bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling biophysical controls on canopy foliage water 18O enrichment in wheat and corn
Authors: Xiao Wei , Lee Xuhui , Wen Xuefa , Sun Xiaomin , Zhang Shichun 
Published: January 2012

AbstractLeaf water 18O enrichment is an important factor controlling the H218O, C18OO, and O18O exchanges between the biosphere and the atmosphere. At present, there is limited capacity to explain the enrichment mechanisms in field conditions. In this study, three models of varying complexity were used to simulate the leaf water 18O enrichment at the canopy scale. Comparisons were made among the models and with high‐frequency isotopic measurements of ecosystem water pools in wheat and corn. The results show that the steady state assumption was a better approximation for ecosystems with lower canopy resistance, that it is important to consider the effect of leaf water turnover in modeling the enrichment and not necessary to deal with time changes in leaf water content, and that the leaf‐scale Péclet effect was incompatible with the big‐leaf modeling framework for canopy‐air interactions. After turbulent diffusion has been accounted for in an apparent kinetic factor parameterization, the mean 18O composition of the canopy foliage water was a well‐behaved property predictable according to the principles established by leaf‐scale studies, despite substantial variations in the leaf water enrichment with leaf and canopy positions. In the online supplement we provided a discussion on the observed variability of leaf water 18O composition with leaf and canopy positions and on the procedure for correcting isotopic measurements for organic contamination.
Natural killer T cells suppress zymosan A‐mediated granuloma formation in the liver by modulating interferon‐γ and interleukin‐10
Authors: Kobayashi Takahiro , Kawamura Hiroki , Kanda Yasuhiro , Matsumoto Hiroaki , Saito Suguru , Takeda Kazuyoshi , Kawamura Toshihiko , Abo Toru 
Published: January 2012

SummaryWild‐type (WT) and CD1d−/− [without natural killer (NK) T cells] mice were treated with zymosan A to induce granuloma formation in the liver. Increased granuloma formation was seen in NKT‐less mice on days 7 and 14 after administration. WT mice showed limited granuloma formation, and zymosan A eventually induced NKT cell accumulation as identified by their surface marker (e.g. CD1d‐tetramer). Zymosan A augmented the expression of Toll‐like receptor 2 on the cell surface of both macrophages and NKT cells. One possible reason for accelerated granuloma formation in NKT‐less mice was increased production of interferon‐ γ (IFN‐γ); a theory that was confirmed using IFN‐γ−/− mice. Also, zymosan A increased interleukin‐10 production in WT mice, which suppresses IFN‐γ production. Taken together, these results suggest that NKT cells in the liver have the potential to suppress zymosan A‐mediated granuloma formation.
Lower numbers of natural killer T cells in HIV‐1 and Mycobacterium leprae co‐infected patients
Authors: Carvalho Karina I. , Bruno Fernanda R. , Snyder‐Cappione Jennifer E. , Maeda Solange M. , Tomimori Jane , Xavier Marilia B. , Haslett Patrick A. , Nixon Douglas F. , Kallas Esper G. 
Published: January 2012

SummaryNatural killer T (NKT) cells are a heterogeneous population of lymphocytes that recognize antigens presented by CD1d and have attracted attention because of their potential role linking innate and adaptive immune responses. Peripheral NKT cells display a memory‐activated phenotype and can rapidly secrete large amounts of pro‐inflammatory cytokines upon antigenic activation. In this study, we evaluated NKT cells in the context of patients co‐infected with HIV‐1 and Mycobacterium leprae. The volunteers were enrolled into four groups: 22 healthy controls, 23 HIV‐1‐infected patients, 20 patients with leprosy and 17 patients with leprosy and HIV‐1‐infection. Flow cytometry and ELISPOT assays were performed on peripheral blood mononuclear cells. We demonstrated that patients co‐infected with HIV‐1 and M. leprae have significantly lower NKT cell frequencies [median 0.022%, interquartile range (IQR): 0.007–0.051] in the peripheral blood when compared with healthy subjects (median 0.077%, IQR: 0.032–0.405, P < 0.01) or HIV‐1 mono‐infected patients (median 0.072%, IQR: 0.030–0.160, P < 0.05). Also, more NKT cells from co‐infected patients secreted interferon‐γ after stimulation with DimerX, when compared with leprosy mono‐infected patients (P = 0.05). These results suggest that NKT cells are decreased in frequency in HIV‐1 and M. leprae co‐infected patients compared with HIV‐1 mono‐infected patients alone, but are at a more activated state. Innate immunity in human subjects is strongly influenced by their spectrum of chronic infections, and in HIV‐1‐infected subjects, a concurrent mycobacterial infection probably hyper‐activates and lowers circulating NKT cell numbers.
B‐cell receptor: from resting state to activate
Authors: Treanor Bebhinn 
Published: January 2012

