bluuebunny/crossref_metadata_2025 huggingface dataset:
Long‐term changes in organic matter of woodland soils cleared for arable cropping in Zimbabwe
Authors: Zingore S. , Manyame C. , Nyamugafata P. , Giller K. E.
Published: September 2005

Subsistence farmers in Africa depend largely on the soil organic matter to sustain crop productivity. Long‐term changes in soil organic carbon and nitrogen were measured after woodland clearance for smallholder subsistence farming or for commercial farming. The contents of organic carbon and nitrogen in soil under reference woodlands were largest (53.3 t C ha−1, 4.88 t N ha−1) in a red clay soil (∼ 50% clay + silt), followed by a granitic sand (∼ 12% clay + silt; 22.8 t C ha−1, 1.47 t N ha−1) and least (19.5 t C ha−1, 0.88 t N ha−1) in a Kalahari sand (∼ 5% clay + silt). Organic carbon declined rapidly under cultivation to attain new equilibria within 10 years on all smallholdings. Greatest losses occurred in soils that initially contained most carbon and nitrogen in the order: red clay (22.4 t C ha−1 and 1.0 t N ha−1) > granitic sand (13.2 t C ha−1 and 0.8 t N ha−1) > Kalahari sand (10.6 t C ha−1 and 0.5 t N ha−1). On the clay soil, commercial farming with intensive use of mineral fertilizers and incorporation of maize stover led to more gradual decline: at equilibrium, contents of carbon and nitrogen were 15 t C ha−1 and 1.7 t N ha−1 greater than on smallholdings with similar soil and climate.

In the Kalahari sand the δ13C of organic C remained constant after woodland clearance, and maize contributed less than 10% of the total C even after 55 years. The δ13C signature increased slightly with increasing duration of cultivation by smallholders in the granitic sands and red clay soil where maize contributed 29% and 35% of the C at equilibrium. Under more productive commercial farming, the carbon derived from maize accounted for 50% of the total after 10 years of cultivation and 67% at equilibrium. The persistence of woodland carbon in the sandy soil is attributed to chemical stabilization resulting from large concentrations of lignin and polyphenols in the tree litter, or as charcoal.
An overview of the permanence of soil organic carbon stocks: influence of direct human‐induced, indirect and natural effects
Authors: Smith P.
Published: September 2005

If biospheric sinks, such as soil organic carbon, are to be used to meet obligations for greenhouse gas emission reduction under the Kyoto Protocol, the permanence of these sinks needs to be considered. Further, since only direct human‐induced carbon sinks can be included, and sinks resulting from indirect and natural effects cannot be used, there is a pressing need to separate direct human‐induced effects from indirect and natural effects. Since these effects also influence the permanence of soil organic stocks, this paper attempts to synthesize existing knowledge in soil science, and use models to examine the likely influence of direct, indirect and natural effects on the permanence of soil organic carbon stocks.
Organo‐mineral associations in sandy acid forest soils: importance of specific surface area, iron oxides and micropores
Authors: Eusterhues K. , Rumpel C. , Kögel‐Knabner I.
Published: September 2005

Organo‐mineral associations stabilize soil organic matter, though the mechanisms by which they do so are unclear. We used particle‐size fractions < 6.3 μm of two soils to examine the importance of Fe oxides, short‐range order Al silicates and the surface areas of minerals and micropores on the formation of organo‐mineral associations. In the subsoil Fe oxides were most strongly statistically correlated with the mineral‐bound organic carbon. We therefore assume that they are the most important substrates for the formation of organo‐mineral associations. There is no indication that this is caused by physical protection of organic matter in their micropores (< 2 nm). In the Haplic Podzol, dithionite–citrate–bicarbonate‐soluble short‐range order Al silicates may also play a role. Fe oxide particles were calculated to offer specific surface areas of ∼ 200 m2 g−1 (goethite) and ∼ 800 m2 g−1 (ferrihydrite), corresponding to crystal diameters of only a few nm. We assume that the resulting large amount of oxide‐specific reactive surface sites (conditionally charged hydroxyl groups) is responsible for their dominant role as sorbents. With maximum C loadings of 1.3 mg C per m2 Fe oxide for the Dystric Cambisol and 1.1 mg C per m2 Fe oxide + short‐range order Al silicates for the Haplic Podzol the subsoils of both soils seem to have reached saturation with respect to organic matter sorption. In contrast to subsoil horizons, organo‐mineral associations from topsoils contain much larger amounts of organic matter. Here a larger C loading on Fe oxides or a greater importance of other sorbents in addition to the oxides must be assumed.
Water flow patterns and pesticide fluxes in an upland soil in northern Thailand
Authors: Ciglasch H. , Amelung W. , Totrakool S. , Kaupenjohann M.
Published: September 2005

