressing uncertainties in model inputs, structure and scaling of results from point locations to regions and the entire country. Overall, SOC stocks increased in US croplands by 14.6 Tg C yr−1 from 1990 to 1995 and 17.5 Tg C yr−1 during 1995 to 2000, and uncertainties were ±22% and ±16% for the two time periods, respectively. Uncertainties were inversely related to spatial scale, with median uncertainties at the regional scale estimated at ±118% and ±114% during the early and latter part of 1990s, and even higher at the site scale with estimates at ±739% and ±674% for the time periods, respectively. This relationship appeared to be driven by the amount of the SOC stock change; changes in stocks that exceeded 200 Gg C yr−1 represented a threshold where uncertainties were always lower than ±100%. Consequently, the amount of uncertainty in estimates derived from process‐based models will partly depend on the level of SOC accumulation or loss. In general, the majority of uncertainty was associated with model structure in this application, and so attaining higher levels of precision in the estimates will largely depend on improving the model algorithms and parameterization, as well as increasing the number of measurement sites used to evaluate the structural uncertainty.
The impacts of classical insect hormones on the expression profiles of a new digestive trypsin‐like protease (TLP) from the cotton bollworm, Helicoverpa armigera
Authors: Sui Y‐P. , Wang J‐X. , Zhao X‐F. 
Published: April 2009

AbstractTrypsin proteinases perform important roles in the protein digestion of an insect midgut. A 1042 bp full‐length cDNA was cloned from Helicoverpa armigera. The gene encoded a 32 kDa protein, with a predicted isoelectric point of 5.7. The amino acid sequence of the protein had a trypsin‐like serine protease domain, and the gene was named Ha‐TLP. The expression of the gene was tissue‐specific and the transcript of Ha‐TLP existed only in the midgut and was not found in the head‐thorax, integument, fat body and haemocytes from 5th instar larvae, with similar expression levels between those in feeding larvae and in molting larvae. In the midgut, the gene transcription level declined from 6th instar 72 h after the larvae entered the wandering stage, and disappeared from 6th instar at 96 h until the pupal stage. By immunohistochemistry, Ha‐TLP was detected in the cytoplasm of the midgut epithelial cells of the 6th instar feeding stage worms. The expression of Ha‐TLP could be up‐regulated by a juvenile hormone (JH) analog methoprene and down‐regulated by 20‐hydroxyecdysone (20E). These facts indicate that Ha‐TLP was involved in food digestion during larval growth and probably up‐regulated by JH and suppressed by extra 20E in vivo.
An investigation to determine the nutritional adequacy and individuals experience of a very low fat diet used to treat type V hypertriglyceridaemia
Authors: Whitfield‐Brown L. , Hamer O. , Ellahi B. , Burden S. , Durrington P. 
Published: April 2009

AbstractBackground:  The management of Type V hypertriglyceridaemia at some centres involves the use of a very low fat diet (15% energy as fat). There is no published research examining compliance with, or nutritional adequacy, of this treatment. This study assesses the nutritional adequacy of the diet and examines barriers and enablers to adherence.Methods:  Fifty‐four eligible patients were invited to take part. Eight males and one female agreed to participate. One male later withdrew. The mean age of participants was 49.4 years (SD 12.9 years), their mean BMI was 30.4 kg m−2 (SD 3.4 kg m−2) and their mean triglyceride level was 8.5 mmol L−1 (SD 5.6 mmol L−1). To assess nutritional adequacy and compliance, 3‐day dietary records and telephone based diet histories were used and analysed using CompEat. Patients’ experience was investigated using semi‐structured telephone based qualitative interviews. Qualitative data was recorded, transcribed and analysed using thematic analysis to allow elucidation of emerging themes.Results:  Fat accounted for 22.5% of dietary energy and compliance was considered difficult. Barriers included lack of accessible nutritional information, increased patient burden defined as inconvenience and the persistent awareness of potential or actual ill health, lack of appropriate food choices, other peoples’ ignorance, lack of flavour and variety, a desire to broaden the palate, cost, social pressure and prior negative experiences with dietitians. Enablers to compliance included nutritional awareness, desire to maintain good health, building on their nutritional knowledge base, behaviour and lifestyle modification, developing a routine, the support of family and friends and supportive eating environments.Conclusion:  Compliance could be improved through extensive education on labelling, eating during special occasions such as Christmas, birthdays and eating out.
Determination of the lactose and galactose content of cheese for use in the galactosaemia diet
Authors: Portnoi P. A. , MacDonald A. 
Published: April 2009