SummaryB‐cell activation is triggered by the binding of antigen to the B‐cell receptor (BCR). The early molecular events triggered by BCR binding of ligand have been well‐characterized both biochemically and using optical microscopy techniques to visualize B‐cell activation as it happens. However, we understand much less about the BCR before activation. For this reason, this review will address recent advances in our view of the structure, organization and dynamics of the resting, unstimulated BCR. These parameters have important implications for our understanding of the initiation of B‐cell activation and will be discussed in the context of current models for BCR activation. These models include the conformation‐induced oligomerization model, in which binding of antigen to monomeric BCR induces a pulling or twisting force causing conformational unmasking of a clustering interface in the Cμ4 domain. Conversely, the dissociation activation model proposes that BCRs exist in auto‐inhibitory oligomers on the resting B‐cell surface and binding of antigen promotes the dissociation of the BCR oligomer exposing phosphorylation residues within Igα/Igβ. Finally, the collision coupling model suggests that BCR are segregated from activating co‐receptors or kinases and activation is associated with changes in BCR mobility on the cell surface, which allows for the functional interaction of these elements.
The development of iron‐free partially stabilized cement for use as dental root‐end filling material
Authors: Ndong F. , Sadhasivam S. , Lin F.‐H. , Savitha S. , Wen‐Hsi W. , Lin C.‐P. 
Published: January 2012

Ndong F, Sadhasivam S, Lin F‐H, Savitha S, Wen‐Hsi W, Lin C‐P. The development of iron‐free partially stabilized cement for use as dental root‐end filling material. International Endodontic Journal, 45, 557–564, 2012.AbstractAim  To determine the effect of increasing the proportion of zinc on partially stabilized cement (PSC) produced using a one‐step sol gel process.Methodology  A one‐step sol‐gel process of Portland cement‐based PSC with Zn was synthesized by replacing iron nitrate. The crystalline phases of the PSC‐Zn powder were analysed by using X‐ray diffraction (XRD). The experimental groups [i.e. MTA, PSC‐Fe (control), PSC with 1% Zn, PSC with 3% Zn, and PSC with 5% Zn] were immersed in simulated body fluid for 3 h, 1 and 3 days to evaluate the hydration product formation. The microstructure and surface morphology were analysed using scanning electron microscopy (SEM). Initial and final setting times of the materials were determined using an ASTM Vicat needle testing machine. To evaluate the cytotoxicity of PSC‐Zn system, primary osteoblasts cell lines were used.Results  The addition of increased weight percentages of Zn, resulted in a more unstable phase which favoured the formation of a monoclinic structure of C3S with an increased hydration reaction of PSC and reduced setting time. The cytotoxicity testing of PSC with Zn revealed that the material was not toxic.Conclusions  The newly synthesized PSC‐Zn material had short setting time and was biocompatible.
Local and landscape management of an expanding range margin under climate change
Authors: Lawson Callum R. , Bennie Jonathan J. , Thomas Chris D. , Hodgson Jenny A. , Wilson Robert J. 
Published: January 2012

Summary1. There is a pressing need to understand how to facilitate species’ range shifts under climate change. However, few empirical studies are available to inform decision‐making, particularly at fine spatial and temporal resolutions.2. We present a case study of a thermally constrained habitat specialist, the silver‐spotted skipper butterflyHesperia comma, at its expanding range margin in south‐eastern Britain. Using data from 724 habitat patches over a 9‐year interval (2000–2009), we examined local and landscape determinants of colonization, survival and population density. We then predicted probabilities of colonization and survival for habitat patches under the observed 1982 and 2009 distributions to investigate how the factors limiting range expansions change through space and time.3. Between 2000 and 2009,Hesperia commacontinued to expand its range in Britain, but the 67 recorded colonization events were offset by 48 local extinctions. Extinctions were strongly linked to climate, occurring predominantly in cooler regions and on shaded north‐facing slopes.4. Population density and probability of survival were closely related to conditions within a site, whereas probability of colonization was largely determined by functional connectivity. Survival probability was also influenced by connectivity, suggesting that immigration helped to support extinction‐prone populations (a ‘rescue effect’).5. Patch occupancy beyond the range margin was primarily constrained by colonization, but close to the expanding front, population survival became the key limiting factor. This pattern was conserved during range expansion, altering management priorities at individual sites.6. Synthesis and applications. Previous studies on facilitating range shifts have stressed the need to increase landscape‐scale connectivity to remove constraints on colonization, and our data substantiate this advice. However, we show that enhancing population survival can also help to facilitate range expansions, because populations at leading range edges face high extinction risk. Population survival can be improved directly through local management actions, such as enlarging patch size and increasing habitat quality, or indirectly by improving connectivity. Thus, local management can secure vulnerable populations at the range edge and provide larger and more stable migrant sources for future expansion and deserves consideration when facilitating range shifts under climate change.
The ecological impact of oceanic island colonization – a palaeoecological perspective from the Azores
Authors: Connor Simon E. , van Leeuwen Jacqueline F.N. , Rittenour Tammy M. , van der Knaap Willem O. , Ammann Brigitta , Björck Svante 
Published: January 2012

