bluuebunny/crossref_metadata_2025 huggingface dataset:
The evolution of morphogenetic fitness landscapes: conceptualising the interplay between the developmental and ecological drivers of morphological innovation
Authors: Marshall Charles R.
Published: February 2014

Here I show how fitness landscapes can be used to understand the relative importance of developmental and ecological change in initiating morphological innovation. Key is the use of morphogenetic ‘rules’ as the axes of the landscape, which enables explicit incorporation of the contribution that specific morphologies make to fitness. Four modes of fitness landscape evolution are identified: (1) change in the density of peaks on the landscape, driven by an increase in the number of selective pressures encountered; (2) change in the dimensionality of the landscape through the addition of morphogenetic rules; (3) change in the size of one or more dimensions of the landscape through elaboration of already existing morphogenetic rules; and, (4) shifting the position of peaks in the landscape. Morphological innovation is initiated by ecological change in Mode (1), for example the Cambrian explosion of animals, and Mode (4), for example, when taxa such as sticklebacks make a shift in environment, or during coevolutionary escalation. Morphological change is initiated by developmental innovation for Mode (2), typified by some macroevolutionary innovations, such as the emergence of jaws, and in Mode (3), for example, in the differentiation of flower morphology facilitated by gene duplication of the B-class developmental genes.
An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function
Authors: Yu Peng , Shaw Chad A.
Published: February 2014

Summary: The Dirichlet-multinomial (DMN) distribution is a fundamental model for multicategory count data with overdispersion. This distribution has many uses in bioinformatics including applications to metagenomics data, transctriptomics and alternative splicing. The DMN distribution reduces to the multinomial distribution when the overdispersion parameter ψ is 0. Unfortunately, numerical computation of the DMN log-likelihood function by conventional methods results in instability in the neighborhood of . An alternative formulation circumvents this instability, but it leads to long runtimes that make it impractical for large count data common in bioinformatics. We have developed a new method for computation of the DMN log-likelihood to solve the instability problem without incurring long runtimes. The new approach is composed of a novel formula and an algorithm to extend its applicability. Our numerical experiments show that this new method both improves the accuracy of log-likelihood evaluation and the runtime by several orders of magnitude, especially in high-count data situations that are common in deep sequencing data. Using real metagenomic data, our method achieves manyfold runtime improvement. Our method increases the feasibility of using the DMN distribution to model many high-throughput problems in bioinformatics. We have included in our work an R package giving access to this method and a vingette applying this approach to metagenomic data.

Availability and implementation: An implementation of the algorithm together with a vignette describing its use is available in Supplementary Data.

Contact:  pengyu.bio@gmail.com or cashaw@bcm.edu

Supplementary information: Supplementary Data are available at Bioinformatics online.
Millimeter Light Curve with Abrupt Jump in Cyg X-3 2008 April–May Outburst
Authors: Tsuboi Masato , Miyazaki Atsushi , Nakanishi Kouichiro , Kotani Taro
Published: February 2014

Cyg X-3 is a well-known microquasar with a bipolar relativistic jet. Its famous giant radio outbursts have been repeated once every several years. However, the behavior of the millimeter-wave emission has remained unclear because of limitations of time resolution in previous observations. We report here on millimeter wave observations of Cyg X-3 experiencing giant outbursts with one of the finest time resolutions. We have found a series of short-lived flares with amplitudes of 1–2 Jy in the millimeter light curve of the 2008 April–May outburst. They have flat spectra at around 100 GHz. We have also found abrupt and large amplitude flux density changes with $e$-folding time of 3.6 min or less. The source size of Cyg X-3 is constrained to within 0.4 AU, and the brightness temperature is estimated to be $T_\mathrm{B}$  $\gtrsim$ 1 $\times$ 10$^{11}\ $K.
A Binary Shaped Mask Coronagraph for a Segmented Pupil
Authors: Enya Keigo , Abe Lyu
Published: February 2014

We present the concept of a binary shaped mask coronagraph applicable to a telescope pupil including obscuration, based on previous work on a binary shaped pupil mask by Kasdin et al. (2005, Appl. Opt., 44, 1117) and Vanderbei (1999, Optimization methods and software, 11, 451). Solutions with multi-barcode masks that “skip over” the obscuration are shown for various types of pupils of the telescope, such as SUBARU, JWST, SPICA, and other examples. The number of diffraction tails in the point-spread function of the coronagraphic image is reduced to two, thus offering a large discovery angle. The concept of mask rotation is also presented, which allows a post-processing removal of diffraction tails, and provides a 360$^{\circ}$ continuous discovery angle. It is suggested that the presented concept offers solutions that potentially will allow large telescopes with a segmented pupil in the future to be used as platforms for coronagraphs.
On the Interpretation of the l–v Features in the Milky Way Galaxy
Authors: Junichi Baba , Takayuki R. Saitoh , Keiichi Wada
Published: February 2014

