bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrating yttrium iron garnet onto nongarnet substrates with faster deposition rates and high reliability
Authors: Sung Sang-Yeob , Qi Xiaoyuan , Stadler Bethanie J. H.
Published: September 2005

Magneto-optical garnets (Y3Fe5O12 or YIG) were grown monolithically by a novel reactive radio-frequency sputtering method that used a partial pressure differential to increase sputtering rates. MgO and quartz substrates were used as they are good buffer layers and optical claddings for integration. A wide single-phase field for annealed YIG was found (26.9–43.2at% Y), and the magnetic properties were measured. The films had refractive indices of 2.1 and out-of-plane Faraday rotations up to 0.2°∕μm at 633nm. The dielectric matrix was used to calculate the difference in the propagation constants of forward and backward traveling light (Δβ=1.999×10−5).
Unsteady fluid-dynamic force solely in terms of control-surface integral
Authors: Wu Jie-Zhi , Pan Ze-Liang , Lu Xi-Yun
Published: September 2005

In experimental aerodynamics (and hydrodynamics) it is well known that, if the flow past a solid body is steady, then the total force on the body can be conveniently estimated by the measured flow data on an appropriate control surface alone. We now show that, for the first time, the steady-flow condition can be removed provided that the flow is incompressible: two innovative formulas for the total force acting on any solid body that moves and deforms arbitrarily in a viscous incompressible fluid, solely in terms of control-surface integrals, are derived based on derivative-moment transformations. The formulas are verified by a numerical test for flow over a two-dimensional fishlike swimming body.
Polymer-based organic field-effect transistor using offset printed source/drain structures
Authors: Zielke Dirk , Hübler Arved C. , Hahn Ulrich , Brandt Nicole , Bartzsch Matthias , Fügmann Uta , Fischer Thomas , Veres Janos , Ogier Simon
Published: September 2005

Organic field-effect transistors were fabricated using offset printed source/drain structures. Interdigitated electrode structures were printed with a poly(3,4–ethylenedioxythiophene) (PEDOT) formulation. A polymeric semiconductor polytriarylamine and different insulator layers were deposited by spin coating. A field-effect mobility of 3×10−3cm2V−1s−1 and on/off ratio of about 103 was achieved, making it possible to produce digital logic elements.
“Bridge Model” of nanoparticles deposited on pores area of the substrate during a membrane fabrication
Authors: Shi Zhongliang , Wu Shanqiang , Szpunar Jerzy A.
Published: September 2005

The initial observations of a palladium membrane deposited by an electroless process and an aluminium membrane deposited by a sputtering process on the porous stainless steel substrates illustrate that the membranes are made of their nanoparticles and the pore areas at the surface of the substrate are covered by palladium or aluminium nanoparticles, which are like building bridges there. A “Bridge Model” is presented to illustrate the deposition progress of the fabrication of a membrane on the porous substrate. Scanning electron microscope micrographs from the cross section of the the palladium membrane deposited on the substrate confirm the presence of this bridge. The result will be beneficial for the design and fabrication of various nanomembranes and micromembranes on the porous substrates as well the effective control of them by the deposition processes.
Filling a spectral hole via self-phase modulation
Authors: Präkelt A. , Wollenhaupt M. , Sarpe-Tudoran C. , Assion A. , Baumert T.
Published: September 2005

The effect of spectral amplitude modulation on self-phase modulation is studied. To that end we remove a small interval of frequency components from the broad spectrum of a femtosecond laser pulse. We investigate the regeneration of these missing frequency components via self-phase modulation. A water jet serves as a transparent sample. A physical model is given which explains the observation that the removed frequency components are not only replenished by self-phase modulation but can even overshoot their adjacent frequencies in power spectral density. In addition, we suggest possible applications in the field of nonlinear microscopy.
Diet among oil-workers on off-shore oil installations in the Norwegian sector of the North Sea
Authors: Oshaug A. , Østgård L. I. , Trygg K. U.
Published: September 2005

Dietary studies based on 24 h recalls were carried out on four oil installations in the Norwegian sector of the North Sea. Two hundred and three persons were interviewed about what they had eaten the previous 24 h. Food purchased for the installations in the previous 5 months was recorded. Results based on 24 h recalls showed that average daily intake of energy was 12.2 MJ of which 17% came from protein, 44% from fat and 39% from carbohydrate, including 8% from sugar. Meat, vegetables, fresh fruits, seafood (shellfish), french fries, eggs, cream and ice-cream were important components of the diet, while bread, fish and cereals played a minor role. Average daily intake (mg) of nutrients were: calcium 1244, iron 15, vitamin A 1049 μg, vitamin D 4.1 μg, thiamin 1.6, riboflavin 2.2, nicotinic acid 22, ascorbic acid 143. Dietary fibre intake, estimated as unavailable carbohydrate, was on average 19 g, and the average daily intake of cholesterol was 755 mg. Intakes were compared with the Norwegian recommended dietary allowance. Most of the employees chose a diet which when eaten over a longer period of time may contribute to the development of coronary heart diseases (CHD) and thereby increase the morbidity and mortality from CHD in the oil industry.
Energy supplementation reverses changes in the basal metabolic rates of chronically undernourished individuals
Authors: Soares M. J. , Kulkarni R. N. , Piers L. S. , Vaz M. , Shetty P. S.
Published: September 2005

