bluuebunny/crossref_metadata_2025_split huggingface dataset:
PAH release from tar‐oil contaminated soil material in response to forced environmental gradients: implications for contaminant transport
Authors: Wehrer M. , Totsche K. U. 
Published: October 2007

SummaryLaboratory test systems are frequently used to assess the release of pollutants from contaminated sites. To infer behaviour in the field, all factors that control the release of such pollutants should be considered in the experiment. We carried out column experiments with varying boundary conditions under saturated flow to identify the processes governing the release and to evaluate the effect of environmental conditions on several polycyclic aromatic hydrocarbons (PAHs). We compared the results with groundwater concentrations monitored in the field. The contaminated soil material originated from a former tar‐processing site. The effluent was analysed in response to forced variations in flow velocity, residence time, ionic strength and temperature. Interruptions to the flow had no effect on concentrations, which were close to those predicted by Raoult’s law. We conclude that release of PAHs is controlled by equilibrium dissolution according to Raoult’s law at moderate ionic strength. Diminishing the ionic strength by a pulse of pure water, however, results in a marked increase in the concentrations of exported PAHs. We attribute this to PAHs being bound to mobile particles. The effect was larger in the column percolated with fast flow, suggesting that the release of carriers is controlled by shear stress. An increase of temperature by 10 K resulted in marked increases in concentrations of the PAHs in the outflow between 6 and 160%. Concentrations in the groundwater correlate well with those in the outflow from the columns with similar ionic strength and temperature. We were able to identify the processes governing the release of PAHs under various conditions and to explain the concentrations observed in the field. The study illustrates that column outflow experiments, which support decisions in risk assessment, must be designed appropriately.
Ammonium uptake and mineralization in prairie streams: chamber incubation and short‐term nutrient addition experiments
Authors: O'BRIEN JONATHAN M. , DODDS WALTER K. 
Published: October 2007

Summary1. We used two separate approaches to estimate ambient ammonium cycling in the north and south branches of Kings Creek, a prairie stream. Chamber experiments were conducted to determine ammonium uptake and mineralization rates associated with epilithic biofilms and filamentous algae collected from the streams. A series of short‐term whole‐stream ammonium addition experiments were also conducted to estimate the rate of uptake at ambient stream concentrations, based on the relationship between ammonium concentrations and uptake rates.2. Chamber experiments were scaled up to whole‐stream levels, resulting in ambient gross uptake estimates of 0.08 μg−2 s−1for the north branch and 0.16 μg−2 s−1for the south branch. The substrata‐specific estimates of mineralization were higher than uptake in both streams.3. Substrata‐specific measurements indicated that ammonium uptake is higher in riffle habitats than in pools habitats. The results of the short‐term ammonium addition experiments support these findings.4. Short‐term ammonium addition experiments show that uptake rates saturate with increasing ammonium concentrations. The observed saturation of uptake rates is consistent with a Michaelis–Menten relationship.5. Scaled estimates of uptake from the chamber experiments were similar to estimates of ambient ammonium uptake based on the whole‐stream experiments, and were comparable with previous estimates of ammonium uptake and mineralization made by using stable isotope tracer methods in Kings Creek.
Acidity versus habitat structure as regulators of littoral microcrustacean assemblages
Authors: WALSENG BJØRN , YAN NORMAN D. , PAWSON TREVOR W. , SKARPAAS OLAV 
Published: October 2007

Summary1. Emergence traps were set overnight on the sediment surface to sample the littoral microcrustaceans of 22 Canadian Shield lakes that ranged in pH from 4.56 to 6.92. Traps were randomly allocated in quintuplicate in both wave‐washed sandy habitats where pipewort (Eriocaulon septangulare) was the dominant macrophyte (termed pipewort habitats), and more protected habitats dominated by floating‐leaved macrophytes (termed floating‐leaved habitats).2. In total, 50 cladoceran and 22 copepod species were found, with 16–45 species in each lake. Lakes that had never acidified exhibited a more diverse fauna than lakes that had acidified.3. There were only minor differences between the numbers of species found in floating‐leaved versus pipewort habitats except for one lake. Non‐chydorid cladoceran, chydorids and copepods constituted 45%, 26% and 29% of the total number of individuals, respectively.4. Based on presence/absence, dominance scores and frequency of occurrences of species, the microcrustacean faunal composition was similar in the two habitats. A detrended correspondence analysis confirmed that there was no separation between the two main types of habitat, and that pH was the parameter most strongly correlated with the dominant microcrustacean compositional gradient among lakes.
Blockade of endogenous B7‐H1 suppresses antibacterial protection after primary Listeria monocytogenes infection
Authors: Seo Su‐Kil , Jeong Hye‐Young , Park Sae‐Gwang , Lee Soo‐Woong , Choi Il‐Whan , Chen Lieping , Choi Inhak 
Published: October 2007

