bluuebunny/crossref_metadata_2025 huggingface dataset:
Vertical shift register using dipolar interaction in magnetic multilayers
Authors: Chin Shin-Liang , Fernández-Pacheco Amalio , Petit Dorothée C. M. C. , Cowburn Russell P.
Published: December 2015

A vertical shift register consisting of multi-layered ferromagnetic bars with in-plane magnetization is investigated numerically using macrospin simulations. These layers are anti-ferromagnetically coupled via dipolar interactions and their in-plane aspect ratio determines their anisotropy. A single data bit is represented by a magnetic kink soliton, which forms at the boundary of two anti-parallel domains with opposite phases. It can be propagated bi-directionally using an externally applied rotating magnetic field. The soliton propagation is dependent on the applied field strength, the magnetic anisotropy of the ferromagnetic layers, and the dipolar coupling energies. For the device investigated here, the largest field range for soliton propagation is found to be from 35 Oe to 235 Oe at a lateral aspect ratio of 1.33. The soliton is also subjected to edge effects where it can be either pinned or reflected rather than being expelled from the stack. It is found that by reducing the thickness of the edge layer, these effects can be reduced substantially. By reducing the thickness of the edge layer by 20%, the field range in which the soliton is expelled increases by more than a factor of two.
Transformer ratio saturation in a beam-driven wakefield accelerator
Authors: Farmer J. P. , Martorelli R. , Pukhov A.
Published: December 2015

We show that for beam-driven wakefield acceleration, the linearly ramped, equally spaced train of bunches typically considered to optimise the transformer ratio only works for flat-top bunches. Through theory and simulation, we explain that this behaviour is due to the unique properties of the plasma response to a flat-top density profile. Calculations of the optimal scaling for a train of Gaussian bunches show diminishing returns with increasing bunch number, tending towards saturation. For a periodic bunch train, a transformer ratio of 23 was achieved for 50 bunches, rising to 40 for a fully optimised beam.
mTOR inhibition activates overall protein degradation by the ubiquitin proteasome system as well as by autophagy
Authors: Zhao Jinghui , Zhai Bo , Gygi Steven P. , Goldberg Alfred Lewis
Published: December 2015

Significance

Lack of nutrients or growth factors rapidly inhibits mTOR kinase and stimulates overall protein breakdown by autophagy, which provides amino acids for new protein synthesis and energy production. Here, we demonstrate that mTOR inhibition also rapidly increases overall protein degradation by the ubiquitin proteasome system by enhancing the ubiquitination of many cell proteins. These findings demonstrate a new general mechanism regulating overall protein breakdown in mammalian cells. This rapid activation of proteolysis not only slows growth and provides essential amino acids upon starvation, but also stimulates ubiquitin-dependent degradation of certain growth-related proteins, including HMG-CoA synthase, which is critical for cholesterol biosynthesis. Accelerated degradation of such proteins represents a new mechanism for rapid suppression of anabolic processes when mTORC1 activity decreases.
CytoGEDEVO—global alignment of biological networks with Cytoscape
Authors: Malek Maximilian , Ibragimov Rashid , Albrecht Mario , Baumbach Jan
Published: December 2015

Motivation: In the systems biology era, high-throughput omics technologies have enabled the unraveling of the interplay of some biological entities on a large scale (e.g. genes, proteins, metabolites or RNAs). Huge biological networks have emerged, where nodes correspond to these entities and edges between them model their relations. Protein–protein interaction networks, for instance, show the physical interactions of proteins in an organism. The comparison of such networks promises additional insights into protein and cell function as well as knowledge-transfer across species. Several computational approaches have been developed previously to solve the network alignment (NA) problem, but only a few concentrate on the usability of the implemented tools for the evaluation of protein–protein interactions by the end users (biologists and medical researchers).

Results: We have created CytoGEDEVO, a Cytoscape app for visual and user-assisted NA. It extends the previous GEDEVO methodology for global pairwise NAs with new graphical and functional features. Our main focus was on the usability, even by non-programmers and the interpretability of the NA results with Cytoscape.

Availability and implementation: CytoGEDEVO is publicly available from the Cytoscape app store at http://apps.cytoscape.org/apps/cytogedevo. In addition, we provide stand-alone command line executables, source code, documentation and step-by-step user instructions at http://cytogedevo.compbio.sdu.dk.

