bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous generation of inertial waves from boundary turbulence in a librating sphere
Authors: Sauret Alban , Cébron David , Le Bars Michael 
Published: July 2013

AbstractIn this work, we report the excitation of inertial waves in a librating sphere even for libration frequencies where these waves are not directly forced. This spontaneous generation comes from the localized turbulence induced by the centrifugal instabilities in the Ekman boundary layer near the equator and does not depend on the libration frequency. We characterize the key features of these inertial waves in analogy with previous studies of the generation of internal waves in stratified flows from localized turbulent patterns. In particular, the temporal spectrum exhibits preferred values of excited frequency. This first-order phenomenon is generic to any rotating flow in the presence of localized turbulence and is fully relevant for planetary applications.
Transparent organic thin film transistors with WO3/Ag/WO3 source-drain electrodes fabricated by thermal evaporation
Authors: Zhang Nan , Hu Yongsheng , Liu Xingyuan 
Published: July 2013

High-performance transparent organic thin film transistors using a WO3/Ag/WO3 (WAW) multilayer as the source and drain electrodes have been developed without breaking the vacuum. The WAW electrodes were deposited by thermal evaporation at room temperature, leading to little damage to organic film. The optimized WAW electrode shows high transmittance (86.57%), low sheet resistance (11 Ω/sq), and a high work function (5.0 eV). Consequently, we obtained high performance devices with mobility of 8.44 × 10−2 cm2/V · s, an on/off ratio of approximately 1.2 × 106, and an average visible range transmittance of 81.5%.
Self-Reporting Bias in Chinook Salmon Sport Fisheries in Idaho: Implications for Roving Creel Surveys
Authors: McCormick Joshua L. , Quist Michael C. , Schill Daniel J. 
Published: July 2013

Abstract
Self-reporting bias in sport fisheries of Chinook Salmon Oncorhynchus tshawytscha in Idaho was quantified by comparing observed and angler-reported data. A total of 164 observed anglers fished for 541 h and caught 74 Chinook Salmon. Fifty-eight fish were harvested and 16 were released. Anglers reported fishing for 604 h, an overestimate of 63 h. Anglers reported catching 66 fish; four less harvested and four less released fish were reported than observed. A Monte Carlo simulation revealed that when angler-reported data were used, total catch was underestimated by 14–15 fish (19–20%) using the ratio-of-means estimator to calculate mean catch rate. Negative bias was reduced to six fish (8%) when the means-of-ratio estimator was used. Multiple linear regression models to predict reporting bias in time fished had poor predictive value. However, actual time fished and a categorical covariate indicating whether the angler fished continuously during their fishing trip were two variables that were present in all of the top a priori models evaluated. Underreporting of catch and overreporting of time fished by anglers present challenges when managing Chinook Salmon sport fisheries. However, confidence intervals were near target levels and using more liberal definitions of angling when estimating effort in creel surveys may decrease sensitivity to bias in angler-reported data.
Received January 3, 2013; accepted May 20, 2013
Disinvestment, Farm Size, and Gradual Farm Exit: The Impact of Subsidy Decoupling in a European Context
Authors: Kazukauskas Andrius , Newman Carol , Clancy Daragh , Sauer Johannes 
Published: July 2013

AbstractThe recent reform of the Common Agricultural Policy, which decouples farm subsidies from production, is expected to impact on farmers' production decisions. We perform a cross‐country farm‐level empirical analysis of farmers' production responses to these reforms using a panel dataset for the EU15 countries for the period 2001–2007. We apply quasi‐experimental empirical methods and find that the probability of a farm disinvesting decreased due to the policy change for most farms. However, the policy change facilitated exit for farms engaged in livestock production and those that were already in the process of leaving the sector.
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming
Authors: Guziolowski Carito , Videla Santiago , Eduati Federica , Thiele Sven , Cokelaer Thomas , Siegel Anne , Saez-Rodriguez Julio 
Published: July 2013