SummaryB7‐H1 (also known as CD274 and PD‐L1) is a cosignalling molecule regulating T‐cell immunity positively or negatively in vivo. However, little is known about the role of endogenous B7‐H1 in bacterial infection. We found that B7‐H1 expression was up‐regulated in various cell populations including CD4+ and CD8+ T cells, natural killer (NK) cells and macrophages following Listeria monocytogenes infection. Administration of the antagonistic B7‐H1 monoclonal antibody resulted in a significant increase in mortality in mice infected with a lethal dose of L. monocytogenes compared with mice given the control immunoglobulin. In vivo blockade of B7‐H1 greatly inhibited the production of tumour necrosis factor (TNF)‐α and nitric oxide, key effector molecules responsible for intracellular killing by macrophages. B7‐H1 blockade also suppressed the expression of granzyme B and interferon (IFN)‐γ by NK cells. Interestingly, blocking of endogenous B7‐H1 selectively inhibited CD8+ T cells rather than CD4+ T cells in response to L. monocytogenes infection, as evidenced by the reduction of IFN‐γ production and the expression of effector surface markers including CD62Lint/low and CD44high in CD8+ T cells from mice given anti‐B7‐H1 monoclonal antibody. In addition, we found that the proliferation of listeriolysin‐O (LLO)‐specific and IFN‐γ‐producing L. monocytogenes‐reactive CD8+ T cells was significantly decreased not only in the effector phase but also in the memory phase in the presence of anti‐B7‐H1 antibody. Our findings thus suggest that endogenous B7‐H1 can provide positive costimulatory signals for innate and adaptive immunity leading to protection against intracellular bacterial infection.
Tumour necrosis factor‐α‐mediated human polymeric immunoglobulin receptor expression is regulated by both mitogen‐activated protein kinase and phosphatidylinositol‐3‐kinase in HT‐29 cell line
Authors: Takenouchi‐Ohkubo N. , Moro I. , Mukae S. , Kaneko Y. , Komiyama K. 
Published: October 2007

SummaryHuman polymeric immunoglobulin receptor (pIgR) is present on the surface of glandular epithelium, and it plays a crucial role in the mucosal immune defence. pIgR expression in HT‐29 cells is up‐regulated by one of the proinflammatory cytokines, tumour necrosis factor (TNF)‐α. However, the mechanism used by the TNF‐α‐mediated signalling pathway has not been examined exclusively. To elucidate this mechanism in detail, HT‐29 cells were cotreated with TNF‐α and mitogen‐activated protein kinase kinase (MAPKK, also called MEK1) inhibitor, PD98059, and the amount of free secretory component (SC) secreted into the culture medium was measured. The amount of free SC stimulated by TNF‐α was increased by addition of PD98059. This up‐regulation occurred at the transcriptional level. The amount of SC was also up‐regulated by addition of TNF‐α with U0126, an inhibitor of MEK1 and MEK2. Nuclear factor (NF)‐κB activity and NF‐κB binding to the κB2 site localized upstream of the pIgR gene did not change after coincubation of HT‐29 cells with TNF‐α and PD98059. The expression level of pIgR by TNF‐α was decreased by LY294002, an inhibitor of phosphatidylinositol‐3‐kinase (PI3K), at the transcriptional level. Extracellular signal‐regulated kinase (ERK)1/2 phosphorylation and NF‐κB binding to the κB2 site were not affected by LY294002 treatment. These data suggest that TNF‐α‐mediated pIgR expression is negatively regulated by ERK pathway, which is independent of NF‐κB. In addition, decrease of SC production by Ly294002 suggests that the presence of PI3K mediated regulation of SC production.
Characterization of suppressive oligodeoxynucleotides that inhibit Toll‐like receptor‐9‐mediated activation of innate immunity
Authors: Peter Mirjam , Bode Konrad , Lipford Grayson B. , Eberle Florian , Heeg Klaus , Dalpke Alexander H. 
Published: October 2007