Contact:  malek@tugraz.at

Supplementary information:  Supplementary data are available at Bioinformatics online.
Observation of polarized hard X-ray emission from the Crab by the PoGOLite Pathfinder
Authors: Chauvin M. , Florén H.-G. , Jackson M. , Kamae T. , Kawano T. , Kiss M. , Kole M. , Mikhalev V. , Moretti E. , Olofsson G. , Rydström S. , Takahashi H. , Iyudin A. , Arimoto M. , Fukazawa Y. , Kataoka J. , Kawai N. , Mizuno T. , Ryde F. , Tajima H. , Takahashi T. , Pearce M.
Published: December 2015

We have measured the linear polarization of hard X-ray emission from the Crab in a previously unexplored energy interval, 20–120 keV. The introduction of two new observational parameters, the polarization fraction and angle stands to disentangle geometrical and physical effects, thereby providing information on the pulsar wind geometry and magnetic field environment. Measurements are conducted using the PoGOLite Pathfinder – a balloon-borne polarimeter. Polarization is determined by measuring the azimuthal Compton scattering angle of incident X-rays in an array of plastic scintillators housed in an anticoincidence well. The polarimetric response has been characterized prior to flight using both polarized and unpolarized calibration sources. We address possible systematic effects through observations of a background field. The measured polarization fraction for the integrated Crab light curve is $18.4^{+9.8}_{-10.6}$ per cent, corresponding to an upper limit (99 per cent credibility) of 42.4 per cent, for a polarization angle of (149.2 ± 16.0)°.
First-generation science cases for ground-based terahertz telescopes
Authors: Hirashita Hiroyuki , Koch Patrick M. , Matsushita Satoki , Takakuwa Shigehisa , Nakamura Masanori , Asada Keiichi , Liu Hauyu Baobab , Urata Yuji , Wang Ming-Jye , Wang Wei-Hao , Takahashi Satoko , Tang Ya-Wen , Chang Hsian-Hong , Huang Kuiyun , Morata Oscar , Otsuka Masaaki , Lin Kai-Yang , Tsai An-Li , Lin Yen-Ting , Srinivasan Sundar , Martin-Cocher Pierre , Pu Hung-Yi , Kemper Francisca , Patel Nimesh , Grimes Paul , Huang Yau-De , Han Chih-Chiang , Huang Yen-Ru , Nishioka Hiroaki , Lin Lupin Chun-Che , Zhang Qizhou , Keto Eric , Burgos Roberto , Chen Ming-Tang , Inoue Makoto , Ho Paul T. P.
Published: December 2015

Ground-based observations at terahertz (THz) frequencies are a newly explorable area of astronomy in the coming decades. We discuss science cases for a first-generation 10-m class THz telescope, focusing on the Greenland Telescope as an example of such a facility. We propose science cases and provide quantitative estimates for each case. The largest advantage of ground-based THz telescopes is their higher angular resolution (∼ 4″ for a 10-m dish), as compared to space or airborne THz telescopes. Thus, high-resolution mapping is an important scientific argument. In particular, we can isolate zones of interest for Galactic and extragalactic star-forming regions. The THz windows are suitable for observations of high-excitation CO lines and [N ii] 205-μm lines, which are scientifically relevant tracers of star formation and stellar feedback. Those lines are the brightest lines in the THz windows, so they are suitable for the initiation of ground-based THz observations. THz polarization of star-forming regions can also be explored since it traces the dust population contributing to the THz spectral peak. For survey-type observations, we focus on “sub-THz” extragalactic surveys, the uniqueness of which is detecting galaxies at redshifts z ∼ 1–2, where the dust emission per comoving volume is the largest in the history of the Universe. Finally we explore possibilities of flexible time scheduling, which enables us to monitor active galactic nuclei, and to target gamma-ray burst afterglows. For these objects, THz and submillimeter wavelength ranges have not yet been explored.
Biomechanical Analysis of an S1 Pedicle Screw Salvage Technique via a Superior Articulating Process Entry Point
Authors: Lee Yu-Po , Ihn Hansel E. , McGarry Michelle H. , Farhan Saifal-Deen , Bhatia Nitin , Lee Thay Q.
Published: December 2015

Study Design.

Biomechanical, cadaveric study.

Objective.

To compare the fixation strength of a novel S1 pedicle screw insertion technique in a revision setting to a standard S1 pedicle screw and an L5 pedicle screw.

Summary of Background Data.

Fusions to the sacrum remain a difficult clinical challenge. Very few salvage techniques exist when a nonunion occurs.

Methods.