Rapid percolation of water through soil facilitates both the recharge and the contamination of groundwater reservoirs. We have studied the variation of water flux and pesticide leaching through a soil in northern Thailand. At a depth of 55 cm, two pits were equipped with tensiometer‐controlled glass suction lysimeters that were connected to a novel on‐line solid‐phase extraction device. Nine insecticides varying in water solubility from 10−2 to 10+6 mg l−1 were applied on the soil surface, and leaching was monitored for 8 weeks. Measured water fluxes were compared with simulated values. Total recovery ranged from traces (malathion, triazophos) to 1.3% (dimethoate) of the applied amount, showing a decreasing retardation with increasing polarity of the substances. All pesticides were detectable in the soil solution during the first rain after application. Due to fingering, 83% of the leachate was transported through 38% of the area at leaching rates of < 2 mm per day. A new adaptation of the Simpson Index revealed that the diversity of the flow pattern increased exponentially with decreasing rates of seepage water flux (R2 = 0.80). No such correlation was found when leaching was faster, indicating that the flow pattern switched from a fingering‐ to a matric‐dominated flux. No long‐term leaching of insecticides was observed. The two profiles studied behaved similarly in terms of both water and pesticide transport. Therefore we suggest that the flow pattern is a stable property of the soil that can be accurately described by our combination of novel experimental setup and statistical analysis of the flow field.
Spatial analysis of categorical soil variables with the wavelet transform
Authors: Lark R. M.
Published: September 2005

This paper describes a wavelet transform for the analysis of categorical (multistate) soil variables, i.e. ones (such as profile classes) that have two or more discrete states. The states are transformed to a continuous variable by a mapping which is optimized by scale and location to highlight local variation.

The method is illustrated with data from a transect across a gilgai landscape in Australia. A categorical variable on relief, with three states, was recorded from the sample sites, from which soil cores had also been collected and analysed. The wavelet analysis showed a transient feature of the variation at scales up to 32 m. There was an interval where the characteristic alternation of depressions with the level plain was interrupted. The variation at scale 64 m appeared to be non‐stationary. The relief was more variable on one side of a change point than it was on the other.

This complex variation of relief was matched by that of the electrical conductivity of the soil, most strongly at the 64‐m scale. The periodicity of conductivity, and the strength of its correlation with relief, were also different either side of the change point identified in the analysis of relief alone. Conductivity also showed similar transient features to relief.

Evidently the wavelet transform can be used to elucidate the variation of categorical soil variables. The information from such an analysis is likely to be useful for planning surveys of the soil to measure continuous variables by sampling and laboratory analysis.
Regulating the mobility of Cd, Cu and Pb in an acid soil with amendments of phosphogypsum, sugar foam, and phosphoric rock
Authors: Garrido F. , Illera V. , Campbell C. G. , García‐González M. T.
Published: September 2005

When acid soil has been contaminated by metals as a result of industrial discharges, accidental spills, or acid mine drainage it may be desirable to retain the metals in the soil rather than allow them to leach away. We have investigated the potential of phosphogypsum (PG), sugar foam (SF), and phosphoric rock (PR) to regulate the availability and mobility of Pb, Cd and Cu. We have also identified changes in attenuation during incubation for 1 year and the effect of aging on metal speciation in amended soils. We studied miscible displacement in columns of undisturbed soil previously treated with solutions of the amendments and soluble metals and, subsequently, single and sequential chemical metal extractions. All amendments increased the soil's metal retention capacity. This, in turn, increased the amount of metal extractable by diethylenetriaminepentaacetic acid (DTPA). However, over time the amounts of DTPA‐extractable metal decreased, particularly for Cu and Pb. Both Cu and Cd were held preferentially within the acetic acid‐extractable fraction (operationally defined exchangeable fraction – EX fraction), whereas Pb was associated mainly with the hydroxylammonium‐extractable fraction (operationally defined bound to Fe and Al hydroxides – OX fraction). Both Pb and Cu in the oxide and organic fractions increased in the PG‐ and SF‐treated soils. In general, the distribution of metal did not change in the PR‐treated columns after the incubation. Finally, scanning electron microscopy in back‐scattered electron mode (SEM–BSE) showed the formation of Al‐hydroxy polymers which provides the soils with additional cation sorption capacity. In the PG‐ and PR‐treated columns, P and S were associated with these formations. The three metals were associated with the Al polymers, probably through direct coordination or the formation of ternary complexes with the inorganic ligands phosphate and sulphate.
Soil sorption–desorption of phosphorus from piggery effluent compared with inorganic sources
Authors: Redding M. R. , Shatte T. , Bell K.
Published: September 2005

The leaching of phosphorus (P) within soils can be a limiting consideration for the sustainable operation of intensive livestock enterprises. Sorption curves are widely used to assist estimation of P retention, though the effect of effluent constituents on their accuracy is not well understood. We conducted a series of P‐sorption–desorption batch experiments with an Oxic Haplustalf (soil 1), Haplusterts (soils 2 and 3), and a Natrustalf (soil 4). Phosphorus sources included effluent, orthophosphate‐P in a matrix replicating the effluent's salt constituents (the reference solution), and an orthophosphate‐P solution. Treated soils were incubated for up to 193 days before sequential desorption extraction. Effluent constituents, probably the organic or particulate components, temporarily increased the vulnerability of sorbed‐P to desorption. The increase in vulnerability was removed by 2–113 days of incubation (25°C). Despite vigorous extraction for 20 consecutive days, some P sorbed as part of the treatments of soils 1 and 2 was not desorbed. The increased vulnerability due to effluent constituents lasted a maximum of about one cropping season and, for all other treatments, adsorption curves overestimated vulnerability to desorption. Therefore, adsorption curves provide a conservative estimate of vulnerability to desorption where effluent is used in continued crop production in these soils.
Organic carbon stocks in the Russian Chernozem
Authors: Mikhailova E. A. , Post C. J.
Published: September 2005

