bluuebunny/crossref_metadata_2025 huggingface dataset:
Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra
Authors: Palmer Katharina , Biasi Christina , Horn Marcus A
Published: December 2011

Cryoturbated peat circles (that is, bare surface soil mixed by frost action; pH 3–4) in the Russian discontinuous permafrost tundra are nitrate-rich ‘hotspots’ of nitrous oxide (N2O) emissions in arctic ecosystems, whereas adjacent unturbated peat areas are not. N2O was produced and subsequently consumed at pH 4 in unsupplemented anoxic microcosms with cryoturbated but not in those with unturbated peat soil. Nitrate, nitrite and acetylene stimulated net N2O production of both soils in anoxic microcosms, indicating denitrification as the source of N2O. Up to 500 and 10 μm nitrate stimulated denitrification in cryoturbated and unturbated peat soils, respectively. Apparent maximal reaction velocities of nitrite-dependent denitrification were 28 and 18 nmol N2O gDW−1 h−1, for cryoturbated and unturbated peat soils, respectively. Barcoded amplicon pyrosequencing of narG, nirK/nirS and nosZ (encoding nitrate, nitrite and N2O reductases, respectively) yielded ≈49 000 quality-filtered sequences with an average sequence length of 444 bp. Up to 19 species-level operational taxonomic units were detected per soil and gene, many of which were distantly related to cultured denitrifiers or environmental sequences. Denitrification-associated gene diversity in cryoturbated and in unturbated peat soils differed. Quantitative PCR (inhibition-corrected per DNA extract) revealed higher copy numbers of narG in cryoturbated than in unturbated peat soil. Copy numbers of nirS were up to 1000 × higher than those of nirK in both soils, and nirS nirK−1 copy number ratios in cryoturbated and unturbated peat soils differed. The collective data indicate that the contrasting N2O emission patterns of cryoturbated and unturbated peat soils are associated with contrasting denitrifier communities.
Local density of trap states in SiO2 and Si3N4 films studied by single electron tunneling force spectroscopy
Authors: Winslow Dustin , Williams Clayton
Published: December 2011

Standard methods used to characterize defect states in dielectric films generally provide spatially averaged defect information. The development of single electron tunneling force spectroscopy provides for the measurement of local density of trap states with atomic scale spatial resolution. In this article, local density of trap states measurements recently obtained on both silicon dioxide and silicon nitride are presented. Local density of states data observed by this method varies from one location to another. The local spectra are compared with previous measurements and theoretical predictions found in the literature.
Vertical design of cubic GaN-based high electron mobility transistors
Authors: Granzner R. , Tschumak E. , Kittler M. , Tonisch K. , Jatal W. , Pezoldt J. , As D. , Schwierz F.
Published: December 2011

Cubic (zinc blende) AlGaN/GaN heterostructures for application in GaN-based high electron mobility transistors are investigated theoretically. The formation of 2DEGs (two-dimensional electron gas) in cubic AlGaN/GaN structures is studied, carrier distributions and threshold voltages are calculated, and design issues are investigated. For the calculations, a Schrödinger-Poisson solver and a simple analytical model developed in the present work are used. It is shown that due to the barrier doping needed for the formation of a pronounced 2DEG in cubic structures, undesirable saturation effects of the 2DEG density may occur. Options to avoid 2DEG saturation and to realize cubic normally-off HEMTs are elaborated. The behavior of cubic AlGaN/GaN structures is compared to that of their hexagonal counterparts.
Bias application hard x-ray photoelectron spectroscopy study of forming process of Cu/HfO2/Pt resistive random access memory structure
Authors: Nagata T. , Haemori M. , Yamashita Y. , Yoshikawa H. , Iwashita Y. , Kobayashi K. , Chikyow T.
Published: December 2011

The forming process of Cu/HfO2/Pt, which is an oxide based resistive random access memory (ReRAM), structure that exhibited resistance switching behavior at a voltage of 1.3 V was investigated by hard x-ray photoelectron spectroscopy under bias operation. A bias application to the structure reduced the Cu2O bonding state at the interface and the intensity ratio of Cu 2p3/2/Hf 3d5/2, providing the evidence of Cu2O reduction and Cu diffusion into the HfO2 layer. We directly observed Cu diffusion at the Cu/HfO2 interface under device operation, which is the evidence of the metal filament formation in the oxide-based ReRAM.
Ab-initio simulations of deformation potentials and electron mobility in chemically modified graphene and two-dimensional hexagonal boron-nitride
Authors: Bruzzone Samantha , Fiori Gianluca
Published: December 2011

We present an ab-initio study of electron mobility and electron-phonon coupling in chemically modified graphene, considering fluorinated and hydrogenated graphene at different percentage coverage. Hexagonal boron carbon nitrogen is also investigated due the increased interest shown by the research community towards this material. In particular, the deformation potentials are computed by means of density functional theory, while the carrier mobility is obtained according to the Takagi model (S. Takagi, A. Toriumi, and H. Tango, IEEE Trans. Electron Devices 41, 2363 (1994)). We will show that graphene with a reduced degree of hydrogenation can compete, in terms of mobility, with silicon technology.
Revenue Autonomy and Regional Growth: An Analysis of the 25-Year Process of Fiscal Decentralisation in Spain
Authors: Gil-Serrate Ramiro , López-Laborda Julio , Mur Jesús
Published: December 2011

