bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of Quasars and Stars by Supervised and Unsupervised Methods
Authors: Zhang Yanxia , Zhao Yongheng , Zheng Hongwen , Wu Xue-bing 
Published: January 2013

AbstractTargeting quasar candidates is always an important task for large spectroscopic sky survey projects. Astronomers never give up thinking out effective approaches to separate quasars from stars. The previous methods on this issue almost belong to supervised methods or color-color cut. In this work, we compare the performance of a supervised method – Support Vector Machine (SVM)– with that of an unsupervised method one-class SVM. The performance of SVM is better than that of one-class SVM. But one-class SVM is an unsupervised algorithm which is helpful to recognize rare or mysterious objects. Combining supervised methods with unsupervised methods is effective to improve the performance of a single classifier.
Application of Stock Density Indices as a Tool for Broad-Scale Population Assessment for Four Cyprinid Species in Central Italy
Authors: Pedicillo Giovanni , Lorenzoni Massimo , Carosi Antonella , Ghetti Lucia 
Published: January 2013

Abstract
Stock-density indices are standardized methods for analyzing length-frequency data that quantify the length structure of a fish population into length categories that are of interest to recreational anglers. We adapted North American relative stock density (RSD) and proportional stock density (PSD) indices to four Italian endemic or native cyprinid species by means of two methods. In accordance with the traditional approach, the benchmarks of length categories were established according to Gabelhouse's percentage classification and calculated on the basis of the largest individual in the data set for each species. In the second method, asymptotic length and size at maturity were used to define the length categories for index calculation. Both methods were tested on length-frequency data from fish collected from sampling sites in the Tiber River basin. The results showed that the traditional approach displayed better applicability, required less sampling effort, and provided a better insight into the length structure of the fish populations studied.
Received January 17, 2012; accepted November 4, 2012
Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries
Authors: DeJesus Michael A. , Zhang Yanjia J. , Sassetti Christopher M. , Rubin Eric J. , Sacchettini James C. , Ioerger Thomas R. 
Published: January 2013

Abstract
Motivation: Next-generation sequencing affords an efficient analysis of transposon insertion libraries, which can be used to identify essential genes in bacteria. To analyse this high-resolution data, we present a formal Bayesian framework for estimating the posterior probability of essentiality for each gene, using the extreme-value distribution to characterize the statistical significance of the longest region lacking insertions within a gene. We describe a sampling procedure based on the Metropolis–Hastings algorithm to calculate posterior probabilities of essentiality while simultaneously integrating over unknown internal parameters.
Results: Using a sequence dataset from a transposon library for Mycobacterium tuberculosis, we show that this Bayesian approach predicts essential genes that correspond well with genes shown to be essential in previous studies. Furthermore, we show that by using the extreme-value distribution to characterize genomic regions lacking transposon insertions, this method is capable of identifying essential domains within genes. This approach can be used for analysing transposon libraries in other organisms and augmenting essentiality predictions with statistical confidence scores.
Availability: A python script implementing the method described is available for download from http://saclab.tamu.edu/essentiality/.
Contact: michael.dejesus@tamu.edu or ioerger@cs.tamu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Large size scatter of passively evolving lensed Galaxies at z ∼ 2 in CLASH
Authors: Fan Lulu , Chen Yang , Er Xinzhong , Li Jinrong , Lin Lin , Kong Xu 
Published: January 2013

