bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial and temporal habitat use by white sharks (Carcharodon carcharias) at an aggregation site in southern New Zealand
Authors: Francis Malcolm P. , Duffy Clinton , Lyon Warrick
Published: April 2015

Subadult and adult white sharks aggregate seasonally near pinniped colonies in several parts of the globe. The time spent there may represent the most vulnerable part of their otherwise migratory life cycle. White sharks have low productivity and may suffer population declines even when afforded legislative protection. White sharks were protected in New Zealand in 2007, but are subject to ongoing incidental fishing mortality. We deployed electronic tags on white sharks at north-eastern Stewart Island in southern New Zealand to identify their temporal and spatial patterns of occupancy, and to inform management measures that aim to separate sharks from fishing effort. White sharks were present almost continuously from late summer to early winter, peaking in autumn (March–June). The population comprised mainly subadult and adult males and subadult females, with males predominating by 2.5:1 during autumn. White shark abundance was greatest in the Titi Islands, and there was fine-scale spatial and temporal variability in abundance. These sharks travel well beyond their aggregation sites, but the behaviour and dynamics of white sharks in other parts of New Zealand remain poorly understood. Any attempts to reduce incidental mortality by protecting white shark habitat must consider a wider spatial context.
The human sex ratio from conception to birth
Authors: Orzack Steven Hecht , Stubblefield J. William , Akmaev Viatcheslav R. , Colls Pere , Munné Santiago , Scholl Thomas , Steinsaltz David , Zuckerman James E.
Published: April 2015

Significance

The human sex ratio has long interested cell biologists, developmental biologists, demographers, epidemiologists, evolutionary biologists, gynecologists, and statisticians. Nonetheless, the trajectory of the human sex ratio from conception to birth has been poorly characterized. We present the most comprehensive analysis of this trajectory ever done. Our dataset is the largest ever assembled to estimate the sex ratio at conception and is the first, to our knowledge, to include data from 3- to- 6-d-old embryos, induced abortions, chorionic villus sampling, amniocentesis, and fetal deaths and live births. Our results indicate that the sex ratio at conception is unbiased, the proportion of males increases during the first trimester, and total female mortality during pregnancy exceeds total male mortality; these are fundamental insights into early human development.
SOX2 primes the epigenetic landscape in neural precursors enabling proper gene activation during hippocampal neurogenesis
Authors: Amador-Arjona Alejandro , Cimadamore Flavio , Huang Chun-Teng , Wright Rebecca , Lewis Susan , Gage Fred H. , Terskikh Alexey V.
Published: April 2015

Significance

Sex-determining region Y-related HMG box 2 (SOX2) is a well-established marker of neural stem and progenitor cells, and its function was shown to be required for the self-renewal of these cells. However, the function of SOX2 in neuronal differentiation is poorly understood. Here we described a novel role of SOX2 in neuronal differentiation in which SOX2 binds to bivalently marked promoters of poised proneural genes in neural progenitor cells and limits the activity of polycomb repressive complex 2 and excessive levels of histone H3 Lys 27 trimethylation. We propose a novel function of SOX2 in maintaining a permissive epigenetic state thus enabling proper activation of the neuronal differentiation program under neurogenic cue.
Structural basis for the geometry-driven localization of a small protein
Authors: Gill Richard L. , Castaing Jean-Philippe , Hsin Jen , Tan Irene S. , Wang Xingsheng , Huang Kerwyn Casey , Tian Fang , Ramamurthi Kumaran S.
Published: April 2015

Significance

Despite extensive studies of protein trafficking across length scales of many microns, how proteins correctly localize within the smaller length scales of bacterial cells is still poorly understood. Recently, we proposed that slight membrane curvature, defined by the surface geometry of a bacterium, can drive the localization of certain shape-sensing proteins. Here, we developed an assay to quantify membrane curvature recognition by the small bacterial protein SpoVM and used NMR to determine the structural basis of curvature recognition. NMR and molecular dynamics simulations suggested a model wherein unusually deep membrane insertion allows the protein to sense subtle acyl chain packing differences between differently curved membranes, a distinct curvature-sensing mechanism from those used by proteins that sense high membrane curvature.
Environmental tipping points significantly affect the cost−benefit assessment of climate policies
Authors: Cai Yongyang , Judd Kenneth L. , Lenton Timothy M. , Lontzek Thomas S. , Narita Daiju
Published: April 2015

Significance

Most current cost−benefit analyses of climate change suggest global climate policy should be relatively weak. However, relatively few studies account for the market or nonmarket impacts of passing environmental tipping points that cause abrupt and irreversible damages. We use a stochastic dynamic model of the climate and economy to quantify the effect of tipping points on climate change policy. We show that environmental tipping points can profoundly alter cost−benefit analysis, justifying a much more stringent climate policy, which takes the form of a higher immediate price on carbon.
Molecular mechanism underlying β1 regulation in voltage- and calcium-activated potassium (BK) channels
Authors: Castillo Karen , Contreras Gustavo F. , Pupo Amaury , Torres Yolima P. , Neely Alan , González Carlos , Latorre Ramon
Published: April 2015