We modeled the gas dynamics of barred galaxies using a three-dimensional, high-resolution, $N$-body $+$ hydrodynamical simulation, and applied it to the Milky Way in an attempt to reproduce both the large-scale structure and the clumpy morphology observed in galactic HI and CO $l$–$v$ diagrams. Owing to including of the multi-phase interstellar medium, self-gravity, star-formation, and supernovae feedback, the clumpy morphology, as well as the large-scale features, in observed $l$–$v$ diagrams were naturally reproduced. We identified in our $l$–$v$ diagrams with a number of not only large-scale peculiar features, such as the `3-kpc arm', `135-km s$^{-1}$ arm', and `Connecting arm', but also clumpy features, such as `Bania clumps', and then linked these features in a face-on view of our model. We give suggestions on the real structure of the Milky Way and on the fate of gas clumps in the central region.
Suzaku Wide-Band X-Ray Observation of the Narrow-Line Seyfert 1 Galaxy Ton S180
Authors: Takahashi Hiroaki , Hayashida Kiyoshi , Anabuki Naohisa
Published: February 2014

We observed the luminous narrow-line Seyfert 1 galaxy Ton S180 with Suzaku, and obtained its wide-band (0.25–55 keV) X-ray spectra for the first time. The spectra were modeled with three components: a power-law component, a reflection from a highly ionized disk component, and an extra soft component either of a disk blackbody or a cutoff power-law. The reflection component accounts for the broad iron K line centered at 6.7 keV, and some fraction of the soft X-ray excess, including the OVIII line emission. The latter two components contribute comparably to the soft X-ray excess. When we adopt the disk blackbody model as the extra soft component, the disk inner radius temperature is 75 eV, much smaller than previously considered. This component is almost consistent with that expected for the slim-disk model assuming edge-on geometry. Hard X-ray emission above 15 keV was marginally detected. To account for the hard X-ray spectrum, we introduced Compton-thick partial absorbers. The absence of the neutral iron K line requires that those absorbers must be preferentially located along the line of sight. Fractional variability has little energy dependence below 10 keV, and is explained with a model in which the covering fraction of the Compton-thick absorber alters the observed flux.
MOIRCS Deep Survey. VII. NIR Morphologies of Star-Forming Galaxies at Redshift z 1
Authors: Konishi Masahiro , Akiyama Masayuki , Kajisawa Masaru , Ichikawa Takashi , Suzuki Ryuji , Tokoku Chihiro , Uchimoto Yuka Katsuno , Yoshikawa Tomohiro , Tanaka Ichi , Onodera Masato , Ouchi Masami , Omata Koji , Nishimura Tetsuo , Yamada Toru
Published: February 2014

We investigated rest-frame near-infrared (NIR) morphologies of a sample of 139 galaxies with $M_{\mathrm{s}}$  $\geq$ 1 $\times$ 10$^{10}\ M_{\odot}$ at z  $=$ 0.8–1.2 in the GOODS-North field using our deep NIR imaging data (MOIRCS Deep Survey, MODS). We focused on Luminous Infrared Galaxies (LIRGs), which dominate a high star formation rate (SFR) density at z  $\sim $ 1, in a sample identified by cross-correlating with the Spitzer/MIPS 24 $\mu $m source catalog. We performed two-dimensional light profile fimonospaceings of z  $\sim $ 1 galaxies in the $K_{\mathrm{s}}$-band (rest-frame $J$-band) with a single-component Sérsic model. We found that at z  $\sim $ 1, $\sim $ 90% of the LIRGs have low Sérsic indices ($n$  $\lt$ 2.5, similar to disk-like galaxies) in the $K_{\mathrm{s}}$-band, and that those disk-like LIRGs consist of $\sim $ 60% of the whole disk-like sample above $M_{\mathrm{s}}$  $\geq$ 3 $\times$ 10$^{10}\ M_{\odot}$. The z  $\sim $ 1 disk-like LIRGs are comparable to or $\sim $ 20% scer at the maximum in size compared to local disk-like galaxies in the same stellar mass range. When we examined rest-frame UV–optical morphologies using the HST/ACS images, the rest-frame $B$-band sizes of the z  $\sim $ 1 disk-like galaxies were found to be comparable to those of the local disk-like galaxies, as reported by previous studies on the size evolution of disk-like galaxies in the rest-frame optical band. By measuring color gradients (galaxy sizes as a function of wavelength) of the z  $\sim $ 1 and local disk-like galaxies, we found that the z  $\sim $ 1 disk-like galaxies have a 3–5 times steeper color gradient than the local ones. Our results indicate that (i) more than a half of the relatively massive disk-like galaxies at z  $\sim $ 1 are in violent star-formation epochs observed as LIRGs, and also (ii) that most of those LIRGs are constructing their fundamental disk structure vigorously. The high SFR density in the universe at z  $\sim $ 1 may be dominated by such star formation in the disk region in massive galaxies.
Discovery of an Excess of H Emitters around 4C 23.56 at z = 2.48
Authors: Tanaka Ichi , De Breuck Carlos , Kurk Jaron D. , Taniguchi Yoshiaki , Kodama Tadayuki , Matsuda Yuichi , Packham Chris , Zirm Andrew , Kajisawa Masaru , Ichikawa Takashi , Seymour Nick , Stern Daniel , Stockton Alan , Venemans Bram P. , Vernet Joël
Published: February 2014