AbstractBackground:  Treatment of galactosaemia requires a low galactose diet. In the UK, traditionally, all cheeses have been excluded from the diet, although some types of mature hard cheese are likely to be low in lactose and galactose. The present study aimed to determine the lactose and galactose content of mature cheeses.Methods:  Over 6 years, the UK Galactosaemia Support Group commissioned the analysis of 109 samples (by two laboratories) of 12 cheese types, in eight batches throughout the year. Cheeses, obtained from retail outlets, were homogenised, sugars were extracted using water or 40% alcohol for fatty samples, and samples were deproteinised. Enzymatic analysis using measuring light absorbance was conducted on filtered extracts.Results:  Cheeses containing undetectable quantities of lactose (<2.8 mg 100 g−1, Leatherhead Food International, Leatherhead, UK (LFI) analysis; <10 mg 100 g−1, Laboratory of Government Chemist, Teddington, UK (LGC Limited) analysis) and galactose were: Gruyere (five samples); Emmental (block, sliced and grated) (16 samples); Jarlsberg (six samples); Parmigiano Reggiano and Grana Padano Italian Parmesan (block and grated) (16 samples); and mature Cheddar cheese from the UK West Country Farmhouse Cheese Makers Association (35 samples) only. Lactose containing cheeses included other mature Cheddar cheeses, Gouda and Edam.Conclusions:  Gruyere, Emmental, Jarlsberg, Italian Parmesan (Parmigiano Reggiano and Grana Padano), and mature Cheddar cheese produced in one area of England where the manufacturing process is standardised and guaranteed are now allowed in the UK galactosaemia diet.
Health‐related quality of life in patients with home nutritional support
Authors: Wanden‐Berghe C. , Nolasco A. , Sanz‐Valero J. , Planas M. , Cuerda C. ,   for the Group NADYA‐SENPE
Published: April 2009

AbstractBackground:  Home nutritional support (HNS) aims to improve or maintain the patient’s quality of life. Given the high social cost of such treatment, however, it is important to investigate whether the perceived quality of life of patients receiving HNS does in fact reflect these objectives. The present study aimed to evaluate the health‐related quality of life (HRQoL) of patients who receive HNS.Methods:  A multicentre, cross‐sectional study of 267 patients was carried out. HRQoL was evaluated using the EuroQoL‐5‐Dimensions (EQ‐5D) questionnaire. The Visual Analogue Scale (VAS) was used to complement the EQ‐5D, aiming to provide an overall estimation of patient quality of life.Results:  The EQ‐5D questionnaire showed that 25% of the subjects valued their HRQoL at between −0.08 and 0.15, 50% at between 0.16 and 0.69 and 25% at between 0.70 and 1. Results from the VAS showed that 75% of patients claimed to have a HRQoL > 40. The median for the VAS was 50.Pathologies were oncological (44.0%), neurological (36.6%) and others (19.3%). The results obtained demonstrate that neurological patients placed a lower value on their HRQoL compared to those of other groups (P < 0.001). In addition, women rated their quality of life lower than men in all pathologies (P = 0.006).Conclusions:  Perceived HRQoL varied depending on pathology and sex. It was difficult to draw conclusions concerning the impact of HNS because of a lack of baseline data and relevant validated measurement tools. The present study highlights the need for more research into the relationship between HNS and HRQoL.
AglZ regulates adventurous (A‐) motility in Myxococcus xanthus through its interaction with the cytoplasmic receptor, FrzCD
Authors: Mauriello Emilia M. F. , Nan Beiyan , Zusman David R. 
Published: April 2009

Summary Myxococcus xanthus moves by gliding motility powered by type IV pili (S‐motility) and distributed motor complexes (A‐motility). The Frz chemosensory pathway controls reversals for both motility systems. However, it is unclear how the Frz pathway can communicate with these different systems. In this article, we show that FrzCD, the Frz pathway receptor, interacts with AglZ, a protein associated with A‐motility. Affinity chromatography and cross‐linking experiments showed that the FrzCD–AglZ interaction occurs between the uncharacterized N‐terminal region of FrzCD and the N‐terminal pseudo‐receiver domain of AglZ. Fluorescence microscopy showed AglZ–mCherry and FrzCD–GFP localized in clusters that occupy different positions in cells. To study the role of the Frz system in the regulation of A‐motility, we constructed aglZ frzCD double mutants and aglZ frzCD pilA triple mutants. To our surprise, these mutants, predicted to show no A‐motility (A‐S+) or no motility at all (A‐S‐), respectively, showed restored A‐motility. These results indicate that AglZ modulates a FrzCD activity that inhibits A‐motility. We hypothesize that AglZ–FrzCD interactions are favoured when cells are isolated and moving by A‐motility and inhibited when S‐motility predominates and A‐motility is reduced.
Manganese import is a key element of the OxyR response to hydrogen peroxide in Escherichia coli
Authors: Anjem Adil , Varghese Shery , Imlay James A. 
Published: April 2009

