bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of soil organic matter associated with particle‐size fractions of water‐stable aggregates
Authors: Puget P. , Chenu C. , Balesdent J. 
Published: December 2008

SummaryStable 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

SummaryMan 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

SummaryThe 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

AbstractThe 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

Abstract 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

AbstractTitle.  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

SummaryIsotopic 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

Summary

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

SummaryTop‐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

SummaryGeographic 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

Summary

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

Abstract.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

Abstract.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

Abstract.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

Abstract.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.