Chernozems (Mollisols) play an important role in the global carbon cycle, but their contribution to the global carbon stock is often underestimated. We have estimated stocks of organic carbon in the upper 2 m in the Russian Chernozem (Haplic Chernozem) under four management regimes: a native grassland (not cultivated for at least 300 years), an adjacent continuous fallow field, a yearly‐cut meadow and an arable field in the Kursk region of Russia. The organic carbon stored in the top 2 m was 462 t ha−1 for the grassland, 451 t ha−1 for the yearly‐cut meadow, 387 t ha−1 for the arable field and 349 t ha−1 for the continuous fallow. From 18 to 26% of the total organic C in the top 2 m was between 1 and 2 m in all four regimes. Vertical distribution of organic C was modelled by an exponential function for which the R2 values lay in the range 0.89–0.95, depending on the regime. This exponential function was used to predict organic C below 2 m in the Haplic Chernozem. Model estimates showed that if we include organic C stored in the Russian Chernozem between 1 and 3 m we shall increase our estimates of C stored by 27–30%.
Sources of nitrite in a permanent grassland soil
Authors: Müller C. , Stevens R. J. , Laughlin R. J.
Published: September 2005

The objective of this study was to separate the observed nitrite (NO2–) concentration in a permanent grassland soil into process‐specific subpools. A laboratory experiment was carried out where either the nitrate and/or ammonium pool was labelled with 15N at 60 atom % excess. The main N transformations that occurred in this experiment were analysed with a 15N tracing model extended with a NO2– submodel. Techniques that have been used to date have been only able to identify NO2– subpools related to nitrification (NO2–nit) and denitrification (NO2–den). With the analysis presented here, we were able to quantify the size of an additional NO2– pool in the soil related to organic N turnover (NO2–org). All transformations related to NO2– turnover of the three subpools occurred simultaneously. After non‐linear parameter optimization the model predicted that on average NO2–den, NO2–nit and NO2–org pools contributed 57, 33 and 10% to the total soil NO2– concentration. The finding that heterotrophic processes can contribute to the NO2– dynamics in permanent grassland soils might also have important implications for the understanding of gaseous N production that are tightly linked to NO2– turnover. Further work is needed to find out how important the conversion of organic N to NO2– is in other soil‐based ecosystems and to identify the microbial groups responsible for this process.
Methane and nitrous oxide fluxes of soils in pure and mixed stands of European beech and Norway spruce
Authors: Borken W. , Beese F.
Published: September 2005

Tree species can affect the sink and source strength of soils for atmospheric methane and nitrous oxide. Here we report soil methane (CH4) and nitrous oxide (N2O) fluxes of adjacent pure and mixed stands of beech and spruce at Solling, Germany. Mean CH4 uptake rates ranged between 18 and 48 μg C m−2 hour−1 during 2.5 years and were about twice as great in both mixed and the pure beech stand as in the pure spruce stand. CH4 uptake was negatively correlated with the dry mass of the O horizon, suggesting that this diminishes the transport of atmospheric CH4 into the mineral soil. Mean N2O emission was rather small, ranging between 6 and 16 μg N m−2 hour−1 in all stands. Forest type had a significant effect on N2O emission only in one mixed stand during the growing season. We removed the O horizon in additional plots to study its effect on gas fluxes over 1.5 years, but N2O emissions were not altered by this treatment. Surprisingly, CH4 uptake decreased in both mixed and the pure beech stands following the removal of the O horizon. The decrease in CH4 uptake coincided with an increase in the soil moisture content of the mineral soil. Hence, O horizons may maintain the gas diffusivity within the mineral soil by storing water which cannot penetrate into the mineral soil after rainfall. Our results indicate that conversion of beech forests to beech–spruce and pure spruce forests could decrease soil CH4 uptake, while the long‐term effect on N2O emissions is expected to be rather small.
Comparative study of six rotary nickel–titanium systems and hand instrumentation for root canal preparation
Authors: Guelzow A. , Stamm O. , Martus P. , Kielbassa A. M.
Published: September 2005

Aim  To compare ex vivo various parameters of root canal preparation using a manual technique and six different rotary nickel–titanium (Ni–Ti) instruments (FlexMaster, System GT, HERO 642, K3, ProTaper, and RaCe).

Methodology  A total of 147 extracted mandibular molars were devided into seven groups (n = 21) with equal mean mesio‐buccal root canal curvatures (up to 70°), and embedded in a muffle system. All root canals were prepared to size 30 using a crown‐down preparation technique for the rotary nickel–titanium instruments and a standardized preparation (using reamers and Hedströem files) for the manual technique. Length modifications and straightening were determined by standardized radiography and a computer‐aided difference measurement for every instrument system. Post‐operative cross‐sections were evaluated by light‐microscopic investigation and photographic documentation. Procedural errors, working time and time for instrumentation were recorded. The data were analysed statistically using the Kruskal–Wallis test and the Mann–Whitney U‐test.