Abstract
In a systematic search over 11 cluster fields from Cluster Lensing And Supernova survey with Hubble (CLASH), we identify 10 passively evolving massive galaxies at redshift z ∼ 2. We derive the stellar properties of these galaxies using Hubble Space Telescope (HST) Wide Field Camera 3 (WFC3)/Advanced Camera for Surveys (ACS) multiband data, together with Spitzer IRAC observations. We also deduce the optical rest-frame effective radius of these high-redshift objects. The derived stellar masses and measured effective radii have been corrected by the lensing magnification factors, which are estimated by simply adopting the spherical NFW model for the foreground cluster lens. The observed near-IR images, obtained by HST WFC3 camera with high spatial resolution and lensed by the foreground clusters, enable us to study the structures of such systems. Nine out of ten galaxies have on average three times smaller effective radius than local early-type Galaxies (ETGs) of similar stellar masses, in agreement with previous works at redshift 1.5 &lt; z &lt; 2.5. Combined with literature data for z ∼ 2, we find that the mass-normalized effective radius scales with redshift as re/M0.56⋆∝(1 + z)− 1.13. We confirm that their size distribution shows a large scatter: from normal size to ∼5 times smaller compared to local ETGs with similar stellar masses. The 1σ scatter σlog re of the size distribution is 0.22 and 0.34 at z ∼ 1.6 and z ∼ 2.1, respectively. The observed large size scatter has to be carefully taken into account in galaxy evolution model predictions.
Activation of Triggering Receptor Expressed on Myeloid Cells-1 Protects Monocyte from Apoptosis through Regulation of Myeloid Cell Leukemia-1
Authors: Cai MeiTing , Chen QiXing , Chen Chi , Liu XiWang , Hou JinChao , Zeng CongLi , Shu Qiang , Fang XiangMing 
Published: January 2013

Abstract

Background:
Triggering receptor expressed on myeloid cells-1 (TREM-1) can amplify the proinflammatory response and may contribute to the pathogenesis of inflammatory disease such as sepsis. However, the role of TREM-1 in monocyte fate and the detailed molecular mechanisms evoked by TREM-1 are unknown.

Methods:
Adenoviruses overexpressing TREM-1 were constructed and transfected into a monocytic cell line. After activation of TREM-1 by agonist antibody with or without lipopolysaccharide, apoptosis was induced and assayed using flow cytometry. The signaling pathways downstream of TREM-1 were illustrated by inhibitory experiments. Proapoptotic/antiapoptotic protein levels were measured using immunoblot. In addition, the relationship between the expression levels of TREM-1 in monocytes and the magnitude of monocyte apoptosis were analyzed in septic patients.

Results:
Activation of TREM-1 protected monocytes from staurosporine-induced apoptosis. This characteristic was also obtained under lipopolysaccharide stimulation. The protection of TREM-1 against monocyte apoptosis was abrogated after inhibition of extracellular signal–regulated kinase or v-akt murine thymoma viral oncogene homologue signaling. Cross-linking of TREM-1 remarkably up-regulated myeloid cell leukemia-1 protein level, and inhibition of extracellular signal–regulated kinase or v-akt murine thymoma viral oncogene homologue resulted in the reduction of myeloid cell leukemia-1 expression. Inhibition of myeloid cell leukemia-1 abolished the antiapoptotic effect of TREM-1. Furthermore, in septic patients, TREM-1 levels were inversely correlated to the magnitude of apoptosis in monocyte.

Conclusions:
TREM-1 played an important role in apoptosis in monocytes. Activation of TREM-1 protected monocytic cells from apoptosis through activation of both extracellular signal–regulated kinase and v-akt murine thymoma viral oncogene homologue pathways and increased expression of myeloid cell leukemia-1 protein. These findings provide a novel additional mechanism for TREM-1–mediated hyperinflammatory response in monocytes.
Anesthetics Interfere with Axon Guidance in Developing Mouse Neocortical Neurons In Vitro via a γ-Aminobutyric Acid Type A Receptor Mechanism
Authors: Mintz C. David , Barrett Kendall M. S. , Smith Sarah C. , Benson Deanna L. , Harrison Neil L. 
Published: January 2013

Abstract

Background:
The finding that exposure to general anesthetics (GAs) in childhood may increase rates of learning disabilities has raised a concern that anesthetics may interfere with brain development. The generation of neuronal circuits, a complex process in which axons follow guidance cues to dendritic targets, is an unexplored potential target for this type of toxicity.