Significance

β-Subunits (β1–β4) play a critical role in defining the properties of the voltage- and calcium-activated potassium (BK) channel, which in turn determines the physiological role that this channel can perform in different tissues. In particular, the β1-subunit causes an increase in the apparent BK Ca
2+
sensitivity due to a stabilization of the voltage sensor in the active configuration. We investigated the molecular details of such voltage-sensor stabilization by mutagenesis and gating current measurements. Mixing regions of β1 and β3 made it possible to identify the N terminus, in particular the third and fourth lysine residues, as the structural element necessary to recover the full effect of β1 on the voltage sensor.
Direct election of regional presidents and party change in Italy
Authors: Wilson Alex
Published: April 2015

This article assesses the impact that direct election of regional presidents has had on party politics in Italy. It finds regional presidents exert a growing personalisation of power within parties at sub-national levels, primarily through their capacity for political nomination and de facto status as party negotiators in the governing coalition. While presidents may shape structures of regional party competition, they remain constrained by coalitional politics and can struggle to assert their authority against powerful governing partners or local powerbrokers rooted in the legislature. They also possess few mechanisms to consolidate their position at national level, consistent with a broader tendency towards ‘stratarchy’ in multi-level parties. Although the distinction between densely and loosely structured parties remains relevant, a common trend towards ‘cartelisation’ at sub-national levels is noted as political parties prioritise the control of state resources and the governing legitimacy this entails. This article contributes to our broader understanding of the multi-level dynamics of party politics in Europe, as well as the unintended consequences of experimenting with an untested hybrid model of ‘directly elected Prime Minister’ in the Italian regions.
A Field-Based Nursery for Headstarting Lobsters to Improve Postrelease Survival for Potential Stock Enhancement in Long Island Sound, Connecticut
Authors: Mercaldo-Allen Renee , Goldberg Ronald , Kuropat Catherine A , Clark Paul , Alix Robert , Schreiner Werner , Roy John
Published: April 2015

Early benthic stage American lobsters Homarus americanus were held in a pilot nursery system in Long Island Sound (LIS), Connecticut, to test field grow out as a step toward potential stock enhancement. A larger size upon release may increase the probability of survival. Lobsters were placed individually in perforated plastic mesh cylindrical “habitats,” and each habitat was housed in an outer protective sleeve with a larger mesh size. During June 2013, 24 lobsters were transferred to each of three wire mesh cages and deployed southwest of Charles Island in Milford, Connecticut (N = 3). The only source of nutrition was naturally occurring organisms. Cages were retrieved monthly, and lobsters were photographed to measure changes in carapace length (CL). After 11 months in the field, lobsters increased 92% in mean size from 6.0- to 11.6-mm CL, with 70.8% overall survival. Headstarting of early benthic stage lobsters shows promise as a tool for possible future stock enhancement in LIS.
Understanding Social Resilience in the Maine Lobster Industry
Authors: Henry Anna M. , Johnson Teresa R.
Published: April 2015

The Maine lobster Homarus americanus fishery is considered one of the most successful fisheries in the world due in part to its unique comanagement system, the conservation ethic of the harvesters, and the ability of the industry to respond to crises and solve collective-action problems. However, recent threats raise the question whether the industry will be able to respond to future threats as successfully as it has to ones in the past or whether it is now less resilient and can no longer adequately respond to threats. Through ethnographic research and oral histories with fishermen, we examined the current level of social resilience in the lobster fishery. We concentrated on recent threats to the industry and the ways in which it has responded to them, focusing on three situations: a price drop beginning in 2008, a recovery in 2010–2011, and a second collapse of prices in 2012. In addition, we considered other environmental and regulatory concerns identified by fishermen. We found that the industry is not responding effectively to recent threats and identified factors that might explain the level of social resilience in the fishery.

