bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prokaryotic diversity of an active mud volcano in the Usu City of Xinjiang, China
Authors: Yang Hong‐Mei , Lou Kai , Sun Jian , Zhang Tao , Ma Xiao‐Long 
Published: June 2011

AbstractThe Usu mud volcanoes are the largest group of terrestrial mud volcanoes in China. The volcanoes are located in a typical arid and semi‐arid region, and the group consists of 36 erupting active mud volcanoes. In this study, the prokaryotic diversity and community structure in the sediment of an active mud volcano were investigated by constructing bacterial and archaeal clone libraries of the 16S rRNA gene. A total of 100 bacterial and 100 archaeal clones were analysed and found to comprise 11 and 7 distinct phylotypes, respectively. The bacterial phylotypes were classified into three phyla (Proteobacteria, Actinobacteria, and Fusobacteria). Of these, Proteobacteria were the most abundant bacterial group, with Deltaproteobacteria dominating the sediment community, and these were affiliated with the order Desulfuromonadales. The archaeal phylotypes were all closely related to uncultivated species, and the majority of the members were related to the orders Methanosarcinales and Halobacteriales of the Euryarchaeota originating from methane hydrate bearing or alkaline sediments. The rest of the archaeal phylotypes belonged to the phylum Crenarchaeota, with representatives from similar habitats. These results suggested that a large number of novel microbial groups and potential methanogenesis may exist in this unique ecosystem. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Evaluating management risks using landscape trajectory analysis: A case study of California fisher
Authors: Thompson Craig M. , Zielinski William J. , Purcell Kathryn L. 
Published: June 2011

AbstractEcosystem management requires an understanding of how landscapes vary in space and time, how this variation can be affected by management decisions or stochastic events, and the potential consequences for species. Landscape trajectory analysis, coupled with a basic knowledge of species habitat selection, offers a straightforward approach to ecological risk analysis and can be used to project the effects of management decisions on species of concern. The fisher (Martes pennanti) occurs primarily in late‐successional forests which, in the Sierra Nevada mountains, are susceptible to high‐intensity wildfire. Understanding the effects of fuels treatments and fire on the distribution of fisher habitat is a critical conservation concern. We assumed that the more a treated landscape resembled occupied female fisher home ranges, the more likely it was to be occupied by a female and therefore the lower the risk to the population. Thus, we characterized important vegetation attributes within the home ranges of 16 female fishers and used the distribution of these attributes as a baseline against which the effects of forest management options could be compared. We used principal components analysis to identify the major axes defining occupied female fisher home ranges and these, in addition to select univariate metrics, became our reference for evaluating the effects of landscape change. We demonstrated the approach at two management units on the Sierra National Forest by simulating the effects of both no action and forest thinning, with and without an unplanned fire, on vegetation characteristics over a 45‐yr period. Under the no action scenario, landscapes remained similar to reference conditions for approximately 30‐yr until forest succession resulted in a loss of landscape heterogeneity. Comparatively, fuel treatment resulted in the reduction of certain forest elements below those found in female fisher home ranges yet little overall change in habitat suitability. Adding a wildfire to both scenarios resulted in divergence from reference conditions, though in the no action scenario the divergence was 4× greater and the landscape did not recover within the 45‐yr timeframe. These examples demonstrate that combining the results of forest growth and disturbance modeling with habitat selection data may be used to quantify the potential effects of vegetation management activities on wildlife habitat. © 2011 The Wildlife Society.
Long‐term outcome after intrauterine laser treatment for twin–twin transfusion syndrome
Authors: Maschke Cornelia , Diemert Anke , Hecher Kurt , Bartmann Peter 
Published: June 2011