By estimating bivariate panel vector autoregressions, this paper analyses the relationship between the revenue autonomy of Spanish regional governments and the regional growth experienced in Spain during the process of fiscal decentralisation from 1984 to 2008. The key finding is the presence of a significant, but marginal, positive effect of regional governments' revenue autonomy on regional growth during the period considered. The small size of the effect can be attributed to the fact that Spanish regional governments have not made extensive use of their important regulatory powers acquired in the 1996 review of the regional financing system or, alternatively, to the fact that the policy of increasing revenue autonomy might have reached saturation point during the period studied, with regard to its effect on economic growth. Both arguments are supported by the identification of an apparent breakpoint, in 1999, in the relationship between revenue autonomy and regional growth in Spain.
Decomposing Residential Self-Selection via a Life-Course Perspective
Authors: Chen Cynthia , Lin Haiyun
Published: December 2011

We propose a decomposition of residential self-selection by understanding the process of its formation. We take a life-course perspective and postulate that locations experienced early in life can have a lasting effect on our locational preferences later in life. In other words, what was experienced spatially is a key factor contributing to our residential self-selection, and our preferences in residential locations are formed long before the onset of our self-selection. We further hypothesize that this prior-location influence is modified by the duration and recency of the prior stay. Using a dataset collected in the New York City Area, we estimated a series of multinomial logit models to test these hypotheses. The results confirm the prior-location influence and demonstrate that this precedes residential self-selection and is impacted by its own properties such as duration and recency. Furthermore, the analysis separating child-bearing households from non-child-bearing households shows an interaction between prior-location influence and the presence of children.
Thinking Habits for Uncertain Subjects: Movement, Stillness, Susceptibility
Authors: Bissell David
Published: December 2011

Stillness occupies an ambivalent position in a world of flows. Opening up space required for reflective, contemplative thought, stillness is often posited as a vital supplement to movement. Yet, in spite of its reverence as a cornerstone of moral responsibility and a key technic of modernity, reflective thought is now taken to be just one modality of thinking amongst many others that compose the body. This paper explores what happens to the capacities of reflective thought when gathered into a vitalist diagram of the body. It does this by tracing how different forms of stillness participate in the constitution of differently susceptible bodies. It considers how habit works to both hold still and move the body in different ways which helps to disrupt an understanding of a body that has a particular capacity for wilful, reflective sovereign thought. As such, and parallel to suggestions that we currently inhabit an era of thought maximisation, this paper argues that reflective thought itself might be better understood as enrolled into a particular diagram of habit that allows us to consider how reflection and contemplation might function not as a redemptive force of liberation from habit, but as the turbulent reverberations of the shock of the outside that can become debilitating.
Blue-Collar Creativity: Reframing Custom-Car Culture in the Imperilled Industrial City
Authors: Warren Andrew , Gibson Chris
Published: December 2011

This paper hitches a ride with young car enthusiasts to explore how their vehicles catalyse a unique form of vernacular creativity, in a seemingly imperilled industrial city setting. While television and print media regularly demonise young drivers for street racing and ‘hoon’ behaviour, this paper purposely adopts a different perspective, on circuits of production and qualitative aspects of the urban custom-car design scene that constitute forms of vernacular creativity. Beyond moral panics little is known about movements, networks, and linkages between custom cars, young enthusiasts, and urban spaces from which their activities emerge. Utilising responsive, in-depth ethnographic methods in Wollongong, Australia, this paper interprets custom-car design as vernacular creativity, valued by young people and located across unassuming and unheralded urban spaces. The possibility that custom-car designers possess skills that are assets for ‘blue-collar’ industrial cities is contrasted against a backdrop of wider discourses depicting such cities as economically vulnerable, as ‘victims' of restructuring—and even ‘uncreative’. Insights relevant to future research on the politics of planning, creative industries, and class identities are also discussed.
Investment in rapid growth shapes the evolutionary rates of essential proteins
Authors: Vieira-Silva Sara , Touchon Marie , Abby Sophie S. , Rocha Eduardo P. C.
Published: December 2011