Received August 20, 2013; accepted October 29, 2014
Against the New Metaphysics of Race
Authors: Ludwig David
Published: April 2015

The aim of this article is to develop an argument against metaphysical debates about the existence of human races. I argue that the ontology of race is underdetermined by both empirical and nonempirical evidence owing to a plurality of equally permissible candidate meanings of “race.” Furthermore, I argue that this underdetermination leads to a deflationist diagnosis according to which disputes about the existence of human races are nonsubstantive verbal disputes. While this diagnosis resembles general deflationist strategies in contemporary metaphysics, I show that my argument does not presuppose controversial metametaphysical assumptions.
Defining Paradigm Darwinian Populations
Authors: Matthewson John
Published: April 2015

This article presents an account of the biological populations that can undergo paradigmatic natural selection. I argue for, and develop Peter Godfrey-Smith’s claim that reproductive competition is a core attribute of such populations. However, as Godfrey-Smith notes, it is not the only important attribute. I suggest what the missing element is, co-opting elements of Alan Templeton’s notion of exchangeability. The final framework is then compared to two recent discussions regarding biological populations proposed by Roberta Millstein and Jacob Stegenga.
Bayesian analysis of a flow meter calibration problem
Authors: Kok G J P , van der Veen A M H , Harris P M , Smith I M , Elster C
Published: April 2015

A turbine flow meter indicates the volume of fluid flowing through the device per unit of time. Such a flow meter is commonly calibrated at a few known flow rates over its measurement range. A calibration curve relating the pulse factor of the meter to the flow rate is then fitted to calibration data using an ordinary least squares approach. This approach does not consider prior knowledge that may exist about the flow meter or the calibration procedure. A Bayesian analysis enables prior knowledge to be taken into account. A Bayesian inference results in a posterior distribution for the unknown parameters of the calibration curve that may be seen as the most comprehensive uncertainty information about these unknowns. This paper investigates for a flow meter calibration problem the effects of appreciating prior knowledge on values of the calibration curve and their associated uncertainties. It presents the results of a Bayesian analysis and compares them to those obtained by an ordinary least squares approach.
Universal enveloping algebras of Poisson Ore extensions
Authors: Lü Jiafeng , Wang Xingting , Zhuang Guangbin
Published: April 2015

We prove that the universal enveloping algebra of a Poisson-Ore extension is a length two iterated Ore extension of the original universal enveloping algebra. As a consequence, we observe certain ring-theoretic invariants of the universal enveloping algebras that are preserved under iterated Poisson-Ore extensions. We apply our results to iterated quadratic Poisson algebras arising from semiclassical limits of quantized coordinate rings and a family of graded Poisson algebras of Poisson structures of rank at most two.
Sutured Khovanov homology, Hochschild homology, and the Ozsváth-Szabó spectral sequence
Authors: Auroux Denis , Grigsby J. , Wehrli Stephan
Published: April 2015

In 2002, Khovanov-Seidel constructed a faithful action of the

(
m
+
1
)

(m+1)

–strand braid group,

B

m
+
1

\mathfrak {B}_{m+1}

, on the derived category of left modules over a quiver algebra,

A
m

A_m

. We interpret the Hochschild homology of the Khovanov-Seidel braid invariant as a direct summand of the sutured Khovanov homology of the annular braid closure.
Photosphere, thermalization surface and spectra of black hole accretion flows under electron scattering
Authors: Masuda Takao , Fukue Jun
Published: April 2015

We examine the expected spectra of black hole accretion flows, which are assumed to be steady and spherically symmetric, considering the separation of the apparent photosphere and thermalization surface under electron scattering. Although the flow itself is spherical, the apparent shape of the photosphere is not spherical, since the density distribution gradually decreases with radius. Furthermore, due to electron scattering, the thermalization surface decouples with the photosphere, and is located deep inside the photosphere for scattering-dominated flows. Since the shape of the thermalization surface is also aspherical, the temperature there is not uniform, which causes a strong limb-darkening effect, and we may observe a non-blackbody spectrum with multi-color-type.
Relationship between extreme ultraviolet microflares and small-scale magnetic fields in the quiet Sun
Authors: Jiang Fayu , Zhang Jun , Yang Shuhong
Published: April 2015

Microflares are small dynamic signatures observed in X-ray and extreme-ultraviolet channels. Because of their impulsive emission enhancements and wide distribution, they are thought to be closely related to coronal heating. By using the high-resolution 171 Å images from the Atmospheric Imaging Assembly and the lines-of-sight magnetograms obtained by the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we trace 10794 microflares in a quiet region near the disk center with a field of view of 960″ × 1068″ during 24 hr. The microflares have an occurrence rate of 4.4 × 103 hr−1 extrapolated over the whole Sun. Their average brightness, size, and lifetime are 1.7I0 (of the quiet Sun), 9.6 Mm2, and 3.6 min, respectively. There exists a mutual positive correlation between the microflares’ brightness, area, and lifetime. In general, the microflares distribute uniformly across the solar disk, but form network patterns locally, which are similar to and matched with the magnetic network structures. Typical cases show that the microflares prefer to occur in magnetic cancellation regions of network boundaries. We roughly calculate the upper limit of energy flux supplied by the microflares and find that the result is still a factor of ∼ 15 below the coronal heating requirement.
Suzaku observations of the old pulsar wind nebula candidate HESS J1356−645
Authors: Izawa Masaharu , Dotani Tadayasu , Fujinaga Takahisa , Bamba Aya , Ozaki Masanobu , Hiraga Junko S.
Published: April 2015