Abstract
Motivation: Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data. The training can be performed using stochastic optimization procedures, but these are unable to guarantee a global optima or to report the complete family of feasible models. This, however, is essential to provide precise insight in the mechanisms underlaying signal transduction and generate reliable predictions.
Results: We propose the use of Answer Set Programming to explore exhaustively the space of feasible logic models. Toward this end, we have developed caspo, an open-source Python package that provides a powerful platform to learn and characterize logic models by leveraging the rich modeling language and solving technologies of Answer Set Programming. We illustrate the usefulness of caspo by revisiting a model of pro-growth and inflammatory pathways in liver cells. We show that, if experimental error is taken into account, there are thousands (11 700) of models compatible with the data. Despite the large number, we can extract structural features from the models, such as links that are always (or never) present or modules that appear in a mutual exclusive fashion. To further characterize this family of models, we investigate the input–output behavior of the models. We find 91 behaviors across the 11 700 models and we suggest new experiments to discriminate among them. Our results underscore the importance of characterizing in a global and exhaustive manner the family of feasible models, with important implications for experimental design.
Availability: caspo is freely available for download (license GPLv3) and as a web service at http://caspo.genouest.org/.
Supplementary information: Supplementary materials are available at Bioinformatics online.
Contact: anne.siegel@irisa.fr or saezrodriguez@ebi.ac.uk
Diagnostic and prognostic value of osteopontin in patients with acute congestive heart failure
Authors: Behnes Michael , Brueckmann Martina , Lang Siegfried , Espeter Florian , Weiss Christel , Neumaier Michael , Ahmad‐Nejad Parviz , Borggrefe Martin , Hoffmann Ursula 
Published: July 2013

AimsTo evaluate the diagnostic and prognostic value of osteopontin in patients with acute dyspnoea and/or peripheral oedema suspected of having acute congestive heart failure (aCHF).Methods and resultsA total of 401 patients presenting with acute dyspnoea and/or peripheral oedema to the emergency department were prospectively enrolled and followed up for up to 5 years. Blood samples for biomarker measurements were collected on admission to the emergency department. Osteopontin combined with NT‐proBNP vs. NT‐proBNP alone for diagnosis of aCHF was tested. Additionally, osteopontin vs. NT‐proBNP for prognostic outcomes (i.e. all‐cause mortality, aCHF‐related rehospitalization, and both in combination) was tested. The diagnostic and prognostic capacity of osteopontin was tested by C‐statistics, reclassification indices, and multivariable Cox prediction models. Osteopontin plus NT‐proBNP improved the diagnostic capacity for aCHF diagnosis [accuracy 76%, 95% confidence interval (CI) 72–80%; specificity 74%, 95% CI 69–79%, net reclassification improvement (NRI) +0.10] compared with NT‐proBNP alone in the emergency department (P = 0.0001). Osteopontin independently predicted all‐cause mortality and aCHF‐related rehospitalization after 1 and 5 years. Compared with NT‐proBNP, osteopontin was of superior prognostic value, specifically in aCHF patients and for the prognostic outcome of aCHF‐related rehospitalization.ConclusionOsteopontin improves aCHF diagnosis when combined with NT‐proBNP. Osteopontin identifies aCHF patients with high 1‐ and 5‐year mortality and rehospitalization risk, and adds prognostic value to NT‐proBNP.Trial registrationNCT00143793
Condition for the formation of micron-sized dust grains in dense molecular cloud cores
Authors: Hirashita Hiroyuki , Li Zhi-Yun 
Published: July 2013

