bluuebunny/crossref_metadata_2025 huggingface dataset:
Tip size effects on atomic force microscopy nanoindentation of a gold single crystal
Authors: Lucas Marcel , Gall Ken , Riedo Elisa
Published: December 2008

The effect of tip radius on atomic force microscopy (AFM) nanoindentation is investigated through indentation on the (111) face of a gold single crystal. The hardness is derived using two different methods: by measuring directly the projected area of the residual indent with AFM images and by measuring the cross-sectional area of the indenter before and after each nanoindentation test. The hardness values obtained from the cross-sectional area of the indenter are comparable with those obtained from images of the residual indent scanned with a sharp tip. Two AFM tips of average radii of 70±12 and 112±26 nm are used to indent the sample to various depths ranging from 4 to 50 nm. For depths above 30 nm, hardness values remain constant around 500 MPa for both indenters. For depths below 30 nm, the hardness increases as the indent depth decreases for the sharp and blunt indenters, and the indent depth dependence is observed over a wider depth range for the sharp indenter. For depths below 30 nm, the hardness values obtained with the sharp indenter are also consistently higher than those obtained with the blunt indenter. The results confirm a size scale effect during nanometer scale indentation for both varying penetration depth and tip radius, both of which influence the volume of material sampled during deformation.
Determining the optimum pentacene channel thickness on hydrophobic and hydrophilic dielectric surface
Authors: Mun Sung-jin , Choi Jeong-M. , Lee Kwang H. , Lee Kimoon , Im Seongil
Published: December 2008

We report that the optimum pentacene channel thickness is dependent on the surface energy state of its dielectric substrate. Pentacene thin-film transistor (TFT) with hydrophobic substrate displays a peak linear mobility at an optimum channel thickness of 50nm, below or above which the linear mobility decreases. In contrast, the linear mobility of the TFT with hydrophilic substrate monotonically increases until the channel thickness decreases to 15nm. According to atomic force microscopy of 15-nm-thin pentacene grown on the SiO2 and poly-4-vinyphenol (PVP) dielectrics, the pentacene islands on PVP are not perfectly interconnected unlike the case on SiO2.
Energy gap modulation in V2O5 nanowires by gas adsorption
Authors: Kim Byung Hoon , Kim Ansoon , Oh Soon-Young , Bae Sung-Soo , Yun Yong Ju , Yu Han Young
Published: December 2008

The current-voltage characteristics at various pressures (2–10 atm) and the scanning tunneling microscopy of vanadium pentoxide nanowires (VONs) with the inert gases (He, Ne, and Ar) and diatomic molecules (H2, N2, O2) have been investigated. The gas dependent conductance (G) is consistent with the inverse energy gap obtained from the scanning tunneling spectroscopy study for the gas-adsorbed single VON. The three possible interactions for gas adsorption of the VON have been discussed. Among them, we have found that the induced dipole-dipole interaction between adsorbed gases plays an important role in conductance variation in the gas adsorbed VON using the conductance per molecule (G/N).
A decade of progress since the birth of Dolly
Authors: Wilmut Ian , Sullivan Gareth , Taylor Jane
Published: December 2008

The greatest effect of the birth Dolly, the first cloned animal derived from an adult, has been in prompting biologists to consider ways of reprogramming adult nuclei to a pluripotent state directly. The first procedure depends upon use of viral vectors to introduce selected transcription factors, but this procedure is slow and very inefficient. Research in our laboratory has demonstrated that exposure of differentiated nuclei to an extract of embryo stem cells induces expression of key pluripotency genes within 8 h, suggesting that it may be possible to identify and use other factors to enhance direct reprogramming. A study of mechanisms that bring about changes in DNA methylation in early sheep embryos identified a developmental isoform of Dnmt1, the expression of which was limited to early stages of pregnancy. Reduction in the level of transcript of this isoform at the time of fertilisation caused sheep embryo development to cease at the early morula stage, revealing a key role for the isoform that remains to be characterised. The ability to obtain pluripotent cells from specific patients is providing important new opportunities to study inherited diseases when the causative mutation is not known. The initial objective of this research is not cell therapy, but to use cells with the characteristics of those in a patient who has inherited the disease to establish a high-throughput screen to identify drugs that are able to prevent progression of the symptoms of the disease. Research is in progress with cells from patients with amyotropic lateral sclerosis.
International Investment Arbitration
Authors: McLachlan Campbell , Shore Laurence , Weiniger Matthew
Published: December 2008

International Investment Arbitration: Substantive Principles provides the first modern detailed analytical survey of the developing substantive principals of international law which are being applied to disputes by international investment tribunals. It considers the key questions that arise, and provides a clear description of the present state of the law as reflected in tribunal practice. The book is divided into three parts. In Part I (Overview) chapter 2 sets out the basic features of investment treaties and is designed to provide a route map to the book as a whole. Chapter 3 : Dispute Settlement looks in more detail at four fundamental issues in the settlement of investment disputes through arbitration: dispute settlement provisions, transparency, the legal nature of the rights at issue and the interpretation of BITs. Part II (Ambit of Protection) is concerned with three major sets of issues related to the ambit of the protections afforded by investment treaties. It is divided into three chapters: Parallel Proceedings, Nationality and Investment. Part III (Substantive Rights) deals with the core substantive rights accorded to investors under an investment treaty. It is divided into three chapters: Treatment of Investors, Expropriation and Compensation.
Effect of pressure on the superionic argyrodite Ag7GeSe5I
Authors: Albert Stéphanie , Haines Julien , Granier Dominique , Pradel Annie , Ribes Michel
Published: December 2008