A largely extended X-ray emission was discovered around the pulsar PSR  J1357−6429 with the Suzaku deep observations. The pulsar, whose characteristic age is 7.3 kyr, is located within the TeV γ-ray source HESS J1356−645. The extended emission is found to have a 1 σ X-ray size of ∼ 4′, or ∼ 3 pc at 2.4 kpc, with a small offset from the pulsar. Its X-ray spectrum is well reproduced by a simple power-law model with a photon index of $1.70_{-0.06}^{+0.07}$. No significant spatial variation was found for the X-ray photon index as a function of distance from the pulsar. We conclude that the extended emission is associated to the pulsar wind nebula (PWN) of PSR  J1357−6429. This is a new sample of largely extended nebulae around middle-aged pulsars. We discuss the evolution of this PWN according to the relic PWN scenario.
Acoustic telemetry reveals cryptic residency of whale sharks
Authors: Cagua E. Fernando , Cochran Jesse E. M. , Rohner Christoph A. , Prebble Clare E. M. , Sinclair-Taylor Tane H. , Pierce Simon J. , Berumen Michael L.
Published: April 2015

Although whale sharks (
Rhincodon typus
) have been documented to move thousands of kilometres, they are most frequently observed at a few predictable seasonal aggregation sites. The absence of sharks at the surface during visual surveys has led to the assumption that sharks disperse to places unknown during the long ‘off-seasons’ at most of these locations. Here we compare 2 years of
R. typus
visual sighting records from Mafia Island in Tanzania to concurrent acoustic telemetry of tagged individuals. Sightings revealed a clear seasonal pattern with a peak between October and February and no sharks observed at other times. By contrast, acoustic telemetry demonstrated year-round residency of
R. typus
. The sharks use a different habitat in the off-season, swimming deeper and further away from shore, presumably in response to prey distributions. This behavioural change reduces the sharks' visibility, giving the false impression that they have left the area. We demonstrate, for the first time to our knowledge, year-round residency of unprovisioned, individual
R. typus
at an aggregation site, and highlight the importance of using multiple techniques to study the movement ecology of marine megafauna.
Multiscale modelling of the feto–placental vasculature
Authors: Clark A. R. , Lin M. , Tawhai M. , Saghian R. , James J. L.
Published: April 2015

The placenta provides all the nutrients required for the fetus through pregnancy. It develops dynamically, and, to avoid rejection of the fetus, there is no mixing of fetal and maternal blood; rather, the branched placental villi ‘bathe’ in blood supplied from the uterine arteries. Within the villi, the feto–placental vasculature also develops a complex branching structure in order to maximize exchange between the placental and maternal circulations. To understand the development of the placenta, we must translate functional information across spatial scales including the interaction between macro- and micro-scale haemodynamics and account for the effects of a dynamically and rapidly changing structure through the time course of pregnancy. Here, we present steps towards an anatomically based and multiscale approach to modelling the feto–placental circulation. We assess the effect of the location of cord insertion on feto–placental blood flow resistance and flow heterogeneity and show that, although cord insertion does not appear to directly influence feto–placental resistance, the heterogeneity of flow in the placenta is predicted to increase from a 19.4% coefficient of variation with central cord insertion to 23.3% when the cord is inserted 2 cm from the edge of the placenta. Model geometries with spheroidal and ellipsoidal shapes, but the same volume, showed no significant differences in flow resistance or heterogeneity, implying that normal asymmetry in shape does not affect placental efficiency. However, the size and number of small capillary vessels is predicted to have a large effect on feto–placental resistance and flow heterogeneity. Using this new model as an example, we highlight the importance of taking an integrated multi-disciplinary and multiscale approach to understand development of the placenta.
A multiscale model for the study of cardiac biomechanics in single-ventricle surgeries: a clinical case
Authors: Meoli Alessio , Cutrì Elena , Krishnamurthy Adarsh , Dubini Gabriele , Migliavacca Francesco , Hsia Tain-Yen , Pennati Giancarlo ,   Modeling of Congenital Hearts Alliance (MOCHA) Group, Taylor Andrew , Giardini Alessandro , Khambadkone Sachin , Schievano Silvia , de Leval Marc , Hsia T. -Y. , Bove Edward , Dorfman Adam , Baker G. Hamilton , Hlavacek Anthony , Migliavacca Francesco , Pennati Giancarlo , Dubini Gabriele , Marsden Alison , Feinstein Jeffrey , Vignon-Clementel Irene , Figliola Richard , McGregor John
Published: April 2015

