bluuebunny/crossref_metadata_2025 huggingface dataset:
Inclusion of photoinhibition in simulation of carbon dynamics of an alpine meadow on the Qinghai‐Tibetan Plateau
Authors: Zhang Yongqiang , Tang Yanhong
Published: September 2005

The Qinghai‐Tibetan Plateau is the highest plateau in the world. Covered mainly by alpine grasslands, the plateau plays an important role in the region's carbon budget. The plateau is characterized by high irradiance, low atmospheric pressure, and low temperature. To examine the carbon dynamics of grassland ecosystems on the plateau, we developed a new model, the carbon dynamics model for alpine grasslands (CDMag). CDMag is composed of a gross photosynthesis (Ac) submodel including photoinhibition simulation, an ecosystem respiration (ER) submodel that considers both autotrophic and heterotrophic respiration, and an intercellular CO2 partial pressure and canopy conductance submodel. The photoinhibition simulation is included to describe the gross production of alpine ecosystems in response to the high‐irradiance environment. A multilayered irradiance transfer scheme is adopted to estimate the irradiance on sunlit and shaded leaves within grassy canopies, and a coupled canopy conductance–net photosynthesis function is integrated into the Ac submodel. CDMag was used to simulate the carbon dynamics of the most extensively distributed alpine grassland, a Kobresia meadow ecosystem on the Qinghai‐Tibetan Plateau. CDMag reproduces well the diurnal and seasonal variation of net ecosystem exchange (NEE) and nighttime ER based on data obtained from 2001 to 2003 using the eddy‐covariance method. The mean measured NEE was about 1.62 μmol m−2 s−1 for the measured periods of the 3 years; the mean of the deviations between measured and simulated NEE was −0.16 to 0.33 μmol m−2 s−1. Owing to photoinhibition, daily gross photosynthesis lost about 5.3–5.6%. The losses were mainly contributed by the 7.5–7.8% reduction in Ac of sunlit leaves of the upper canopy layer. In addition, the light‐use efficiency of the alpine meadow had seasonal dynamics, with the highest values in the middle of the growing season. We have generalized CDMag for other alpine grasslands on the entire plateau.
Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water
Authors: Elmer Sidney P. , Park Sanghyun , Pande Vijay S.
Published: September 2005

In this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (pPA) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. The solvent quality has a dramatic effect on the time scales in which pPA 12-mers fold. Acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of ∼100–200ns, depending on temperature. In contrast, chloroform and water were observed to hinder the folding of the pPA 12-mer due to extreme solvation conditions relative to acetonitrile; chloroform denatures the oligomer, whereas water promotes aggregation and traps. The pPA 12-mer in a pure methanol solution folded in ∼400ns at 300K, compared relative to the experimental 12-mer folding time of ∼160ns measured in a 1:1 v/v THF/methanol solution. Requisite in drawing the aforementioned conclusions, analysis techniques based on Markov state models are applied to multiple short independent trajectories to extrapolate the long-time scale dynamics of the 12-mer in each respective solvent. We review the theory of Markov chains and derive a method to impose detailed balance on a transition-probability matrix computed from simulation data.
Foldamer dynamics expressed via Markov state models. II. State space decomposition
Authors: Elmer Sidney P. , Park Sanghyun , Pande Vijay S.
Published: September 2005

The structural landscape of poly-phenylacetylene (pPA), otherwise known as m-phenylene ethynylene oligomers, has been shown to consist of a very diverse set of conformations, including helices, turns, and knots. Defining a state space decomposition to classify these conformations into easily identifiable states is an important step in understanding the dynamics in relation to Markov state models. We define the state decomposition of pPA oligomers in terms of the sequence of discretized dihedral angles between adjacent phenyl rings along the oligomer backbone. Furthermore, we derive in mathematical detail an approach to further reduce the number of states by grouping symmetrically equivalent states into a single parent state. A more challenging problem requires a formal definition for knotted states in the structural landscape. Assuming that the oligomer chain can only cross the ideal helix path once, we propose a technique to define a knotted state derived from a helical state determined by the position along the helical nucleus where the chain crosses the ideal helix path. Several examples of helical states and knotted states from the pPA 12-mer illustrate the principles outlined in this article.
Nonlinear distortion of a laser pulse in a magnetized plasma
Authors: Sharma Anamika , Tripathi V. K.
Published: September 2005

Nonlinear propagation of a circularly polarized intense short-pulse laser through a plasma, immersed in a strong axial magnetic field, is examined. The relativistic mass effect makes the group velocity of the laser intensity-dependent. Different portions of the laser pulse travel with different group velocities. For an initially Gaussian pulse, steepening of the laser-pulse amplitude profile occurs, which is then followed by shock formation. The propagation characteristic of the laser is also sensitive to the choice of the ratio of laser frequency to electron cyclotron frequency, and the ratio of plasma frequency to electron cyclotron frequency.
Intermixing and phase separation at the atomic scale in Co-rich (Co,Fe) and Cu multilayered nanostructures
Authors: Ladwig Peter F. , Olson Jesse D. , Bunton Joseph H. , Larson David J. , Ulfig Robert M. , Martens Richard L. , Gribb Tye T. , Kelly Thomas F. , Bonsager Martin C. , Schultz Allan E. , Pant Bharat B. , Chang Y. Austin
Published: September 2005