Results  No significant differences were detected between the rotary Ni–Ti instruments for alteration of working length. All Ni–Ti systems maintained the original curvature well, with minor mean degrees of straightening ranging from 0.45° (System GT) to 1.17° (ProTaper). ProTaper had the lowest numbers of irregular post‐operative root canal diameters; the results were comparable between the other systems. Instrument fractures occurred with ProTaper in three root canals, whilst preparation with System GT, HERO 642, K3 and the manual technique resulted in one fracture each. Ni–Ti instruments prepared canals more rapidly than the manual technique. The shortest time for instrumentation was achieved with System GT (11.7 s).

Conclusions  Under the conditions of this ex vivo study all Ni–Ti systems maintained the canal curvature, were associated with few instrument fractures and were more rapid than a standardized manual technique. ProTaper instruments created more regular canal diameters.
Shear bond strength of Resilon to a methacrylate‐based root canal sealer
Authors: Hiraishi N. , Papacchini F. , Loushine R. J. , Weller R. N. , Ferrari M. , Pashley D. H. , Tay F. R.
Published: September 2005

Aim  To evaluate the adhesive strength of Resilon to NextTM root canal sealant (Heraeus–Kulzer), a methacrylate‐based root canal sealer, using a modified microshear bond testing design.

Methodology  Flat Resilon surfaces of different roughnesses (smooth surface and surface roughness equivalent to 320‐grit and 180‐grit) were prepared by compression moulding for bonding to the sealer and compared with a composite control. The shear strength data were statistically analysed using Kruskal–Wallis one‐way anova on ranks and Dunn's multiple comparison tests (α = 0.05). After shear testing, fractured specimens were examined using a field emission‐scanning electron microscope for detailed analysis of the failure modes.

Results  The composite control exhibited significantly higher mean shear strength (7.62 MPa) that was 4.4–4.7 times those of the Resilon groups (1.64–1.74 MPa; P < 0.001). Increasing the surface roughness of the Resilon surface did not contribute to further improvement in shear bond strength for this methacrylate‐based sealer (P > 0.05). Failure modes in the composite control were cohesive and mixed failures, while those in the Resilon groups were predominantly adhesive failures, with a small percentage of mixed failures. Ultrastructural evidence of phase separation of polymeric components could be identified in Resilon. Both intact, non deformed and plastically deformed Resilon surfaces could be observed in specimens that exhibited adhesive failures.

Conclusion  The low shear strength of Resilon to a methacrylate‐based sealer compared with a composite control suggests that the amount of dimethacrylate incorporated in this filled, polycaprolactone‐based thermoplastic composite may not yet be optimized for effective chemical coupling to methacrylate resins.
Soil feedback and pathogen activity in Prunus serotina throughout its native range
Authors: REINHART KURT O. , ROYO ALEJANDRO A. , VAN DER PUTTEN WIM H. , CLAY KEITH
Published: September 2005

Oomycete soil pathogens are known to have a negative effect on Prunus serotina seedling establishment and to promote tree diversity in a deciduous forest in Indiana, USA. Here, we investigate whether negative feedbacks operate widely in its native range in eastern USA.

In laboratory experiments, soil sterilization was used to test the net effect of soil biota (pathogens and mutualists) and fungicide treatments to test the effects of soil pathogens (oomycetes) on survival of P. serotina seedlings in soils from 22 P. serotina populations throughout the eastern USA.

In soil associated with P. serotina trees, there was a significant positive effect of both soil sterilization and fungicide on seedling survival. The two effects were positively correlated, suggesting that oomycetes were responsible for the observed mortality of seedlings in untreated soils relative to sterilized soils.

We determined the host‐specificity of these interactions by comparing the effects of the soil biota associated with conspecific and heterospecific trees. There was no interaction between the effects of soil origin and soil sterilization, or of soil origin and fungicide, on seedling survival, although an effect of soil origin on the relative oomycete effect suggested that soil pathogens associated with conspecifics had a more negative influence than those from heterospecifics.

Fungicide treatment decreased pre‐emergence mortality of P. serotina seedlings at two of three field sites in the northern USA.

The overall consistency between the laboratory experiments and the field experiment strongly suggests that oomycete soil pathogens have a negative effect on the survival of P. serotina seedlings throughout its native range in the eastern USA.

Soil‐borne pathogens therefore appear to regulate the densities of a common tree species (P. serotina) at larger geographical scales than previously described, providing additional evidence of the important role that soil biota play in regulating plant populations and structuring plant communities.
Soil‐related performance variation and distributions of tree species in a Bornean rain forest
Authors: RUSSO SABRINA E. , DAVIES STUART J. , KING DAVID A. , TAN SYLVESTER
Published: September 2005

Spatial distributions of tropical trees often correlate with environmental variation, suggesting that ecological sorting caused by niche differentiation may be important for maintaining species diversity.

Four soil types have been identified in a 52‐ha forest dynamics plot in Bornean mixed dipterocarp forest (ranked by increasing fertility and moisture: sandy loam, loam, fine loam, and clay). The distributions of 73% of tree species in the plot are significantly aggregated on one of these soil types. We tested the hypothesis that variation in performance (growth and mortality) underlies these edaphically biased species distributions.