Complex congenital heart disease characterized by the underdevelopment of one ventricular chamber (single ventricle (SV) circulation) is normally treated with a three-stage surgical repair. This study aims at developing a multiscale computational framework able to couple a patient-specific three-dimensional finite-element model of the SV to a patient-specific lumped parameter (LP) model of the whole circulation, in a closed-loop fashion. A sequential approach was carried out: (i) cardiocirculatory parameters were estimated by using a fully LP model; (ii) ventricular material parameters and unloaded geometry were identified by means of the stand-alone, three-dimensional model of the SV; and (iii) the three-dimensional model of SV was coupled to the LP model of the circulation, thus closing the loop and creating a multiscale model. Once the patient-specific multiscale model was set using pre-operative clinical data, the virtual surgery was performed, and the post-operative conditions were simulated. This approach allows the analysis of local information on ventricular function as well as global parameters of the cardiovascular system. This methodology is generally applicable to patients suffering from SV disease for surgical planning at different stages of treatment. As an example, a clinical case from stage 1 to stage 2 is considered here.
The inter-sample structural variability of regular tissue-engineered scaffolds significantly affects the micromechanical local cell environment
Authors: Campos Marin A. , Lacroix D.
Published: April 2015

Rapid prototyping techniques have been widely used in tissue engineering to fabricate scaffolds with controlled architecture. Despite the ability of these techniques to fabricate regular structures, the consistency with which these regular structures are produced throughout the scaffold and from one scaffold to another needs to be quantified. Small variations at the pore level can affect the local mechanical stimuli sensed by the cells thereby affecting the final tissue properties. Most studies assume rapid prototyping scaffolds as regular structures without quantifying the local mechanical stimuli at the cell level. In this study, a computational method using a micro-computed tomography-based scaffold geometry was developed to characterize the mechanical stimuli within a real scaffold at the pore level. Five samples from a commercial polycaprolactone scaffold were analysed and computational fluid dynamics analyses were created to compare local velocity and shear stress values at the same scaffold location. The five samples did not replicate the computer-aided design (CAD) scaffold and velocity and shear stress values were up to five times higher than the ones calculated in the CAD scaffold. In addition high variability among samples was found: at the same location velocity and shear stress values could be up to two times higher from sample to sample. This study shows that regular scaffolds need to be thoroughly analysed in order to quantify real cell mechanical stimuli so inspection methods should be included as part of the fabrication process.
Optimal control strategies of eradicating invisible glioblastoma cells after conventional surgery
Authors: de los Reyes V Aurelio A. , Jung Eunok , Kim Yangjin
Published: April 2015

Glioblastoma, the most aggressive type of brain cancer, has median survival time of 1 year after diagnosis. It is characterized by alternating modes of rapid proliferation and aggressive invasion in response to metabolic stress in the microenvironment. A particular microRNA, miR-451, and its downstream signalling molecules, AMPK complex, are known to be key determinants in switching cell fate. These components form a core control system determining a balance between cell growth and migration which is regulated by fluctuating glucose levels in the microenvironment. An important factor from the treatment point of view is that low levels of glucose affect metabolism and activate cell migration through the miR-451-AMPK control system, creating ‘invisible’ migratory cells and making them inaccessible by conventional surgery. In this work, we apply optimal control theory to deal with the problem of maintaining upregulated miR-451 levels that prevent cell infiltration to surrounding brain tissue and thus induce localization of these cancer cells at the surgical site. The model also considers the effect of a drug that blocks inhibitive pathways of miR-451 from AMPK complex. Glucose infusion control and drug infusion control are chosen to represent dose rates of glucose and drug intravenous administrations, respectively. The characteristics of optimal control lead us to investigate the structure of optimal intravenous infusion regimen under various circumstances and predict best clinical outcomes with minimum expense possible.
Coastal foredune evolution: the relative influence of vegetation and sand supply in the US Pacific Northwest
Authors: Zarnetske Phoebe L. , Ruggiero Peter , Seabloom Eric W. , Hacker Sally D.
Published: April 2015

Biophysical feedbacks between vegetation and sediment are important for forming and modifying landscape features and their ecosystem services. These feedbacks are especially important where landscape features differ in their provision of ecosystem services. For example, the shape of coastal foredunes, a product of both physical and biological forces, determines their ability to protect communities from rising seas and changing patterns of storminess. Here we assessed how sand supply and changes in vegetation over interannual (3 year) and decadal (21 year) scales influenced foredune shape along 100 km of coastline in the US Pacific Northwest. Across 21 years, vegetation switched from one congeneric non-native beachgrass to another (
Ammophila arenaria
to
A. breviligulata
) while sand supply rates were positive. At interannual timescales, sand supply rates explained the majority of change in foredune height (64–69%) and width (56–80%). However, at decadal scales, change in vegetation explained the majority of the change in foredune width (62–68%), whereas sand supply rates explained most of the change in foredune height (88–90%). In areas with lower shoreline change rates (±2 m yr
−1
), the change in vegetation explained the majority of decadal changes in foredune width (56–57%) and height (59–76%). Foredune shape directly impacts coastal protection, thus our findings are pertinent to coastal management given pressures of development and climate change.
Chloroform alters interleaflet coupling in lipid bilayers: an entropic mechanism
Authors: Reigada Ramon , Sagués Francesc
Published: April 2015