We report on the discovery of a significant excess of candidate H$\alpha $ emitters (HAEs) in the field of the radio galaxy 4C 23.56 at z$=$ 2.483. Using the MOIRCS near-infrared imager on the Subaru Telescope we found 11 candidate emission-line galaxies to a flux limit of $\sim$7.5 $\times$ 10$^{-17}\ $erg s$^{-1}\ $cm$^{-2}$, which is about 5-times excess from the expected field counts with an $\sim$ 3-$\sigma$ significance. Three of these have been spectroscopically confirmed as redshifted H$\alpha $ at z$=$ 2.49. The distribution of candidate emitters on the sky is tightly confined to a 1.2-Mpc-radius area at z$=$ 2.49, locating 4C 23.56 at the western edge of the distribution. An analysis of the deep Spitzer MIPS 24$\ \mu$m imaging shows that there is also an excess of faint MIPS sources. All but two of the 11 HAEs are also found in the MIPS data. The inferred star-formation rate (SFR) of the HAEs based on the extinction-corrected H$\alpha $ luminosity (median SFR$\gtrsim$ 100$\ M_{\odot}\ $yr$^{-1}\ $) is similar to those of HAEs in random fields at z$\sim$ 2. On the other hand, the MIPS-based SFR for the HAEs is on average 3.6-times larger, suggesting the existence of star-formation significanly obscured by dust. A comparison of the H$\alpha $-based star-formation activities of the HAEs in the 4C 23.56 field to those in another proto-cluster around PKS 1138$-$262 at z$=$ 2.16 reveals that the latter tend to have fainter H$\alpha $ emission despite similar $K$-band magnitudes. This suggests that star-formation may be suppressed in the PKS 1138$-$262 protocluster relative to the 4C 23.56 protocluster. This difference among the HAEs in the two proto-clusters at z$\gt$ 2 may imply that some massive cluster galaxies are just forming at these epochs with some variation among them.
Spectropolarimetry of the Superwind Filaments of the Starburst Galaxy M 82: Kinematics of Dust Outflow
Authors: Yoshida Michitoshi , Kawabata Koji S. , Ohyama Youichi
Published: February 2014

Spectropolarimetry results for the starburst galaxy M 82 are presented. The optical emission lines of the filaments in the energetic outflow (``superwind'') from the nuclear starburst region of M 82 are substantially polarized. The H$\alpha$ polarization degrees and angles measured by our study are consistent with previous narrowband imaging polarimetry data. The polarized emission lines are redshifted with respect to the emission lines in the total light and systemic motion of the galaxy. The emission line intensity ratios [N II]$/$H$\alpha$ and [S II]$/$H$\alpha$ in the polarized light are similar to those of the nuclear star-forming region. In addition, the electron density $N_{\rm e}$ derived from the [S II]$\lambda$6731$/\lambda$6717 line ratio of the polarized light is $\sim\ $600–1000 cm$^{-3}$ at a distance of more than 1 kpc from the nucleus, whereas the $N_{\rm e}$ derived from the total light are less than 300 cm$^{-3}$. These facts strongly suggest that the emission from the nuclear starburst of M 82 is scattered by dust grains entrained and transported outward by the superwind. A simple hollow biconical outflow model shows that the velocity of the outflowing dust grains, $v_{\rm d}$, ranges from 100 to 200 km s$^{-1}$ near the nucleus, decreases monotonically with the distance from the nucleus, and reaches $\sim\ $10 km s$^{-1}$ at around 1 kpc. The motion of the dust is substantially slower than that of both ionized gas ($v_{{\rm H}\alpha}$  $\sim\ $ 600 km s$^{-1}$) and molecular gas ($v_{\rm CO}$  $\sim\ $ 200 km s$^{-1}$) at the same distance from the nucleus of M 82. This indicates that dust grains in the superwind are kinematically decoupled from both gas components at large radii. Since the dust velocity $v_{\rm d}$ is much less than the escape velocity of M 82 ($v_{\rm esc}$  $\approx$ 170 km s$^{-1}$ at 1.5 kpc from the nucleus), most of the dust entrained by the superwind cannot escape to intergalactic space, and may fall back into the galaxy disk if there is no additional acceleration mechanism (such as radiation pressure).
Diffraction-Limited Subaru Imaging of M 82: Sharp Mid-Infrared View of the Starburst Core*
Authors: Gandhi Poshak , Isobe Naoki , Birkinshaw Mark , Worrall Diana M. , Sakon Itsuki , Iwasawa Kazushi , Bamba Aya
Published: February 2014