Annual growth and mortality rates over 5 years were estimated for trees ≥ 1 cm in diameter and compared among soil types, life histories and species‐aggregation patterns.

Overall, growth and mortality rates were lowest on the poorest soil (sandy loam). Growth rates on each soil type correlated with soil fertility for pioneers, while mortality rates correlated with soil fertility for both pioneers and late‐successional species.

There was little evidence that soil specialists had a home‐soil performance advantage. Soil‐specific ranks of growth and mortality rates of each species‐aggregation group largely mirrored the ranks of their rates across the plot and did not shift substantially among soil types. On every soil, species aggregated on sandy loam or clay ranked last or next‐to‐last, and species aggregated on loam ranked the highest.

Ecological sorting of species among soils was strong. With increasing diameter, species were lost from the soils on which they were not aggregated more frequently than would be expected based on random mortality. The underlying mechanisms of ecological sorting may involve low mortality rates as a requirement for species to achieve high abundance on the poorest soil, whereas for the richer soils, having high growth rates appears relatively more important for achieving high abundance.

Thus, species’ demographic responses to resource variation among soil types, especially related to the poorest soil, affects tree species distribution patterns in this forest and thereby influences the structure of tropical forest communities.
Effects of long‐distance dispersal for metapopulation survival and genetic structure at ecological time and spatial scales
Authors: BOHRER GIL , NATHAN RAN , VOLIS SERGEI
Published: September 2005

Long‐distance dispersal (LDD) of seeds by wind plays an important role in population survival and structure, especially in naturally patchy or human‐fragmented metapopulations. However, no study has tested its effects using a realistic dispersal kernel in a metapopulation context with explicit spatial structure and local extinctions.

We incorporated such kernels into a newly proposed simulation model, which combines within‐patch (population) demographic processes and a simplified maternally inherited single‐locus, two‐allele genetic make‐up of the populations. As a test case, we modelled a typical conservation scenario of Aleppo pine (Pinus halepensis) populations.

The effects of LDD were rather diverse and depended on initial population conditions and local extinction rates. LDD increased metapopulation survival at intermediate local‐extinction probabilities. LDD helped maintain higher total genetic variability in populations that were initially drifted, but facilitated random genetic loss through drift in initially ‘well mixed’ populations. LDD prevented population differentiation in low extinction rates but increased it at intermediate to high extinction rates.

Our results suggest that LDD has broader evolutionary implications and would be selected for in populations facing intermediate local‐extinction pressures. Our modelling approach provides a strong tool to test the effects of LDD on metapopulation survival and genetic variability and to identify the parameters to which such effects are most sensitive, in ecological and conservational scenarios.
Do health care professionals underestimate severe pain more often than mild pain? Statistical pitfalls using a data simulation model
Authors: Idvall Ewa , Brudin Lars
Published: September 2005

Rationale  When comparing patients’ pain ratings with the health care professional's conception of pain assessed by Visual Analogue Scales (VAS) ratings, statistical problems arise.

Method and Result  In this data simulation study we have shown that the tendency for health care professionals to underestimate severe pain compared with mild pain is probably not attributed to difficulties in judging severe pain more often than mild but the result of professionals having a different and often narrower distribution of their ratings compared with patients.
Morphological and physiological characteristics of Saprolegnia spp. strains pathogenic to Atlantic salmon, Salmo salar L.
Authors: Stueland S , Hatai K , Skaar I
Published: September 2005

Seventeen strains of Saprolegnia spp. were examined for morphological and physiological characteristics, and seven were examined for their pathogenicity to Atlantic salmon, Salmo salar L. Two of the Saprolegnia strains tested caused 89 and 31% cumulative mortality in challenged salmonids and were significantly more pathogenic than the other strains tested. The positive control (Saprolegnia parasitica ATCC 90213) caused 18% mortality, but this was not significantly higher than non‐pathogenic strains (0–3% cumulative mortality). All the pathogenic Saprolegnia strains and two non‐pathogenic strains had secondary cysts with long, hooked hairs, a characteristic which is claimed to be typical of S. parasitica. This characteristic is apparently necessary, but does not in itself determine the ability to cause mortality in Atlantic salmon. However, all the pathogenic Saprolegnia strains in the present study showed a significantly higher initial growth rate of cysts in sterilized tap water than did non‐pathogenic strains. The results of the present study suggest that initial growth rate of germinating cysts in pure water, together with the presence of long hooked hairs on the secondary cysts, may be indicators of pathogenicity of Saprolegnia strains to Atlantic salmon.
Isolation of the salmonid rhamnose‐binding lectin STL2 from spores of the microsporidian fish parasite Loma salmonae
Authors: Booy A , Haddow J D , Olafson R W
Published: September 2005

The microsporidian parasite, Loma salmonae, is the causative agent of gill disease in both wild and netpen‐reared salmonids worldwide. In this paper we report the finding of a rhamnose‐binding lectin from steelhead trout, Oncorhynchus mykiss, which was found bound in high concentration to the surface coat of L. salmonae spores. SDS‐PAGE, immunoblot, N‐terminal sequencing and mass spectrometric analyses were used to determine that the dominant 24 kDa protein lectin observed on SDS‐PAGE analysis of intact spore extracts is the O. tshawytscha variant of the previously identified rhamnose‐binding lectin STL2 from rainbow trout, O. mykiss. Although the physiological role of these lectins has not been clearly delineated, they have been implicated in a variety of functions, including inhibition of pathogenic bacteria by opsonization and macrophage‐mediated tumour lysis.
Energy intakes of children with Crohn's disease treated with enteral nutrition as primary therapy
Authors: Gavin J. , Anderson C. E. , Bremner A. R. , Beattie R. M.
Published: September 2005