The interaction of the two leaflets of the plasmatic cell membrane is conjectured to play an important role in many cell processes. Experimental and computational studies have investigated the mechanisms that modulate the interaction between the two membrane leaflets. Here, by means of coarse-grained molecular dynamics simulations, we show that the addition of a small and polar compound such as chloroform alters interleaflet coupling by promoting domain registration. This is interpreted in terms of an entropic gain that would favour frequent chloroform commuting between the two leaflets. The implication of this effect is discussed in relation to the general anaesthetic action.
‘Parabolic’ trapped modes and steered Dirac cones in platonic crystals
Authors: McPhedran R. C. , Movchan A. B. , Movchan N. V. , Brun M. , Smith M. J. A.
Published: April 2015

This paper discusses the properties of flexural waves governed by the biharmonic operator, and propagating in a thin plate pinned at doubly periodic sets of points. The emphases are on the design of dispersion surfaces having the Dirac cone topology, and on the related topic of trapped modes in plates for a finite set (cluster) of pinned points. The Dirac cone topologies we exhibit have at least two cones touching at a point in the reciprocal lattice, augmented by another band passing through the point. We show that these Dirac cones can be steered along symmetry lines in the Brillouin zone by varying the aspect ratio of rectangular lattices of pins, and that, as the cones are moved, the involved band surfaces tilt. We link Dirac points with a parabolic profile in their neighbourhood, and the characteristic of this parabolic profile decides the direction of propagation of the trapped mode in finite clusters.
Stokes phenomena in discrete Painlevé I
Authors: Joshi N. , Lustri C. J.
Published: April 2015

In this study, we consider the asymptotic behaviour of the first discrete Painlevé equation in the limit as the independent variable becomes large. Using an asymptotic series expansion, we identify two types of solutions which are pole-free within some sector of the complex plane containing the positive real axis. Using exponential asymptotic techniques, we determine Stokes phenomena effects present within these solutions, and hence the regions in which the asymptotic series expression is valid. From a careful analysis of the switching behaviour across Stokes lines, we find that the first type of solution is uniquely defined, while the second type contains two free parameters, and that the region of validity may be extended for appropriate choice of these parameters.
The nature of nurture in a wild mammal's fitness
Authors: McFarlane S. Eryn , Gorrell Jamieson C. , Coltman David W. , Humphries Murray M. , Boutin Stan , McAdam Andrew G.
Published: April 2015

Genetic variation in fitness is required for the adaptive evolution of any trait but natural selection is thought to erode genetic variance in fitness. This paradox has motivated the search for mechanisms that might maintain a population's adaptive potential. Mothers make many contributions to the attributes of their developing offspring and these maternal effects can influence responses to natural selection if maternal effects are themselves heritable. Maternal genetic effects (MGEs) on fitness might, therefore, represent an underappreciated source of adaptive potential in wild populations. Here we used two decades of data from a pedigreed wild population of North American red squirrels to show that MGEs on offspring fitness increased the population's evolvability by over two orders of magnitude relative to expectations from direct genetic effects alone. MGEs are predicted to maintain more variation than direct genetic effects in the face of selection, but we also found evidence of maternal effect trade-offs. Mothers that raised high-fitness offspring in one environment raised low-fitness offspring in another environment. Such a fitness trade-off is expected to maintain maternal genetic variation in fitness, which provided additional capacity for adaptive evolution beyond that provided by direct genetic effects on fitness.
Stable isotopes reveal links between human food inputs and urban ant diets
Authors: Penick Clint A. , Savage Amy M. , Dunn Robert R.
Published: April 2015

The amount of energy consumed within an average city block is an order of magnitude higher than that consumed in any other ecosystem over a similar area. This is driven by human food inputs, but the consequence of these resources for urban animal populations is poorly understood. We investigated the role of human foods in ant diets across an urbanization gradient in Manhattan using carbon and nitrogen stable isotopes. We found that some—but not all—ant species living in Manhattan's most urbanized habitats had δ
13
C signatures associated with processed human foods. In particular, pavement ants (
Tetramorium
sp. E) had increased levels of δ
13
C similar to δ
13
C levels in human fast foods. The magnitude of this effect was positively correlated with urbanization. By contrast, we detected no differences in δ
15
N, suggesting
Tetramorium
feeds at the same trophic level despite shifting to human foods. This pattern persisted across the broader ant community; species in traffic islands used human resources more than park species. Our results demonstrate that the degree urban ants exploit human resources changes across the city and among species, and this variation could play a key role in community structure and ecosystem processes where human and animal food webs intersect.
Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities
Authors: Friman Ville-Petri , Guzman Laura Melissa , Reuman Daniel C. , Bell Thomas
Published: April 2015