The objective of the present study was to examine the influence of energy supplementation and its cessation thereafter on the basal metabolic rates (BMR) of chronically undernourished individuals. Seven apparently healthy males were supplemented daily with 3.35 MJ (15 g protein, 35 g fat, 105 g carbohydrate) for 12 weeks. The average gain in body-weight was 1.9 kg (body fat, 58%; fat-free mass (FFM), 42%). The rise in BMR exceeded that accounted for by the increases in FFM during the 12 weeks of supplementation and was attributed to increases in the amount and activity of the visceral tissue as well as to an added cost of lipogenesis. At 12 weeks after cessation of the supplement, body-weights and FFM had decreased to presupplementation levels. BMR at this stage were significantly lower than at the 12th week of supplementation, when expressed per kg FFM or when adjusted for FFM using an analysis of covariance. These results suggest an increase in the metabolic efficiency during this negative energy balance period. The study demonstrates that, in the chronically undernourished, the changes in BMR are reversible and, hence, physiologically important to the process of adaptation to low-energy intakes.
The digestibility in piglets of faba bean (Vicia faba L.) as affected by breeding towards the absence of condensed tannins
Authors: Van Der Poel A. F. B. , Dellaert L. M. W. , Van Norel A. , Helsper J. P. F. G.
Published: September 2005

Seed samples from two near-isogenic faba bean (Vicia faba L.) lines were examined for the levels of so-called anti-nutritional factors (ANF). From the ANF known to be present in faba beans, trypsin inhibitor activity, functional lectins, condensed tannins and pyrimidine glycosides were analysed. It was concluded that the lines differed only in the content of condensed tannins being < 0.5 g/kg and 5.2 (sd 0.2) g/kg for the low (LT)- and high (HT)-tannin lines respectively. In addition, the level of pyrimidine glycosides in the LT line was slightly higher than that in the HT line. The LT line showed a reduced proportion of the seed coat (105 v. 119 g/kg) and a lower seed weight (0.85 v. 1.01 g). The apparent ileal and faecal digestibility values of dry matter and nitrogen from the HT and LT line were determined for piglets which were fed on diets containing chromium oxide as a marker. The mean apparent ileal and faecal digestibility values for dry matter for the LT line were 0.694 and 0.889 and for N 0.828 and 0.879 respectively. For the HT line, these values were approximately 0.05 and 0.10 lower (P > 0.05). A multi-enzyme technique was used to predict the in vitro protein digestibility (IVPD) of the two lines. The IVPD of the LT line was 0.965 and about 0.05 higher than the HT line, confirming the difference in digestibility as measured in vivo. The present study shows the positive effects on digestibility of removal of condensed tannins in faba beans which was achieved by plant breeding.
Oligonucleotide arrays: information from replication and spatial structure
Authors: Upton Graham J. G. , Lloyd Julie C.
Published: September 2005

Motivation: The introduction of oligonucleotide DNA arrays has resulted in much debate concerning appropriate models for the measurement of gene expression. By contrast, little account has been taken of the possibility of identifying the physical imperfections in the raw data.

Results: This paper demonstrates that, with the use of replicates and an awareness of the spatial structure, deficiencies in the data can be identified, the possibility of their correction can be ascertained and correction can be effected (by use of local scaling) where possible. The procedures were motivated by data from replicates of Arabidopsis thaliana using the GeneChip® ATH1-121501 microarray. Similar problems are illustrated for GeneChip® Human Genome U133 arrays and for the newer and larger GeneChip® Wheat Genome microarray.

Availability: R code is freely available on request.

Contact:  gupton@essex.ac.uk
Energy landscape of k-point mutants of an RNA molecule
Authors: Clote P. , Waldispühl J. , Behzadi B. , Steyaert J.-M.
Published: September 2005

Motivation: A k-point mutant of a given RNA sequence s = s1, …, sn is an RNA sequence s′=s1′,…,sn′ obtained by mutating exactly k-positions in s; i.e. Hamming distance between s and s′ equals k. To understand the effect of pointwise mutation in RNA, we consider the distribution of energies of all secondary structures of k-point mutants of a given RNA sequence.

Results: Here we describe a novel algorithm to compute the mean and standard deviation of energies of all secondary structures of k-point mutants of a given RNA sequence. We then focus on the tail of the energy distribution and compute, using the algorithm AMSAG, the k-superoptimal structure; i.e. the secondary structure of a ≤k-point mutant having least free energy over all secondary structures of all k′-point mutants of a given RNA sequence, for k′ ≤ k. Evidence is presented that the k-superoptimal secondary structure is often closer, as measured by base pair distance and two additional distance measures, to the secondary structure derived by comparative sequence analysis than that derived by the Zuker minimum free energy structure of the original (wild type or unmutated) RNA.