SummarySynthetic oligodeoxynucleotides containing unmethylated CpG sequences (CpG‐ODNs) stimulate Toll‐like receptor‐9 (TLR‐9), thereby activating innate immunity. Stimulatory CpG‐ODNs have been shown to be valuable in modifying immune responses in allergy, infection and cancer. Recently, it has been reported that the stimulation of TLR‐9 by endogenous DNA might contribute to the pathogenesis of autoimmune diseases. We here report the identification of a suppressive, guanosine‐rich ODN (G‐ODN) that inhibited the activation of TLR‐9 by stimulatory CpG‐ODNs. The G‐ODN was suppressive in murine macrophages and dendritic cells as well as in human plasmacytoid dendritic cells in vitro. G‐ODN blocked the secretion of tumour necrosis factor‐α (TNF‐α) and interleukin‐12p40 and interfered with the up‐regulation of major histocompatibility complex (MHC) class II and costimulatory molecules. G‐ODN was inhibitory even at a molar ratio of 1 : 10 (G‐ODN:CpG‐ODN) and when administered up to 7 hr after stimulation with CpG. G‐ODN specifically inhibited TLR‐9 but not other TLRs. Inhibition was dependent on a string of five guanosines. G‐ODN was also inhibitory in an in vivo model of CpG/galactosamin (GalN) lethal shock. G‐ODN interfered with upstream TLR‐9 signalling. However, by extensive analysis we can exclude that G‐ODN acts at the stage of cellular uptake. G‐ODN therefore represents a class of suppressive ODNs that could be of therapeutic use in situations with pathologic TLR‐9 activation, as has been proposed for certain autoimmune diseases.
A new method for estimating visitation rates of cryptic animals via repeated surveys of indirect signs
Authors: Gruber Bernd , Reineking Björn , Calabrese Justin M , Kranz Andreas , Poledníková Katerina , Poledník Luká , Klenke Reinhard , Valentin Anett , Henle Klaus 
Published: October 2007

Summary

Visitation rate is a measure of the frequency with which animals visit specific locations of interest. This information is crucial for various problems in the conservation and management of animal species, e.g. to determine the risk wildlife poses to human managed resources or the predation risks of nests. An important assessment tool, especially for cryptic animals, is to count indirect signs of presence, such as tracks or faeces.
Here we propose a maximum likelihood‐based method that uses information on the age of tracks or signs, and we show that existing visitation rate/probability estimators are special cases of this more general approach.
Using simulated data, we compared the performance of the new visitation rate estimator to three other estimators, including the most commonly used estimator. These estimators make use of either fresh, aged or total signs, whereas our approach uses information simultaneously on both fresh and aged signs. The new estimator is, on average, in excess of three times more accurate than the next best estimator. Moreover, the new approach is very flexible and can be applied for sampling regimens with irregular time intervals between sampling.
We demonstrate the application of the method to field data by estimating the visitation rate of Eurasian otters (Lutra lutra) to a commercial fish pond. To facilitate the use of this method, we provide an easy‐to‐use Excel workbook and give recommendations on the most efficient sampling regimens.
Synthesis and applications. Visitation rate is an important quantity that can be estimated by repetitive sampling of indirect signs. We demonstrate the advantage of incorporating information explicitly on the age of signs over existing approaches. The new estimator can be applied to any species for which it is possible to discriminate between aged and new signs or tracks, and should be widely applicable in ecology and conservation biology.
Mangrove forest distributions and dynamics (1975–2005) of the tsunami‐affected region of Asia†
Authors: Giri C. , Zhu Z. , Tieszen L. L. , Singh A. , Gillette S. , Kelmelis J. A. 
Published: October 2007