Background  Enteral nutrition (EN) is widely used and is effective in the treatment of children with Crohn's disease given as an exclusive feed for 6–8 weeks. Current dietetic practice during EN is to recommend an energy intake based on estimated average requirement (EAR) for energy for age [Department of Health (1991) Report on Health and Social Subjects No. 41. Dietary Reference Values for Food Energy and Nutrients for the United Kingdom. London: HMSO].

Aims  To examine factors affecting energy intake and weight gain during EN in relation to disease site and nutritional status.

Methods  A retrospective cohort study examining energy intake and weight gain during the exclusive EN feeding period in 40 patients newly diagnosed with Crohn's in relation to EAR, nutritional status, disease site.

Results  All patients improved clinically and gained weight during EN with improvement in the CRP as a marker of the systemic inflammatory response. Energy intake was higher than EAR in 82% (33/40 patients), with the median 117.5% of EAR. Weight gain correlated with body mass index standard deviation score (P = 0.001) at start of treatment, but not energy intake or CRP.

Conclusion  Estimated average requirement underestimates energy intakes in most children with newly diagnosed Crohn's disease. During EN, an energy intake in the range of 100–149% (median 117.5%) EAR for energy for age may be required. Energy balance studies in children with active disease are required.
A study to investigate women's experiences of radiation enteritis following radiotherapy for cervical cancer
Authors: Abayomi J. , Kirwan J. , Hackett A. , Bagnall G.
Published: September 2005

Background  Radiotherapy remains the standard treatment for cervical cancer, especially for more advanced disease. It is estimated that the prevalence of chronic radiation enteritis (CRE) post‐radiotherapy is in the region of 5–15% (http://www.nci.nih.gov/cancertopics). However, preliminary studies at the study hospital suggest the problem to be more widespread (C. Israel, unpublished data).

Aim  This qualitative study of 10 cervical cancer patients investigates experiences of CRE and its impact on quality of life.

Methods  Informed volunteers participated in one‐to‐one tape‐recorded in‐depth interviews exploring experiences following treatment. These interviews were transcribed verbatim and analysed using NUD*IST Nvivo.

Results  The majority of women reported side‐effects from radiotherapy, predominantly diarrhoea. CRE had a significant impact upon the physical, psychological and social aspects of life of sufferers, enforcing some to be virtually housebound. Other sufferers were managing their symptoms with regular medication and/or self‐imposed restricted diets. Few of these women had ever sought professional help in dealing with their problems because of embarrassment or reluctance to complain.

Conclusions  If untreated the side‐effects of CRE have a disabling affect on sufferers, who may be reluctant to seek help about their symptoms. Health professionals need to be more pro‐active in identifying and caring for sufferers of CRE.
Tackling obesity in men – preliminary evaluation of men‐only groups within a commercial slimming organization
Authors: Bye C. , Avery A. , Lavin J.
Published: September 2005

Background  Over Slimming World's 36‐year history men have always made up a small percentage of the slimming organization's membership. Past company research suggested that men would feel more comfortable in men‐only groups rather than mixed. In 2002, Slimming World set a target to raise the awareness among men about the dangers of being overweight and made practical weight‐management solutions more accessible through a national network of men's groups.

Aim  To evaluate men's weight loss within these ‘men‐only’ groups.

Methods  Data analysed included those men having attended a group for at least 8 weeks.

Results  At the point of data collection average BMI had decreased from 35.9 to 32.5 kg m−2. At least 5% weight loss was achieved in 90% of the sample. In those who had been members for 24 weeks 69% achieved a 10% weight loss. Shift working did not affect weight loss success.

Conclusion  This data shows that overweight and obese men attending Slimming World are successful at losing weight in this environment and can achieve recommended health‐related weight loss targets. There should be a move to get away from the mis‐perception that slimming groups are only for women and raise awareness of the commercial option to men.
A novel 3D wavelet‐based filter for visualizing features in noisy biological data
Authors: MOSS W. C. , HAASE S. , LYLE J. M. , AGARD D. A. , SEDAT J. W.
Published: September 2005

We have developed a three‐dimensional (3D) wavelet‐based filter for visualizing structural features in volumetric data. The only variable parameter is a characteristic linear size of the feature of interest. The filtered output contains only those regions that are correlated with the characteristic size, thus de‐noising the image. We demonstrate the use of the filter by applying it to 3D data from a variety of electron microscopy samples, including low‐contrast vitreous ice cryogenic preparations, as well as 3D optical microscopy specimens.
Cross‐sectional TEM investigation of nickel‐catalysed carbon nanotube films grown by plasma‐enhanced CVD
Authors: YAO Y. , FALK L. K. L. , MORJAN R. E. , NERUSHEV O. A. , CAMPBELL E. E. B.
Published: September 2005