AbstractTwin–twin transfusion syndrome (TTTS) is a severe complication occurring in about 10% of monochorionic twin pregnancies. The chronic unbalanced transfusion of blood across placental vascular communications from the donor to the recipient twin may lead to impairment of various organ systems in the affected twins. In Hamburg, Germany, since 1995 patients with TTTS were treated with fetoscopic laser coagulation as the first causal therapeutic strategy. All survivors after laser surgery were followed up in the University Children's Hospital in Bonn, Germany. In this article, we summarize long‐term follow‐up studies from our German study population and compare our results with data from the literature. Copyright © 2011 John Wiley & Sons, Ltd.
Achieving high‐growth‐rate in GaN homoepitaxy using high‐density nitrogen radical source
Authors: Kawai Yohjiro , Chen Shang , Honda Yoshio , Yamaguchi Masahito , Amano Hiroshi , Kondo Hiroki , Hiramatsu Mineo , Kano Hiroyuki , Yamakawa Koji , Den Shoji , Hori Masaru 
Published: June 2011

AbstractThe key issue in GaN growth by radio‐frequency plasma‐assisted molecular beam epitaxy is the low growth rate compared with that obtained using an ammonia source. To reduce the processing time and to improve the crystalline quality of the epilayer, a high‐density radical source (HDRS) with high stability has been developed. The growth rate of the GaN epilayer was improved using the HDRS rather than a conventional radical source. During the growth, a sharp streak pattern obtained by reflection high‐energy electron diffraction was maintained. An atomically smooth surface was confirmed by atomic force microscopy observation (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Reliability study on micro‐structured InGaN light‐emitting diodes
Authors: Li Z. L. , Li K. H. , Choi H. W. 
Published: June 2011

AbstractMicro‐structured InGaN light‐emitting diodes (µLED) are capable of delivering enhanced light output due to additional light extraction through exposed sidewalls. However, these sidewalls formed by plasma etching can potentially affect the lifetime and reliability of the devices as a result of plama damage. A study on the electrical characteristics and reliability of µLED arrays has been carried out in this work. Although improved optical performance can be expected based on previous studies, expanded device sidewalls prove to accelerate the rate of optical degradation, adversely affect the lifetimes of devices. Through precise current‐voltage measurement vertical current conduction along the plasma‐damaged sidewalls was identified as the key mechanism contributing to degraded reliability. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Direct study of nonlinear carrier recombination in InGaN quantum well structures
Authors: Malinauskas Tadas , Miasojedovas Saulius , Aleksiejūnas Ramūnas , Juršėnas Saulius , Jarašiūnas Kęstutis , Nomura Masahiro , Arakawa Yasuhiko , Shimura Tsutomu , Kuroda Kazuo 
Published: June 2011

AbstractDirect measurements of carrier recombination dynamics in In0.1Ga0.9N/In0.03Ga0.97N multiple quantum well (QW) structures with different well thickness (d = 5.5, 17, 34 nm) are presented. The measurements by light‐induced picosecond transient grating and time‐resolved photoluminescence techniques revealed three contributing carrier recombination mechanisms at high carrier injections (“efficiency droop” conditions): stimulated emission (SE), bimolecular, and Shockley‐Read‐Hall. The study indicates on absence of Auger recombination rate with quadratic dependence, 1/τ ∝ N2, which was not observed up to ∼5x1019 cm‐3 excess carrier density (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Injection efficiency in AlGaN‐based UV laser diodes
Authors: Nagata Kengo , Takeda Kenichiro , Oshimura Yoshinori , Takehara Kosuke , Aoshima Hiroki , Ito Shun , Iwaya Motoaki , Takeuchi Tetsuya , Kamiyama Satoshi , Akasaki Isamu , Amano Hiroshi , Yoshida Harumasa , Kuwabara Masakazu , Yamashita Yoji , Kan Hirofumi 
Published: June 2011