AbstractAim  We aimed to estimate the present extent of tsunami‐affected mangrove forests and determine the rates and causes of deforestation from 1975 to 2005.Location  Our study region covers the tsunami‐affected coastal areas of Indonesia, Malaysia, Thailand, Burma (Myanmar), Bangladesh, India and Sri Lanka in Asia.Methods  We interpreted time‐series Landsat data using a hybrid supervised and unsupervised classification approach. Landsat data were geometrically corrected to an accuracy of plus‐or‐minus half a pixel, an accuracy necessary for change analysis. Each image was normalized for solar irradiance by converting digital number values to the top‐of‐the atmosphere reflectance. Ground truth data and existing maps and data bases were used to select training samples and also for iterative labelling. We used a post‐classification change detection approach. Results were validated with the help of local experts and/or high‐resolution commercial satellite data.Results  The region lost 12% of its mangrove forests from 1975 to 2005, to a present extent of c. 1,670,000 ha. Rates and causes of deforestation varied both spatially and temporally. Annual deforestation was highest in Burma (c. 1%) and lowest in Sri Lanka (0.1%). In contrast, mangrove forests in India and Bangladesh remained unchanged or gained a small percentage. Net deforestation peaked at 137,000 ha during 1990–2000, increasing from 97,000 ha during 1975–90, and declining to 14,000 ha during 2000–05. The major causes of deforestation were agricultural expansion (81%), aquaculture (12%) and urban development (2%).Main conclusions  We assessed and monitored mangrove forests in the tsunami‐affected region of Asia using the historical archive of Landsat data. We also measured the rates of change and determined possible causes. The results of our study can be used to better understand the role of mangrove forests in saving lives and property from natural disasters such as the Indian Ocean tsunami, and to identify possible areas for conservation, restoration and rehabilitation.
Close anthropogenic control of Fagus sylvatica establishment and expansion in a Swedish protected landscape – implications for forest history and conservation
Authors: Lindbladh Matts , Niklasson Mats , Karlsson Matts , Björkman Leif , Churski Marcin 
Published: October 2007

AbstractAim   The dominant forces behind the expansion of Fagus sylvatica (beech) in northern Europe during the late Holocene have been much debated. Palaeoecological analyses were performed for a biodiversity hotspot reserve in order to study the processes behind the local establishment of Fagus, as well as the historical vegetational development in relation to present‐day biodiversity and conservation.Location  Biskopstorp Forest Reserve in south‐west Sweden.Methods  Pollen and charcoal were analysed from three small‐hollow sites in the reserve. Two of the investigated wetlands were located adjacent to old‐growth stands of Fagus, and the third was located near a stand of old Quercus.Results  The 2500‐year record shows that Fagus was first established around the two Fagus old‐growth sites, c. ad 900 and 1200, respectively, and that this was followed by an expansion around ad 1600. During the establishment phase, and more so in the expansion phase, there were simultaneous increases in types of pollen indicative of human activity. These indicators are also frequent throughout the record from the Quercus site, but here Fagus never became common.Main conclusions  The dynamics behind the establishment and expansion of Fagus in the reserve seems to have been influenced to a large degree by human activity, for example selective cutting, human‐induced fires, and agriculture. Fagus became established in the reserve more than 1000 years after it became established regionally, making climate less probable as the dominant force behind the species’ stand‐scale establishment. The spreading of Fagus across southern Scandinavia has previously been shown to be a patchy process in time and space. Our study suggests that this patchiness is evident also at a small spatial scale (a few kilometres). At the Quercus site, relatively high amounts of pollen from the field layer throughout the record indicate open conditions that probably favoured Quercus. The degree of human impact at this site was probably too high to allow the expansion of Fagus. With the long‐term perspective provided by our study it was possible to identify the last 200–300 years as an unrepresentative period with respect to tree species composition and forest dynamics. The large increase of Picea locally and regionally over the last several hundred years, combined with dramatic levels of human impact, have altered the tree composition and forest dynamics to such an extent that active management is necessary in order to maintain biodiversity in the reserve.
Bone mass in young adults with Down syndrome
Authors: Guijarro M. , Valero C. , Paule B. , Gonzalez‐Macias J. , Riancho J. A. 
Published: October 2007