Abstract
We investigate the condition for the formation of micron-sized grains in dense cores of molecular clouds. This is motivated by the detection of mid-infrared emission from deep inside a number of dense cores, the so-called ‘coreshine,’ which is thought to come from scattering by micron (μm)-sized grains. Based on numerical calculations of coagulation starting from the typical grain-size distribution in the diffuse interstellar medium, we obtain a conservative lower limit to the time t to form μm-sized grains: t/tff &gt; 3(5/S)(nH/105 cm−3)−1/4 (where tff is the free-fall time at hydrogen number density nH in the core and S the enhancement factor of the grain–grain collision cross-section to account for non-compact aggregates). At the typical core density nH = 105 cm−3, it takes at least a few free-fall times to form the μm-sized grains responsible for coreshine. The implication is that those dense cores observed in coreshine are relatively long-lived entities in molecular clouds, rather than dynamically transient objects that last for one free-fall time or less.
REVIEW: Refuges for fauna in fire‐prone landscapes: their ecological function and importance
Authors: Robinson Natasha M. , Leonard Steve W.J. , Ritchie Euan G. , Bassett Michelle , Chia Evelyn K. , Buckingham Sebastian , Gibb Heloise , Bennett Andrew F. , Clarke Michael F. 
Published: July 2013

SummaryRapid environmental change is placing increasing pressure on the survival of many species globally. Ecological refuges can mitigate the impacts of change by facilitating the survival or persistence of organisms in the face of disturbance events that would otherwise lead to their mortality, displacement or extinction. Refuges may have a critical influence on the successional trajectory and resilience of ecosystems, yet their function remains poorly understood.We review and describe the role of refuges in faunal conservation in the context of fire, a globally important disturbance process.Refuges have three main functions in relation to fire: they enhance immediate survival during a fire event, facilitate the persistence of individuals and populations after fire and assist in the re‐establishment of populations in the longer term. Refuges may be of natural or anthropogenic origin, and in each case, their creation can arise from deterministic or stochastic processes. The specific attributes of refuges that determine their value are poorly known, but include within‐patch attributes relating to vegetation composition and structure; patch‐scale attributes associated with their size and shape; and the landscape context and spatial arrangement of the refuge in relation to fire patterns and land uses.Synthesis and applications. Refuges are potentially of great importance in buffering the effects of wildfire on fauna. There is an urgent need for empirical data from a range of ecosystems to better understand what constitutes a refuge for different taxa, the spatial and temporal dynamics of species' use of refuges and the attributes that most influence their value to fauna. Complementary research is also required to evaluate threats to naturally occurring refuges and the potential for management actions to protect, create and enhance refuges. Knowledge of the spatial arrangement of refuges that enhance the persistence of fire‐sensitive species will aid in making decisions concerning land and fire management in conservation reserves and large natural areas. Global change in the magnitude and extent of fire regimes means that refuges are likely to be increasingly important for the conservation of biodiversity in fire‐prone environments.
Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing
Authors: Wang X. Q. , Zhao L. , Eaton D. A. R. , Li D. Z. , Guo Z. H. 
Published: July 2013

AbstractPhylogenetic relationships among temperate species of bamboo are difficult to resolve, owing to both the challenge of detecting sufficiently variable markers and their polyploid history. Here, we use restriction site–associated DNA sequencing to identify candidate loci with fixed allelic differences segregating between and within two temperate species of bamboos: Arundinaria faberi and Yushania brevipaniculata. Approximately 27 million paired‐end sequencing reads were generated across four samples. From pooled data, we assembled 67 685 and 70 668 de novo contigs from partial overlap among paired‐end reads, with an average length of 240 and 241 bp for the two species, respectively, which were used to investigate functional classification of RAD tags in a blastx search. Analysed separately by population, we recovered 29 443 putatively orthologous RAD tags shared across the four sampled populations, containing 28 023 sequence variants, of which c. 13 000 are segregating between species, and c. 3000 segregating between populations within each species. Analyses based on these RAD tags yielded robust phylogenetic inferences, even with data set constructed from surprisingly few loci. This study illustrates the potential for reduced‐representation genome data to resolve difficult phylogenetic relationships in temperate bamboos.
Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all‐taxa biotic surveys
Authors: Geller J. , Meyer C. , Parker M. , Hawk H. 
Published: July 2013