Proteins evolve at very different rates and, most notably, at rates inversely proportional to the level at which they are produced. The relative frequency of highly expressed proteins in the proteome, and thus their impact on the cell budget, increases steeply with growth rate. The maximal growth rate is a key life-history trait reflecting trade-offs between rapid growth and other fitness components. We show that the maximal growth rate is weakly affected by genetic drift. The negative correlation between protein expression levels and evolutionary rate and the positive correlation between expression levels of highly expressed proteins and growth rates, suggest that investment in growth affects the evolutionary rate of proteins, especially the highly expressed ones. Accordingly, analysis of 61 families of orthologs in 74 proteobacteria shows that differences in evolutionary rates between lowly and highly expressed proteins depend on maximal growth rates. Analyses of complexes with key roles in bacterial growth and strikingly different expression levels, the ribosome and the replisome, confirm these patterns and suggest that the growth-related sequence conservation is associated with protein synthesis. Maximal growth rates also shape protein evolution in the other bacterial clades. Long-branch attractions associated with this effect might explain why clades with persistent history of slow growth are attracted to the root when the tree of prokaryotes is inferred using highly, but not lowly, expressed proteins. These results indicate that reconstruction of deep phylogenies can be strongly affected by maximal growth rates, and highlight the importance of life-history traits and their physiological consequences for protein evolution.
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
Authors: Karnovsky Alla , Weymouth Terry , Hull Tim , Tarcea V. Glenn , Scardoni Giovanni , Laudanna Carlo , Sartor Maureen A. , Stringer Kathleen A. , Jagadish H. V. , Burant Charles , Athey Brian , Omenn Gilbert S.
Published: December 2011

Motivation: Metabolomics is a rapidly evolving field that holds promise to provide insights into genotype–phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges is providing tools that link metabolite data with other types of high-throughput molecular data (e.g. transcriptomics, proteomics), and incorporate prior knowledge of pathways and molecular interactions.

Results: We describe a new, substantially redesigned version of our tool Metscape that allows users to enter experimental data for metabolites, genes and pathways and display them in the context of relevant metabolic networks. Metscape 2 uses an internal relational database that integrates data from KEGG and EHMN databases. The new version of the tool allows users to identify enriched pathways from expression profiling data, build and analyze the networks of genes and metabolites, and visualize changes in the gene/metabolite data. We demonstrate the applications of Metscape to annotate molecular pathways for human and mouse metabolites implicated in the pathogenesis of sepsis-induced acute lung injury, for the analysis of gene expression and metabolite data from pancreatic ductal adenocarcinoma, and for identification of the candidate metabolites involved in cancer and inflammation.

Availability: Metscape is part of the National Institutes of Health-supported National Center for Integrative Biomedical Informatics (NCIBI) suite of tools, freely available at http://metscape.ncibi.org. It can be downloaded from http://cytoscape.org or installed via Cytoscape plugin manager.

Contact:  metscape-help@umich.edu; akarnovs@umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ontogeny of Cytochrome P450 Aromatase mRNA Expression in the Developing Sheep Brain
Authors: Roselli C. E. , Stormshak F.
Published: December 2011

The intraneuronal conversion of testosterone to oestradiol constitutes a critical step in the development and sexual differentiation of the brain of many short gestation mammalian species and has been inferred to play a similar role in long gestation sheep. This conversion is catalysed by cytochrome P450 aromatase (CYP19), which is expressed in specific brain structures during foetal development. The present study was undertaken to examine the specific neuroanatomical distribution and relative expression of aromatase mRNA in the developing sheep hypothalamus. The foetal sheep is a highly tractable model system for localising the region‐specific expression of aromatase in the brain during prenatal development that can help predict regions where oestrogen acts to shape neural development. Our results, obtained using real time quantitative reverse transcriptase‐polymerase chain reaction, revealed that aromatase mRNA was expressed throughout mid to late gestation in the foetal preoptic area and amygdala. In the preoptic area, aromatase expression declined with advancing gestation, whereas, it increased in the amygdala. No sex differences were observed in either brain area. We next investigated the anatomical distribution of aromatase using in situ hybridisation histochemistry and found that the pattern of mRNA expression was largely established by midgestation. High expression was observed in the medial preoptic nucleus, bed nucleus of the stria terminalis and corticomedial amygdala. We also observed substantial expression in the dorsal striatum. These results extend our understanding of the developmental expression of aromatase in the foetal sheep brain and lend support to the view that it plays an essential role in sexual differentiation and maturation of the neuroendocrine, motor and reward control systems.
Somatostatin Dramatically Stimulates Growth Hormone Release from Primate Somatotrophs Acting at Low Doses Via Somatostatin Receptor 5 and Cyclic AMP
Authors: Córdoba‐Chacón J. , Gahete M. D. , Culler M. D. , Castaño J. P. , Kineman R. D. , Luque R. M.
Published: December 2011

Somatostatin and cortistatin have been shown to act directly on pituitary somatotrophs to inhibit growth hormone (GH) release. However, previous results from nonprimate species indicate that these peptides can also directly stimulate GH secretion, at low concentrations. The relevance of this phenomenon in a nonhuman primate model was investigated in the present study by testing the impact of somatostatin/cortistatin on GH release in primary pituitary cell cultures from baboons. High doses (> 10−10 m) of somatostatin/cortistatin did not alter basal GH secretion but blocked GH‐releasing hormone (GHRH)‐ and ghrelin‐induced GH release. However, at low concentrations (10−17–10−13 m), somatostatin/cortistatin dramatically stimulated GH release to levels comparable to those evoked by GHRH or ghrelin. Use of somatostatin receptor (sst) specific agonists/antagonists, and signal transduction blockers indicated that sst2 and sst1 activation via intact adenylate cylcase and mitogen‐activated protein kinase systems mediated the inhibitory actions of high‐concentration somatostatin. By contrast, the stimulatory actions of low‐dose somatostatin on GH release were mediated by sst5 signalling through adenylate cylcase/cAMP/protein kinase A and intracellular Ca2+ pathways, and were additive with ghrelin (not GHRH). Notably, low‐concentrations of somatostatin, similar to sst5‐agonists, inhibited prolactin release. These results clearly demonstrate that the ultimate impact of somatostatin/cortistatin on hormone release is dose‐dependent, cell type‐selective and receptor‐specific, where the stimulatory effects of low‐concentration somatostatin/cortistatin on GH release extend to primates, thereby supporting the notion that this action is relevant in regulating GH secretion in humans.
The levels of zearalenone and its metabolites in plasma, urine and faeces of horses fed with naturally, Fusarium toxin–contaminated oats
Authors: Songsermsakul P. , Böhm J. , Aurich C. , Zentek J. , Razzazi‐Fazeli E.
Published: December 2011