Contact:  clote@bc.edu

Supplementary information:
METIS: multiple extraction techniques for informative sentences
Authors: Mitchell A. L. , Divoli A. , Kim J.-H. , Hilario M. , Selimas I. , Attwood T. K.
Published: September 2005

Summary: METIS is a web-based integrated annotation tool. From single query sequences, the PRECIS component allows users to generate structured protein family reports from sets of related Swiss-Prot entries. These reports may then be augmented with pertinent sentences extracted from online biomedical literature via support vector machine and rule-based sentence classification systems.

Availability:  

Contact:  mitchell@ebi.ac.uk

Supplementary information:
MILVA: An interactive tool for the exploration of multidimensional microarray data
Authors: D'Alimonte Davide , Lowe David , Nabney Ian T. , Mersinias Vassilis , Smith Colin P.
Published: September 2005

Motivation: Clustering techniques such as k-means and hierarchical clustering are commonly used to analyze DNA microarray derived gene expression data. However, the interactions between processes underlying the cell activity suggest that the complexity of the microarray data structure may not be fully represented with discrete clustering methods.

Results: A newly developed software tool called MILVA (microarray latent visualization and analysis) is presented here to investigate microarray data without separating gene expression profiles into discrete classes. The underpinning of the MILVA software is the two-dimensional topographic representation of multidimensional microarray data. On this basis, the interactive MILVA functions allow a continuous exploration of microarray data driven by the direct supervision of the biologist in detecting activity patterns of co-regulated genes.

Availability: The MILVA software is freely available. The software and the related documentation can be downloaded from . User ‘surrey’ as username and ‘3245’ as password to login. The software is currently available for Windows platform only.

Contact:  d.lowe@aston.ac.uk
Functional richness, functional evenness and functional divergence: the primary components of functional diversity
Authors: Mason Norman W. H. , Mouillot David , Lee William G. , Wilson J. Bastow
Published: September 2005

Functional diversity is hypothesised as being beneficial for ecosystem functions, such as productivity and resistance to invasion. However, a precise definition of functional diversity, and hence a framework for its quantification, have proved elusive. We present a definition based on the analogy of the components of species diversity – richness, evenness and divergence. These concepts are applied to functional characters to give three components of functional diversity – functional richness, functional evenness and functional divergence. We demonstrate how each of these components may be calculated. It is hoped that our definition of functional diversity and its components will aid in elucidation of the mechanisms behind diversity/ecosystem‐function relationships.
Compensatory growth for free? A field experiment on brown trout, Salmo trutta
Authors: Johnsson Jörgen I. , Bohlin Torgny
Published: September 2005

Laboratory studies suggest that animals may be capable of compensatory growth after periods of food shortage. There is, however, a lack of field experiments investigating the incidence and consequences of compensatory growth in the wild, and the relevance of compensatory responses in natural populations has recently been questioned. Here we addressed the hypotheses that (1) food restriction during critical growth periods can induce compensatory growth, and (2) that compensatory growth is associated with delayed costs in natural populations. These hypotheses were addressed by (1) manipulating the food intake of brown trout in spring, (2) measuring growth rate responses over the first month following release, and (3) measuring growth and mortality (i.e. recapture rate) over the subsequent fall and winter. We found that brown trout restored lost body weight and condition within a month, providing the first experimental demonstration of compensatory growth in the wild. However, no delayed costs of the compensatory response could be detected within the timespan of the experiment. We suggest that wild brown trout have an adapted “buffer capacity” to withstand fluctuations in food supply, allowing restoration of lost lipid reserves when feeding conditions improve. However, when prolonged food deprivation affect structural components, compensation may not be possible without compromising long‐term performance.
Nitrogen deposition and herbivory affect biomass production and allocation in an annual plant
Authors: Throop Heather L.
Published: September 2005

Atmospheric nitrogen (N) deposition is leading to large‐scale changes in N availability in terrestrial ecosystems. Nitrogen availability is known to affect herbivore consumption rates, insect population dynamics and plant response to herbivory, but few studies have investigated these factors in combination. I tested the hypotheses that a) simulated N deposition alone would positively affect plant performance, b) herbivory alone would detrimentally affect plant performance and c) when combined, the positive impacts of N deposition would be mitigated by N‐induced increases in herbivore consumption rates and population sizes. I assessed the response of Ambrosia artemisiifolia (Asteraceae, common ragweed) to simulated N deposition and herbivory by aphids and beetles. In greenhouse and field studies, I caged multivoltine herbivores on plants and allowed damage rates to differ among N treatments due to N‐driven changes in herbivore populations and consumption rates. Simulated N deposition led to increased vegetative and seed biomass and decreased root:shoot ratios. Both types of herbivory caused decreases in seed biomass, reproductive allocation, and root biomass. The combined influences of N deposition and herbivory varied with plant tissue type. The positive influences of N deposition on root and seed biomass were generally suppressed by herbivory, while positive impacts of N on shoot biomass were typically not significantly suppressed by herbivory. These data suggest that in addition to substantial direct influences on plant production and allocation, N deposition may indirectly affect biomass production and allocation through affecting the rates and consequences of insect herbivory. However, these strength of these indirect effects will differ among herbivore species. The particularly strong influence of both herbivory and N deposition on A. artemisiifolia reproduction suggest potential population and community‐level consequences.
Overcompensation and adaptive plasticity of apical dominance in Erysimum strictum (Brassicaceae) in response to simulated browsing and resource availability
Authors: Rautio P. , Huhta A‐P. , Piippo S. , Tuomi J. , Juenger T. , Saari M. , Aspi J.
Published: September 2005