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics.
Biogeography of worm lizards (Amphisbaenia) driven by end-Cretaceous mass extinction
Authors: Longrich Nicholas R. , Vinther Jakob , Pyron R. Alexander , Pisani Davide , Gauthier Jacques A.
Published: April 2015

Worm lizards (Amphisbaenia) are burrowing squamates that live as subterranean predators. Their underground existence should limit dispersal, yet they are widespread throughout the Americas, Europe and Africa. This pattern was traditionally explained by continental drift, but molecular clocks suggest a Cenozoic diversification, long after the break-up of Pangaea, implying dispersal. Here, we describe primitive amphisbaenians from the North American Palaeocene, including the oldest known amphisbaenian, and provide new and older molecular divergence estimates for the clade, showing that worm lizards originated in North America, then radiated and dispersed in the Palaeogene following the Cretaceous-Palaeogene (K-Pg) extinction. This scenario implies at least three trans-oceanic dispersals: from North America to Europe, from North America to Africa and from Africa to South America. Amphisbaenians provide a striking case study in biogeography, suggesting that the role of continental drift in biogeography may be overstated. Instead, these patterns support Darwin and Wallace's hypothesis that the geographical ranges of modern clades result from dispersal, including oceanic rafting. Mass extinctions may facilitate dispersal events by eliminating competitors and predators that would otherwise hinder establishment of dispersing populations, removing biotic barriers to dispersal.
Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait
Authors: Husby Arild , Kawakami Takeshi , Rönnegård Lars , Smeds Linnéa , Ellegren Hans , Qvarnström Anna
Published: April 2015

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.
Insect antimicrobial peptides show potentiating functional interactions against Gram-negative bacteria
Authors: Rahnamaeian Mohammad , Cytryńska Małgorzata , Zdybicka-Barabas Agnieszka , Dobslaff Kristin , Wiesner Jochen , Twyman Richard M. , Zuchner Thole , Sadd Ben M. , Regoes Roland R. , Schmid-Hempel Paul , Vilcinskas Andreas
Published: April 2015

Antimicrobial peptides (AMPs) and proteins are important components of innate immunity against pathogens in insects. The production of AMPs is costly owing to resource-based trade-offs, and strategies maximizing the efficacy of AMPs at low concentrations are therefore likely to be advantageous. Here, we show the potentiating functional interaction of co-occurring insect AMPs (the bumblebee linear peptides hymenoptaecin and abaecin) resulting in more potent antimicrobial effects at low concentrations. Abaecin displayed no detectable activity against
Escherichia coli
when tested alone at concentrations of up to 200 μM, whereas hymenoptaecin affected bacterial cell growth and viability but only at concentrations greater than 2 μM. In combination, as little as 1.25 μM abaecin enhanced the bactericidal effects of hymenoptaecin. To understand these potentiating functional interactions, we investigated their mechanisms of action using atomic force microscopy and fluorescence resonance energy transfer-based quenching assays. Abaecin was found to reduce the minimal inhibitory concentration of hymenoptaecin and to interact with the bacterial chaperone DnaK (an evolutionarily conserved central organizer of the bacterial chaperone network) when the membrane was compromised by hymenoptaecin. These naturally occurring potentiating interactions suggest that combinations of AMPs could be used therapeutically against Gram-negative bacterial pathogens that have acquired resistance to common antibiotics.
A simple model for the influence of habitat resource availability on lateral clonal spread
Authors: Weiser Martin , Smyčka Jan
Published: April 2015

Plant clonal spread is ubiquitous and of great interest, owing both to its key role in plant community assembly and its suitability for plant behaviour research. However, mechanisms that govern spreading distance are not well known. Here we link spacer costs and below-ground competition in a simple model of growth in a homogeneous below-ground environment, in which optimal distance between ramets is based on minimizing the sum of these costs. Using this model, we predict a high prevalence of clonal growth that does not employ spacers in resource-poor environments and a nonlinear increase in spreading distance in response to increasing below-ground resource availability. Analysis of database data on clonal growth in relationship to below-ground resource availability revealed that patterns of the spread based on stolons is compatible with the model's predictions. As expected, model prediction failed for rhizomatous species, where spacer sizes are likely to be selected mainly to play roles other than spread. The model's simplicity makes it useful as a null model in testing hypotheses about the effects of environmental heterogeneity on clonal spread.
Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment
Authors: Wang Yun-xiang , Huang Fa-qi , Nogi Yuichi , Pang Shou-ji , Wang Ping-kang , Lv Jie
Published: April 2015