Concentration profile of zearalenone (ZON) and its metabolites in plasma, urine and faeces samples of horses fed with Fusarium toxin–contaminated oats is described. In plasma, β‐zearalenol (β‐ZOL) was detected at high levels on day 10 of the study (3.21–6.24 μg/l). β‐Zearalenol and α‐zearalenol were the major metabolites in urine. Zearalenone, α‐ZOL and β‐ZOL were predominantly found in faeces. Zearalanone could also be detected in urine (1.34–5.79 μg/l) and faeces (1 μg/kg). The degree of glucuronidation was established in all sample types, approximately 100% in urine and plasma. Low per cent of glucuronidation (4–15%) was found in faeces samples. The results indicate the main conversion of ZON into β‐ZOL in horse. This finding could explain why horse is not susceptible to ZON in comparison with swine which produce α‐ZOL as a predominant metabolite.
Effect of dietary protein and lipid levels on growth, nutrient utilization and whole‐body composition of blue gourami, Trichogaster trichopterus fingerlings
Authors: Mohanta K. N. , Subramanian S. , Korikanthimath V. S.
Published: December 2011

Nine semi‐purified diets were prepared with three levels each of protein (300, 350 and 400 g/kg) and lipid (60, 80 and 100 g/kg) and fed ad libitum to Trichogaster trichopterus fingerlings (0.61 ± 0.03 g) in triplicate groups (10 fish/replicate) for 90 days to determine optimum dietary protein and lipid levels. Twenty‐seven flow‐through fibre‐reinforced plastic tanks (200 l capacity each with 100 l of water) were used for rearing the fish. The dietary protein, lipid and their interactions had significant effects (p < 0.05) on weight gain, feed conversion ratio, specific growth rate, nutrient retention and digestibility, but not on hepato‐ and viscerosomatic indexes (p > 0.05). Dietary protein and the interaction of protein with lipid had significant effect (p < 0.05) on whole‐body dry matter, lipid and energy contents, but not on protein and ash contents (p > 0.05). But, the dietary lipid had significant (p < 0.05) effect on whole‐body dry matter, protein, lipid and energy contents except the ash contents (p > 0.05). For each level of dietary protein, the increase in dietary lipid resulted significant increase (p < 0.05) in whole‐body lipid contents without affecting the protein and ash contents (p > 0.05). Based on better growth and dietary performances, the optimum dietary protein and lipid levels of blue gourami fingerling are 350 and 80 g/kg diet respectively.
Genetic variability of the blue and red shrimp Aristeus antennatus in the Western Mediterranean Sea inferred by DNA microsatellite loci
Authors: Cannas Rita , Sacco Flavio , Follesa Maria Cristina , Sabatini Andrea , Arculeo Marco , Lo Brutto Sabrina , Maggio Teresa , Deiana Anna Maria , Cau Angelo
Published: December 2011

Genetic variation at eight microsatellite loci was studied in nine populations of the blue and red shrimp Aristeus antennatus to investigate whether distinct stocks are present in the Western Mediterranean Sea. A high level of gene flow and no evidence of genetic partitioning were discovered. No significant variation was found (FST = 0.00673, P‐value = 0.067) even when shrimps from exploited and those from deep‐water unexploited grounds were compared. No evidence of reduction or expansion of population size in the recent past was found, as indicated by the bottleneck and interlocus g‐tests. Our results are consistent with previous studies using mitochondrial gene methods and allozymes, indicating that, for this species, extensive pelagic larval dispersal and adult migration are probably responsible for the genetic homogeneity observed. In particular, due to a different bathymetric distribution of males and females, reported to be associated with different water masses and hence with possible differential dispersal capacity between sexes, the hypothesis of sex‐biased dispersal was tested. Mean values of corrected assignment indices and mean relatedness values were higher for males, suggesting that females are the more widely dispersing sex. Molecular assessment of A. antennatus from the Western Mediterranean provides data of biological and evolutionary interest for the successful management of such a highly valuable fishery resource.
Treatment of high‐frequency gastric electrical stimulation for gastroparesis
Authors: Chu Huikuan , Lin Zhiyue , Zhong Likun , McCallum Richard W , Hou Xiaohua
Published: December 2011

Background and Aims:  The aim of this study was to assess the effects of gastric electrical stimulation (GES) on symptoms and gastric emptying in patients with gastroparesis, and the effects of GES on the three subgroups of gastroparesis.