In the cases where overcompensation has been observed in monocarpic herbs, overcompensation is associated with an apically dominant shoot architecture of intact plants, increased lateral branching following herbivory, and increased reproductive success as a consequence of damage. The compensatory continuum hypothesis expects overcompensation to be more prevalent in resource rich environments compared to poor environments. This is paradoxical since in resource rich conditions the intact plants should branch most vigorously and hence any further increase in branch number should lead to lower seed yield. An explanation could be that apical dominance is rather insensitive to changes in resource availability, and that overcompensation is possible in conditions where plants experience meristem limitation (due to apical dominance) in relation to available resources.

We explored the branching patterns and fitness responses of tall wormseed mustard (Erysimum strictum) to simulated browsing, soil nutrients, and competition in common garden. Competition increased apical dominance and reduced plant fitness whereas fertilization had the reverse effects. Simulated browsing increased lateral branching and had little impact on plant fitness. Fitness overcompensation was observed only among plants grown in competition and in the absence of fertilization – the most resource poor treatment combination in the experiment. The results contradict both with the compensation continuum and the assumption that apical dominance shows no or very little plasticity in relation to growing conditions. Because directional selection gradients on branch number were invariantly positive irrespective of growing conditions, we propose that, in spite of phenotypic plasticity of apical dominance, the plants appear to be meristem rather than resource limited, and that meristem limitation is strongest in conditions where intact plants produce fewest lateral branches. Our results deviate from the compensation continuum because resource availability affected compensation ability more strongly through phenotypic plasticity of shoot architecture rather than via changes in resource availability per se.
Effects of phenanthraquinone on allergic airway inflammation in mice
Authors: Hiyoshi K. , Takano H. , Inoue K.‐I. , Ichinose T. , Yanagisawa R. , Tomura S. , Kumagai Y.
Published: September 2005

Background

Diesel exhaust particles (DEP) enhance allergic airway inflammation in mice (Takano et al., Am J Respir Crit Care Med 1997; 156: 36–42). DEP consist of carbonaceous nuclei and a vast number of organic chemical compounds. However, it remains to be identified which component(s) from DEP are responsible for the enhancing effects. 9,10‐Phenanthraquinone (PQ) is a quinone compound involved in DEP.

Objective
To investigate the effects of PQ inoculated intratracheally on allergic airway inflammation related to ovalbumin (OVA) challenge.

Materials and Methods
We evaluated effects of PQ on airway inflammation, local expression of cytokine proteins, and allergen‐specific immunoglobulin production in mice in the presence or absence of OVA.

Results
In the presence of OVA, PQ (2.1 ng/animal) significantly increased the numbers of eosinophils and mononuclear cells in bronchoalveolar lavage fluid as compared with OVA alone. In contrast, the numbers of these cells around the airways were not significantly different between OVA challenge and OVA plus PQ challenge in lung histology. PQ exhibited adjuvant activity for the allergen‐specific production of IgG1 and IgE. OVA challenge induced significant increases in the lung expression of IL‐4, IL‐5, eotaxin, macrophage chemoattractant protein‐1, and keratinocyte chemoattractant as compared with vehicle challenge. However, the combination of PQ with OVA did not alter the expression levels of these proteins as compared with OVA alone.

Conclusion
These results indicate that PQ can enhance the immunoglobulin production and the infiltration of inflammatory cells into alveolar spaces that are related to OVA, whereas PQ seems to be partially responsible for the DEP toxicity on the allergic airway inflammation.
Common human Toll‐like receptor 9 polymorphisms and haplotypes: association with atopy and functional relevance
Authors: Berghöfer B. , Frommer T. , König I. R. , Ziegler A. , Chakraborty T. , Bein G. , Hackstein H.
Published: September 2005

Background
Toll‐like receptor 9 (TLR9) is a pattern‐recognition receptor that detects unmethylated CpG motifs prevalent in bacterial and viral DNA. TLR9 stimulation is a key event after bacterial infection, triggering innate immunity and T‐helper type 1 skewed adaptive immunity. Synthetic CpG‐oligodeoxynucleotides (CpG‐ODNs) represent a promising and novel class of immune adjuvants for allergy treatment, vaccination, and cancer therapy. However, common functional TLR9 gene variants could interfere with the clinical utilization of CpG‐ODN in immunotherapy. Recently, a possible association of TLR9 polymorphism C‐1237T with asthma has been reported.

Objective
The aim of the present study was to investigate whether TLR9 polymorphisms or haplotypes have functional relevance and are associated with atopy.

Methods
We genotyped five common TLR9 single‐nucleotide polymorphisms (SNPs) in promoter, exon, and intron regions of the gene in 527 healthy blood donors, and estimated four common haplotypes. The total IgE and specific IgE levels against the most common aeroallergens were measured (n=303). IFN‐α production by plasmacytoid dendritic cells (pDCs) was analysed after stimulation with TLR9 ligand CpG‐ODN (n=220).