Methods:
GA exposures were conducted in developing neocortical neurons in culture and in early postnatal neocortical slices overlaid with fluorescently labeled neurons. Axon targeting, growth cone collapse, and axon branching were measured using quantitative fluorescence microscopy.

Results:
Isoflurane exposure causes errors in Semaphorin-3A–dependent axon targeting (n = 77 axons) and a disruption of the response of axonal growth cones to Semaphorin-3A (n = 2,358 growth cones). This effect occurs at clinically relevant anesthetic doses of numerous GAs with allosteric activity at γ-aminobutyric acid type A receptors, and it was reproduced with a selective agonist. Isoflurane also inhibits growth cone collapse induced by Netrin-1, but does not interfere branch induction by Netrin-1. Insensitivity to guidance cues caused by isoflurane is seen acutely in growth cones in dissociated culture, and errors in axon targeting in brain slice culture occur at the earliest point at which correct targeting is observed in controls.

Conclusions:
These results demonstrate a generalized inhibitory effect of GAs on repulsive growth cone guidance in the developing neocortex that may occur via a γ-aminobutyric acid type A receptor mechanism. The finding that GAs interfere with axon guidance, and thus potentially with circuit formation, represents a novel form of anesthesia neurotoxicity in brain development.
HISTONE DEACETYLASE19 Interacts with HSL1 and Participates in the Repression of Seed Maturation Genes inArabidopsisSeedlings
Authors: Zhou Yi , Tan Bin , Luo Ming , Li Yin , Liu Chen , Chen Chen , Yu Chun-Wei , Yang Songguang , Dong Shuai , Ruan Jiuxiao , Yuan Liangbin , Zhang Zhou , Zhao Linmao , Li Chenlong , Chen Huhui , Cui Yuhai , Wu Keqiang , Huang Shangzhi 
Published: January 2013

AbstractThe seed maturation genes are specifically and highly expressed during late embryogenesis. In this work, yeast two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays revealed that HISTONE DEACETYLASE19 (HDA19) interacted with the HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2-LIKE1 (HSL1), and the zinc-finger CW [conserved Cys (C) and Trp (W) residues] domain of HSL1 was responsible for the interaction. Furthermore, we found that mutations in HDA19 resulted in the ectopic expression of seed maturation genes in seedlings, which was associated with increased levels of gene activation marks, such as Histone H3 acetylation (H3ac), Histone H4 acetylation (H4ac), and Histone H3 Lys 4 tri-methylation (H3K4me3), but decreased levels of the gene repression mark Histone H3 Lys 27 tri-methylation (H3K27me3) in the promoter and/or coding regions. In addition, elevated transcription of certain seed maturation genes was also found in the hsl1 mutant seedlings, which was also accompanied by the enrichment of gene activation marks but decreased levels of the gene repression mark. Chromatin immunoprecipitation assays showed that HDA19 could directly bind to the chromatin of the seed maturation genes. These results suggest that HDA19 and HSL1 may act together to repress seed maturation gene expression during germination. Further genetic analyses revealed that the homozygous hsl1 hda19 double mutants are embryonic lethal, suggesting that HDA19 and HSL1 may play a vital role during embryogenesis.
PECTIN METHYLESTERASE INHIBITOR6 Promotes Arabidopsis Mucilage Release by Limiting Methylesterification of Homogalacturonan in Seed Coat Epidermal Cells
Authors: Saez-Aguayo Susana , Ralet Marie-Christine , Berger Adeline , Botran Lucy , Ropartz David , Marion-Poll Annie , North Helen M. 
Published: January 2013