We present new imaging at 12.81 and 11.7 $\mu$m of the central $\sim$ 40$”$$\times$ 30$”$ ($\sim$ 0.7 kpc $\times$ 0.5 kpc) of the starburst galaxy M 82. The observations were carried out with the COMICS mid-infrared (mid-IR) imager on the 8.2 m Subaru Telescope, and are diffraction-limited at an angular resolution of $\lt$0$″$4. The images show extensive diffuse structures, including a 7-long linear chimneylike feature and another resembling the edges of a ruptured bubble. This is the clearest view to date of the base of the kpc-scale dusty wind known in this galaxy. These structures do not trace back to a single central point, implying multiple ejection sites for the dust. In general, the distribution of dust probed in the mid-IR anticorrelates with the locations of massive star clusters that appear in the near-infrared. The 10–21 $\mu$m mid-IR emission, spatially integrated over the field of view, may be represented by hot dust with temperature of $\sim$ 160 K. Most discrete sources are found to have extended morphologies. Several radio H II regions are identified for the first time in the mid-IR. The only potential radio supernova remnant to have a mid-IR counterpart is a source which has previously also been suggested to be a weak active galactic nucleus. This source has an X-ray counterpart in Chandra data which appears prominently above 3 keV and is best described as a hot ($\sim$ 2.6 keV) absorbed thermal plasma with a 6.7 keV Fe K emission line, in addition to a weaker and cooler thermal component. The mid-IR detection is consistent with the presence of strong [NeII]$\lambda$12.81 $\mu$m line emission. The broad-band source properties are complex, but the X-ray spectra do not support the active galactic nucleus hypothesis. We discuss possible interpretations regarding the nature of this source.
A Possible Tilted Orbit of the Super-Neptune HAT-P-11b
Authors: Hirano Teruyuki , Narita Norio , Shporer Avi , Sato Bun'ei , Aoki Wako , Tamura Motohide
Published: February 2014

We report on the detection of the Rossiter–McLaughlin effect for the eccentric, super-Neptune exoplanet HAT-P-11b, based on radial-velocity measurements taken with the High Dispersion Spectrograph mounted on the Subaru 8.2 m telescope, and simultaneous photometry with the LCOGT 2.0 m Faulkes Telescope North, both located in Hawaii. The observed radial velocities during a planetary transit of HAT-P-11b show a persistent blue-shift, suggesting a spin–orbit misalignment in the system. The best-fit value for the projected spin–orbit misalignment angle is ${\lambda}$$=$ 103$^\circ$$_{-18^\circ}^{+22^\circ}$. This fact suggests that not only hot-Jupiters, but also super-Neptunes like HAT-P-11b had once experienced dynamical processes, such as planet–planet scattering or Kozai migration.
Grisms Developed for FOCAS
Authors: Ebizuka Noboru , Kawabata Koji S. , Oka Keiko , Yamada Akiko , Kashiwagi Masako , Kodate Kashiko , Hattori Takashi , Kashikawa Nobunari , Iye Masanori
Published: February 2014

Faint Object Camera and Spectrograph (FOCAS) is a versatile common-use optical instrument for the 8.2 m Subaru Telescope, offering imaging and spectroscopic observations. FOCAS employs grisms with resolving powers ranging from 280 to 8200 as dispersive optical elements. A grism is a direct-vision grating composed of a transmission grating and prism(s). FOCAS has five grisms with replica surface-relief gratings including an echelle-type grism, and eight grisms with volume-phase holographic (VPH) gratings. The size of these grisms is 110 mm $\times$ 106 mm in aperture with a maximum thickness of 110 mm. We employ not only the dichromated gelatin, but also the hologram resin as a recording material for VPH gratings. We discuss the performance of these FOCAS grisms measured in the laboratory, and verify it by test observations, and show examples of astronomical spectroscopic observations.
Knocking Out Bcsas1 in Botrytis cinerea Impacts Growth, Development, and Secretion of Extracellular Proteins, Which Decreases Virulence
Authors: Zhang Zhanquan , Qin Guozheng , Li Boqiang , Tian Shiping
Published: February 2014

Pathogenic fungi usually secrete a series of virulence factors to the extracellular environment to facilitate infection. Rab GTPases play a central role in the secretory pathway. To explore the function of Rab/GTPase in filamentous fungi, we knocked out a Rab/GTPase family gene, Bcsas1, in Botrytis cinerea, an aggressive fungal pathogen that infects more than 200 plant species. A detailed analysis was conducted on the virulence and the secretory capability of the mutants. The results indicated that knockout of Bcsas1 inhibited hyphal development and reduced sporulation of B. cinerea on potato dextrose agar plates resulting in reduced virulence on various fruit hosts. Knocking out the Bcsas1 gene led to an accumulation of transport vesicles at the hyphal tip, significantly reduced extracellular protein content, and lowered the activity of polygalacturonase and xylanase in the extracellular medium. However, mutation of Bcsas1 did not affect the expression of genes encoding polygalacturonase and xylanase, suggesting the secretion of these two family enzymes was suppressed in the mutant. Moreover, a comparative analysis of the secretome provided further evidence that the disruption of Bcsas1 in mutant strains significantly depressed the secretion of polysaccharide hydrolases and proteases. The results indicate that Bcsas1, the Rab8/SEC4-like gene, plays a crucial role in development, protein secretion, and virulence of B. cinerea.
A Systematic Review of the Unintended Consequences of Clinical Interventions to Reduce Adverse Outcomes
Authors: Manojlovich Milisa , Lee Soohee , Lauseng Deborah
Published: February 2014