Results
No significant influence of common TLR9 polymorphisms and haplotypes on the total and specific IgE levels was found. Functional analysis of CpG‐ODN‐induced IFN‐α did not indicate a significant role for common TLR9 gene polymorphisms in TLR9 function.

Conclusion
We conclude that common genetic differences in the TLR9 gene exert no major influence on allergy susceptibility, and are unlikely to have on impact on clinical application of CpG‐ODNs.
Environmental risk factors and allergic bronchial asthma
Authors: D'Amato G. , Liccardi G. , D'Amato M. , Holgate S.
Published: September 2005

The prevalence of allergic respiratory diseases such as bronchial asthma has increased in recent years, especially in industrialized countries. A change in the genetic predisposition is an unlikely cause of the increase in allergic diseases because genetic changes in a population require several generations. Consequently, this increase may be explained by changes in environmental factors, including indoor and outdoor air pollution. Over the past two decades, there has been increasing interest in studies of air pollution and its effects on human health. Although the role played by outdoor pollutants in allergic sensitization of the airways has yet to be clarified, a body of evidence suggests that urbanization, with its high levels of vehicle emissions, and a westernized lifestyle are linked to the rising frequency of respiratory allergic diseases observed in most industrialized countries, and there is considerable evidence that asthmatic persons are at increased risk of developing asthma exacerbations with exposure to ozone, nitrogen dioxide, sulphur dioxide and inhalable particulate matter. However, it is not easy to evaluate the impact of air pollution on the timing of asthma exacerbations and on the prevalence of asthma in general. As concentrations of airborne allergens and air pollutants are frequently increased contemporaneously, an enhanced IgE‐mediated response to aeroallergens and enhanced airway inflammation could account for the increasing frequency of allergic respiratory allergy and bronchial asthma. Pollinosis is frequently used to study the interrelationship between air pollution and respiratory allergy. Climatic factors (temperature, wind speed, humidity, thunderstorms, etc) can affect both components (biological and chemical) of this interaction. By attaching to the surface of pollen grains and of plant‐derived particles of paucimicronic size, pollutants could modify not only the morphology of these antigen‐carrying agents but also their allergenic potential. In addition, by inducing airway inflammation, which increases airway permeability, pollutants overcome the mucosal barrier and could be able to ‘prime’ allergen‐induced responses. There are also observations that a thunderstorm occurring during pollen season can induce severe asthma attacks in pollinosis patients. After rupture by thunderstorm, pollen grains may release part of their cytoplasmic content, including inhalable, allergen‐carrying paucimicronic particles.
Population dynamics of the exploited sea cucumber Isostichopus fuscus in the western Galápagos Islands, Ecuador
Authors: HEARN ALEX , MARTÍNEZ PRISCILLA , VERONICA TORAL‐GRANDA M. , MURILLO JUAN CARLOS , POLOVINA JEFFREY
Published: September 2005

Long‐term density data for the sea cucumber, Isostichopus fuscus, from Canal Bolivar (separating western Isabela and eastern Fernandina Islands), Galápagos, were compared with catch statistics and used in a stock depletion model to determine the extent of the effects of the fishery on the existing population and the potential for the population to recover after each fishing season. Recruitment indices were found to be low from 1994 until mid‐1999, when a mass recruitment event was registered and numbers of small individuals increased dramatically. The increase in density of juveniles peaked in 2001 and has declined since. Recruitment in this species of sea cucumber appears to be highly sporadic and may depend on intense climatic events such as the warm El Niño. Current levels of fishing activity are unsustainable. The management implications of pulse recruitment in this fishery are discussed.
Response of fish and plankton to nutrient loading reduction in eight shallow Danish lakes with special emphasis on seasonal dynamics
Authors: JEPPESEN ERIK , JENSEN JENS PEDER , SØNDERGAARD MARTIN , LAURIDSEN TORBEN L.
Published: September 2005

1. For 13 years the response of the plankton and fish community to a decline in external phosphorus loading was studied in eight lakes with a mean depth <5 m. We conducted chi‐square analyses of sign of slope (positive or negative) of bimonthly averages of plankton variables for the eight lakes versus time. For fish, we compared results from two periods, i.e. 1989–1994 versus 1994–2001 as less data were available.

2. Fish community structure tended to respond to the lowered concentration of total phosphorus (TP), although not all changes were significant. While catch per unit effort (multi‐mesh sized gill nets) of cyprinids (especially bream, Abramis brama and roach, Rutilus rutilus) was highest in the first 5‐year period, the quantitative importance particularly of perch (Perca fluviatilis), pike (Esox lucius) and rudd (Scardinius erythropthalmus), a littoral species, increased significantly after 1994.

3. No changes occurred in zooplankton biomass, except for an increase in November and December. Biomass of small cladocerans, however, declined during summer and autumn, and the proportion of Daphnia to cladoceran biomass also increased. Average body weight of Daphnia and that of all cladocerans increased. The proportion of calanoids among copepods decreased in summer and the average body weight of cyclopoids and calanoids decreased during summer and autumn/early winter.