Methods:  A literature search of clinical trials using high‐frequency GES to treat patients with gastroparesis from January 1995 to January 2011 was performed. Data on the total symptom severity score (TSS), nausea severity score, vomiting severity score, and gastric emptying were extracted and analyzed. The statistic effect index was weighted mean differences.

Results:  Ten studies (n = 601) were included in this study. In the comparison to baseline, there was significant improvement of symptoms and gastric emptying (P < 0.00001). It was noted that GES significantly improved both TSS (P < 0.00001) and gastric retention at 2 h (P = 0.003) and 4 h (P < 0.0001) in patients with diabetic gastroparesis (DG), while gastric retention at 2 h (P = 0.18) in idiopathic gastroparesis (IG) patients, and gastric retention at 4 h (P = 0.23) in postsurgical gastroparesis (PSG) patients, did not reach significance.

Conclusions:  Based on this meta‐analysis, the substantial and significant improvement of symptoms and gastric emptying, and the good safety we observed, indicate that high‐frequency GES is an effective and safe method for treating refractory gastroparesis. DG patients seem the most responsive to GES, both subjectively and objectively, while the IG and PSG subgroups are less responsive and need further research.
A Low‐Memory, Straightforward and Fast Bilateral Filter Through Subsampling in Spatial Domain
Authors: Banterle Francesco , Corsini Massimiliano , Cignoni Paolo , Scopigno Roberto
Published: December 2011

In this work we present a new algorithm for accelerating the colour bilateral filter based on a subsampling strategy working in the spatial domain. The base idea is to use a suitable subset of samples of the entire kernel in order to obtain a good estimation of the exact filter values. The main advantages of the proposed approach are that it has an excellent trade‐off between visual quality and speed‐up, a very low memory overhead is required and it is straightforward to implement on the GPU allowing real‐time filtering. We show different applications of the proposed filter, in particular efficient cross‐bilateral filtering, real‐time edge‐aware image editing and fast video denoising. We compare our method against the state of the art in terms of image quality, time performance and memory usage.
Gender as a moderator of the relationship between materialism and fashion clothing involvement among Indian youth
Authors: Handa Meenakshi , Khare Arpita
Published: December 2011

The research examines the role of gender in moderating the relationship between materialism and product involvement with fashion clothing among the Indian youth. The Richins materialism scale and the product involvement and purchase involvement scales developed by O'Cass were used to understand the behaviour of Indian youth towards fashion clothing. The sample (n = 254) comprised of university students from different parts of India. The findings indicate that Indian youth do not possess a high level of materialistic tendencies. Gender has a moderating influence on the relationship between materialism and involvement with fashion clothing. Young men and women differ with respect to their involvement with fashion clothing and even more with regard to their involvement with the purchase of fashion clothing, with women reporting a higher level of involvement in both cases.
Crystallization of Lithium Disilicate Glass Using Microwave Processing
Authors: Mahmoud Morsi M. , Folz Diane C. , Suchicital Carlos T. A. , Clark David E.
Published: December 2011

The crystallization of lithium disilicate (LS2) glass using a variable frequency microwave (VFM) processing technique was investigated. Lithium disilicate glass samples were prepared from commercial frit using a conventional glass melting and casting technique. A two‐stage heat‐treatment regime was used to crystallize the glass samples. The nucleation and crystallization temperatures were determined by the thermal analysis of the prepared LS2 glass. The LS2 glass samples were nucleated by conventional heating, followed by the crystallization step using two different techniques: conventional and microwave crystallization. Characterization of the prepared glass‐ceramic samples by both techniques was conducted using X‐ray diffraction, Fourier transform infrared reflectance spectroscopy, Raman spectroscopy, and scanning electron microscopy. Variable frequency microwave processing was successfully used to crystallize LS2 glass. Enhanced kinetics and slightly different crystallization mechanisms were observed in the VFM crystallization process as compared with the conventional one.
High‐Frequency Negative Permittivity from Fe/Al2O3 Composites with High Metal Contents
Authors: Gao Meng , Shi Zhi‐cheng , Fan Run‐hua , Qian Lei , Zhang Zi‐dong , Guo Jing‐yan
Published: December 2011

For conventional metal/ceramic composites, we report an interesting negative permittivity behavior, which was usually observed in artificial metamaterials. The Fe/Al2O3 composites with different Fe volume contents ranging from 10% to 40% were prepared through hot‐pressing sintering. The impedance and dielectric properties of the composites in high frequency range present a distinct dependence on the composition, and the negative permittivity is obtained when Fe content exceeds 20 vol%. The experimental results of negative permittivity from the composites above percolation threshold are in good agreement with fitting results from Drude model. The tunability of negative permittivity makes Fe/Al2O3 composites promising candidates for the double negative materials.
Climate‐based empirical models show biased predictions of butterfly communities along environmental gradients
Authors: Pellissier Loïc , Pradervand Jean‐Nicolas , Pottier Julien , Dubuis Anne , Maiorano Luigi , Guisan Antoine
Published: December 2011