The effect of pressure on both the structure and the electrical conductivity of the superionic Ag7GeSe5I phase has been studied at room temperature (i) by powder X-ray diffraction from 0.1 MPa to 10 GPa, (ii) by single-crystal X-ray diffraction from 0.1 MPa to 2 GPa and (iii) by impedance spectroscopy from 0.1 MPa to 1.5 GPa. The decrease in conductivity of about one order of magnitude when the pressure increases up to 1.5 GPa can be explained by compression of the cell. For a pressure increase up to 10 GPa, compression of the cell is about 6% in volume. The compressibility of the cell affects mainly two sites,i.e.I and one of the two Ag sites. Both sites have a very largeBisothat increases even further with pressure, to reach a value close to 11.5 Å2at 1.5 GPa. The occupancy of both Ag sites changes with pressure and becomes similar above 0.8 GPa. On the whole, it appears that the conduction mechanism is affected by pressure. While the conduction pathway is not changed, the limiting jump for ionic diffusion changes from an intercluster jump with a pseudo-potential barrier of about 257 meV at ambient pressure to an indirect jump with a pseudo-potential value of 240 meV at 1.8 GPa.
Strain profiles in thin films: influence of a coherently diffracting substrate and thickness fluctuations
Authors: Boulle A. , Conchon F. , Guinebretière R.
Published: December 2008

A simple least-squares fitting-based method is described for the determination of strain profiles in epitaxial films using high-resolution X-ray diffraction. The method is model-independent,i.e.it does not require any `guess' model for the shape of the strain profile. The shape of the vertical displacement profile is modelled using the versatile cubicB-spline functions, which puts smoothness and curvature constraints on the fitting procedure. The effect of a coherently diffracting substrate is taken into account as well as the effects of film thickness fluctuations. The model is applied to the determination of strain profiles in SmNiO3films epitaxically grown on SrTiO3(001) substrates. The shape of the retrieved strain profile is discussed in terms of oxygen vacancies.
Water retention properties of the clay in soils developed on clayey sediments: significance of parent material and soil history
Authors: Bruand A. , Tessier D.
Published: December 2008

We have investigated the water retention properties of clayey subsoil horizons according to the variation of clay characteristics. The horizons studied developed on a large range of age and facies of calcareous or calcium‐saturated clayey sediments. The water retention properties were studied from −10 hPa to −15 000 hPa water potential using small clods collected in winter when swelling is at a maximum and water content close to field capacity. The specific water content and volume of the clods at field conditions, their specific volume at −15 000 hPa water potential, the clay content, the organic carbon content, the cation exchange capacity, the N2‐BET surface area and calcareous content were measured. The clay fabric, which is the spatial distribution of the elementary clay particles, was quantified when the soil was close to field capacity and we could attribute the whole pore volume to the porosity of the clay fabric. Our results show that the water retention properties of the clay vary greatly from one soil to another with respect to the clay fabric. The variation of the latter depends on the cation exchange capacity, the size of elementary particles and hydric stress history of the clay. We show that the water retention properties of the studied clayey soils vary according to the clay content and fabric, the latter being related either to parent material fabric or to both the hydric history of the soil and size of the elementary clay particles.
Dissolved components in precipitation water percolated through forest litter
Authors: Hongve D. , Van Hees P. A. W. , Lundström U. S.
Published: December 2008

Leaves lying on the forest floor are a major source of dissolved organic substances in soil and surface waters, and these substances have important effects in those environments. We used zero‐tension lysimeters to study the chemical characteristics of water percolating through litter from various species of forest trees. The leaching rates were greatest in the autumn and declined rapidly thereafter, especially for deciduous litter. During an annual cycle, 2.5–17% of the initial contents of the carbon in the litter was recovered as dissolved organic carbon in percolates. Humus‐like substances, hydrophilic acids and hydrophilic neutral compounds constituted the major fractions of dissolved C. Leachates from deciduous leaf litter were only partly biodegradable, and those from spruce needles were scarcely biodegradable.