AbstractWe evaluated AlGaN‐based 355 nm UV laser diodes prepared under two different Mg activation conditions. The annealing processes for Mg activation in p‐layers were carried out under N2 or O2 ambient to investigate the effect of the ambient gas on the laser characteristics. The threshold current densities and operating voltages of the UV laser diodes were improved by annealing under O2 compared with those under N2. We then estimated the injection efficiencies of the laser diode structures by considering the internal quantum efficiencies of optical excitation and electrical excitation. The internal quantum efficiency of the electrically excited spontaneous emission from the laser structure annealed under O2 reached 50% at a carrier density of 7.0×1018 cm‐3, while the structure annealed under N2 required a 1.8‐fold higher carrier density of 1.2×1019 cm‐3 to reach the same internal quantum efficiency. In addition, the internal quantum efficiency estimated from optical excitation reached 50% even at a carrier density of 3.0×1018 cm‐3. This implies that the injection efficiencies in the UV laser diode structures annealed under N2 and O2 were 25% and 45%, respectively. Mg activation by O2 annealing is effective for increasing the injection efficiency. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
GaNAs alloys over the whole composition range grown on crystalline and amorphous substrates
Authors: Yu K. M. , Novikov S. V. , Broesler R. , Levander A. X. , Liliental‐Weber Z. , Luckert F. , Martin R. W. , Dubon O. , Wu J. , Walukiewicz W. , Foxon C. T. 
Published: June 2011

AbstractUsing low temperature molecular beam epitaxy (LT‐MBE) technique we have overcome the miscibility gap of GaAs and GaN alloys and successfully synthesized GaN1‐xAsx alloys in the whole composition range on crystalline (sapphire and silicon) and amorphous (Pyrex glass) substrates. On the N‐rich side we found an increased incorporation of As with decreasing growth temperature. At high enough As content the films lose their crystallinity and become amorphous. On sapphire substrate, the alloys are amorphous in the composition range of 0.17<x<0.75. For the films grown on glass substrates, the composition range for amorphous alloys extends to x∼0.1. However, films grown on silicon shows small fraction of As‐rich and N‐rich GaNAs nanocrystals for films with As content up to 36%. These amorphous GaNAs films have smooth morphology, homogeneous composition and sharp, well defined optical absorption edges. The bandgap energy of the GaN1‐xAsx alloys covers a broad energy range from ∼3.4 eV in GaN to∼0.8 eV at x∼0.85. This provides an almost perfect fit to the solar spectrum offering the opportunity to design high efficiency multijunction solar cells using a single ternary alloy system. The amorphous nature of this alloy over a wide alloy range can also be advantageous since they can be deposited on low‐cost glass substrate. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Evaluation of behavior factor of tunnel‐form concrete building structures using Applied Technology Council 63 methodology
Authors: Tavafoghi Alireza , Eshghi Sassan 
Published: June 2011

SUMMARYTunnel‐form construction system is used for buildings made up of slabs and walls. This system has represented fast construction technique, low cost and time saving in the construction period. However, there are no special requirements for seismic design of this type of buildings, and some provisions of the concrete bearing wall system are used. None of the seismic codes addresses the R factor for tunnel‐form buildings directly, and some doubts remained about prediction of the fundamental period. Meanwhile the force‐based methods, which depended on R factor and fundamental period, are still used for seismic design of this type of buildings. There is a need for evaluating the R factor for tunnel‐form buildings. The methodology was developed by the Applied Technology Council (ATC) entitled ATC‐63 Project for quantifying building system performance and response parameters for use in seismic design. Here, this methodology is used to estimate more reliable R factor for tunnel‐form buildings. An experimental program was carried out to decrease the uncertainty of finite element modeling and using it as a part of the methodology. A database was created, and some analyses were performed. The results of analysis were summarized to propose more accurate R factor for tunnel‐form buildings. Copyright © 2011 John Wiley & Sons, Ltd.
An analysis of mutualistic interactions between exotic ants and honeydew producers in the Yanbaru district of Okinawa Island, Japan
Authors: Tanaka Hirotaka , Ohnishi Hitoshi , Tatsuta Haruki , Tsuji Kazuki 
Published: June 2011