A better understanding of the factors that mould ecological community structure is required to accurately predict community composition and to anticipate threats to ecosystems due to global changes. We tested how well stacked climate‐based species distribution models (S‐SDMs) could predict butterfly communities in a mountain region. It has been suggested that climate is the main force driving butterfly distribution and community structure in mountain environments, and that, as a consequence, climate‐based S‐SDMs should yield unbiased predictions. In contrast to this expectation, at lower altitudes, climate‐based S‐SDMs overpredicted butterfly species richness at sites with low plant species richness and underpredicted species richness at sites with high plant species richness. According to two indices of composition accuracy, the Sorensen index and a matching coefficient considering both absences and presences, S‐SDMs were more accurate in plant‐rich grasslands. Butterflies display strong and often specialised trophic interactions with plants. At lower altitudes, where land use is more intense, considering climate alone without accounting for land use influences on grassland plant richness leads to erroneous predictions of butterfly presences and absences. In contrast, at higher altitudes, where climate is the main force filtering communities, there were fewer differences between observed and predicted butterfly richness. At high altitudes, even if stochastic processes decrease the accuracy of predictions of presence, climate‐based S‐SDMs are able to better filter out butterfly species that are unable to cope with severe climatic conditions, providing more accurate predictions of absences. Our results suggest that predictions should account for plants in disturbed habitats at lower altitudes but that stochastic processes and heterogeneity at high altitudes may limit prediction success of climate‐based S‐SDMs.
Global periodontal disease epidemiology
Authors: Dye Bruce A.
Published: December 2011

Our understanding of the global epidemiology of periodontal disease has changed considerably over the past 50 years. This change has been influenced not only by our evolving knowledge of the natural history and distribution of the disease, but also by changing measurement methodologies. Although great strides have been made in describing the underlying contributions of microorganisms and plaque ecology, as well as the inflammatory and host responses, there is still much that is not known regarding risk susceptibility and prevention effectiveness. The focus of global periodontal epidemiology during the last half century has been on identifying populations who have periodontal disease and situations where disparities in disease prevalence exist between groups. Unlike dental public health activities directed toward dental caries, less effort has been made in periodontal epidemiology with regard to surveying or monitoring groups who may be at greater risk for moderate or severe disease and evaluating public health initiatives directed at mitigating risk or reducing such periodontal disease prevalence. Additionally, there is limited information regarding current national estimates of periodontal disease in most countries. Although numerous periodontal studies have been performed globally, very few are epidemiological studies using nationally representative samples. The aim of this critical review is to discuss the historical context of global periodontal disease epidemiology, highlight key activities and findings over the past decade in global periodontal epidemiology, and comment on how changes in the practice of epidemiology may affect global periodontology over the coming decade.
Genetic susceptibility to periodontitis
Authors: Laine Marja L. , Crielaard Wim , Loos Bruno G.
Published: December 2011

In this systematic review, we explore and summarize the peer‐reviewed literature on putative genetic risk factors for susceptibility to aggressive and chronic periodontitis. A comprehensive literature search on the PubMed database was performed using the keywords ‘periodontitis’ or ‘periodontal disease’ in combination with the words ‘genes’, ‘mutation’, ‘SNP’ or ‘polymorphism’. The studies selected were written in English, had a case–control design, and reported genotype distribution. Only studies with at least 100 individuals in either the case or control group were included. Research on genetic polymorphisms has only had limited success in identifying significant and reproducible genetic factors for susceptibility to aggressive periodontitis and chronic periodontitis. Taking together the data published on gene polymorphisms in aggressive and chronic periodontitis, we conclude that there are differences among the various studies for the rare allele carriage rates. Nevertheless, there is some evidence that polymorphisms in the IL1B, IL1RN, FcγRIIIb, VDR and TLR4 genes may be associated with aggressive periodontitis susceptibility, and polymorphisms in the IL1B, IL1RN, IL6, IL10, VDR, CD14, TLR4 and MMP1 genes may be associated with chronic periodontitis susceptibility as a single genetic factor in certain populations. Future studies should apply stricter disease classifications, use larger study cohorts, adjust for relevant risk factors in aggressive and chronic periodontiti,s and include analysis of multiple genes and polymorphisms. Establishing consortia and performing collaborative studies may help to conquer the limitations of small sample size and limited statistical power.
Hydrologic Connectivity Affects Fish Assemblage Structure, Diversity, and Ecological Traits in the Unregulated Gambia River, West Africa
Authors: White Seth M. , Ondračková Markéta , Reichard Martin
Published: December 2011