Abstract
Imbibed seeds of the Arabidopsis thaliana accession Djarly are affected in mucilage release from seed coat epidermal cells. The impaired locus was identified as a pectin methylesterase inhibitor gene, PECTIN METHYLESTERASE INHIBITOR6 (PMEI6), specifically expressed in seed coat epidermal cells at the time when mucilage polysaccharides are accumulated. This spatio-temporal regulation appears to be modulated by GLABRA2 and LEUNIG HOMOLOG/MUCILAGE MODIFIED1, as expression of PMEI6 is reduced in mutants of these transcription regulators. In pmei6, mucilage release was delayed and outer cell walls of epidermal cells did not fragment. Pectin methylesterases (PMEs) demethylate homogalacturonan (HG), and the majority of HG found in wild-type mucilage was in fact derived from outer cell wall fragments. This correlated with the absence of methylesterified HG labeling in pmei6, whereas transgenic plants expressing the PMEI6 coding sequence under the control of the 35S promoter had increased labeling of cell wall fragments. Activity tests on seeds from pmei6 and 35S:PMEI6 transgenic plants showed that PMEI6 inhibits endogenous PME activities, in agreement with reduced overall methylesterification of mucilage fractions and demucilaged seeds. Another regulator of PME activity in seed coat epidermal cells, the subtilisin-like Ser protease SBT1.7, acts on different PMEs, as a pmei6 sbt1.7 mutant showed an additive phenotype.
A direct physiological trade‐off between personal and social immunity
Authors: Cotter Sheena C. , Littlefair Joanne E. , Grantham Peter J. , Kilner Rebecca M. 
Published: January 2013

Summary

Recent work shows that organisms possess two strategies of immune response: personal immunity, which defends an individual, and social immunity, which protects other individuals, such as kin. However, it is unclear how individuals divide their limited resources between protecting themselves and protecting others.

Here, with experiments on female burying beetles, we challenged the personal immune system and measured subsequent investment in social immunity (antibacterial activity of the anal exudates).

Our results show that increased investment in one aspect of personal immunity (wound repair) causes a temporary decrease in one aspect of the social immune response.

Our experiments further show that by balancing investment in personal and social immunity in this way during one breeding attempt, females are able to defend their subsequent lifetime reproductive success.

We discuss the nature of the physiological trade‐off between personal and social immunity in species that differ in the degree of eusociality and coloniality, and suggest that it may also vary within species in relation to age and partner contributions to social immunity.
Effects of tree species richness and composition on moose winter browsing damage and foraging selectivity: an experimental study
Authors: Milligan Harriet T. , Koricheva Julia 
Published: January 2013

SummaryThe optimal foraging theory, the nutrient balance hypothesis, and the plant association theories predict that foraging decisions and resulting tree damage by large mammalian browsers may be influenced by the species richness and species composition of forest stands. This may lead to either associational susceptibility (increased damage on a focal plant in a mixed stand) or associational resistance (reduced damage in a mixed stand).Better understanding of the mechanisms and the relative importance of tree species richness and composition effects on foraging by mammalian browsers is needed to support sustainable management of forests and mammal populations. However, existing knowledge of forest diversity effects on foraging by large mammalian browsers comes largely from observational studies while experimental evidence is limited.We analysed winter browsing by moose (Alces alcesL.) in a long‐term, large‐scale experiment in Finland, which represents a tree species richness gradient from monocultures to 2‐, 3‐ and 5‐species mixtures composed of Scots pine (Pinus sylvestrisL.), Norway spruce (Picea abiesL.), Siberian larch (Larix sibiricaLedeb.), silver birch (Betula pendulaRoth.) and black alder (Alnus glutinosaL.).The intensity of browsing per plot increased with tree species richness while browsing selectivity decreased with tree species being targeted more equally in species‐rich mixtures. Tree species composition of a plot was also an important determinant of intensity of browsing. The greatest browsing occurred in plots containing preferred species (pine and birch) while intermediate preference species (larch and alder) experienced associational susceptibility when growing with pine and birch compared with their monocultures or mixtures without pine and birch. In contrast, we found no evidence of associational resistance; the presence of a least preferred species (spruce) in a mixture had no significant effect on moose browsing on other tree species.We demonstrate that the presence of alternative forage species allows moose to spend longer opportunistically foraging in a plot, resulting in increased level of damage in species‐rich stands and stands containing preferred tree species. Our results highlight the limitations of the optimal foraging theory in predicting browsing patterns and demonstrate the importance of associational effects within mixed stands.
Fearing the feline: domestic cats reduce avian fecundity through trait‐mediated indirect effects that increase nest predation by other species
Authors: Bonnington Colin , Gaston Kevin J. , Evans Karl L. 
Published: January 2013