AbstractInvasive exotic ants often have a mutualistic relationship with other insects excreting honeydew, and this is considered to play a key role in their invasion success. We investigated the multispecies association patterns between ants and hemipteran insects in the Yanbaru forests, Okinawa, Japan, an Asian biodiversity hotspot. We especially focused on roadside environments, which are the frontlines of invasion for exotic ants. We found that only a small number of herbaceous and pioneer plants were predominant on the roadsides. Four honeydew producers, Melanaphis formosana, Dysmicoccus sp. A, Heteropsylla cubana, and Sogata hakonensis, living on these roadside plants accounted for 94.9% of the total honeydew‐producer aggregations observed. Only a few exotic ants, such as Technomyrmex brunneus and Anoplolepis gracilipes, were observed with these honeydew‐producer aggregations, and densities of these ants and honeydew producers were often positively correlated. An ant exclusion experiment showed that exotic ant occurrence improved the survival of some of the hemipteran colonies. Interestingly, the abundance of native ants was not correlated with the abundance of honeydew producers, and the local density of Pheidole noda was negatively correlated with that of M. formosana. These findings, i.e., only a few ants, all exotic, tended to hemipteran honeydew producers despite the existence of many native ants, and the abundances of those exotic ants and those hemipteran insects had positive correlations, provide some insights into the mechanism of biological invasion and provide information for the management of exotic ants.
Do molecules matter more than morphology? Promises and pitfalls in parasites
Authors: PERKINS S. L. , MARTINSEN E. S. , FALK B. G. 
Published: June 2011

SUMMARYSystematics involves resolving both the taxonomy and phylogenetic placement of organisms. We review the advantages and disadvantages of the two kinds of information commonly used for such inferences – morphological and molecular data – as applied to the systematics of metazoan parasites generally, with special attention to the malaria parasites. The problems that potentially confound the use of morphology in parasites include challenges to consistent specimen preservation, plasticity of features depending on hosts or other environmental factors, and morphological convergence. Molecular characters such as DNA sequences present an alternative data source and are particularly useful when not all the parasite's life stages are present or when parasitaemia is low. Nonetheless, molecular data can bring challenges that include troublesome DNA isolation, paralogous gene copies, difficulty in developing molecular markers, and preferential amplification in mixed species infections. Given the differential benefits and shortcomings of both molecular and morphological characters, both should be implemented in parasite taxonomy and phylogenetics.
Gay and lesbian carers: ageing in the shadow of dementia
Authors: PRICE ELIZABETH 
Published: June 2011

ABSTRACTThis article reports on findings from a qualitative study, undertaken in England, which explored the experiences of 21 gay men and lesbian women who care, or cared, for a person with dementia. The aim of the study was to explore this experience through the lens of a person's gay or lesbian sexuality. The paper reports two related themes that emerged from the wider study – respondents' hopes, fears and plans for the future and, specifically, the way in which their caring experiences had coloured their views and expectations of how their own health and social care needs may be met. Respondents' narratives reflect a range of pervasive anxieties about the future. First, about the possibility that they might be diagnosed with a condition such as dementia and, consequently, the myriad ways in which their sexualities and lifestyle choices may be perceived and interpreted as they themselves age and, possibly, require health and/or social care and support. In light of these concerns, respondents reflected upon the need for specialist service provision for older gay and lesbian people – an idea that was, perhaps surprisingly, not universally welcomed.
China's export restriction policies: complying with ‘WTO plus’ or undermining multilateralism
Authors: KARAPINAR BARIS 
Published: June 2011