A Gram-reaction-negative bacterial strain, designated fig4T, was isolated from a subsurface sediment core of Qiangtang Basin permafrost in China. Cells were catalase- and oxidase-positive and rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain fig4T was a member of the family Hyphomicrobiaceae and was most closely related to members of the genera Pelagibacterium, Vasilyevaea and Devosia with 93.8–96.2 % sequence similarities. The major cellular fatty acids were C16 : 0, C18 : 0, 11-methyl C18 : 1ω7c, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major respiratory quinone was Q-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The DNA G+C content was 60.7 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain fig4T is considered to represent a novel species of a new genus in the family Hyphomicrobiaceae, for which the name Youhaiella tibetensis gen. nov., sp. nov. is proposed. The type strain is fig4T ( = CGMCC 1.12719T = JCM 19854T).
Microbacterium enclense sp. nov., isolated from sediment sample
Authors: Mawlankar Rahul R. , Mual Poonam , Sonalkar Vidya V. , Thorat Meghana N. , Verma Ashish , Srinivasan Krishnamurthi , Dastager Syed G.
Published: April 2015

A novel bacterium (strain NIO-1002T) belonging to the genus Microbacterium was isolated from a marine sediment sample in Chorao Island, Goa Province, India. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Cells of this strain were Gram-stain-positive, non-motile, non-spore-forming rods that formed yellow-pigmented colonies. It grew in 0–12 % (w/v) NaCl and at 25–37 °C, with optimal growth at 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1002T is associated with members of the genus Microbacterium, with highest sequence similarity with Microbacterium hominis CIP 105731T (98.1 %) and Microbacterium testaceum KCTC 9103T (98.0 %). Within the phylogenetic tree, this novel strain shared a branching point with M. hominis CIP 105731T. The DNA G+C content was 66.5 mol% and DNA–DNA hybridization relatedness between NIO-1002T, M. hominis CIP 105731T and M. testaceum KCTC 9103T was 39.0 ± 2.0 % and 41.0 ± 2.0 %, respectively. The major fatty acids were ai-C15 : 0, i-C16 : 0 and ai-C17 : 0 and the diamino acid in the cell-wall peptidoglycan of NIO-1002T was lysine. Data obtained from DNA–DNA hybridization and chemotaxonomic phenotypic analysis support the conclusion that strain NIO-1002T represents a novel species within the genus Microbacterium. The name Microbacterium enclense sp. nov. is proposed, with NIO-1002T ( = NCIM 5454T = DSM 25125T = CCTCC AB 2011120T) as the type strain.
Simple genetic models for autism spectrum disorder
Authors: Mukhopadhyay Swagatam , Wigler Michael , Levy Dan
Published: April 2015

To explore the interplay between new mutation, transmission, and gender bias in genetic disease requires formal quantitative modeling. Autism spectrum disorders offer an ideal case: they are genetic in origin, complex, and show a gender bias. The high reproductive costs of autism ensure that most strongly associated genetic mutations are short-lived, and indeed the disease exhibits both transmitted andde novocomponents. There is a large body of both epidemiologic and genomic data that greatly constrain the genetic mechanisms that may contribute to the disorder. We develop a computational framework that assumes classes of additive variants, each member of a class having equal effect. We restrict our initial exploration to single class models, each having three parameters. Only one model matches epidemiological data. It also independently matches the incidence ofde novomutation in simplex families, the gender bias in unaffected siblings in simplex populations, and rates of mutation in target genes. This model makes strong and as yet not fully tested predictions, namely that females are the primary carriers in cases of genetic transmission, and that the incidence ofde novomutation in target genes for families at high risk for autism are not especially elevated. In its simplicity, this model does not account for MZ twin concordance or the distorted gender bias of high functioning children with ASD, and does not accommodate all the known mechanisms contributing to ASD. We point to the next steps in applying the same computational framework to explore more complex models.

Author summary

For understanding complex genetic diseases one needs both data and molecular/genetic models. In the absence of any model, it is impossible to do more than summarize observations. A good model will be consistent with much or all of the existing data and puts the data in the context of known genetic principles. Ideally the model will make testable predictions. Where the good models fail often shows the directions that require more thought about mechanisms. In this paper we describe a new computational framework that we use to explore a complex genetic disorder with many gene targets, with bothde novoand transmitted variants, and with gender bias. The disorder we consider is autism spectrum disorder (ASD), and our framework rules out some previous models that make unsustainable predictions. We identify a formal model that satisfies diverse epidemiologic and genomic observations. This model makes strong and untested predictions and thereby suggests new studies that would resolve outstanding aspects of autism genetics.