The Gambia River of West Africa is a large unobstructed river, characterized by a natural flow regime and lateral connectivity across its floodplain. Construction of a major dam, however, is planned. We compared patterns of fish diversity, habitat use, assemblage structure, and the distribution of trophic position and body morphology in riverine and floodplain habitats in Niokolo Koba National Park, located downstream of the planned dam site. A total of 49 fish species were captured, revealing a lognormal distribution as expected for species‐rich assemblages. Fish species exhibited a range of habitat use patterns, from generalist to highly habitat‐specific, and appeared to migrate laterally among habitats between seasons. Species richness was homogenous among habitats in the wet season yet appeared to increase with isolation from the main river in the dry season. Fish assemblage structure was best explained by the interaction between habitat type and season, underlining the importance of the natural flow regime and lateral connectivity among floodplain habitats. The abundance of fishes having elongate bodies increased with isolation from the main channel in the wet season only. The distribution of fishes having compressed cross‐sectional morphology decreased with isolation from the main channel in the dry season only. These patterns of trait distribution support the conclusion that variation in hydrologic connectivity structures the fish assemblage. Our results suggest that altered flow regimes and loss of floodplain habitats after damming could lead to both decreased taxonomic and functional diversity of the fish assemblage.
Immunodeficiency due to defects in store‐operated calcium entry
Authors: Feske Stefan
Published: December 2011

Mutations in genes encoding the calcium‐release activated calcium (CRAC) channel abolish calcium influx in cells of the immune system and cause severe congenital immunodeficiency. Patients with autosomal recessive mutations in the CRAC channel gene ORAI1, its activator stromal interaction molecule 1 (STIM1), and mice with targeted deletion of Orai1, Stim1, and Stim2 genes reveal important roles for CRAC channels in adaptive and innate immune responses to infection and in autoimmunity. Because CRAC channels have important functions outside the immune system, deficiency of either ORAI1 or STIM1 is associated with a unique clinical phenotype. This review will give an overview of CRAC channel function in the immune system, examine the consequences of CRAC channel deficiency for immunity in human patients and mice, and discuss genetic defects in immunoreceptor‐associated signaling molecules that compromise calcium influx and cause immunodeficiency.
The association between childhood overweight and obesity and otitis media
Authors: Kuhle S. , Kirk S. F. L. , Ohinmaa A. , Urschitz M. S. , Veugelers P. J.
Published: December 2011

Objective

The objective of this study was to examine the association between otitis media and childhood obesity in a population‐based sample of elementary school children in the Canadian province of Nova Scotia.

Methods

The study design is a prospective cohort study, linking data from a population‐based survey of Grade 5 students (aged 10–11 years) in the Canadian province of Nova Scotia in 2003 with Nova Scotia administrative health data. Measured body mass index was used to define weight status based on the age‐ and gender‐specific cut‐off points of the International Obesity Task Force. Health administration data for each child was linked via Health Card numbers. The primary outcome was healthcare utilization (physician visits and costs) for suppurative otitis media (International Classification of Diseases [ICD]9: 382; ICD10: H65–66) with no previous diagnosis of otitis in the last 30 days.

Results

Relative to normal weight children, obese children had more healthcare provider contacts for otitis media (adjusted incidence rate ratio 2.03, 95% confidence interval [CI] 1.66–2.49), incurred more costs per otitis media‐related visit ($47 vs. $24,
P
 = 0.0001) and had higher odds to have repeated otitis media (adjusted odds ratio 2.27, 95% CI 1.54–3.35). Socioeconomic factors, a history of breastfeeding, presence of an allergic disorder or chronic adenoid/tonsil disorder did not change the association between obesity and otitis media.

Conclusion

There is a clear association between childhood obesity and otitis media that cannot be explained by confounding by socioeconomic factors or clinically associated disorders.
Voyager Measurements of Hydrogen Lyman-α Diffuse Emission from the Milky Way
Authors: Lallement Rosine , Quémerais Eric , Bertaux Jean-Loup , Sandel Bill R. , Izmodenov Vlad
Published: December 2011

This emission, observed in other galaxies mainly from regions around newborn stars, has now been detected in our Galaxy.
The Race to X-ray Microbeam and Nanobeam Science
Authors: Ice Gene E. , Budai John D. , Pang Judy W. L.
Published: December 2011

X-ray microbeams are an emerging characterization tool with broad implications for science, ranging from materials structure and dynamics, to geophysics and environmental science, to biophysics and protein crystallography. We describe how submicrometer hard x-ray beams with the ability to penetrate tens to hundreds of micrometers into most materials and with the ability to determine local composition, chemistry, and (crystal) structure can characterize buried sample volumes and small samples in their natural or extreme environments. Beams less than 10 nanometers have already been demonstrated, and the practical limit for hard x-ray beam size, the limit to trace-element sensitivity, and the ultimate limitations associated with near-atomic structure determinations are the subject of ongoing research.
Modeling Effects of Environmental Change on Wolf Population Dynamics, Trait Evolution, and Life History
Authors: Coulson Tim , MacNulty Daniel R. , Stahler Daniel R. , vonHoldt Bridgett , Wayne Robert K. , Smith Douglas W.
Published: December 2011

Analysis of a 20-year data set on Yellowstone wolves reveals that environmental change generates eco-evolutionary responses.
The Intraepithelial T Cell Response to NKG2D-Ligands Links Lymphoid Stress Surveillance to Atopy
Authors: Strid Jessica , Sobolev Olga , Zafirova Biljana , Polic Bojan , Hayday Adrian
Published: December 2011

Epidermal abrasion and T cells in the skin work together to drive the type of immune responses seen in allergy and asthma.
RNA Elimination Machinery Targeting Meiotic mRNAs Promotes Facultative Heterochromatin Formation
Authors: Zofall Martin , Yamanaka Soichiro , Reyes-Turcu Francisca E. , Zhang Ke , Rubin Chanan , Grewal Shiv I. S.
Published: December 2011

Making Heterochromatin

Heterochromatin is a particularly compact DNA-protein assembly that can repress gene expression. Constitutive heterochromatin is found, for example, at centromeres and the subtelomeric regions. Working with
Schizosaccharomyces pombe
,

Zofall
et al.