Nickel‐catalysed multiwall carbon nanotubes synthesized by plasma‐enhanced chemical vapour deposition on a silicon substrate with acetylene and ammonia at 700 °C have been characterized by high‐resolution and analytical transmission electron microscopy. The nucleation of the carbon nanotubes occurs as a consequence of the carburization and dusting of supported preformed nickel‐ and silicon‐rich particles. This process yields disintegrated silicon‐containing nickel particles dispersed in dome‐shaped carbon islands adherent to the substrate. The particles act as catalysts for tube growth, resulting in aligned multiwall carbon nanotubes with a bamboo‐like structure anchored to the dome‐shaped carbon islands. The bottom part of the carbon islands contains bundles of graphene sheets orientated parallel to the substrate. The nanotubes are capped with fcc nickel particles containing dissolved silicon. Most of these particles have a conical shape orientated with a <110> direction along the tube growth axis, and with {110} and {111} planes as exposed faces.
Genetic estimates of contemporary effective population size: to what time periods do the estimates apply?
Authors: WAPLES ROBIN S.
Published: September 2005

Although most genetic estimates of contemporary effective population size (Ne) are based on models that assumeNeis constant, in real populationsNechanges (often dramatically) over time, and estimates (N̂e) will be influenced byNein specific generations. In such cases, it is important to properly match N̂eto the appropriate time periods (for example, in computingNe/Nratios). Here I consider this problem for semelparous species with two life histories (discrete generations and variable age at maturity — the ‘salmon’ model), for two different sampling plans, and for estimators based on single samples (linkage disequilibrium, heterozygote excess) and two samples (temporal method). Results include the following.Discrete generations: (i) Temporal samples from generations 0 andtestimate the harmonic meanNein generations 0 throught − 1 but do not provide information aboutNein generationt; (ii) Single samples provide an estimate ofNein the parental generation, not the generation sampled; (iii) single‐sample and temporal estimates never provide information aboutNein exactly the same generations; (iv) Recent bottlenecks can downwardly bias estimates based on linkage disequilibrium for several generations.Salmon model: (i) A pair of single‐cohort (typically juvenile) samples from years 0 andtprovide a temporal estimate of the harmonic mean of the effective numbers of breeders in the two parental years (Nb(0)andNb(t)), but adult samples are more difficult to interpret because they are influenced byNbin a number of previous years; (ii) For single‐cohort samples, both one‐sample and temporal methods provide estimates ofNbin the same years (contrast with results for discrete generation model); (iii) Residual linkage disequilibrium associated with past population size will not affect single‐sample estimates ofNbas much as in the discrete generation model because the disequilibrium diffuses among different years of breeders. These results lead to some general conclusions about genetic estimates ofNein iteroparous species with overlapping generations and identify areas in need of further research.
DNA taxonomy, phylogeny and Pleistocene diversification of the Cicindela hybrida species group (Coleoptera: Cicindelidae)
Authors: CARDOSO A. , VOGLER A. P.
Published: September 2005

Species delimitation is complicated where morphological variation is continuous or poorly subdivided, but for taxonomic convenience it is common practice to separate and name geographical groups to capture this variation. DNA‐based approaches may be used to test if these groups in fact represent historically divided, discrete species entities. The Cicindela hybrida complex (Coleoptera: Cicindelidae) is an assemblage of up to seven morphologically recognized species and 15 subspecies with wide distribution in the Palaearctic region. We sequenced a discontinuous segment of 1899 bp of mtDNA including three regions (coxI, rrnL+trnL2+nad1, cob) for a total of 99 specimens from 36 sampling localities across Europe, revealing 48 haplotypes. Four major clades could be identified corresponding to geographical groups from central Iberia, Ukraine, central Europe, and a band from the Atlantic Iberian coast to northern Europe. Taking into account further subdivisions within these clades, four of the six named species included in the analysis were recognizable by applying various procedures for species delimitation. Age estimates from calibrated molecular clocks date the diversification of the hybrida group within the past 2 million years (Myr), and the separation of the northern clade within 0.4 Myr. Nested clade analysis revealed the rapid range expansion of the northern group consistent with postglacial dispersal, but we did not find support for specific source population(s) in the postulated southern refugia. The evolutionary framework based on mtDNA sequences is shown to identify species entities as discrete clusters of closely related sequences and provides an objective system for delineating and recognizing hierarchically structured groups. In the case of the C. hybrida complex, these groups largely coincided with those established from morphology. The study adds further support to the utility of mtDNA‐based sequence profiles (the ‘DNA taxonomy’) as a rapid and objective synthesis of evolutionary diversity and as reference system for communication.
Heterozygosity, inbreeding and neonatal traits in Soay sheep on St Kilda
Authors: OVERALL A. D. J. , BYRNE K. A. , PILKINGTON J. G. , PEMBERTON J. M.
Published: September 2005