AbstractAim  In many cases, human colonization drastically modified the ecosystems of remote oceanic islands before scientists arrived to document the changes. Palaeoecological records before and after human colonization provide insights into the original ecosystems and an assessment of subsequent human impact. We used pollen analysis to compare the impact of 15th century colonization of the Azores with that of natural disturbances such as volcanic eruptions and climate changes.Location  Azores archipelago, Atlantic Ocean.Methods  Sediment records from three highland sites in the Azores (on the islands of Pico and Flores) were dated radiometrically and analysed palynologically. Pollen taxa were classified as native, endemic or introduced based on comparison with flora lists. Data were statistically zoned and temporal trends identified using detrended correspondence analysis.Results  Human colonization of the Azores resulted in rapid, widespread, persistent vegetation changes on a scale unprecedented in the last 2700 years, detectable through the decline of dominant trees, the spread of grasses and fire‐tolerant species, the introduction of exotic plants, evidence for grazing and fire, and changes to soils and moisture availability. During the same period, volcanic eruptions appear to have had more localized impacts on the vegetation, lasting 500–1000 years and favouring endemic taxa. The effect of late Holocene climatic changes on the highland vegetation of the Azores seems to have been minor. Palaeoecological data indicate that at least two plant species went extinct on Pico after human colonization and that some plants regarded as introduced were almost certainly part of the original flora of the islands. Despite a consistent signal of human impact, compositional differences between Juniperus brevifolia communities on Pico and Flores remained after colonization.Main conclusions  Human colonization had a greater impact on the pristine vegetation of Pico and Flores than climatic changes and volcanic activity during recent millennia. The similarity between post‐colonization changes on the Azores and other oceanic islands suggests a consistent pattern and scale to historical‐era human impact on otherwise pristine ecosystems. These characteristics could be used to further elaborate biogeographical theory and direct conservation efforts towards species that appear most susceptible to human activity.
Cryo‐SEM specimen preparation under controlled temperature and concentration conditions
Authors: ISSMAN L. , TALMON Y. 
Published: January 2012

SummaryCryogenic temperature scanning electron microscopy (cryo‐SEM) is an excellent technique for imaging liquid and semi‐liquid materials of high vapour pressure, which are highly viscous or contain large (>0.5 μm) aggregates, in which nanometric details are to be studied. However, so far there have been no adequate tools for controlled cryo‐specimen preparation. The specimen preparation stage is critical, because most of those samples are very sensitive to concentration and temperature changes, leading to nanostructural artefacts in the specimens. We designed and built a system for easy and reliable cryo‐SEM specimen preparation under controlled conditions of fixed temperature and humidity. We describe this new methodology, and demonstrate its applicability, by showing imaging data of three liquid material systems. We have studied carbon nanotubes (CNTs) dispersions in superacid. We also characterized a number of systems made of water/isooctane/nonionic and cationic surfactant that showed different microemulsion phases as function of the system composition and temperature. In all of the examples given, we demonstrate artefact‐ and contamination‐free specimens, which have preserved their native nanostructure. Our new system paves the way for a new methodology for the newly emerging field of cryo‐SEM.
Proteomics in evolutionary ecology: linking the genotype with the phenotype
Authors: DIZ ANGEL P. , MARTÍNEZ‐FERNÁNDEZ MÓNICA , ROLÁN‐ALVAREZ EMILIO 
Published: January 2012

AbstractThe study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein–protein interactions, as well as the combined use of the different ‐omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.
Monitoring adaptive genetic responses to environmental change
Authors: HANSEN MICHAEL M. , OLIVIERI ISABELLE , WALLER DONALD M. , NIELSEN EINAR E. ,   The GeM Working Group
Published: January 2012