AbstractBackground  Down syndrome (DS) is a frequent cause of intellectual disability. With the increasing life expectancy of these patients, concerns have been raised about the risk of osteoporosis. In fact, several investigators have reported a reduced bone mass in DS. However, the results may be confounded by comorbid diseases, and differences in lifestyle habits and body size. Therefore, we planned to determine anthropometric and lifestyle factors influencing bone mineral density (BMD) in young adults with DS.Methods  Thirty‐nine patients with DS (mean age 26 years) and 78 controls were studied. Areal BMD was measured by dual x‐ray decsitometry (DXA); volumetric BMD at the lumbar spine and femoral neck was estimated with published formulae.Results  DS patients had lower areal BMD than controls at all regions (spine, hip and total body). Height and projected bone area were also lower. There were no differences between both groups regarding estimated volumetric BMD at the femoral neck. However, spine volumetric BMD was also lower in DS than controls. In multivariate analysis, DS, male sex, little physical activity and low sunlight exposure were associated with lower spine volumetric BMD; on the other hand, fat mass and sunlight exposure were associated with femoral neck volumetric BMD.Conclusion  This study shows that patients with DS had a reduced areal BMD, but it is in part a consequence of the reduced body size, particularly at the femoral neck. Physical activity and sunlight exposure are associated to volumetric BMD and should be stimulated in order to maintain an adequate bone mass in these patients.
Deletion of the OPHN1 gene detected by aCGH
Authors: Madrigal I. , Rodríguez‐Revenga L. , Badenas C. , Sánchez A. , Milà M. 
Published: October 2007

AbstractBackground  The oligophrenin 1 gene (OPHN1) is an Rho‐GTPase‐activating protein involved in the regulation of the G‐protein cycle required for dendritic spine morphogenesis. Mutations in this gene are implicated in X‐linked mental retardation (XLMR).Methods  We report a deletion spanning exons 21 and 22 of the OPHN1 gene identified by a tiling path X‐chromosome array comparative genomic hybridization (CGH) and multiplex ligation‐dependent probe amplification, confirmed by polymerase chain reaction (PCR), in a family with four males with intellectual disabilities.Results  Patients harbouring mutations in this gene share the same clinical manifestations reinforcing the idea of a syndromic XLMR. The most important neurological findings are cerebellar hypoplasia and ventriculomegaly.Conclusions  We recommend screening of the OPHN1 gene in male patients with XLMR and cerebellar anomalies. This case highlights the value of high‐resolution techniques as Multiplex Ligation Probe Amplification (MLPA) and CGH array for a better characterization of copy number changes and suggests that MLPA technology may be very useful for an initial screening of small deletions and duplications in XLMR patients.
SEM investigation of interfacial dislocations in nickel‐base superalloys
Authors: EPISHIN ALEXANDER , LINK THOMAS , NOLZE GERT 
Published: October 2007

SummaryA new technique for investigation of interfacial dislocations in nickel‐base superalloys by scanning electron microscopy is presented. At high temperatures the pressure of interfacial dislocations against the γ/γ′‐interface causes grooves. This ‘fingerprint of the dislocation network’ is visualized by deep selective etching, which removes the γ′‐phase down to the γ/γ′‐interface. Compared with transmission electron microscopy, the proposed method has important advantages: observation of large sample areas, no superposition of dislocations lying in different specimen depths, possibility of three‐dimensional view of dislocation configurations, information about the dislocation mobility, reduced time for preparation and visualization. The method can be applied for multiphase materials where the interface is grooved by interfacial dislocations.
In vivo dynamic light scattering microscopy of tumour blood vessels
Authors: KALCHENKO V. , PREISE D. , BAYEWITCH M. , FINE I. , BURD K. , HARMELIN ALON 
Published: October 2007

SummaryWe present a study investigating the use of dynamic light scattering microscopy based on the temporal laser speckle's contrast that is produced over time by red blood cells (RBCs) flowing inside tumour blood vessels. The proposed noninvasive methodology is capable of producing high‐resolution images of tumour vasculature. The technique is effective at producing images from tissue at a significant depth, as well as potentially having the ability to monitor tumour perfusion. An advantage of this methodology is that it has improved depth penetration compared with conventional imaging techniques (such as reflected‐light microscopy), and one can avoid the use of any fluorescent or artificial chemicals for labeling. This is advantageous since labeling materials can affect imaging and animal welfare with respect to experiments that require continuous and repetitive monitoring.