Despite the fact that Co-rich (Co,Fe) alloys and Cu are immiscible materials in bulk form, evidence of thermally induced mixing at the atomic scale has been observed in thin-film multilayers of (Co,Fe) and Cu. However, long term anneals at lower temperatures produced a breakup of the multilayers into a two-phase mixture of (Co,Fe) and Cu particles. The observations were made with the use of the three-dimensional atom probe technique, with supporting evidence from differential scanning calorimetry and x-ray diffraction. Besides their scientific importance, these results are of interest where these (Co,Fe) and Cu thin films are used to produce the giant magnetoresistive effect.
Effect of DNA charge helicity on B-Z DNA transition
Authors: Cherstvy A. G.
Published: September 2005

We construct a linear Poisson-Boltzmann model for a description of the electrostatics of the B-Z DNA conformational transition. The model takes into account the helicity and double strandedness of DNA charge distribution and provides a good agreement with experimental data on the stabilization of Z-DNA at high concentrations of simple salt. The results of other models are discussed.
Fabrication and optical measurements of germanium-doped silica ridge waveguides using a colloidal suspension approach
Authors: Kim Deok-Yang , Du Henry , Kowach Glen R. , White Christopher A. , McGee David J.
Published: September 2005

Germanium-doped silica ridge waveguides for planar lightwave circuits were fabricated using colloidal suspensions. After consolidation at 1300 °C, fully dense micron-scale thick films were obtained. The refractive index of these films was tuned with germanium dopant up to 11.1 mol %. The propagation loss of a 3.1 mol % germanium-doped silica sample without an overcladding layer was 3.3±0.5dB∕cm. Postannealing of the patterned waveguides at 1200 °C for 30 min was conducted in order to reflow waveguides, but it did not significantly smooth the sidewall roughness due to the high viscosity of the 3.1 mol % germanium-doped silica at that temperature.
Electro-optically tunable photonic crystals
Authors: Schmidt M. , Eich M. , Huebner U. , Boucher R.
Published: September 2005

We report on electro-optical modulation with a sub-1-V sensitivity in a photonic crystal slab waveguide resonator which contains a nanostructured second-order nonlinear optical polymer. The electro-optical susceptibility in the core was induced by high electric-field poling. A square lattice of holes carrying a linear defect was transferred into the slab by electron-beam lithography and reactive ion etching, creating a photonic crystal slab-based resonator. Applying an external electric modulation voltage to electrodes leads to a linear electro-optical shift of the resonance spectrum and thus to a modulation of the transmission at a fixed wavelength based on the electronic displacement polarization in a noncentrosymmetric medium (Pockels effect). This effect is therefore inherently faster than other reported electro-optic modulation effects in nanophotonics.
Diocotron instability in non-neutral plasmas with a stationary point in the rotation frequency profile
Authors: Kotelnikov I. A. , Pozzoli R. , Romé M.
Published: September 2005

A new analytical solution to the problem of the l=1 diocotron mode instability in a hollow density non-neutral plasma column with finite lenght is presented. The starting point of the analysis is the paper of Finn et al. [J. M. Finn, D. del-Castillo-Negrete, and D. C. Barnes, Phys. Plasmas 6, 3744 (1999)], where the instability mechanism involves compression of the plasma in the direction parallel to the magnetic field, with conservation of its line-integrated density. In the limit of small curvature of the plasma end-fronts, the method presented here provides both eigenvalue and eigenfunction for the unstable l=1 “extreme mode.”
Application of cascaded frequency multiplication to molecular spectroscopy
Authors: Drouin Brian J. , Maiwald Frank W. , Pearson John C.
Published: September 2005

Laboratory molecular spectroscopy provides the basis for interpretation of atmospheric, planetary, and astrophysical data gathered by remote sensing. Laboratory studies of atomic and molecular signatures across the electromagnetic spectrum provide high-precision, quantitative data used to interpret the observed environment from remote measurements. Historically, the region of the spectrum above 500 GHz has been relatively unexplored due to atmospheric absorption and technical difficulties generating and detecting radiation. Laboratory spectroscopy at these frequencies has traditionally involved measurement of one or two absorption features and relied on fitting of models to the limited data. We report a new spectrometer built around a computer-controlled commercial synthesizer and millimeter-wave module driving a series of amplifiers followed by a series of wide-bandwidth frequency doublers and triplers. The spectrometer provides the ability to rapidly measure large pieces of frequency space with higher resolution, accuracy, and sensitivity than with Fourier transform infrared techniques. The approach is simple, modular, and requires no custom-built electronics or high voltage and facilitates the use of infrared data analysis techniques on complex submillimeter spectra.
Peculiar ZnO nanopushpins and nanotubes synthesized via simple thermal evaporation
Authors: Zhang Xianghui , Zhang Ye , Xu Jun , Wang Zhe , Chen Xihong , Yu Dapeng , Zhang Peng , Qi Hanhong , Tian Yongjun
Published: September 2005