Summary

Urban areas contain high densities of non‐native species, which in the UK include the domestic cat Felis catus (Linnaeus 1758) and the grey squirrel Sciurus carolinensis (Gmelin 1788). The direct predation effects of domestic cats on prey populations attract intense debate, and such influences of the nest‐predatory grey squirrel are receiving increasing attention. In contrast, theory predicts that sublethal and indirect effects are more important, but empirical evidence is currently lacking.

We conducted controlled model presentation experiments at active urban blackbird Turdus merula (Linnaeus 1758) nests to provide the first empirical evidence that quantifies the potential sublethal and indirect effects of predators (domestic cat and grey squirrel) on avian reproductive success.

Domestic cat models reduced subsequent parental provisioning rates, a strong indicator of sublethal effects, by one‐third relative to a nonpredatory rabbit Oryctolagus cuniculus (Linnaeus 1758) control. There was no compensatory increase in food load size. Previous experiments demonstrate that this magnitude of reduced food delivery will reduce nestling growth rates by c. 40%. The grey squirrel model induced similar but weaker effects.

Following the brief presence of the domestic cat model, subsequent daily nest predation rates, chiefly by corvids, increased by an order of magnitude relative to the squirrel and rabbit models. The intensity of parental nest defence elicited in response to model presentations predicts the probability of such third‐party predator predation events, and the domestic cat model generated significant increases in nest defence behaviour.

Synthesis and applications. The brief presence of a domestic cat at avian nest sites reduces subsequent provisioning rates and induces lethal trait‐mediated indirect effects. We provide the first robust evidence for these latter effects in any avian predator–prey system, although they are likely to be common in many avian assemblages with high predator densities. It is imperative that future assessments of the impact of predatory species on avian prey species take lethal trait‐mediated indirect effects into account, as so doing will prevent biased estimates of predator effects and facilitate the design of more effective control strategies. Full mitigation of the sublethal and indirect effects of domestic cats would problematically require permanent indoor housing.
Deliberative Pragmatic Equilibrium Review: A Framework for Comparing Institutional Devices and Their Enactment of Deliberative Democracy in the UK
Authors: Elstub Stephen 
Published: January 2013

Research Highlights and Abstract This article: Presents a framework for comparing institutions and their ability to enact various norms of deliberative democracy across various stages of the policy process and different levels of governance. Specifically contextualises this framework for application in the UK. A range of institutional mechanisms have been advocated to ensure the practical application of deliberative democracy, and these are now being employed in practice throughout the UK. However, different institutional mechanisms will be suited to the enactment of variant democratic principles and will be able to adapt to some features of complexity and not others. This means certain institutional devices will be able to operate effectively at different levels of governance, but not at others, and contribute to some, but not all, stages of a decision-making sequence, within different political systems. A comprehensive and systematic comparison of the relationship these institutions have to deliberative democracy is therefore required so that these institutions can be effectively sequenced to ensure all the key elements of deliberative democracy are enacted in the UK political system, at each level of governance and stage of decision-making. This article therefore develops the ‘Deliberative Pragmatic Equilibrium Review’ (DePER) framework to enable such a comparison of institutional mechanisms, with respect to how they enact key principles of deliberative democracy, by combining normative and empirical analysis through the employment of Fung's ‘pragmatic equilibrium’ approach. The framework is applicable to all political systems, but is here tailored specifically for institutional comparison in the UK, although it is not applied to concrete cases in this article.