Low molecular weight organic acids constituted 0–12% of the dissolved organic carbon in the percolates of the first autumn sampling and decreased over time. Acetic and formic acids were present at the largest concentrations, up to 30 μmol l−1 per g litter, and gluconic, pyruvic, fumaric, oxalic and citric acids were also frequent in significant concentrations. Among the aromatic acids, p‐hydroxybenzoic acid was identified in four out of five autumn samples. The organic components in litter leachates are important for the microbial activity in soil and surface waters. The organic acids enhance weathering and translocation of metals by their ability to form complexes. Litter is also a source of inorganic ions in soil solutions. The dominant cations in the percolates were K+, Ca2+ and Mg2+, and spruce litter also yielded large quantities of Al and Fe.
Characteristics of non‐allophanic Andisols derived from low‐activity clay regoliths in the Nilgiri Hills (Southern India)
Authors: Caner L. , Bourgeon G. , Toutain F. , Herbillon A. J.
Published: December 2008

Low‐activity clay soils on old planation surfaces of the tropics are generally considered as stable end points of soil formation. It is therefore surprising to find Andisols on them. We characterized the properties of six profiles representative of these soils in the western part of the Nilgiri Hills (2000–2500 m above mean sea level), Southern India, where the present climatic conditions are cool (mean annual temperature 15°C) and humid (mean annual rainfall 2500 mm). Thick (50–80 cm) dark‐reddish brown topsoil overlies strongly desilicated yellowish‐red materials. This horizon has andic properties to a sufficient depth and the carbon content requirement of the melanic epipedon to place these soils in the Andisol order. Our data as well as the history of the Nilgiri Hills suggest that the formation of these non‐allophanic Andisols resulted from the succession of two main steps. First, a ‘lateritic’ weathering cycle led to the relative accumulation of secondary Al and Fe oxides. Later, the accumulation of organic matter favoured by a more recent climatic change induced complexation by organic acids of Al and Fe oxides, and the production of enough metal–humus complexes to give rise to andic properties. Such soils, in which secondary Al and Fe oxides, generally considered as indicators of an advanced weathering stage, are involved in a new cycle of soil formation, are original Andisols.
Effect of root mucilage and modelled root exudates on soil structure
Authors: Traoré O. , Groleau‐Renaud V. , Plantureux S. , Tubeileh A. , Boeuf‐Tremblay V.
Published: December 2008

Plant roots release in the rhizosphere diverse organic materials which may have different effects on soil structure. We have evaluated the effect of natural and modelled root‐released materials on soil aggregates and the biodegradation of carbon from roots in the soil. The effects of root mucilage from maize and of a modelled soluble exudate were compared with those of simple compounds (glucose, polygalacturonic acid). For all treatments, soil was amended with 2 g C kg−1 soil and incubated for 30 days at 25°C. The biodegradation of mucilage was similar to that of polygalacturonic acid, and slower than the decomposition of modelled exudates and glucose. Addition of all substrates increased the stability of aggregates, but the duration of this effect depended on the chemical nature of the material. Compared with the control, the proportion of stable aggregates after 30 days of incubation was multiplied by 3.8 for root mucilage, by 4.2 for modelled soluble exudates, by 2.5 for polygalacturonic acid and by 2.0 for glucose. The different fractions of root exudates in the rhizosphere evidently affected the aggregate stability.
Chemical heterogeneity of humic substances: characterization of size fractions obtained by hollow‐fibre ultrafiltration
Authors: Christl I. , Knicker H. , Kögel‐Knabner I. , Kretzschmar R.
Published: December 2008

To investigate the chemical heterogeneity of humic substances in relation to molecular size, fulvic and humic acids were extracted and purified from the surface horizon of a Humic Gleysol in northern Switzerland. A fractionation scheme using hollow‐fibre ultrafiltration cartridges was developed and used to obtain four size fractions of the humic acid with nominal molecular weight ranges > 300 kDa, 100–300 kDa, 30–100 kDa, and 10–30 kDa. The fulvic acid and all humic acid fractions were characterized by size exclusion chromatography, elemental analysis (C, H, N, S), as well as spectroscopic techniques including UV‐VIS, CP‐MAS 13C‐NMR, FT‐IR, and fluorescence spectroscopy.

Clear chemical differences between the humic acid size fractions were observed. Smaller size fractions of the soil humic acid contained more chargeable functional groups and a larger percentage of aromatic carbon than the larger size fractions. Conversely, the percentage of aliphatic carbon increased with increasing apparent molecular weight. The chemical composition of the smallest humic acid fraction differed clearly from the fulvic acid fraction, despite similar apparent molecular size and carboxyl carbon content. Small humic acids contained much more aromatic carbon and less aliphatic carbon than the fulvic acid fraction. Apparently, humic size fractions differ in their chemical composition, which can have important implications for their environmental behaviour.
Dynamics of soil organic matter associated with particle‐size fractions of water‐stable aggregates
Authors: Puget P. , Chenu C. , Balesdent J.
Published: December 2008

Stable macroaggregates (> 200 μm) of cultivated soils are reported in the literature to be richer in organic carbon, and in young organic carbon in particular, than microaggregates (< 200 μm). However, the nature of this additional carbon is not yet known. To determine it, we compared the composition of organic matter in stable macroaggregates with that in unstable ones. Macroaggregates 2–3 mm in diameter were separated from two silty cultivated soils from the Paris basin. They were slaked, and the primary particle composition of the resulting fractions was analysed. We used the natural abundance of 13C to quantify the amount of young carbon, derived from a maize crop, in the various size fractions.