AbstractDNA barcoding is a powerful tool for species detection, identification and discovery. Metazoan DNA barcoding is primarily based upon a specific region of the cytochrome c oxidase subunit I gene that is PCR amplified by primers HCO2198 and LCO1490 (‘Folmer primers’) designed by Folmer et al. (Molecular Marine Biology and Biotechnology, 3, 1994, 294). Analysis of sequences published since 1994 has revealed mismatches in the Folmer primers to many metazoans. These sequences also show that an extremely high level of degeneracy would be necessary in updated Folmer primers to maintain broad taxonomic utility. In primers jgHCO2198 and jgLCO1490, we replaced most fully degenerated sites with inosine nucleotides that complement all four natural nucleotides and modified other sites to better match major marine invertebrate groups. The modified primers were used to amplify and sequence cytochrome c oxidase subunit I from 9105 specimens from Moorea, French Polynesia and San Francisco Bay, California, USA representing 23 phyla, 42 classes and 121 orders. The new primers, jgHCO2198 and jgLCO1490, are well suited for routine DNA barcoding, all‐taxon surveys and metazoan metagenomics.
Avian functional group responses to rainfall across four vegetation types in theSimpsonDesert, centralAustralia
Authors: Tischler Max , Dickman Christopher R. , Wardle Glenda M. 
Published: July 2013

AbstractTemporal and spatial variability in rainfall and subsequent resource flows often drive large changes in bird demography and the structure of avian assemblages in arid regions. Here, we describe broad avian functional group responses to rainfall across four vegetation classes in theSimpsonDesert, centralAustralia, over a period when both dry and wet conditions prevailed. Birds were surveyed in eucalypt woodlands, gidyea woodlands, mixedAcacia(mulga) shrublands and spinifex‐dominated hummock grasslands in this region between 2006 and 2008 using a spatially nested hierarchical sampling design with fixed radius point counts as replicates. Predictably, the composition of bird communities varied across vegetation classes as well as over time. Generalist feeders and insectivorous birds dominated assemblages during dry periods, whereas granivorous species were most abundant and widespread following heavy rains. Carnivores and specialist nectarivores responded variably throughout the sampling period regardless of habitat. The dynamics of granivores were especially interesting; large numbers of nomadic species moved into the study area in response to rainfall, highlighting a key role for this group in shaping community structure. This study represents the first attempt to investigate avian functional group dynamics across differing vegetation types in a variable but low productivity landscape. The findings confirm that community composition is spatially and temporally dynamic, and prompt further investigation into the roles that habitat and resource limitation play in defining bird communities in aridAustralia.
Soft scale insects (Hemiptera: Coccoidea: Coccidae) on grapevines in Australia
Authors: Rakimov Adrian , Ben‐Dov Yair , White Vanessa , Hoffmann Ary A. 
Published: July 2013

AbstractThere is little information on the distribution and pest status of soft scale insects (Hemiptera: Coccoidea: Coccidae) in vineyards in Australia despite the potential of this group to spread ampeloviruses and directly damage vines. A survey of coccid species in the main vineyard regions was therefore undertaken. Parthenolecanium persicae (62% of sites), Part. pruinosum (46%) and Coccus hesperidum (8%) were the most common species collected, while Co. longulus, Parasaissetia nigra and Saissetia species were also recorded. Rare male Part. persicae were collected from one location. A 385 base pair fragment of the cytochrome oxidase subunit I (CO1) region was sequenced to provide a species‐specific marker for identification applicable across live stages. CO1 detected reasonable levels of sequence variation within some species and high levels of variation between species. The phylogenetic tree based on CO1 was able to discriminate between all species and showed Part. pruinosum from Gumeracha (SA), Part. nigra from West Swan (WA) and Co. longulus to be quite unique. These findings indicate that Part. pruinosum is much more common than previously appreciated and may include multiple species but also highlights the dominant pest status of Part. persicae in Australian vineyards and provides support for the application of CO1 to future molecular studies of Coccidae within Australia.
Technology and the future bioeconomy
Authors: Zilberman David , Kim Eunice , Kirschner Sam , Kaplan Scott , Reeves Jeanne 
Published: July 2013