4. Total biovolume of phytoplankton declined significantly in March to June and tended to decline in November and December as well, while no significant changes were observed during summer and autumn. Non‐heterocystous cyanobacteria showed a decreasing trend during summer and autumn, while heterocystous cyanobacteria increased significantly in late summer. An increase in late summer was also evident for cryptophytes and chrysophytes, while diatoms tended to decline during most seasons.

5. We conclude that phytoplankton, and probably also fish, responded rapidly to reduced loading, whereas the effect on zooplankton was less pronounced. However, increases in body weight of cladocerans and the zooplankton to phytoplankton biomass ratio during summer indicate reduced top‐down control on zooplankton and enhanced grazing on phytoplankton. This conclusion is supported by a tendency for fish biomass to decline and a shift towards greater dominance by piscivores and, thus, an increased likelihood of predator control of zooplanktivorous cyprinids.
Combining palaeolimnological and limnological approaches in assessing lake ecosystem response to nutrient reduction
Authors: BATTARBEE RICHARD W. , JOHN ANDERSON N. , JEPPESEN ERIK , LEAVITT PETER R.
Published: September 2005

1. Palaeolimnological data and limnological time‐series data are highly complementary. Sediment records extend time‐scales, integrate subannual variability and expand the range of sites that can be studied, but they suffer from taphonomic biases and occasionally from uncertain chronology. Observational time‐series data, on the other hand, are highly resolved but are very limited in extent both in space and time.

2. Palaeolimnological and observational data‐sets need to be combined in oligotrophication research to establish (i) the past and present status of lakes needed to identify reference conditions; (ii) changes in ecosystem state; (iii) responses to nutrient reduction; and (iv) the potential role of other factors (e.g. additional stressors, climate change) that might confound predictions of future state.
A comparison of diatom phosphorus transfer functions and export coefficient models as tools for reconstructing lake nutrient histories
Authors: BENNION HELEN , JOHNES PENNY , FERRIER ROBERT , PHILLIPS GEOFF , HAWORTH ELIZABETH
Published: September 2005

1. We compared the baseline phosphorus (P) concentrations inferred by diatom‐P transfer functions and export coefficient models at 62 lakes in Great Britain to assess whether the techniques produce similar estimates of historical nutrient status.

2. There was a strong linear relationship between the two sets of values over the whole total P (TP) gradient (2–200 μg TP L−1). However, a systematic bias was observed with the diatom model producing the higher values in 46 lakes (of which values differed by more than 10 μg TP L−1 in 21). The export coefficient model gave the higher values in 10 lakes (of which the values differed by more than 10 μg TP L−1 in only 4).

3. The difference between baseline and present‐day TP concentrations was calculated to compare the extent of eutrophication inferred by the two sets of model output. There was generally poor agreement between the amounts of change estimated by the two approaches. The discrepancy in both the baseline values and the degree of change inferred by the models was greatest in the shallow and more productive sites.

4. Both approaches were applied to two lakes in the English Lake District where long‐term P data exist, to assess how well the models track measured P concentrations since approximately 1850. There was good agreement between the pre‐enrichment TP concentrations generated by the models. The diatom model paralleled the steeper rise in maximum soluble reactive P (SRP) more closely than the gradual increase in annual mean TP in both lakes. The export coefficient model produced a closer fit to observed annual mean TP concentrations for both sites, tracking the changes in total external nutrient loading.

5. A combined approach is recommended, with the diatom model employed to reflect the nature and timing of the in‐lake response to changes in nutrient loading, and the export coefficient model used to establish the origins and extent of changes in the external load and to assess potential reduction in loading under different management scenarios.

6. However, caution must be exercised when applying these models to shallow lakes where the export coefficient model TP estimate will not include internal P loading from lake sediments and where the diatom TP inferences may over‐estimate TP concentrations because of the high abundance of benthic taxa, many of which are poor indicators of trophic state.
Long‐term response of a shallow, moderately flushed lake to reduced external phosphorus and nitrogen loading
Authors: KÖHLER J. , HILT S. , ADRIAN R. , NICKLISCH A. , KOZERSKI H. P. , WALZ N.
Published: September 2005

1. The responses of nutrient concentrations, plankton, macrophytes and macrozoobenthos to a reduction in external nutrient loading and to contemporary climatic change were studied in the shallow, moderately flushed Lake Müggelsee (Berlin, Germany). Weekly to biweekly data from 1979 to 2003 were compared with less frequently collected historical data.

2. A reduction of more than 50% in both total phosphorus (TP) and total nitrogen (TN) loading from the hypertrophic (1979–90) to the eutrophic period (1997–2003) was followed by an immediate decline in TN concentrations in the lake. TP concentrations only declined during winter and spring. During summer, phosphorus (P) release from the sediments was favoured by a drastic reduction in nitrate import. Therefore, Müggelsee acted as a net P source for 6 years after the external load reduction despite a mean water retention time of only 0.1–0.16 years.

3. Because of the likely limitation by P in spring and nitrogen (N) in summer, phytoplankton biovolume declined immediately after nutrient loading was reduced. The formerly dominant cyanobacteria (Oscillatoriales) Limnothrix redekei and Planktothrix agardhii disappeared, but the mean biovolume of the N2‐fixing species Aphanizomenon flos‐aquae remained constant.