The stable macroaggregates were richer in total C and in young C (younger than 6 and 23 years respectively in the two soils studied) than the unstable ones. This young C comprised 50% particulate organic matter, 20% associated with silt and 30% with clay particles. We propose a schematic composition of aggregates in these soils in which stable aggregates are formed by the binding of microaggregates by additional young organic matter, predominantly plant debris. Young organic matter is preferentially incorporated and is responsible for aggregation, though it is eventually redistributed among aggregate classes through the destruction and re‐formation of the aggregates. We have developed a model to simulate this redistribution. The model shows that stable macroaggregates have a life of a few years, but that microaggregates may exist for decades. We suggest that the stabilization and de‐stabilization of macroaggregates in soils is linked to the incorporation and biodegradation of plant debris.
Review series on helminths, immune modulation and the hygiene hypothesis: The broader implications of the hygiene hypothesis
Authors: Rook Graham A. W.
Published: December 2008

Man has moved rapidly from the hunter–gatherer environment to the living conditions of the rich industrialized countries. The hygiene hypothesis suggests that the resulting changed and reduced pattern of exposure to microorganisms has led to disordered regulation of the immune system, and hence to increases in certain inflammatory disorders. The concept began with the allergic disorders, but there are now good reasons for extending it to autoimmunity, inflammatory bowel disease, neuroinflammatory disorders, atherosclerosis, depression associated with raised inflammatory cytokines, and some cancers. This review discusses these possibilities in the context of Darwinian medicine, which uses knowledge of evolution to cast light on human diseases. The Darwinian approach enables one to correctly identify some of the organisms that are important for the ‘Hygiene’ or ‘Old Friends’ hypothesis, and to point to the potential exploitation of these organisms or their components in novel types of prophylaxis with applications in several branches of medicine.
Review series on helminths, immune modulation and the hygiene hypothesis: How might infection modulate the onset of type 1 diabetes?
Authors: Cooke Anne
Published: December 2008

The development of type 1 diabetes is influenced by both genetic and environmental factors. The current rise in the incidence of diabetes is occurring more rapidly than can be accounted for by genetic change, highlighting the influence of environmental modifiers. Considerable effort has been expended to identify infectious agents that might be responsible for this rise in incidence, but no single infectious agent has been linked to this dramatic increase in type 1 diabetes. There has been increasing interest in the possibility that infections of historical importance that might have shaped our immune systems over evolutionary time may also have played a role in down‐modulating some autoimmune and allergic disorders. In this review, some of the ways in which certain organisms might have influenced the onset of autoimmunity are discussed.
Genomic structure and promoter analysis of pathogen‐induced repat genes from Spodoptera exigua
Authors: Hernández‐Rodríguez C. S. , Ferré J. , Herrero S.
Published: December 2008

The repat gene family encodes midgut proteins overexpressed in response to pathogen infection in the lepidopteran Spodoptera exigua. Up‐regulation of repat genes has been observed after challenging the larvae with both Bacillus thuringiensis toxins and after infection with the baculovirus Autographa californica multiple nucleopolyhedrovirus. In our study, PCR amplification of the genomic region and genome walking were used to obtain the genomic structure and the sequence of the 5′‐upstream region of repat1 and repat2, two of the most phylogenetically distant members of the repat family. A similar gene structure between repat1 and repat2 has been found, with conserved exon‐intron positions and junction sequences, suggesting a common origin for these genes. Recombinant baculoviruses carrying the firefly luciferase gene under the control of different 5′‐upstream regions of the repat1 gene were constructed to elucidate the influence of these regions in gene expression. Infection of Helicoverpa zea gut‐derived cells with the recombinant baculoviruses revealed the upstream regions of the repat1 gene which are involved in gene transcription and demonstrated the role of an intron located in the 5′‐untranslated region in the enhancement of gene expression.
Septic injury‐inducible genes in medicinal maggots of the green blow fly Lucilia sericata
Authors: Altincicek B. , Vilcinskas A.
Published: December 2008

Lucilia sericata maggots are used world‐wide in biosurgery for the medical treatment of nonhealing wounds because they ingest necrotic tissues and significantly promote healing. To gain further insight into interdependencies between ecological adaptation and molecular evolution of innate immunity in Diptera, we used the suppression subtractive hybridization method to screen for genes that are differentially expressed in response to septic wounding of sterile second instar larvae of L. sericata. This approach resulted in the identification of 65 novel Lucilia genes including potential signalling proteins (e.g. inhibitor of apoptosis 2 protein) and a number of digestive enzymes including lipases and proteinases. Additionally, we found numerous putative antimicrobial peptides (AMPs), such as a potential Lucilia defensin, diptericin and three novel proline‐rich AMPs. The identified genes may facilitate access to both peptides and proteins within the beneficial excretions, secretions and haemolymph of medicinal maggots and provide novel insights into the evolution of innate immunity in Diptera.
Clients’ experiences of living at home with a mechanical ventilator
Authors: Ballangrud Randi , Bogsti Wenche Bergseth , Johansson Inger Signe
Published: December 2008

Title.  Clients’ experiences of living at home with a mechanical ventilator.