ZnO nanostructures with peculiar morphology were synthesized in large quantities via catalyst-free thermal evaporation. Both ZnO nanopushpins with very thin and flat cap on top of the nanorods, and regular hexagonal nanotubes, can be obtained in the same run of growth in different regions. The ZnO nanopushpins and nanotubes were characterized by using scanning electron microscopy and transmission electron microscopy. Cathodoluminescence measurements revealed that the emission from oxygen vacancy overwhelmed that of the near band gap in the as-grown ZnO nanotube arrays.
Lateral phase separation in AlGaN grown on GaN with a high-temperature AlN interlayer
Authors: Sun Q. , Huang Y. , Wang H. , Chen J. , Jin R. Q. , Zhang S. M. , Yang H. , Jiang D. S. , Jahn U. , Ploog K. H.
Published: September 2005

The influences of a high-temperature (HT) AlN interlayer (IL) on the phase separation in crack-free AlGaN grown on GaN have been studied. The depth-dependent cathodoluminescence (CL) spectra indicate a relatively uniform Al distribution in the growth direction, but the monochromatic CL images and the CL spectra obtained by line scan measurements reveal a lateral phase separation in AlGaN grown on relatively thick HT-AlN ILs. Moreover, when increasing the thickness of HT-AlN IL, the domain-like distribution of the AlN mole fraction in AlGaN layers is significantly enhanced through a great reduction of the domain size. The morphology of mesa-like small islands separated by V trenches in the HT-AlN IL, and the grain template formed by the coalescence of these islands during the subsequent AlGaN lateral overgrowth, are attributed to be responsible for the formation of domain-like structures in the AlGaN layer.
Applying the transtheoretical model to eating behaviour change: challenges and opportunities
Authors: Horwath Caroline C.
Published: September 2005

This review provides a rigorous investigation of the question of whether the transtheoretical model (TTM) (or stages of change model) is applicable to eating behaviour change. The TTM is currently the most popular of a number of stage theories being used to examine health behaviour change. Stage theories specify an ordered set of ‘stages of readiness to change’ into which people can be classified and identify the factors that can facilitate movement from one stage to the next. If eating behaviour change follows a stage process, then nutritionists could identify the predominant stage or stages in a population and focus resources on those issues most likely to move people to the next stage (e.g. from no intention of changing, to thinking about changing). In addressing this question, the review draws on the defining characteristics of stage theories as clarified by Weinstein et al. (1998), provides an in-depth coverage of methodological considerations, and a detailed summary table of dietary studies applying the TTM. Specific recommendations are made for improving the accuracy of dietary stage classifications. Among the key conclusions are: (1) dietary studies using the TTM have been hampered by a focus on nutritional outcomes such as dietary fat reduction, rather than clearly understood food behaviours (e.g. five servings of fruit and vegetables per day); (2) accurate stage classification systems are possible for food-based goals, but major misclassification problems occur with nutrient-based goals; (3) observation of an association between stage and dietary intake is not sufficient to demonstrate the validity of the model for dietary behaviour; (4) there is a need for valid questionnaires to measure all aspects of the TTM, and more research on the whole model, particularly the ‘processes of change’, rather than on single constructs such as ‘stage’ (5) cross-sectional studies generally support the predicted patterns of between-stage differences in decisional balance, self-efficacy, and processes of change; (6) studies which test the key hypothesis that different factors are important in distinguishing different stages are rare, as are prospective studies and stage-matched interventions. Only such studies can conclusively determine whether the TTM is applicable to eating behaviour. Since the ultimate test of the TTM will be the effectiveness of stage-matched dietary interventions, the review ends by exploring the requirements for such studies.
Effects of an iron supplementation trial on the Fe status of Thai schoolchildren
Authors: Hathirat Phongjan , Valyasevi Aree , Kotchabhakdi Nittaya J. , Rojroongwasinkul Nipa , Pollitt Ernesto
Published: September 2005

A double-blind clinical trial was conducted among 9- to 11-year-old children in sixteen schools in the Chon Buri province of Thailand to assess the effects of an iron supplement combined with an anthelminthic agent (i.e. albendazole). In addition to the albendazole, Fe or placebo tablets were distributed to 2268 children enrolled in grades three to five without knowledge of the Fe status of the children. Criteria for case inclusion were: (a) absence of A E Bart's or haemoglobin (Hb) H disease, (b) absence of abnormal Hb EE, and (c) age, 108–144 months. The results showed a significant improvement in the Fe status of the children after 16 weeks of treatment. The increments were: Hb from 124 to 128 g/l, serum ferritin from 34.54 to 104.72 μg/l, transferrin saturation from 24.09 to 35.05%; free erythrocyte protoporphyrin decreased from 444.7 to 281.4 μg/l erythrocytes. These changes were significantly greater than in the control group that received only the anthelminthic agent. However, the administration of albendazole only also resulted in significant changes in the same Fe indicators.
Influence of low dietary lipid content on anorexia and [14C]glucose uptake in the intestine of zinc-deficient mice
Authors: Taneja S. K. , Arya P.
Published: September 2005