4. The abundance of Daphnia spp. in summer decreased by half, while that of cyclopoid copepod species increased. Abundances of benthic macroinvertebrates (mainly chironomids) decreased by about 80%. A resource control of both phytoplankton and zooplankton is indicated by significant positive correlations between nutrient concentrations and phytoplankton biovolume and between phytoplankton and zooplankton biomass.

5. Water transparency in spring increased after nutrient reduction and resulted in re‐colonisation of the lake by Potamogeton pectinatus. However, this process was severely hampered by periphyton shading and grazing by waterfowl and fish.

6. Water temperatures in Müggelsee have increased in winter, early spring and summer since 1979. The earlier development of the phytoplankton spring bloom was associated with shorter periods with ice cover, while direct temperature effects were responsible for the earlier development of the daphnid maximum in spring.
The recovery of a very shallow eutrophic lake, 20 years after the control of effluent derived phosphorus
Authors: PHILLIPS GEOFF , KELLY ANDREA , PITT JO‐ANNE , SANDERSON RORY , TAYLOR ELIOT
Published: September 2005

1. Monitoring at fortnightly to monthly intervals of a very shallow, lowland lake over 24 years has enabled the time course of recovery from nutrient enrichment to be investigated after high external P loading of the lake (>10 g P m−2 year−1) was reduced between 1977 and 1980.

2. The lake showed a relatively rapid response during the spring and early summer, with a reduction in phytoplankton biomass occurring after 5 years when soluble reactive phosphorus concentration was <10 μg L−1.

3. However, during the later summer the response was delayed for 15 years because of sustained remobilisation of phosphorus from the sediment. The greater water clarity in spring and a gradual shift from planktonic to benthic algal growth may be related to the reduction in internal loading after 15 years.

4. Changes in the phytoplankton community composition were also observed. Centric diatoms became less dominant in the spring, and the summer cyanobacteria populations originally dominated by non‐heterocystous species (Limnothrix/Planktothrix spp.) almost disappeared. Heterocystous species (Anabaena spp. and Aphanizomenon flos‐aquae) were slower to decline, but after 20 years the phytoplankton community was no longer dominated by cyanobacteria.

5. There were no substantial changes in food web structure following re‐oligotrophication. Total zooplankton biomass decreased but body size of Daphnia hyalina, the largest zooplankton species in the lake, remained unchanged, suggesting that the fish population remained dominated by planktivorous species.

6. Macrophyte growth was still largely absent after 20 years, although during the spring water clarity may have become sufficient for macrophytes to re‐establish.
Response of a eutrophic, shallow subtropical lake to reduced nutrient loading
Authors: COVENEY M. F. , LOWE E. F. , BATTOE L. E. , MARZOLF E. R. , CONROW R.
Published: September 2005

1. Lake Apopka (FL, U.S.A.) was subjected to decades of high nutrient loading from farms developed in the 1940s on converted riparian wetlands. Consequences included perennially high densities of cyanobacteria, low water transparency, elimination of submerged vegetation, modified fish community, and deposition of nutrient‐rich, flocculent sediments.

2. Initial steps were taken to reduce phosphorus (P) loading. Through strengthened regulation and purchase of farms for restoration, external P loading was reduced on average from 0.56 to 0.25 g P m−2 year−1 (55%) starting in 1993. The P loading target for the lake is 0.13 g P m−2 year−1.

3. For the first 6 years of P loading reduction the annual sedimentation coefficient (σ) averaged 13% less than the prior long‐term value (0.97 versus 1.11 year−1). The sedimentation coefficient, σ, was lower in the last 3 years of the study, but this period included extreme low‐water conditions and may not be representative. Annual σ was negative (net P flux to the water column) only 1 year.

4. Wind velocity explained 43% of the variation in σ during the period before reductions in total phosphorus (TP) concentration of lake water, but this proportion dropped to 6% after TP reductions.

5. Annual mean TP concentrations differed considerably from values predicted from external loading and hydraulic retention time using the Vollenweider–Organization for Economic Co‐operation and Development relationship. Reductions in lake water TP concentration fit model predictions better when multiyear (3‐year) mean values were used.

6. Evidence available to date indicates that this shallow, eutrophic lake responded to the decrease in external P loading. Neither recycling of sediment P nor wind‐driven resuspension of sediments prevented improvements in water quality. Reductions in TP concentration were evident about two TP‐resident times (2 × 0.9 year) after programmes began to reduce P loading. Improvements in concentrations of chlorophyll a and total suspended solids as well as in Secchi transparency lagged changes in lake‐water TP concentration but reached similar magnitudes during the study.
Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes
Authors: Ishihara Shuji , Fujimoto Koichi , Shibata Tatsuo
Published: September 2005