Aim.  This paper reports on a study of how clients experience living with home mechanical ventilation and how they experience care and supervision of healthcare personnel.

Background.  The number of people living at home with mechanical ventilators is increasing, and this is considered a successful approach to reducing incapacity and mortality.

Method.  Qualitative interviews were conducted with 10 service users in 2006. The informants were 18–75 years old and had varying diagnoses and levels of functioning. The interviews were tape recorded, transcribed and analysed by qualitative content analysis.

Findings.  Two main themes emerged: Theme 1. Having a home ventilator enhances quality of life – a life worth living. The ventilator treatment builds up strength and improves well‐being. Participants emphasized that it was important to feel in control of their own situation and had an overriding wish to live a normal and active life; Theme 2. Competence and continuity of healthcare personnel are factors for success. The experience was that competence and follow‐up by healthcare personnel varied, and that good quality teaching and information were important.

Conclusion.  Users of home mechanical ventilators should be active partners in their own care so that their experience is taken into account. It is important for clients having home mechanical ventilation to be empowered and have control in their daily lives, as well as having competent caregivers and continuity of care.
Estimating the scale of fish feeding movements in rivers using δ13Csignature gradients
Authors: Rasmussen Joseph B. , Trudeau Veronique , Morinville Genevieve
Published: December 2008

Isotopic signatures of consumers provide a time integration of their feeding history, and as a result of movements, are often out of line with signatures of their local resources. Such disequilibrium can be useful for inferring the spatial scale of consumer movement.

δ13Csignatures of dissolved inorganic carbon as well as periphyton and invertebrates, exhibit pronounced gradients along rivers. We outline an analytical framework to estimate the spatial scale of movement of riverine fish by comparing the slopes of their δ13Csignature gradients to that of the stream invertebrates they consume. For free‐ranging juvenile Atlantic salmon (Salmo salarL.), unconstrained by barriers, δ13Csignatures departed considerably from invertebrate signatures, and along‐stream slopes were as little as half those recorded for stream invertebrates. Movement estimates for these fish, based on their signature slopes, are ~20 km.

By contrast, stream resident salmonids (whose movements are constrained by physical barriers) and sedentary taxa such as sculpins and sticklebacks, have carbon signatures much closer to invertebrate signatures where they were collected. For these groups, our method yields negligible estimates of movement, similar to those of invertebrates.

Although this method cannot provide precise estimates of how much individual organisms move, or reveal details of movement history, it may provide an effective complement to telemetric and other methods of studying movement.
Large river floodplain restoration: predicting species richness and trait responses to the restoration of hydrological connectivity
Authors: Paillex Amael , Dolédec Sylvain , Castella Emmanuel , Mérigoux Sylvie
Published: December 2008

Floodplains are species‐rich environments often strongly impacted by human activities. In particular, the negative effects of progressive and rapid disconnection of secondary channels have led to restoration programmes and a growing interest in restoration ecology.

Current restoration strategies in large river floodplains focus on the macroinvertebrate response related to the increases in lateral connectivity of the secondary channels. We constructed a framework to assess a gradient of hydrological connectivity among 13 secondary channels and the main channel of a large river, and we modelled the response of a set of macroinvertebrate metrics to this gradient. Comparisons between predicted and observed metrics in restored channels allowed us to measure the effect of an increase in the hydrological connectivity on the biological characteristics of macroinvertebrate assemblages.

The pre‐restoration framework enabled a clear ordering of channels into three types according to levels of hydrological connectivity. Rarefied richness and species traits, responding to the connectivity gradient, showed a net difference between disconnected channels and the main river channel. We were able to highlight a predation–colonization trade‐off along the gradient of hydrological connectivity with a maximum colonization potential in the most connected channels.

Post‐restoration sampling showed deviations of the restored channels from their expected ecological state. A large proportion of colonizers were favoured by the restoration operations and non‐native species occurred in the restored channels.

Synthesis and applications. Macroinvertebrate biodiversity in large river floodplains is shaped by lateral hydrological connectivity. Increasing hydrological connectivity led to an increase in colonization rate. One year after restoration, the increase in lateral connectivity had shifted the restored sites away from the predicted state. This unpredictability is, in part, a consequence of the rapid colonization by non‐native species of new habitats created by the restoration measures. We recommend that floodplain‐scale restoration should focus on diversification of the hydrological connectivity of channels, thereby conserving a maximum of functional characteristics in macroinvertebrate communities.
What controls woodland regeneration after elephants have killed the big trees?
Authors: Moe Stein R. , Rutina Lucas P. , Hytteborn Håkan , Du Toit Johan T.
Published: December 2008

Top‐down regulation of ecosystems by large herbivores is a topic of active debate between scientists and managers, and a prime example is the interaction between elephantsLoxodonta africanaand trees in African savannas. A common assumption among wildlife managers is that a local reduction in elephant numbers will ultimately allow woodland to self‐restore to a desired former state. Such regeneration is, however, dependent on the survival of seedlings of impacted tree species. We conducted a field experiment to investigate seedling predation in the elephant‐transformed Chobe riparian woodland of northern Botswana.