Zinc deficiency was induced in adult male mice by feeding them for 8 weeks on a purified semi-synthetic Zn-deficient diet (ZD) containing 90 g lipid/kg (60 g maize oil plus 30 g cod-liver oil). One group was then fed on a low-lipid Zn-deficient diet (ZDLR) containing 30 g cod-liver oil/kg as the sole lipid source for a further 8 weeks. At the end of the experiment the stomach clearance rate, daily food intake, body-weight gain and [14C]glucose uptake in the intestine were significantly higher in group ZDLR than in mice that continued eating the Zn-deficient lipid-adequate diet ZD, and were comparable to results for a group given a Zn-supplemented diet. These results suggest that the pathogenesis of anorexia, nutrient malabsorption and growth retardation are secondary to lipid malabsorption resulting from Zn deficiency
Erythrocytes, erythrocyte membranes, neutrophils and platelets as biopsy materials for the assessment of zinc status in humans
Authors: Ruz Manuel , Cavan Kelley R. , Bettger William J. , Gibson Rosalind S.
Published: September 2005

During a controlled zinc depletion-repletion study, fifteen men aged 25.3 (sd 3.3) years were fed on a low-Zn diet with high phytate:Zn and phytate × calcium: Zn molar ratios for 7 weeks, followed by a 2 week repletion period when 30 mg supplemental Zn/d was given. Changes in plasma, urine, and hair Zn concentrations, taste acuity, and cellular immune response confirmed the development of mild Zn deficiency. Zn concentrations in neutrophils, platelets, erythrocytes and erythrocyte membranes, mean platelet volume, and activities of alkaline phosphatse (EC3.1.3.1) and α-d-mannosidase (EC3.2.1.24) in neutrophils did not respond to changes in Zn status. In contrast, alkaline phosphatase activity in erythrocyte membranes showed a significant decline which was consistent in all subjects (nmol product formed/min per mg protein; baselinev.7-week Zn depletion, 0.656 (sd 0.279)v.0.506 (sd 0.230), at 7 weeks;P< 0.05); neutral phosphatase activity remained unchanged. Alkaline phosphatase activity in erythrocyte membranes may be a potential index of Zn status in humans
Nutritional intake, height and weight of 11–12-year-old Northumbrian children in 1990 compared with information obtained in 1980
Authors: Adamson Ashley , Rugg-Gunn Andrew , Butler Timothy , Appleton David , Hackett Allan
Published: September 2005

There is little age-specific information on changes in dietary intake over time in this country, yet this is valuable in assessing the effectiveness of health education programmes particularly in vulnerable groups such as adolescents. In 1990, 379 children aged 12 years completed two 3 d dietary records. They were interviewed by one dietitian on the day after completion of each diary to verify and enlarge on the information provided and, with the aid of food models, obtain a quantitative record of food intake. Nutrient intake was calculated using computerized food tables. These children attended the same seven Middle schools in Northumberland as 405 children of the same age who recorded their diet using the same method, 10 years previously. Heights and weights were also recorded in both studies in the same manner. Comparing the nutrient intakes in 1990 with 1980, energy intake fell in the boys (to 8.6 MJ) but not in the girls (8.3 MJ). The contribution of fat to energy intake was unchanged at about 40% (about 90 g/d). Likewise, intake of sugars was unchanged at about 22% of energy (about 118 g/d). Calcium intake remained the same in the girls (763 mg/d in 1990) but fell in the boys (786 mg/d in 1990). Iron, vitamin C and unavailable carbohydrate intakes increased in both sexes, and the nutrient density of the diet improved in all sex and social-class groups. However, a social trend evident in 1980 still existed in 1990 with low social groups having the poorest-quality diet. It is concluded that there is little evidence of substantial progress towards improving the diet of adolescents in this country.
Self-organized 2D nanopatterns after low-coverage Ga adsorption on Si (1 1 1)
Authors: Schmidt Thomas , Gangopadhyay Subhashis , Flege Jan Ingo , Clausen Torben , Locatelli Andrea , Heun Stefan , Falta Jens
Published: September 2005

The evolution of the Si(1 1 1) surface after submonolayer deposition of Ga has been observedin situby low-energy electron microscopy and scanning tunnelling microscopy. A phase separation of Ga-terminated-R 30° reconstructed areas and bare Si(1 1 1)-7 × 7 regions leads to the formation of a two-dimensional nanopattern. The shape of this pattern can be controlled by the choice of the surface miscut direction, which is explained in terms of the anisotropy of the domain boundary line energy and a high kink-formation energy. A general scheme for the nanopattern formation, based on intrinsic properties of the Si(1 1 1) surface, is presented. Experiments performed with In instead of Ga support this scheme.
Using information theory to search for co-evolving residues in proteins
Authors: Martin L. C. , Gloor G. B. , Dunn S. D. , Wahl L. M.
Published: September 2005

Motivation: Some functionally important protein residues are easily detected since they correspond to conserved columns in a multiple sequence alignment (MSA). However important residues may also mutate, with compensatory mutations occurring elsewhere in the protein, which serve to preserve or restore functionality. It is difficult to distinguish these co-evolving sites from other non-conserved sites.