AbstractNew discoveries in life sciences and the challenge of climate change are leading to the emergence of the bioeconomy where basic methods of advanced biology are applied to produce a wide array of products while also improving environmental quality. The emergence of the bioeconomy is a continuing evolutionary process of transition from systems of mining nonrenewable resources to farming renewable ones. This transition benefits from the modern tools of molecular biology that have expanded the human capacity to breed new organisms and utilize them to increase productivity in agriculture and fisheries as well as produce a wide array of products that were extracted in the past. This transition is leading to the integration of the agricultural sector with the energy and mineral sectors. The introduction of biotechnology has already improved the productivity of medicine as well as agriculture but, in the case of agriculture, has encountered resistance and regulatory constraints. The evolution of the bioeconomy requires continuous public investment in research and innovation as well as the establishment of a regulatory framework and financial incentives and institutions that would lead to continuous private sector investment in the development and commercialization of new products. One of the biggest challenges is the development of a regulatory framework that would control possible human and environmental externalities from new biotechnology products and, at the same time, not stifle innovation.
Serum Autoantibodies in Mice Immunized with Syngeneic Testicular Germ Cells Alone
Authors: Hirai Shuichi , Naito Munekazu , Terayama Hayato , Hatayama Naoyuki , Qu Ning , Musha Muhetaerjiang , Itoh Masahiro 
Published: July 2013

ProblemThe aim of this study was to identify the characteristics of serum autoantibodies in experimental autoimmune orchitis (EAO) induced by immunization with syngeneic testicular germ cells (TGC) alone in mice.Method of studyThe serum autoantibodies were analyzed by enzyme‐linked immunosorbent assay (ELISA), Western blotting, and immunohistochemical staining.ResultsSerum autoantibody titers against TGC and epididymal spermatozoa (ES) gradually increased with the development of EAO. At the initial stage of EAO, serum autoantibodies reacted with only a few antigens of TGC and ES, while in the later stage, the reactions with various antigens of TGC and ES occurred. However, the autoantibodies were specific to the testis and epididymis but not to other organs.ConclusionThese results indicate that titers and kinds of autoantibodies in TGC‐immunized mice increase with EAO development and they are specific to TGC and ES.
Reason for the increasing use of vacuum extraction in Sweden: a population‐based study
Authors: Elvander Charlotte , Ekéus Cecilia , Gemzell‐Danielsson Kristina , Cnattingius Sven 
Published: July 2013

AbstractObjectiveTo explain the increasing rates of vacuum extraction in Sweden.DesignPopulation‐based register study.SettingNationwide study in Sweden.PopulationA total of 589 108 primiparous women with singleton, term live births in 1992–2010.MethodsOdds ratios with 95% confidence intervals were estimated for potential risk factors for vacuum extraction and emergency cesarean. To explain the increase in vacuum extraction over time, we successively adjusted for maternal and infant characteristics in four different models.Main outcome measuresVacuum extraction.ResultsRates of vacuum extraction increased from 11.5% in 1992 to 14.8% in 2010. The risk of vacuum extraction increased with maternal age and gestational length, but decreased with increasing maternal height. The increased use of vacuum extraction over time was partly explained by increasing maternal age and increased use of epidural anesthesia. Among women with and without epidural analgesia, the increase in vacuum extraction over time was confined to vacuum extraction due to signs of fetal distress.ConclusionsDepending on risk factors, the odds of being delivered by vacuum extraction can vary immensely from one woman to another. Increasing maternal age explains a substantial fraction of the increase in vacuum extraction use since 1992. Whether the increase in vacuum extractions due to fetal distress reflects a true increase in fetal distress during labor remains to be explained.