SummaryVery little manganese is imported into Escherichia coli under routine growth conditions: the import system is weakly expressed, the manganese content is low, and a manganese‐dependent enzyme is not correctly metallated. Mutants that lack MntH, the importer, grow at wild‐type rates, indicating that manganese plays no critical role. However, MntH supports the growth of iron‐deficient cells, suggesting that manganese can substitute for iron in activating at least some metalloenzymes. MntH is also strongly induced when cells are stressed by hydrogen peroxide. This adaptation is essential, as E. coli cannot tolerate peroxide stress if mntH is deleted. Other workers have observed that manganese improves the ability of a variety of microbes to tolerate oxidative stress, and the prevailing hypothesis is that manganese does so by chemically scavenging hydrogen peroxide and/or superoxide. We found that manganese does not protect peroxide‐stressed cells by scavenging peroxide. Instead, the beneficial effects of manganese correlate with its ability to metallate mononuclear enzymes. Because iron‐loaded enzymes are vulnerable to the Fenton reaction, the substitution of manganese may prevent protein damage. Accordingly, during H2O2 stress, mutants that cannot import manganese and/or are unable to sequester iron suffer high rates of protein oxidation.
TagR promotes PpkA‐catalysed type VI secretion activation in Pseudomonas aeruginosa
Authors: Hsu FoSheng , Schwarz Sandra , Mougous Joseph D. 
Published: April 2009

SummaryType VI secretion systems (T6SSs) contribute to interactions of bacterial pathogens and symbionts with their hosts. Previously, we showed that Pseudomonas aeruginosa T6S is posttranslationally activated upon phosphorylation of Fha1, an FHA domain protein, by PpkA, a membrane‐spanning threonine kinase. Herein, additional structural, enzymatic and genetic requirements for PpkA‐catalysed T6SS activation are identified. We found that PpkA plays an essential structural role in the T6SS, and that this role is intimately linked to its ability to promote secretion and phosphorylate Fha1. Protein localization and protein–protein interaction studies show that a complex containing Fha1 and the T6S ATPase, ClpV1 is recruited to the T6S apparatus in a phosphorylation‐dependent manner. The mechanism of PpkA activation was also investigated. We identified critical PpkA autophosphorylation sites and showed that small molecule‐induced dimerization of the extracellular domains of PpkA is sufficient to activate the T6SS. Finally, we discovered TagR, a component of the T6S posttranslational regulatory pathway that functions upstream of PpkA to promote kinase activity. We present a model whereby an unknown cue causes dimerization of the extracellular domains of PpkA, leading to its autophosphorylation, recruitment of the Fha1‐ClpV1 complex, phosphorylation of Fha1, and T6SS activation. Our findings should facilitate approaches for identifying physiological activators of T6S.
Molecular analysis of restriction endonuclease EcoRII from Escherichia coli reveals precise regulation of its enzymatic activity by autoinhibition
Authors: Szczepek Michal , Mackeldanz Petra , Möncke‐Buchner Elisabeth , Alves Jürgen , Krüger Detlev H. , Reuter Monika 
Published: April 2009

SummaryBacterial restriction endonuclease EcoRII requires two recognition sites to cleave DNA. Proteolysis of EcoRII revealed the existence of two stable domains, EcoRII‐N and EcoRII‐C. Reduction of the enzyme to its C‐terminal domain, EcoRII‐C, unleashed the enzyme activity; this truncated form no longer needed two recognition sites and cleaved DNA much more efficiently than EcoRII wild‐type. The crystal structure of EcoRII showed that probably the N‐terminal domain sterically occludes the catalytic site, thus apparently controlling the cleavage activity. Based on these data, EcoRII was the first restriction endonuclease for which an autoinhibition mechanism as regulatory strategy was proposed. In this study, we probed this assumption and searched for the inhibitory element that mediates autoinhibition. Here we show that repression of EcoRII‐C is achieved by addition of the inhibitory domain EcoRII‐N or by single soluble peptides thereof in trans. Moreover, we perturbed contacts between the N‐ and the C‐terminal domain of EcoRII by site‐directed mutagenesis and proved that β‐strand B1 and α‐helix H2 are essential for autoinhibition; deletion of either secondary structural element completely relieved EcoRII autoinhibition. This potent regulation principle that keeps EcoRII enzyme activity controlled might protect bacteria against suicidal restriction of rare unmodified recognition sites in the cellular genome.
FtsN‐like proteins are conserved components of the cell division machinery in proteobacteria
Authors: Möll Andrea , Thanbichler Martin 
Published: April 2009

SummaryIn bacteria, cytokinesis is mediated by a ring‐shaped multiprotein complex, called divisome. While some of its components are widely conserved, others are restricted to certain bacterial lineages. FtsN is the last essential cell division protein to localize to the division septum in Escherichia coli and is poorly conserved outside the enteric bacteria. We have identified a homologue of FtsN in the α‐proteobacterium Caulobacter crescentus and show that it is essential for cell division. C. crescentus FtsN is recruited to the divisome significantly after cell division initiates and remains associated with the new cell poles after cytokinesis is finished. All determinants necessary for localization and function are located in a largely unstructured periplasmic segment of the protein. Its conserved SPOR‐domain, by contrast, is dispensable for cytokinesis, although it supports targeting of FtsN to the division site. Interestingly, the SPOR‐domain is recruited to the division plane when produced in isolated form and retains its localization potential in a heterologous host background. Searching for proteins that share the characteristic features of FtsN from E. coli and C. crescentus, we identified FtsN‐like cell division proteins in β‐ and δ‐proteobacteria, suggesting that FtsN is widespread among bacteria, albeit highly variable at the sequence level.