We investigated whether birth weight and neonatal survival, a period within which 24% of all mortalities occur, were correlated with levels of inbreeding in St Kilda Soay sheep, using pedigree inbreeding coefficients and four marker‐based estimators of inbreeding. None of the inbreeding estimators, either of the offspring, or of their mothers, explained significant variation in a lamb's birth weight or probability of surviving the neonatal period, suggesting low inbreeding depression for these traits. We evaluated the correlation between the marker‐based measures of inbreeding and inbreeding coefficients obtained from the Soay pedigree, where paternal links were inferred using the same panel of microsatellite markers. Even when using a relatively complete portion of the pedigree, in which all individuals had known maternal and paternal grandparents, the correlation was found to be weak (r = −0.207, where meanf = 0.0168). These results add support to the recent prediction that when the mean and variance in inbreeding are low in a population, heterozygosity–fitness correlations can be very weak or even undetectable. The pursuit of more detailed pedigrees offers the best prospect for identifying inbreeding depression within this study population.
Molecular evidence for glacial refugia of mountain plants in the European Alps
Authors: SCHÖNSWETTER P. , STEHLIK I. , HOLDEREGGER R. , TRIBSCH A.
Published: September 2005

Many mountain ranges have been strongly glaciated during the Quaternary ice ages, and the locations of glacial refugia of mountain plants have been debated for a long time. A series of detailed molecular studies, investigating intraspecific genetic variation of mountain plants in the European Alps, now allows for a first synopsis. A comparison of the phylogeographic patterns with geological and palaeoenvironmental data demonstrates that glacial refugia were located along the southwestern, southern, eastern and northern border of the Alps. Additional glacial refugia were present in central Alpine areas, where high‐elevation plants survived the last glaciation on ice‐free mountain tops. The observed intraspecific phylogeographies suggest general patterns of glacial survival, which conform to well‐known centres of Alpine species diversity and endemism. This implies that evolutionary or biogeographic processes induced by climatic fluctuations act on gene and species diversity in a similar way.
Mitochondrial DNA analysis of the bark beetle predator Thanasimus dubius F. (Coleoptera: Cleridae) reveals regional genetic differentiation
Authors: SCHREY NATALIE M. , REEVE JOHN D. , ANDERSON FRANK E.
Published: September 2005

The checkered beetle, Thanasimus dubius F., is an important predator of scolytid bark beetles that attack conifers. Relatively few studies exist that have addressed the population genetics of predatory beetles, especially those with potential as biological control agents. This study was conducted to investigate the population genetics of T. dubius across a large part of its range in the eastern United States. A 464‐base pair portion of the mitochondrial cytochrome c oxidase subunit I was sequenced for 85 individuals resulting in 60 haplotypes. Analysis of molecular variance was conducted on the resulting haplotypes for all populations and as a hierarchical analysis between populations defined as broad‐scale northern and southern groups. Results indicate a significant overall ΦST = 0.220 (P < 0.001) for all populations with the hierarchical analysis revealing that this significant ΦST is due to structuring of the populations between northern and southern regions (ΦCT = 0.388, P < 0.009). The observed genetic structure is possibly due to the discontinuous distribution of pine trees, which act as hosts for the prey of T. dubius, which has occurred historically in the central region of the United States that has been covered by prairie.
Deciphering host migrations and origins by means of their microbes
Authors: WIRTH THIERRY , MEYER AXEL , ACHTMAN MARK
Published: September 2005

Mitochondrial DNA and microsatellite sequences are powerful genetic markers for inferring the genealogy and the population genetic structure of animals but they have only limited resolution for organisms that display low genetic variability due to recent strong bottlenecks. An alternative source of data for deciphering migrations and origins in genetically uniform hosts can be provided by some of their microbes, if their evolutionary history correlates closely with that of the host. In this review, we first discuss how a variety of viruses, and the bacterium Helicobacter pylori, can be used as genetic tracers for one of the most intensively studied species, Homo sapiens. Then, we review statistical problems and limitations that affect the calculation of particular population genetic parameters for these microbes, such as mutation rates, with particular emphasis on the effects of recombination, selection and mode of transmission. Finally, we extend the discussion to other host–parasite systems and advocate the adoption of an integrative approach to both sampling and analysis.
Co‐infected C57BL/6 mice mount appropriately polarized and compartmentalized cytokine responses to Litomosoides sigmodontis and Leishmania major but disease progression is altered
Authors: LAMB T. J. , GRAHAM A. L. , LE GOFF L. , ALLEN J. E.
Published: September 2005

This study examines the capacity of the mammalian host to fully compartmentalize the response to infection with type 1 vs. type 2 inducing organisms that infect different sites in the body. For this purpose, C57BL/6 mice were infected with the rodent filarial nematode Litomosoides sigmodontis followed by footpad infection with the protozoan parasite Leishmania major. In this host, nematode infection is established in the thoracic cavity but no microfilariae circulate in the bloodstream. We utilized quantitative ELISPOT analysis of IL‐4 and IFN‐γ producing cells to assess cytokine bias and response magnitude in the lymph nodes draining the sites of infection as well as more systemic responses in the spleen and serum. Contrary to other systems where co‐infection has a major impact on bias, cytokine ratios were unaltered in either local lymph node. The most notable effect of co‐infection was an unexpected increase in the magnitude of the IFN‐γ response to L. major in mice previously infected with L. sigmodontis. Further, lesion development was significantly delayed in these mice. Thus, despite the ability of the immune system to appropriately compartmentalize the immune response, interactions between responses at distinct infection sites can alter disease progression.