Results: We used Mutual Information (MI) to identify co-evolving positions. Using in silico evolved MSAs, we examined the effects of the number of sequences, the size of amino acid alphabet and the mutation rate on two sources of background MI: finite sample size effects and phylogenetic influence. We then assessed the performance of various normalizations of MI in enhancing detection of co-evolving positions and found that normalization by the pair entropy was optimal. Real protein alignments were analyzed and co-evolving isolated pairs were often found to be in contact with each other.

Availability: All data and program files can be found at

Contact:  lwahl@uwo.ca

Supplementary information:
Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation
Authors: Zwir Igor , Huang Henry , Groisman Eduardo A.
Published: September 2005

Motivation: A critical challenge of the post-genomic era is to understand how genes are differentially regulated even when they belong to a given network. Because the fundamental mechanism controlling gene expression operates at the level of transcription initiation, computational techniques have been developed that identify cis regulatory features and map such features into expression patterns to classify genes into distinct networks. However, these methods are not focused on distinguishing between differentially regulated genes within a given network. Here we describe an unsupervised machine learning method, termed GPS for gene promoter scan, that discriminates among co-regulated promoters by simultaneously considering both cis-acting regulatory features and gene expression. GPS is particularly useful for knowledge discovery in environments with reduced datasets and high levels of uncertainty.

Results: Application of this method to the enteric bacteria Escherichia coli and Salmonella enterica uncovered novel members, as well as regulatory interactions in the regulon controlled by the PhoP protein that were not discovered using previous approaches. The predictions made by GPS were experimentally validated to establish that the PhoP protein uses multiple mechanisms to control gene transcription, and is a central element in a highly connected network.

Availability: The scripts and programs used in this work are accessible from the gps-tools.wustl.edu website. Data and predictions are available by request.

Contact:  groisman@borcim.wustl.edu

Supplementary information:
Design of long oligonucleotide probes for functional gene detection in a microbial community
Authors: Chung Won-Hyong , Rhee Sung-Keun , Wan Xiu-Feng , Bae Jin-Woo , Quan Zhe-Xue , Park Yong-Ha
Published: September 2005

Motivation: Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes.

Results: We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set.

Availability:  

Contact:  yhpark@kribb.re.kr

Supplementary information:
A comparison study: applying segmentation to array CGH data for downstream analyses
Authors: Willenbrock Hanni , Fridlyand Jane
Published: September 2005

Motivation: Array comparative genomic hybridization (CGH) allows detection and mapping of copy number of DNA segments. A challenge is to make inferences about the copy number structure of the genome. Several statistical methods have been proposed to determine genomic segments with different copy number levels. However, to date, no comprehensive comparison of various characteristics of these methods exists. Moreover, the segmentation results have not been utilized in downstream analyses.

Results: We describe a comparison of three popular and publicly available methods for the analysis of array CGH data and we demonstrate how segmentation results may be utilized in the downstream analyses such as testing and classification, yielding higher power and prediction accuracy. Since the methods operate on individual chromosomes, we also propose a novel procedure for merging segments across the genome, which results in an interpretable set of copy number levels, and thus facilitate identification of copy number alterations in each genome.

Availability:  

Contact:  jfridlyand@cc.ucsf.edu

Supplementary Information:
BADASP: predicting functional specificity in protein families using ancestral sequences
Authors: Edwards Richard J. , Shields Denis C.
Published: September 2005

Summary: Burst After Duplication with Ancestral Sequence Predictions (BADASP) is a software package for identifying sites that may confer subfamily-specific biological functions in protein families following functional divergence of duplicated proteins. A given protein phylogeny is grouped into subfamilies based on orthology/paralogy relationships and/or user definitions. Ancestral sequences are then predicted from the sequence alignment and the functional specificity is calculated using variants of the Burst After Duplication method, which tests for radical amino acid substitutions following gene duplications that are subsequently conserved. Statistics are output along with subfamily groupings and ancestral sequences for an easy analysis with other packages.