This is a systematic review of the literature on unintended consequences of clinical interventions to reduce falls, catheter-related urinary tract infection, and vascular catheter-related infections in hospitalized patients. A systematic search of the literature was conducted in CINAHL and PubMed. We developed a screening tool and a two-stage screening process to identify relevant articles. Nine articles met inclusion criteria, and of those, 8 reported on interventions to reduce patient falls. Four studies reported a positive, unexpected benefit; 3 studies reported a negative, unexpected detriment; and 4 reported a perverse effect (different from what was expected). Three studies reported both positive and perverse effects arising from the intervention. In 4 of the studies, despite fall prevention interventions, patients fell while trying to get to the bathroom, suggesting that interventions to reduce one adverse outcome (i.e., CAUTI) may be associated with another outcome (i.e., patient falls). In some cases, there were positive outcomes for those who implemented and/or evaluated interventions. We encourage colleagues to collect and report data on possible unintended consequences of their interventions to allow a fuller picture of the relationship between intervention and all outcomes to emerge.
Stiffest elastic networks
Authors: Gurtner Gérald , Durand Marc
Published: February 2014

The rigidity of a network of elastic beams is closely related to its microstructure. We show both numerically and theoretically that there is a class of isotropic networks, which are stiffer than any other isotropic network of same density. The elastic moduli of thesestiffest elastic networksare explicitly given. They constitute upper-bounds, which compete or improve the well-known Hashin–Shtrikman bounds. We provide a convenient set of criteria (necessary and sufficient conditions) to identify these networks and show that their displacement field under uniform loading conditions is affine down to the microscopic scale. Finally, examples of such networks with periodic arrangement are presented, in both two and three dimensions. In particular, we present anoptimalandisotropicthree-dimensional structure which, to our knowledge, is the first one to be presented as such.
Immediate replacement of fishing with dairying by the earliest farmers of the northeast Atlantic archipelagos
Authors: Cramp Lucy J. E. , Jones Jennifer , Sheridan Alison , Smyth Jessica , Whelton Helen , Mulville Jacqui , Sharples Niall , Evershed Richard P.
Published: February 2014

The appearance of farming, from its inception in the Near East around 12 000 years ago, finally reached the northwestern extremes of Europe by the fourth millennium BC or shortly thereafter. Various models have been invoked to explain the Neolithization of northern Europe; however, resolving these different scenarios has proved problematic due to poor faunal preservation and the lack of specificity achievable for commonly applied proxies. Here, we present new multi-proxy evidence, which qualitatively and quantitatively maps subsistence change in the northeast Atlantic archipelagos from the Late Mesolithic into the Neolithic and beyond. A model involving significant retention of hunter–gatherer–fisher influences was tested against one of the dominant adoptions of farming using a novel suite of lipid biomarkers, including dihydroxy fatty acids, ω-(
o
-alkylphenyl)alkanoic acids and stable carbon isotope signatures of individual fatty acids preserved in cooking vessels. These new findings, together with archaeozoological and human skeletal collagen bulk stable carbon isotope proxies, unequivocally confirm rejection of marine resources by early farmers coinciding with the adoption of intensive dairy farming. This pattern of Neolithization contrasts markedly to that occurring contemporaneously in the Baltic, suggesting that geographically distinct ecological and cultural influences dictated the evolution of subsistence practices at this critical phase of European prehistory.
The emergence of the rescue effect from explicit within- and between-patch dynamics in a metapopulation
Authors: Eriksson Anders , Elías-Wolff Federico , Mehlig Bernhard , Manica Andrea
Published: February 2014

Immigration can rescue local populations from extinction, helping to stabilize a metapopulation. Local population dynamics is important for determining the strength of this rescue effect, but the mechanistic link between local demographic parameters and the rescue effect at the metapopulation level has received very little attention by modellers. We develop an analytical framework that allows us to describe the emergence of the rescue effect from interacting local stochastic dynamics. We show this framework to be applicable to a wide range of spatial scales, providing a powerful and convenient alternative to individual-based models for making predictions concerning the fate of metapopulations. We show that the rescue effect plays an important role in minimizing the increase in local extinction probability associated with high demographic stochasticity, but its role is more limited in the case of high local environmental stochasticity of recruitment or survival. While most models postulate the rescue effect, our framework provides an explicit mechanistic link between local dynamics and the emergence of the rescue effect, and more generally the stability of the whole metapopulation.
The influence of social norms on the dynamics of vaccinating behaviour for paediatric infectious diseases
Authors: Oraby Tamer , Thampi Vivek , Bauch Chris T.
Published: February 2014

Mathematical models that couple disease dynamics and vaccinating behaviour often assume that the incentive to vaccinate disappears if disease prevalence is zero. Hence, they predict that vaccine refusal should be the rule, and elimination should be difficult or impossible. In reality, countries with non-mandatory vaccination policies have usually been able to maintain elimination or very low incidence of paediatric infectious diseases for long periods of time. Here, we show that including injunctive social norms can reconcile such behaviour-incidence models to observations. Adding social norms to a coupled behaviour-incidence model enables the model to better explain pertussis vaccine uptake and disease dynamics in the UK from 1967 to 2010, in both the vaccine-scare years and the years of high vaccine coverage. The model also illustrates how a vaccine scare can perpetuate suboptimal vaccine coverage long after perceived risk has returned to baseline, pre-vaccine-scare levels. However, at other model parameter values, social norms can perpetuate depressed vaccine coverage during a vaccine scare well beyond the time when the population's baseline vaccine risk perception returns to pre-scare levels. Social norms can strongly suppress vaccine uptake despite frequent outbreaks, as observed in some small communities. Significant portions of the parameter space also exhibit bistability, meaning long-term outcomes depend on the initial conditions. Depending on the context, social norms can either support or hinder immunization goals.
A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers
Authors: Aronson Myla F. J. , La Sorte Frank A. , Nilon Charles H. , Katti Madhusudan , Goddard Mark A. , Lepczyk Christopher A. , Warren Paige S. , Williams Nicholas S. G. , Cilliers Sarel , Clarkson Bruce , Dobbs Cynnamon , Dolan Rebecca , Hedblom Marcus , Klotz Stefan , Kooijmans Jip Louwe , Kühn Ingolf , MacGregor-Fors Ian , McDonnell Mark , Mörtberg Ulla , Pyšek Petr , Siebert Stefan , Sushinsky Jessica , Werner Peter , Winter Marten
Published: February 2014

Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being
Columba livia
and
Poa annua
. The density of bird and plant species (the number of species per km
2
) has declined substantially: only 8% of native bird and 25% of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education.
Trait‐based scaling of temperature‐dependent foliar respiration in a species‐rich tropical forest canopy
Authors: Slot Martijn , Rey‐Sánchez Camilo , Winter Klaus , Kitajima Kaoru
Published: February 2014

The scarcity of empirical data on leaf respiration (R) and its temperature sensitivity (e.g. Q10, defined as the proportional increase in R per 10 °C warming) causes uncertainty in current estimates of net primary productivity of tropical forests.

We measured temperature response curves of R on 123 upper‐canopy leaves of 28 species of trees and lianas from a tropical forest in Panama and analysed variations in R and Q10 in relation to other leaf functional traits.

Respiration rates per leaf area at 25 °C (RA) varied widely among species and were significantly higher in trees than in lianas. RA was best predicted by a multiple regression model containing leaf phosphorus concentration, photosynthetic capacity and leaf mass per area (r2 = 0·64). The mean Q10 value (2·4) was significantly higher than the commonly assumed value of 2·0. Q10 was best predicted by the combination of leaf carbohydrate concentration and growth form (trees vs lianas) (r2 = 0·26).

The night‐time leaf respiratory carbon flux from this tropical forest was calculated from these multiple regression models to be 4·5 Mg C ha−1 year−1, with an estimated additional 2·9 Mg C ha−1 year−1 being released by respiration during the day.

Trait‐based modelling has potential for estimating R, thus facilitating carbon flux estimation in species‐rich tropical forests. However, in contrast to global analyses, leaf phosphorus content was the most important correlate of R and not leaf nitrogen, so calibration of trait models to the tropics will be important. Leaf traits are poor predictors of Q10 values, and more empirical data on the temperature sensitivity of respiration are critically needed to further improve our ability to scale temperature‐dependent respiration in species‐rich tropical forests.
Coil response inversion for very early time modelling of helicopter‐borne time‐domain electromagnetic data and mapping of near‐surface geological layers
Authors: Schamper Cyril , Auken Esben , Sørensen Kurt
Published: February 2014

Very early times in the order of 2–3 μs from the end of the turn‐off ramp for time‐domain electromagnetic systems are crucial for obtaining a detailed resolution of the near‐surface geology in the depth interval 0–20 m. For transient electromagnetic systems working in the off time, an electric current is abruptly turned off in a large transmitter loop causing a secondary electromagnetic field to be generated by the eddy currents induced in the ground. Often, however, there is still a residual primary field generated by remaining slowly decaying currents in the transmitter loop. The decay disturbs or biases the earth response data at the very early times. These biased data must be culled, or some specific processing must be applied in order to compensate or remove the residual primary field. As the bias response can be attributed to decaying currents with its time constantly controlled by the geometry of the transmitter loop, we denote it the ‘Coil Response’. The modelling of a helicopter‐borne time‐domain system by an equivalent electronic circuit shows that the time decay of the coil response remains identical whatever the position of the receiver loop, which is confirmed by field measurements. The modelling also shows that the coil response has a theoretical zero location and positioning the receiver coil at the zero location eliminates the coil response completely. However, spatial variations of the coil response around the zero location are not insignificant and even a few cm deformation of the carrier frame will introduce a small coil response. Here we present an approach for subtracting the coil response from the data by measuring it at high altitudes and then including an extra shift factor into the inversion scheme. The scheme is successfully applied to data from the SkyTEM system and enables the use of very early time gates, as early as 2–3 μs from the end of the ramp, or 5–6 μs from the beginning of the ramp. Applied to a large‐scale airborne electromagnetic survey, the coil response compensation provides airborne electromagnetic methods with a hitherto unseen good resolution of shallow geological layers in the depth interval 0–20 m. This is proved by comparing results from the airborne electromagnetic survey to more than 100 km of Electrical Resistivity Tomography measured with 5 m electrode spacing.
An evolutionary perspective on reproductive individual heterogeneity in a marine vertebrate
Authors: Chambert Thierry , Rotella Jay J. , Garrott Robert A.
Published: February 2014

Although the quantification of individual heterogeneity in wild populations' vital rates has recently attracted growing interest among ecologists, the investigation of its evolutionary consequences remains limited, mainly because of the difficulties in assessing fitness and heritability from field studies on free‐ranging animals. In the presence of individual variability, evaluation of fitness consequences can notably be complicated by the existence of trade‐offs among different vital rates.