We planted seedling gardens in (i) complete exclosures that excluded all herbivores except small rodents and invertebrates, (ii) semi‐permeable exclosures that excluded ungulates but included primates, lagomorphs, all rodents, gallinaceous birds, etc, and (iii) completely open plots. Seedlings were of two tree species decreasing in the area (Faidherbia albidaandGarcinia livingstonei) and two that are increasing (Combretum mossambicenseandCroton megalobotrys).

After 9 months, seedling survival ranged from >75% for all species in the complete exclosure to <20% forFaidherbia albidain the open plots. Survival of all seedlings exceptC. megalobotrysdeclined precipitously in open plots during the dry season when invertebrates are largely dormant but when impalasAepyceros melampus(locally abundant ungulates) increase the browse components of their diets.

Seedling survival in the open plots was negatively related to local impala density but unrelated to that of any other browser.

Synthesis and applications. Our findings relate to the current debate about managing elephants to restore southern African savanna landscapes to desired historical states. Various seedling predators, including the ubiquitous impalaAepyceros melampus, regulate the regeneration of trees from seedlings, and our experiments support the hypothesis that tall closed‐canopy woodlands originate during episodic windows of opportunity for seedling survival. To artificially recreate such a window would require the decimation of seedling predators as well as elephants, which is impractical at the landscape scale.
The sizes of species’ geographic ranges
Authors: Gaston Kevin J. , Fuller Richard A.
Published: December 2008

Geographic range size and how it changes through time is one of the fundamental ecological and evolutionary characteristics of a species, and a strong predictor of extinction risk. However, the measurement of range size remains a substantial challenge. Indeed, there is significant confusion in the literature as to how this should be done, particularly in the context of the distinction between the fundamentally different concepts of extent of occurrence (EOO) and area of occupancy (AOO), and the use of these quantities, including in assessments of the threat status of species.

Here we review the different approaches to determining the geographic distributions of species, the measurement of their range sizes, the relationships between the two, and other difficulties posed by range size measurement (especially those of range discontinuities when measuring EOO, and spatial scale when measuring AOO).

We argue that it is important to (i) distinguish the estimation of the distribution of a species from the measurement of its geographic range size; (ii) treat measures of EOO and AOO as serving different purposes, rather than regarding them as more or less accurate ways of measuring range size; and (iii) measure EOO including discontinuities in habitat or occupancy.

Synthesis and applications.With the availability and collation of extensive data sets on species occurrences, a rapidly increasing number of studies are investigating geographic range size, and particularly how various measures of range size predict macroecological patterns and inform assessments of the conservation status of species and areas. The distinction between EOO and AOO is becoming blurred in many contexts, but most particularly in that of threatened species assessments for Red Listing. Continued progress in these fields demands greater clarity in the meaning and derivation of measures of geographic range size. The two principal measures serve different purposes, and should not be regarded as alternatives that simply differ in accuracy.
Forecasting the combined effects of urbanization and climate change on stream ecosystems: from impacts to management options
Authors: Nelson Kären C. , Palmer Margaret A. , Pizzuto James E. , Moglen Glenn E. , Angermeier Paul L. , Hilderbrand Robert H. , Dettinger Michael , Hayhoe Katharine
Published: December 2008

Streams collect runoff, heat, and sediment from their watersheds, making them highly vulnerable to anthropogenic disturbances such as urbanization and climate change. Forecasting the effects of these disturbances using process‐based models is critical to identifying the form and magnitude of likely impacts. Here, we integrate a new biotic model with four previously developed physical models (downscaled climate projections, stream hydrology, geomorphology, and water temperature) to predict how stream fish growth and reproduction will most probably respond to shifts in climate and urbanization over the next several decades.

The biotic submodel couples dynamics in fish populations and habitat suitability to predict fish assemblage composition, based on readily available biotic information (preferences for habitat, temperature, and food, and characteristics of spawning) and day‐to‐day variability in stream conditions.

We illustrate the model using Piedmont headwater streams in the Chesapeake Bay watershed of the USA, projecting ten scenarios: Baseline (low urbanization; no on‐going construction; and present‐day climate); one Urbanization scenario (higher impervious surface, lower forest cover, significant construction activity); four future climate change scenarios [Hadley CM3 and Parallel Climate Models under medium‐high (A2) and medium‐low (B2) emissions scenarios]; and the same four climate change scenarios plus Urbanization.

Urbanization alone depressed growth or reproduction of 8 of 39 species, while climate change alone depressed 22 to 29 species. Almost every recreationally important species (i.e. trouts, basses, sunfishes) and six of the ten currently most common species were predicted to be significantly stressed. The combined effect of climate change and urbanization on adult growth was sometimes large compared to the effect of either stressor alone. Thus, the model predicts considerable change in fish assemblage composition, including loss of diversity.