Availability: BADASP is freely available from

Contact:  redwards@rcsi.ie

Supplementary information: A manual with further details can be downloaded from
Tradeoffs between height growth rate, stem persistence and maximum height among plant species in a post‐fire succession
Authors: Falster Daniel S. , Westoby Mark
Published: September 2005

One way species of low maximum height can accrue sufficient light income to persist in vegetation is via rapid height growth immediately following disturbance. By surveying patches of known time since fire, we reconstructed height–growth trajectories for 19 post‐fire recruiting species from fire‐prone vegetation in south‐eastern Australia. Cross‐species patterns of height growth were compared to several plant traits thought to influence height strategy, including leaf mass per area, stem tissue density, stem diameter and capacity to resprout. Shorter species were found to temporarily outpace taller species, both as resprouters and within reseeders. Among reseeders, a single axis of variation summarised patterns of height–growth, time to onset of reproduction and longevity. This axis was tightly correlated with maximum height, leaf mass per area and stem diameter at a given height. These results illustrate how a range of height strategies can coexist in fire‐prone vegetation, via the time‐process initiated by disturbance.
Functional stability of microbial communities in contaminated soils
Authors: Tobor‐Kapłon M. A. , Bloem J. , Römkens P. F. A. M. , Ruiter P. C. de
Published: September 2005

Functional stability, measured in terms of resistance and resilience of respiration and growth rate of bacteria and fungi, was studied in soils that have been exposed to copper and low pH for more than twenty years. We used treatments, consisting of soil with no or high copper load (0 or 750 kg ha−1) and low or neutral pH (4.0 or 6.1). Stability was examined by applying an additional stress in the form of lead or salt. After addition of lead, respiration (decomposition of freshly added lucerne meal) showed lower resistance at low than at neutral pH and at high copper than at low copper. The most acid and contaminated soil was the least resistant. Respiration showed no resilience after addition of lead. Bacterial growth rate (thymidine incorporation) also showed resistance at low pH but only in soils that were not contaminated with copper.

After addition of salt, respiration showed no differences in resistance but the soils without copper contamination showed higher resilience. Bacterial growth rate showed lower resistance at low pH than at neutral pH, the latter in which the growth rate increased by on average 123%. This increase at high pH was faster in soil without copper than in soil with copper contamination in which the growth rate initially decreased and then increased. The effects of secondary stress depended on the nature of the stress (lead or salt) and on the parameter measured (respiration or bacterial growth rate). In general the highest resistance and/or resilience were found in the least contaminated soils with neutral pH and/or no copper contamination. Thus, the microbial communities in the cleaner soils showed the highest functional stability. The results seem to confirm the notion that environmental stress alters ecosystems such that supplementary stress will have stronger impacts than in an unstressed system. The results may also confirm the insurance‐hypothesis that reduced biodiversity due to the first stress negatively affected community stability. As an alternative, we discuss the observed effects in terms of altered energy budget.
Lack of ant attendance may induce compensatory plant growth
Authors: Offenberg Joachim , Nielsen Mogens Gissel , Macintosh Donald J. , Havanon Sopon , Aksornkoae Sanit
Published: September 2005

Three levels in ant–plant protection systems need to be considered to fully understand how these symbiotic systems work. Here we present the effect of Oecophylla smaragdina ants on (1) the arthropod community, (2) herbivory, and (3) plant performance, within a studied mangrove ant–plant protection system. On Rhizophora mucronata trees in Thailand ants successfully colonised ant trees attached with a string to a natural ant tree, whereas they were unable to colonise control trees without this connection. Trees were monitored and arthropods (numbers and composition), leaf damage, leaf turnover and growth rates (stem diameter, tree height and total leaf area) were recorded in two surveys covering a period of 12 months. The number of herbivorous arthropods, but not the number of predators, was significantly lower on ant trees compared to control trees. Likewise, the amount of leaf damage inflicted by the four major groups of herbivores (Chrysomelidae, Tortricidae, Geometridae and Sesarminae) was significantly lower on ant trees compared to control trees and so was the leaf turnover rate. In spite of this, the released herbivore pressure on ant trees did not translate into higher growth rates. In contrast, all growth responses increased more on control trees compared to ant trees. Differences between the two groups were insignificant but leaf area increase was only marginally nonsignificant (P=0.062). The results show that ants remove herbivorous arthropods more efficiently than predators but ant‐colonised mangroves do not necessarily benefit from this despite the resulting decrease in herbivory.
Relieving substrate limitation‐soil moisture and temperature determine gross N transformation rates
Authors: Bengtson Per , Falkengren‐Grerup Ursula , Bengtsson Göran
Published: September 2005

A field experiment was designed with the objective to reveal the interactions between soil moisture, temperature, total, dissolved, and phosphate buffer extractable C and N, and microbial activity in the control of in situ gross N mineralization and immobilization rates in a deciduous forest. We had three alternative hypotheses to explain variations of the gross N transformations: 1) microorganisms are C limited, 2) microorganisms are N limited, or 3) neither C nor N limit the microorganisms but moisture and temperature conditions. Each hypothesis had specific criteria to be fulfilled for its acceptance. The results demonstrated that gross N transformation rates were more dependent on and variable with soil moisture and temperature than the size of the different C and N pools. The immobilization of N was dependent on the gross mineralization rate, suggesting that the production of enzymes for mineralization of organic N and the immobilization of N from the surrounding soil is disconfirmed when the intracellular N content of the microorganisms is sufficiently high. If the microorganisms are starved for N, enzyme systems involved in both the assimilation and mineralization of N are activated.