In this study, to further assess the evolutionary significance of previously quantified levels of individual heterogeneity in female Weddell seal (Leptonychotes weddellii Lesson) reproductive rates (Chambert et al. ), we investigated how several life‐history characteristics of female offspring were related to their mother's reproductive rate, as well as to other maternal traits (age and experience) and environmental conditions at birth.

The probability and age of first reproduction (recruitment) of female offspring was not related to their mother's reproductive rate, suggesting the absence of a maternal trade‐off between the number and quality of offspring a female produces. Evidence of a positive, but relatively weak, relationship between the reproductive rates of a mother and her female offspring was found, suggesting some degree of heritability in this trait.

Using a simulation approach based on these statistical findings, we showed that substantial differences in the number of grandchildren, produced through female progeny, can be expected among females with different reproductive rates.

Despite the presence of substantial stochastic variability, due to environmental fluctuations and other unidentified mechanisms, and in the light of the fact that the metrics obtained do not provide a full measure of real fitness, our results do suggest that the individual reproductive variability found in female Weddell seals could potentially have important fitness consequences.
Environmental Democratisation: Assessing the Impact of Democratisation on Environmental Capacity in South and Southeastern Europe
Authors: O'Brien Thomas
Published: February 2014

Although a relationship between established democratic political systems and environmental capacity has been described, the impact of the democratisation process on environmental capacity is not clear. The aim of this article is to determine the effect of both prior regime type and mode of transition on environmental capacity, through consideration of the cases of Bulgaria, Portugal, Romania and Spain. In addition, the importance of the European Union (EU) as an external actor shaping environmental capacity building is assessed. Findings indicate that variations in prior regime type and mode of transition had limited impact on environmental capacity development. Of greater importance were the persistent non-democratic legacies that influenced behaviours and actions during the democratisation period. The requirements of the EU were fundamental in ensuring that environmental issues remained on the domestic political agenda in such a context.
Explaining Territorial Change in Federal Democracies: A Comparative Historical Institutionalist Approach
Authors: Tillin Louise
Published: February 2014

This article builds a framework drawn from historical institutionalism to analyse changes to the territorial composition of federal systems arising from the creation or admission of new sub-units. Despite the sustained interest among political scientists in the effects of federal design on ethnic conflict, economic development and prospects for democratic stability, there has been little sustained attempt to explain when and why territorial maps change over time. A historical institutionalist framework draws attention to the ways in which constellations of internal borders are underpinned by – and reproduce – patterns of power. The framework explains territorial change by studying the multiple layers that structure political life in federal settings and which through their interactions produce change. The article proceeds to explain territorial change in two countries with contrasting federal origins: India and the United States. In so doing, it questions the tendency within comparative politics to treat both countries as places of exception.
The Militant Strain: An Analysis of Anti-Secular Discourse in Britain
Authors: Kettell Steven
Published: February 2014

Issues about the relationship between the religious and the secular have become increasingly prominent in recent years. In Britain, one of the central themes around this topic has been the emergence and propagation by leading religious and political figures of a concerted anti-secular discourse. This warns of the dangers posed by a militant, aggressive and intolerant form of secularism which is said to be driven by an ideological desire to force religion out of the public square, representing a clear threat to religious freedoms and social morality. This discourse has been shaped by a number of interrelated causal dynamics, but the religious and political influences involved differ substantially. Respectively, these relate to ongoing processes of secularisation and the increasing use of identity politics, set against the changing capacities of the British state and the electoral considerations of the Conservative Party.
Serum vascular endothelial growth factor levels following luteal gonadotrophin‐releasing hormone antagonist administration in women with severe early ovarian hyperstimulation syndrome
Authors: Lainas GT , Kolibianakis EM , Sfontouris IA , Zorzovilis IZ , Petsas GK , Lainas TG , Tarlatzis BC
Published: February 2014

Objective

To investigate the kinetics of serum vascular endothelial growth factor (VEGF) following gonadotrophin‐releasing hormone (GnRH) antagonist administration in the luteal phase in women with established severe early ovarian hyperstimulation syndrome (OHSS).

Design

Pilot observational cohort study.

Setting

Private in vitro fertilisation (IVF) Unit.

Population

Twelve IVF women diagnosed with established severe early OHSS 5 days post oocyte retrieval (POR).

Methods

Women undergoing IVF diagnosed with severe early OHSS 5 days POR were given 0.25 mg GnRH antagonist for 4 days, from day 5 until and including day 8 POR, combined with elective blastocyst cryopreservation. Serum VEGF was measured from the day of oocyte retrieval until day 11 POR. Ovarian volume, ascites, serum estradiol and progesterone, haematocrit and white blood cells were monitored during the same period.

Main outcome measures

Kinetics of VEGF following luteal GnRH antagonist administration in women with established severe early OHSS.

Results

The concentration of VEGF was highest (390.9 ± 137.4 pg/ml) 5 days POR, coinciding with the day of diagnosis of severe OHSS. There was a significant decline of VEGF on day 7 (302.8 ± 104.9 pg/ml; P = 0.026), day 9 (303.3 ± 148.3 pg/ml; P = 0.007), and day 11 (252.6 ± 182.7 pg/ml; P = 0.010) compared with day 5 POR. This decline was associated with an improvement of ultrasound and laboratory parameters, indicating regression of severe OHSS. All women were managed at an outpatient level.