Synthesis and applications. The interaction of climate change and urban growth may entail significant reconfiguring of headwater streams, including a loss of ecosystem structure and services, which will be more costly than climate change alone. On local scales, stakeholders cannot control climate drivers but they can mitigate stream impacts via careful land use. Therefore, to conserve stream ecosystems, we recommend that proactive measures be taken to insure against species loss or severe population declines. Delays will inevitably exacerbate the impacts of both climate change and urbanization on headwater systems.
Mucosal T‐cell responses to HIV: responding at the front lines
Authors: Shacklett B. L. , Critchfield J. W. , Ferre A. L. , Hayes T. L.
Published: December 2008

Mucosal surfaces of the body serve as the major portal of entry for human immunodeficiency virus (HIV). These tissues also house a majority of the body’s lymphocytes, including the CD4+ T cells that are the major cellular target for HIV infection. Mucosal surfaces are defended by innate and adaptive immune mechanisms, including secreted antibodies and CD8+ cytotoxic T cells (CTL). CTL in mucosal lymphoid tissues may serve to limit viral replication, decreasing the host’s viral burden as well as reducing the likelihood of sexual transmission to a naïve host. This review summarizes recent literature on HIV‐specific T‐cell responses in mucosal tissues, with an emphasis on the gastrointestinal tract.
NK cells in HIV‐1 infection: evidence for their role in the control of HIV‐1 infection
Authors: Alter G. , Altfeld M.
Published: December 2008

Increasing evidence supports the notion that the innate immune response, and in particular, natural killer cells play a central role in determining the quality of the host immune response to infection. In this review we highlight recent evidence that suggests that NK cells influence the clinical fate of HIV‐infected individuals.
Human immunodeficiency virus‐1 acquisition in genital mucosa: Langerhans cells as key‐players
Authors: De Jong M. A. W. P. , Geijtenbeek T. B. H.
Published: December 2008

Human immunodeficiency virus‐1 (HIV‐1) infection occurs primarily via genital mucosal tissues and the cellular mechanisms that affect HIV‐1 acquisition are largely unclear. Langerhans cells (LCs) are professional antigen presenting cells lining the mucosal stratified squamous epithelium. It is becoming evident that LCs have different functions in HIV‐1 transmission. HIV‐1 can infect mucosal LCs, which subsequently efficiently transmit the virus to T cells in the lymphoid tissues. However, this seems to be dependent on the activation status of LCs, as immature LCs prevent HIV‐1 infection by clearing invading HIV‐1 though the C‐type lectin langerin. Recent data demonstrate that co‐infections with sexual transmitted infection (STIs) negate the protective function of LCs by different mechanisms, thereby allowing LC infection with HIV‐1 and subsequently HIV‐1 transmission. Here, we will discuss the function of LCs under normal circumstances and in the presence of STIs or inflammation. A better understanding of LCs function during homeostasis and inflammation is necessary for the development of new strategies to prevent HIV‐1 infection.
Dendritic cell‐based human immunodeficiency virus vaccine
Authors: Rinaldo C. R.
Published: December 2008

Dendritic cells (DC) have profound abilities to induce and coordinate T‐cell immunity. This makes them ideal biological agents for use in immunotherapeutic strategies to augment T‐cell immunity to HIV infection. Current clinical trials are administering DC‐HIV antigen preparations carried out ex vivo as proof of principle that DC immunotherapy is safe and efficacious in HIV‐infected patients. These trials are largely dependent on preclinical studies that will provide knowledge and guidance about the types of DC, form of HIV antigen, method of DC maturation, route of DC administration, measures of anti‐HIV immune function and ultimately control of HIV replication. Additionally, promising immunotherapy approaches are being developed based on targeting of DC with HIV antigens in vivo. The objective is to define a safe and effective strategy for enhancing control of HIV infection in patients undergoing antiretroviral therapy.
Immunity in natural SIV infections
Authors: Silvestri G.
Published: December 2008

In stark contrast to human immunodeficiency virus (HIV)‐infected individuals who, if left untreated, almost invariably progress to acquired immunodeficiency syndrome (AIDS), natural hosts for the simian immunodeficiency viruses (SIV) remain asymptomatic throughout the course of infection. This observation represents one of the main unresolved puzzles of AIDS research, particularly if one considers that natural SIV infections are characterized by chronically high levels of viraemia as well as intrinsic virus cytopathicity comparable with that of HIV. In this review, I discuss the basic immunological features of natural, nonpathogenic SIV infections, the evidence suggesting that attenuated, rather than extraordinarily strong, immune responses to the virus may favour their benign course, and the implications of these findings in terms of HIV therapy and vaccines.
Signalling pathways leading to IFN‐α production in human plasmacytoid dendritic cell and the possible use of agonists or antagonists of TLR7 and TLR9 in clinical indications
Authors: Guiducci C. , Coffman R. L. , Barrat F. J.
Published: December 2008