AbstractWidespread environmental changes including climate change, selective harvesting and landscape alterations now greatly affect selection regimes for most organisms. How animals and plants can adapt to these altered environments via contemporary evolution is thus of strong interest. We discuss how to use genetic monitoring to study adaptive responses via repeated analysis of the same populations over time, distinguishing between phenotypic and molecular genetics approaches. After describing monitoring designs, we develop explicit criteria for demonstrating adaptive responses, which include testing for selection and establishing clear links between genetic and environmental change. We then review a few exemplary studies that explore adaptive responses to climate change in Drosophila, selective responses to hunting and fishing, and contemporary evolution in Daphnia using resurrected resting eggs. We further review a broader set of 44 studies to assess how well they meet the proposed criteria, and conclude that only 23% fulfill all criteria. Approximately half (43%) of these studies failed to rule out the alternative hypothesis of replacement by a different, better‐adapted population. Likewise, 34% of the studies based on phenotypic variation did not test for selection as opposed to drift. These shortcomings can be addressed via improved experimental designs and statistical testing. We foresee monitoring of adaptive responses as a future valuable tool in conservation biology, for identifying populations unable to evolve at sufficiently high rates and for identifying possible donor populations for genetic rescue. Technological advances will further augment the realization of this potential, especially next‐generation sequencing technologies that allow for monitoring at the level of whole genomes.
Calcretes, fluviolacustrine sediments and subsidence patterns in Permo‐Triassic salt‐walled minibasins of the south Urals, Russia
Authors: NEWELL ANDREW J. , BENTON MICHAEL J. , KEARSEY TIMOTHY , TAYLOR GRAEME , TWITCHETT RICHARD J. , TVERDOKHLEBOV VALENTIN P. 
Published: January 2012

AbstractThe south Uralian foreland basin forms part of the giant, yet sparsely documented, PreCaspian salt tectonic province. The basin can potentially add much to the understanding of fluviolacustrine sedimentation within salt‐walled minibasins, where the literature has been highly reliant on only a few examples (such as the Paradox Basin of Utah). This paper describes the Late Permian terrestrial fill of the Kul’chumovo salt minibasin near Orenburg in the south Urals in which sediments were deposited in a range of channel, overbank and lacustrine environments. Palaeomagnetic stratigraphy shows that, during the Late Permian, the basin had a relatively slow and uniform subsidence pattern with widespread pedogenesis and calcrete development. Angular unconformities or halokinetic sequence boundaries cannot be recognized within the relatively fine‐grained fill, and stratigraphic and spatial variations in facies are therefore critical to understanding the subsidence history of the salt minibasin. Coarse‐grained channel belts show evidence for lateral relocation within the minibasin while the development of a thick stack of calcrete hardpans indicates that opposing parts of the minibasin became largely inactive for prolonged periods (possibly in the order of one million years). The regular vertical stacking of calcrete hardpans within floodplain mudstones provides further evidence that halokinetic minibasin growth is inherently episodic and cyclical.
Sea‐level rise, depth‐dependent carbonate sedimentation and the paradox of drowned platforms
Authors: KIM WONSUCK , FOUKE BRUCE W. , PETTER ANDREW L. , QUINN TERRENCE M. , KERANS CHARLES , TAYLOR FRED 
Published: January 2012

AbstractA mathematical model of carbonate platform evolution is presented in which depth‐dependent carbonate growth rates determine platform‐top accumulation patterns in response to rising relative sea‐level. This model predicts that carbonate platform evolution is controlled primarily by the water depth and sediment accumulation rate conditions at the onset of relative sea‐level rise. The long‐standing ‘paradox of a drowned platform’ arose from the observation that maximum growth rate potentials of healthy platforms are faster than those of relative sea‐level rise. The model presented here demonstrates that a carbonate platform could be drowned during a constant relative sea‐level rise whose rate remains less than the maximum carbonate production potential. This scenario does not require environmental changes, such as increases in nutrient supply or siliciclastic sedimentation, to have taken place. A rate of relative sea‐level rise that is higher than the carbonate accumulation rate at the initial water depth is the only necessary condition to cause continuous negative feedbacks to the sediment accumulation rates. Under these conditions, the top of the carbonate platform gradually deepens until it is below the active photic zone and drowns despite the strong maximum growth potential of the carbonate production factory. This result effectively resolves the paradox of a drowned carbonate platform. Test modelling runs conducted with 2·5 m and 15 m initial sea water depths at bracketed rates of relative sea‐level rise have determined how fast the system catches up and maintains the ‘keep‐up’ phase. This is the measure of time necessary for the basin to respond fully to external forcing mechanisms. The duration of the ‘catch‐up’ phase of platform response (termed ‘carbonate response time’) scales with the initial sea water depth and the platform‐top aggradation rate. The catch‐up duration can be significantly elongated with an increase in the rate of relative sea‐level rise. The transition from the catch‐up to the keep‐up phases can also be delayed by a time interval associated with ecological re‐establishment after platform flooding. The carbonate model here employs a logistical equation to model the colonization of carbonate‐producing marine organisms and captures the initial time interval for full ecological re‐establishment. This mechanism prevents the full extent of carbonate production to be achieved at the incipient stage of relative sea‐level rise. The increase in delay time due to the carbonate response time and self‐organized processes associated with biological colonization increase the chances for platform drowning due to deepening of water depth (> ca 10 m). Furthermore this implies a greater likelihood for an autogenic origin for high‐frequency cyclic strata than has been estimated previously.