Conclusions

GnRH antagonist administration in the luteal phase is associated with a significant decline of VEGF and with regression of established severe early OHSS.
Safety of oseltamivir during pregnancy: a comparative study using the EFEMERIS database
Authors: Beau A‐B , Hurault‐Delarue C , Vial T , Montastruc J‐L , Damase‐Michel C , Lacroix I
Published: February 2014

Objective

To compare pregnancy outcome between women exposed and unexposed to oseltamivir during pregnancy.

Design

A comparative observational cohort study of women exposed to oseltamivir during pregnancy.

Setting

A French prescription database (EFEMERIS) that includes data for pregnant women was used. EFEMERIS records prescribed and dispensed reimbursed drugs during pregnancy and pregnancy outcomes in Haute‐Garonne, South West France.

Population

Women who delivered from 1 July 2004 to 31 December 2010.

Methods

The study compared exposed and unexposed pregnant women. Two women unexposed to oseltamivir were individually matched, by maternal age, month, and year of delivery, with one women exposed to oseltamivir. Multivariable conditional logistic regression and multivariable Cox proportional hazards regression were used to evaluate associations between each outcome and exposure to oseltamivir during pregnancy.

Main outcome measures

Pregnancy loss for any cause, preterm delivery, low birthweight, neonatal pathology, and congenital malformation.

Results

A cohort of 337 (0.58% of women included in EFEMERIS) women exposed to oseltamivir were compared with 674 unexposed women. The risk for pregnancy loss (HR 1.52; 95 % CI 0.80–2.91), for preterm birth (adjusted OR 0.64; 95% CI 0.31–1.27), and for neonatal pathology (adjusted OR 0.62; 95% CI 0.23–1.54) did not differ between exposed and unexposed groups. When exposure during organogenesis was considered, one case of congenital anomaly (2.0%) among 49 exposed women and one case (1.0%) among 99 unexposed women were observed (crude OR 2.00; 95% CI 0.13–32.00).

Conclusions

There was no significant association between adverse pregnancy outcomes and exposure to oseltamivir during pregnancy.
Global Politics and Us
Authors: May Christopher
Published: February 2014

This review article explores how individuals are involved in global politics, and asks whether such involvement can only be easily understood when mediated through nongovernmental organisations (NGOs) or whether there are opportunities for recognising direct (global) political engagement differently. It investigates (albeit briefly) whether the political agency of individuals is meaningful in global politics, and whether analyses that might foreground such engagement can balance more structuralist approaches as well as those that seek to suggest that only collective action (organised through NGOs) can be effective on the global political stage. One might anecdotally see a role for individuals at crucial (global) political junctures, but the question is what opportunities might there be for making a more strident argument for the role of the individual in global politics? In different ways the five books explored in the review offer different paths to such recognition, and although none of the books completely help resolve this lacuna, all offer ways to think about the shape that such a project might take if it is to be successful.
Use of Sodium Dodecyl Sulfate Pretreatment and 2‐stage Curing for Improved Quality of Salted Duck Eggs
Authors: Lian Zixuan , Qiao Longshan , Zhu Guanghong , Deng Yun , Qian Bingjun , Yue Jin , Zhao Yanyun
Published: February 2014

The effects of use of sodium dodecyl sulfate (SDS) pretreatment and 2‐stage curing on the microbial, physicochemical, and microstructural qualities of salted duck eggs were studied. After pretreatment in 0.5% (w/v) SDS solution at room conditions for 15 min, no discolorations were observed and no microorganisms were detected on the egg shells. In the 2‐stage curing process, 25% (w/v) and 30% (w/v) saline solutions were evaluated in the 1st step (Stage I, approximately 18 d), whereas 4% (w/v) saline solution was applied in the 2nd step (Stage II, approximately 15 d). Along with increased curing time, water content decreased and NaCl content increased in the egg yolks from approximately 0.40% to 0.86%, whereas the water content of egg albumen remained at approximately 85% during the 2‐stage curing. More importantly, the NaCl content of albumen maintained at approximately 4.0% at Stage II curing. Yolk index as a sign of maturity for salted duck eggs reached 1 at the end of Stage I (18 d) and retained the same value during Stage II curing regardless of the NaCl concentration in the Stage I saline solution. Oil exudation in egg yolks increased as the time of curing increased. As seen from scanning electron microscopy, oil was released from yolk granules. This study indicated that SDS pretreatment is effective to reduce microbial load on the shells of fresh duck eggs and the 2‐stage curing can improve physicochemical qualities of the salted duck eggs and shortened curing time to about 7 to 17 d as compared to the traditional 1‐step curing method.

Practical Application

Spoiled saline solution and uneven distribution of salt are the 2 major problems in producing salted duck eggs. Sodium dodecyl sulfate (SDS) pretreatment and 2‐stage curing process have shown effective to solve these problems, respectively. The SDS pretreatment was able to remove microorganisms and soil from the surface of fresh egg shells, thus preventing the spoilage of the saline solution. The 2‐stage curing process successfully controlled the NaCl content of egg albumen and yolk in the final product, and shortened the curing time compared to the traditional 1‐step curing method.