The mean in situ gross N mineralization rate was two orders of magnitude higher than the natural N deposition in the area and the N addition in the NITREX experiments, meaning that a reduction in the gross N mineralization rate of about 1% would be enough to compensate for the addition of inorganic N. This decrease would hardly be detectable given the great spatial and temporal variability of N transformation rates.
Nest predation and habitat change interact to influence Siberian jay numbers
Authors: Eggers Sönke , Griesser Michael , Andersson Tommy , Ekman Jan
Published: September 2005

We studied Siberian jays, breeding in northern Sweden, to examine the potential for interactions between nest predation and reduced vegetation heterogeneity around nest sites to cause a decrease in jay numbers. Parent behaviour and nests are highly cryptic in the species. Our 12‐year data showed, however, that nests had a probability of only 0.46 to be successful and produce at least one nestling. Nest predation was intense and a main cause of nest failure. All predators that could be identified were visually oriented hunters, mostly other corvids able to colonize taiga forest only close to human settlements. Consistent with the idea that predators used visual cues, nest predation increased with parental activity, which suggests that predators used parental provisioning trips to locate nests. Furthermore, a reduction in daily nest survival rates with decreasing amount of nesting cover was more pronounced in areas with high corvid activity as predicted when cover mediates the hunting efficiency of visual oriented predators. Declining temperatures interacted with the effects of habitat characteristics to further reduce daily nest survival rates suggesting that parents were not able to increase nest visitation rates to satisfy the higher energy demands of their nestlings without endangering the nest. Our results identify a mechanism through which predation and human‐induced reduction in nesting cover on a larger scale may interact to cause a reduction in Siberian jay numbers larger than expected from habitat loss alone.
Evaluation of alternate harvesting strategies using experimental microcosms
Authors: Fryxell J. M. , Smith I. M. , Lynn D. H.
Published: September 2005

Experimental evidence to evaluate alternate conservation policies for harvested populations is currently meager. We used populations of the ciliateTetrahymena thermophilagrowing in test tube microcosms to experimentally evaluate the effects of alternate harvesting policies in a controlled, replicable setting. Simple density‐dependent models were effective in predicting patterns of ciliate population growth in the microcosms. We evaluated several univariate models, finding that a Ricker logistic model was a better predictor of ciliate population dynamics than Gompertz logistic, non‐linear logistic, or random walk models. Using the Ricker logistic model as a demographic skeleton, we modeled ciliate population dynamics with respect to three alternate harvesting policies (fixed quota, fixed proportion, and fixed escapement), each conducted at four comparable levels of harvest intensity. The parameterized demographic models predicted that fixed quota harvesting would lead to lower mean ciliate abundance and higher temporal variability in ciliate abundance than fixed proportion or fixed escapement policies, with an appreciable risk of extinction, even under the controlled environmental conditions of our experimental system. For each harvesting policy, the intensity of harvest had demonstrable effects on population density. Population variability was higher for fixed quota harvesting than the other policies. The stochastic demographic model successfully predicted heightened extinction risk in the fixed quota system, relative to the other management treatments. Our experimental evidence lends support to the theoretical prediction that fixed quota harvesting is riskier than fixed proportion or fixed escapement policies.
Host‐plant species modifies the diet of an omnivore feeding on three trophic levels
Authors: Magalhães Sara , Janssen Arne , Montserrat Marta , Sabelis Maurice W.
Published: September 2005

The diet choice of omnivores feeding on two adjacent trophic levels (either plants and herbivores or herbivores and predators) has been studied extensively. However, omnivores usually feed on more than two trophic levels, and this diet choice and its consequences for population dynamics have hardly been studied. We report how host‐plant quality affects the diet choice of western flower thrips feeding on three trophic levels: plants (cucumber or sweet pepper), eggs of spider mites and eggs of a predatory mite that attacks spider mites. Spider mites feed on the same host plants as thrips and produce a web that hampers predator mobility. To assess the indirect effects of spider mites on predation by thrips, the thrips were offered spider‐mite eggs and predatory‐mite eggs on cucumber or sweet pepper leaf discs that were either clean, damaged by spider mites but without spider‐mite web, or damaged and webbed. We show that, overall, thrips consumed more eggs on sweet pepper, a plant of low quality, than on cucumber, a high quality host plant. On damaged and webbed leaf discs (mimicking the natural situation), thrips killed more predator eggs than spider‐mite eggs on sweet pepper, but they killed equal numbers of eggs of each species on cucumber. This is because web hampered predation on spider‐mite eggs by thrips on sweet pepper, but not on cucumber, whereas it did not affect predation on predatory‐mite eggs. We used the data obtained to parameterize a model of the local dynamics of this system. The model predicts that total predation by the omnivore has little effects on population dynamics, whereas differential attack of predator eggs and spider‐mite eggs by the omnivore has large effects on the dynamics of both mite species on the two host plants.
Among population variation in specialist and generalist seed predation – the importance of host plant distribution, alternative hosts and environmental variation
Authors: Östergård Hannah , Ehrlén Johan
Published: September 2005

Pre‐dispersal seed predators can have important effects on population dynamics and trait selection in their host plants. However, the factors determining spatial variation in predation intensity are poorly known. We assessed the relative importance of host plant distribution, alternative hosts and environmental factors for among‐population variation in predation in a system with three host plants, a specialist and a generalist pre‐dispersal seed predator.