AbstractExport restrictions imposed on various food products and natural resources have been subject to extensive public attention. Most recently, China's restrictions of its exports of certain minerals and rare earth metals have led to heated debates. The United States (US), European Union (EU), and Mexico have already filed a WTO dispute case against China on this matter. This paper describes the policy objectives and the global welfare implications of export restrictions. It summarizes the relevant WTO regulation, and offers a detailed analysis of the China–Raw Materials case which is before the Dispute Settlement Body (DSB). It argues that although export restrictions is arguably an area of ‘under-regulation’ or ‘regulatory deficiency’ in the WTO law, it is strongly biased against the late accession Members, including China. Yet, the way that China institutes its export restrictions raises serious questions about its role in the multilateral trading system, which it relies on for its economic prosperity. Hence, this is an area where China is likely to feel the implications of its so-called ‘WTO-plus’ commitments on its domestic and trade policies.
MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects
Authors: Westra Harm-Jan , Jansen Ritsert C. , Fehrmann Rudolf S. N. , te Meerman Gerard J. , van Heel David , Wijmenga Cisca , Franke Lude 
Published: June 2011

Abstract
Motivation: Sample mix-ups can arise during sample collection, handling, genotyping or data management. It is unclear how often sample mix-ups occur in genome-wide studies, as there currently are no post hoc methods that can identify these mix-ups in unrelated samples. We have therefore developed an algorithm (MixupMapper) that can both detect and correct sample mix-ups in genome-wide studies that study gene expression levels.
Results: We applied MixupMapper to five publicly available human genetical genomics datasets. On average, 3% of all analyzed samples had been assigned incorrect expression phenotypes: in one of the datasets 23% of the samples had incorrect expression phenotypes. The consequences of sample mix-ups are substantial: when we corrected these sample mix-ups, we identified on average 15% more significant cis-expression quantitative trait loci (cis-eQTLs). In one dataset, we identified three times as many significant cis-eQTLs after correction. Furthermore, we show through simulations that sample mix-ups can lead to an underestimation of the explained heritability of complex traits in genome-wide association datasets.
Availability and implementation: MixupMapper is freely available at http://www.genenetwork.nl/mixupmapper/
Contact: lude@ludesign.nl
Supplementary Information: Supplementary data are available at Bioinformatics online.
Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays
Authors: Paliy Oleg , Foy Brent D. 
Published: June 2011

Abstract
Motivation: Many current studies of complex microbial communities rely on the isolation of community genomic DNA, amplification of 16S ribosomal RNA genes (rDNA) and subsequent examination of community structure through interrogation of the amplified 16S rDNA pool by high-throughput sequencing, phylogenetic microarrays or quantitative PCR.
Results: Here we describe the development of a mathematical model aimed to simulate multitemplate amplification of 16S ribosomal DNA sample and subsequent detection of these amplified 16S rDNA species by phylogenetic microarray. Using parameters estimated from the experimental results obtained in the analysis of intestinal microbial communities with Microbiota Array, we show that both species detection and the accuracy of species abundance estimates depended heavily on the number of PCR cycles used to amplify 16S rDNA. Both parameters initially improved with each additional PCR cycle and reached optimum between 15 and 20 cycles of amplification. The use of more than 20 cycles of PCR amplification and/or more than 50 ng of starting genomic DNA template was, however, detrimental to both the fraction of detected community members and the accuracy of abundance estimates. Overall, the outcomes of the model simulations matched well available experimental data. Our simulations also showed that species detection and the accuracy of abundance measurements correlated positively with the higher sample-wide PCR amplification rate, lower template-to-template PCR bias and lower number of species in the interrogated community. The developed model can be easily modified to simulate other multitemplate DNA mixtures as well as other microarray designs and PCR amplification protocols.
Contact: oleg.paliy@wright.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
nucleR: a package for non-parametric nucleosome positioning
Authors: Flores Oscar , Orozco Modesto 
Published: June 2011

Abstract
Summary: nucleR is an R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.
Availability: Additional information and methodological details can be found at http://mmb.pcb.ub.es/nucleR
Contact: modesto.orozco@irbbarcelona.org
Supplementary Information: Supplementary data are available at Bioinformatics online.