(p.
96
, published online 1 December) examined the heterochromatin islands often found near meiotic genes, which are maintained in a silenced state during vegetative growth. Heterochromatin formation at these loci did not generally involve the RNA interference machinery, as is observed at centromeres, but did require transcription. The exosome, an RNA-degrading machine, was involved in the formation of the heterochromatin islands, which could be remodeled in response to sexual differentiation.
Replication in Field Biology: The Case of the Frog-Eating Bat
Authors: Ryan Michael J.
Published: December 2011

Studies conducted in the field offer unique opportunities to observe nature, but achieving true replication under natural conditions is challenging. As demonstrated by the discovery of frog eating by a charismatic bat, biology conducted in the field generally follows an interesting progression that includes discovery, demonstration, experimentation, and verification.
Controversial Studies Give a Deadly Flu Virus Wings
Authors: Enserink Martin
Published: December 2011

H5N1 avian influenza strains genetically altered to be more easily transmissible are the subject of a heated debate among scientists, biosecurity experts, and U.S. government officials.
Dengue Virus Capsid Protein Binding to Hepatic Lipid Droplets (LD) Is Potassium Ion Dependent and Is Mediated by LD Surface Proteins
Authors: Carvalho Filomena A. , Carneiro Fabiana A. , Martins Ivo C. , Assunção-Miranda Iranaia , Faustino André F. , Pereira Renata M. , Bozza Patricia T. , Castanho Miguel A. R. B. , Mohana-Borges Ronaldo , Da Poian Andrea T. , Santos Nuno C.
Published: December 2011

Dengue virus (DENV) affects millions of people, causing more than 20,000 deaths annually. No effective treatment for the disease caused by DENV infection is currently available, partially due to the lack of knowledge on the basic aspects of the viral life cycle, including the molecular basis of the interaction between viral components and cellular compartments. Here, we characterized the properties of the interaction between the DENV capsid (C) protein and hepatic lipid droplets (LDs), which was recently shown to be essential for the virus replication cycle. Zeta potential analysis revealed a negative surface charge of LDs, with an average surface charge of −19 mV. The titration of LDs with C protein led to an increase of the surface charge, which reached a plateau at +13.7 mV, suggesting that the viral protein-LD interaction exposes the protein cationic surface to the aqueous environment. Atomic force microscopy (AFM)-based force spectroscopy measurements were performed by using C protein-functionalized AFM tips. The C protein-LD interaction was found to be strong, with a single (un)binding force of 33.6 pN. This binding was dependent on high intracellular concentrations of potassium ions but not sodium. The inhibition of Na
+
/K
+
-ATPase in DENV-infected cells resulted in the dissociation of C protein from LDs and a 50-fold inhibition of infectious virus production but not of RNA replication, indicating a biological relevance for the potassium-dependent interaction. Limited proteolysis of the LD surface impaired the C protein-LD interaction, and force measurements in the presence of specific antibodies indicated that perilipin 3 (TIP47) is the major DENV C protein ligand on the surface of LDs.
The effect of sports specialization on musculus quadriceps function after exercise-induced muscle damage
Authors: Skurvydas Albertas , Brazaitis Marius , Venckūnas Tomas , Kamandulis Sigitas , Stanislovaitis Aleksas , Zuoza Aurelijus
Published: December 2011

The primary aim of the present study was to examine the effect of eccentric exercise-induced (100 submaximal eccentric contractions at an angular velocity of 60° s–1, with 20-s rest intervals) muscle damage on peripheral and central fatigue of quadriceps muscle in well-trained long-distance runners, sprint runners, volleyball players, and untrained subjects. We found that (i) indirect symptoms of exercise-induced muscle damage (prolonged decrease in maximal voluntary contraction, isokinetic concentric torque, and electrically induced (20 Hz) torque) were most evident in untrained subjects, while there were no significant differences in changes of muscle soreness and plasma creatine kinase 48 h after eccentric exercise between athletes and untrained subjects; (ii) low-frequency fatigue was greater in untrained subjects and volleyball players than in sprint runners and long-distance runners; (iii) in all subjects, electrically induced (100 Hz) torque decreased significantly by about 20%, while central activation ratio decreased significantly by about 8% in untrained subjects and sprint runners, and by about 3%–5% in long-distance runners and volleyball players. Thus, trained subjects showed greater resistance to exercise-induced muscle damage for most markers, and long-distance runners had no advantage over sprint runners or volleyball players.