Effects of host plant population size were relatively more important in the specialist than in the generalist seed predator. The specialist seed predatorApion opeticum, utilizing onlyLathyrus vernusoccurred in less than half of the patches, and specialist seed predation was influenced only by host plant population size. The generalistBruchus atomariuswas present in nearly all patches, and generalist predation was influenced by environmental factors and availability of alternative hosts. Predation on alternative hosts was not affected byL. vernuspresence.

The results suggest that a wide range of factors influences the strength of plant–seed–predator interactions, and that the relative importance of different factors depend on the degree of specialization. This will result in highly complex selection mosaics and coevolutionary trajectories.
Ecological traps in isodars: effects of tallgrass prairie management on bird nest success
Authors: Shochat Eyal , Patten Michael A. , Morris Douglas W. , Reinking Dan L. , Wolfe Donald H. , Sherrod Steve K.
Published: September 2005

Ecological traps occur when habitat selection and habitat suitability (measured in terms of fitness) are decoupled. We developed a graphical model based on isodar theory to distinguish between an ideal distribution and an ecological trap. We tested the model's predictions using data on breeding bird populations in managed tallgrass prairie in Oklahoma. Between 1992 and 1996 we monitored success for 2600 nests of 26 breeding species in undisturbed, grazed, and burned and grazed plots. We also sampled arthropod biomass and nest predator abundance. Using the isodar model we determined that managed plots are ecological traps: compared with success on plots left undisturbed, nest success on plots that were only grazed was lower, and success on plots that were burned and grazed was substantially lower. Yet birds preferred to nest on managed plots, where arthropod abundance was measurably higher. Reptiles were the most abundant taxon of nest predators, and their abundance was highest in managed plots. Consequently, tree‐nesting species had higher nest success than shrub‐ and ground‐nesting birds. Nest success also increased with tree height. We concluded that isodar theory is a useful tool for detecting ecological traps if any component of fitness is measured in addition to animal densities. Our study also suggests that (1) human modification of the environment may alter simultaneously food and predator abundance, (2) the former affects nest site selection and the latter nest success, and (3) such ecosystems are likely to become traps for breeding birds.
Importance of correlations among matrix entries in stochastic models in relation to number of transition matrices
Authors: Ramula Satu , Lehtilä Kari
Published: September 2005

Stochastic matrix models are used to predict population viability and the risk of extinction. Different stochastic methods require different amounts of estimation effort and may lead to divergent estimates. We used 16 transition matrices collected from ten populations of the perennial herb Primula veris to compare population estimates produced by different stochastic methods, such as selection of matrices, selection of vital rates, selection of matrix elements, and Tuljapurkar's approximation. Specifically, we tested the reliability of the methods using different numbers of transition matrices, and examined the importance of correlations among matrix entries. When correlations among matrix entries were included in the models, selection of vital rates produced the lowest and Tuljapurkar's approximation produced the highest estimates of mean population growth rates. Selection of matrices and matrix elements often produced nearly similar population estimates. Simulations based on incompletely estimated correlations among matrix entries considerably differed from those based on all correlations estimated, particularly when correlations were strong. The magnitude of correlations among matrix entries depended on the number of matrices, which made it difficult to generalize correlations within a species. Given that selection of vital rates or matrix elements is used, correlations among matrix entries should usually be included in the model, and they should preferably be estimated from the present data rather than according to other information of the species.
Erythropoietic activity in patients with sickle cell anaemia before and after treatment with hydroxyurea
Authors: Ballas Samir , Marcolina Mary , Dover George , Barton Franca ,   the Investigators of the Multicenter Study of Hydroxyurea Sickle Cell Anemia
Published: September 2005

In this project we have prospectively studied the erythropoietic activity in patients with sickle cell anaemia (SS) before and after treatment with hydroxyurea (HU). Some of the patients were enrolled in a double‐blind placebo controlled trial of HU in patients with SS and others were enrolled in an open label study. Determinants of erythropoietic activity included the reticulocyte count, red blood cell (RBC) survival by the 51Cr method, plasma 59Fe clearance, plasma iron turnover (PIT), erythron transferrin uptake (ETU), RBC production/destruction rate, and RBC Fe utilization. Therapy with HU increased the mean corpuscular volume (MCV), haemoglobin (Hb)F, RBC survival and t1/259Fe clearance; it decreased the reticulocyte count, the white blood cell (WBC) count, ETU, and the PIT. Most of the changes in parameters of erythropoiesis could be explained by the increase in 51Cr RBC survival after therapy with HU. Together the data showed that in selected patients the net effect of HU on Hb level was a function of the difference between the suppressive effect of HU (decreased RBC production) and the increase in RBC survival. In the majority of patients who responded to HU, there was a preferential effect on RBC survival.