Plasmacytoid dendritic cells (PDC) are highly specialized immune cells capable of producing large amounts of type I and III IFN in response to viral infection. This response is mediated through TLR7 and TLR9 signalling pathways. In addition, PDC can differentiate into fully mature dendritic cells able to efficiently crosspresent viral antigens, thus playing an important role in adaptive immunity. This dual property of PDC is being used in clinical settings where synthetic TLR7 and TLR9 ligands are currently evaluated in clinical trials for the treatment of viral infections, allergies and cancers. Interestingly, there is evidence suggesting that chronic activation of PDC by endogenous RNA and DNA containing immune complexes maybe an important mechanism of driving autoimmunity and significant efforts to develop bi‐functional antagonists of TLR7 and TLR9 are currently underway.
Antiviral CD8+ T cells in the genital tract control viral replication and delay progression to AIDS after vaginal SIV challenge in rhesus macaques immunized with virulence attenuated SHIV 89.6
Authors: Genescà M. , McChesney M. B. , Miller C. J.
Published: December 2008

The recently failed clinical efficacy trial of an acquired immunodeficiency syndrome (AIDS) vaccine that elicits antiviral CD8+ T‐cell responses has emphasized the challenge of producing an effective vaccine against human immunodeficiency virus (HIV). In the simian immunodeficiency virus (SIV)/ rhesus monkey model of AIDS, live‐attenuated lentivirus ‘vaccines’ provide the best protection from uncontrolled viral replication and clinical disease after pathogenic SIV challenge. This review summarizes a recent series of studies in which we show that after vaginal SIV challenge of rhesus macaques immunized with an attenuated lentivirus protection from uncontrolled viral replication is primarily mediated by CD8+ T cells in the vaginal mucosa. Immunization with a chimeric simian/human immunodeficiency virus (SHIV) results in a systemic infection that induces a moderate population of SIV‐specific CD8+ and CD4+ T cells with cytolytic potential in the vaginal mucosa. Depletion of CD8+ T cells at the time of SIV challenge completely abrogates the protection mediated by prior infection with attenuated SHIV. Further after vaginal SIV challenge, the only significant expansion of SIV‐specific T cells occurs in the vagina in these animals. No significant expansion of T‐cell responses was observed in systemic lymphoid tissues. Thus, the presence of SIV‐specific CD8+ T cells in the vagina on the day of vaginal SIV challenge and a modest expansion of local effector T cells is sufficient to stop uncontrolled SIV replication. It seems that T‐cell based vaccine strategies that can elicit mucosal effector CD8+ T‐cell populations and avoid inducing systemic T‐cell proliferation upon exposure to HIV have the greatest potential for mimicking the success of live‐attenuated lentiviral vaccines.
Developing an HIV cytotoxic T‐lymphocyte vaccine: issues of CD8 T‐cell quantity, quality and location
Authors: Masopust D.
Published: December 2008

Issues of quantity, quality and location impact the ability of CD8 T cells to mediate protection from infection. These issues are considered in light of human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) vaccination. Methods are reviewed that result in 100‐ to 1000‐fold higher frequencies of vaccine‐specific memory CD8 T cells than that achieved by current HIV/SIV vaccine approaches. Data demonstrating that location within mucosal tissues has a direct impact on memory CD8 T‐cell function are discussed. Arguments are made that establishing memory CD8 T cells within mucosal sites of transmission, a priori to natural infection, may be essential for conferring optimal and rapid protection. Lastly, it is proposed that heterologous prime‐boost vaccination with recombinant live replicating vectors, which has the potential to induce tremendous numbers of cytolytic memory CD8 T cells within mucosal tissues, would provide a far more stringent test of the hypothesis that memory CD8 T cells could, in principal, form the basis for a preventative HIV vaccine.
Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches
Authors: AGUILAR RAMIRO , QUESADA MAURICIO , ASHWORTH LORENA , HERRERIAS‐DIEGO YVONNE , LOBO JORGE
Published: December 2008

Conservation of genetic diversity, one of the three main forms of biodiversity, is a fundamental concern in conservation biology as it provides the raw material for evolutionary change and thus the potential to adapt to changing environments. By means of meta‐analyses, we tested the generality of the hypotheses that habitat fragmentation affects genetic diversity of plant populations and that certain life history and ecological traits of plants can determine differential susceptibility to genetic erosion in fragmented habitats. Additionally, we assessed whether certain methodological approaches used by authors influence the ability to detect fragmentation effects on plant genetic diversity. We found overall large and negative effects of fragmentation on genetic diversity and outcrossing rates but no effects on inbreeding coefficients. Significant increases in inbreeding coefficient in fragmented habitats were only observed in studies analyzing progenies. The mating system and the rarity status of plants explained the highest proportion of variation in the effect sizes among species. The age of the fragment was also decisive in explaining variability among effect sizes: the larger the number of generations elapsed in fragmentation conditions, the larger the negative magnitude of effect sizes on heterozygosity. Our results also suggest that fragmentation is shifting mating patterns towards increased selfing. We conclude that current conservation efforts in fragmented habitats should be focused on common or recently rare species and mainly outcrossing species and outline important issues that need to be addressed in future research on this area.