Gene regulatory networks contain several substructures called network motifs, which frequently exist throughout the networks. One of such motifs found in Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster is the feed‐forward loop, in which an effector regulates its target by a direct regulatory interaction and an indirect interaction mediated by another gene product. Here, we theoretically analyze the behavior of networks that contain feed‐forward loops cross talking to each other. In response to levels of the effecter, such networks can generate multiple rise‐and‐fall temporal expression profiles and spatial stripes, which are typically observed in developmental processes. The mechanism to generate these responses reveals the way of inferring the regulatory pathways from experimental results. Our database study of gene regulatory networks indicates that most feed‐forward loops actually cross talk. We discuss how the feed‐forward loops and their cross talks can play important roles in morphogenesis.
The politics of post‐implementation reviews
Authors: Gwillim David , Dovey Ken , Wieder Bernhard
Published: September 2005

Abstract.  The post‐implementation review (PIR) literature emphasizes the benefits of ex post evaluations of information technology (IT) projects. However, empirical studies of actual practice show that few organizations undertake any substantive form of ex post evaluation. This article presents the results of case study research in the Australian offices of two global corporations. These results support the findings reported in the literature and contribute new insights into the political factors that discourage the undertaking of PIRs in organizations. Furthermore, the results reveal a significant gap between theory and practice with respect to IT investment and IT governance practices, with no evidence found of such practices influencing ex post evaluation behaviour in these two organizations.
Island biogeography of the Mediterranean sea: the species–area relationship for terrestrial isopods
Authors: Gentile Gabriele , Argano Roberto
Published: September 2005

Aim  We looked at the biogeographical patterns of Oniscidean fauna from the small islands of the Mediterranean Sea in order to investigate the species–area relationship and to test for area‐range effects.

Location  The Mediterranean Sea.

Methods  We compiled from the literature a data set of 176 species of Oniscidea (terrestrial isopods) distributed over 124 Mediterranean islands. Jaccard's index was used as input for a UPGMA cluster analysis. The species–area relationship was investigated by applying linear, semi‐logarithmic, logarithmic and sigmoid models. We also investigated a possible ‘small island effect’ (SIE) by performing breakpoint regression. We used a cumulative and a sliding‐window approach to evaluate scale‐dependent area‐range effects on the log S/log A regression parameters.

Results  Based on similarity indexes, results indicated that small islands of the Mediterranean Sea can be divided into two major groups: eastern and western. In general, islands from eastern archipelagos were linked together at similarity values higher than those observed for western Mediterranean islands. This is consistent with a more even distribution of species in the eastern Mediterranean islands. Separate archipelagos in the western Mediterranean could be discriminated, with the exception of islets, which tended to group together at the lowest similarity values regardless of the archipelago to which they belong. Islets were characterized by a few common species with large ranges. The species–area logarithmic model did not always provide the best fit. Most continental archipelagos showed very similar intercepts, higher than the intercept for the Canary island oceanic archipelago. Sigmoid regression returned convex curves. Evidence for a SIE was found, whereas area‐range effects that are dependent on larger scale analyses were not unambiguously supported.

Main conclusions  The Oniscidea fauna from small islands of the Mediterranean Sea is highly structured, with major and minor geographical patterns being identifiable. Some but not all of the biogeographical complexity can be explained by interpreting the different shapes of species–area curves. Despite its flexibility, the sigmoid model tested did not always provide the best fit. Moreover, when the model did provide a good fit the curves looked convex, not sigmoid. We found evidence for a SIE, and minor support for scale‐dependent area‐range effects.
Gene diversity in a fragmented population of Briza media: grassland continuity in a landscape context
Authors: PRENTICE HONOR C. , LÖNN MIKAEL , ROSQUIST GABRIELLE , IHSE MARGARETA , KINDSTRÖM MERIT
Published: September 2005

We investigated patterns of allozyme variation in demes of the grass Briza media in semi‐natural grassland fragments within a mosaic agricultural landscape on the Baltic island of Öland. In the study area, Briza is both a characteristic species of old pastures and an early colonizer of young grasslands developing on previously forested or arable sites.

Generalized linear models revealed that descriptors of both present landscape structure and past grassland history are significant determinants of genetic variation in the Briza demes. Genetic structure and levels of within‐deme diversity are influenced by the size of grassland fragments, the type of habitat surrounding the grasslands, the size/spatial extent of the demes, the geographic position of the demes and the historical continuity of the grassland fragments.

Gene diversity (H) was higher in demes from grassland polygons with a high proportion of adjacent grassland, higher in the more extensive demes, and decreased northwards within the study area.

The negative association between the inbreeding coefficient (FIS) and grassland continuity is interpreted in terms of a two‐stage colonization process: recruitment into young grasslands leads initially to spatial patchiness, but subsequent selection in maturing pastures occurs within an increasingly uniform and dense sward.

Despite a weak overall genetic structure (as indicated by Bayesian cluster analysis) the between‐deme FST was significant. Linear discriminant analysis of within‐deme allele frequencies grouped the demes according to the age and previous land‐use history of their grassland polygons. The convergence of the allele frequency profiles in the younger grasslands towards those of the old grasslands is consistent with convergence of selective regimes as pastures mature towards an increasingly uniform, dense sward and characteristic species assemblage.

The genetic composition of demes of a grassland species appears to be influenced by the process of plant community convergence during grassland development – complementing the recent finding that convergence of species composition in experimental assemblages of grassland plants is dependent on the genotypic composition of the component species.