The biomechanical integrity of three screw fixations, L5 pedicle screws, a standard S1 pedicle screw, and an S1 pedicle screw placed via a superior articulating process entry point (SAP S1), was characterized by performing pullout tests using cadaveric specimens including L5 and sacrum.

Results.

SAP S1 constructs (735.5 ± 110.1 N/mm) were significantly stiffer than standard S1 (P = 0.005) and L5 (P = 0.02) constructs. There was no statistically significant difference between the L5 constructs and the standard S1 constructs for linear stiffness. There was no statistical difference between the three fixations for yield load, displacement at yield load, and energy absorbed to yield load.

The ultimate pullout force for the SAP S1 was statistically higher than the standard S1 (1213.7 ± 579.6 vs. 478.6 ± 452.9 N; P = 0.004). Displacement at ultimate load was significantly greater for L5 screw fixation (3.3 ± 1.1 mm) compared to the other two constructs. Both the L5 (2277.4 ± 1873.3 N-mm) and SAP S1 (2628.2 ± 2054.4 N-mm) constructs had significantly greater energy absorbed to ultimate load than the standard S1 construct (811.7 ± 937.6 N-mm), but there was no statistical difference between the L5 and SAP S1 constructs.

Conclusion.

S1 pedicle screw fixation via an SAP entry point provides biomechanical advantages compared to screws placed via the standard S1 or L5 entry point and may be a viable option for revision of a failed L5-S1 fusion with a compromised standard S1 entry point.

Level of Evidence: N/A
MRI-Guided Stereotactic System for Delivery of Intraspinal Microstimulation
Authors: Grahn Peter J. , Goerss Stephan J. , Lujan J. Luis , Mallory Grant W. , Kall Bruce A. , Mendez Aldo A. , Trevathan James K. , Felmlee Joel P. , Bennet Kevin E. , Lee Kendall H.
Published: December 2015

Study Design.

Laboratory/animal-based proof of principle study.

Objective.

To validate the accuracy of a magnetic resonance imaging (MRI)-guided stereotactic system for intraspinal electrode targeting and demonstrate the feasibility of such a system for controlling implantation of intraspinal electrodes.

Summary of Background Data.

Intraspinal microstimulation (ISMS) is an emerging preclinical therapy, which has shown promise for the restoration of motor function following spinal cord injury. However, targeting inaccuracy associated with existing electrode implantation techniques remains a major barrier preventing clinical translation of ISMS.

Methods.

System accuracy was evaluated using a test phantom comprised of nine target locations. Targeting accuracy was determined by calculating the root mean square error between MRI-generated coordinates and actual frame coordinates required to reach the target positions. System performance was further validated in an anesthetized pig model by performing MRI-guided intraspinal electrode implantation and stimulation followed by computed tomography of electrode location. Finally, system compatibility with a commercially available microelectrode array was demonstrated by implanting the array and applying a selection of stimulation amplitudes that evoked hind limb responses.

Results.

The root mean square error between actual frame coordinates and software coordinates, both acquired using the test phantom, was 1.09 ± 0.20 mm. Postoperative computed tomography in the anesthetized pig confirmed spatially accurate electrode placement relative to preoperative MRI. Additionally, MRI-guided delivery of a microwire electrode followed by ISMS evoked repeatable electromyography responses in the biceps femoris muscle. Finally, delivery of a microelectrode array produced repeatable and graded hind limb evoked movements.

Conclusion.

We present a novel frame-based stereotactic system for targeting and delivery of intraspinal instrumentation. This system utilizes MRI guidance to account for variations in anatomy between subjects, thereby improving upon existing ISMS electrode implantation techniques.

Level of Evidence: N/A
US State-Level Policy Responses to the Ebola Outbreak, 2014-2015
Authors: Sell Tara Kirk , McGinty Emma E. , Pollack Keshia , Smith Katherine Clegg , Burke Thomas A. , Rutkow Lainie
Published: December 2015

Context:

The 2014-2015 Ebola epidemic in West Africa raised concerns about the potential occurrence of an Ebola outbreak in the United States. The federal government and individual states developed guidance and policies to determine how to manage individuals within the United States who may have been exposed to Ebola.

Design:

A total of 139 documents describing state policies for individuals considered at risk for Ebola and the requirements, as well as restrictions these individuals may be subject to, were systematically identified and analyzed.

Results:

A wide range of policy responses and variations on quarantine, movement restrictions, exposure categories, and monitoring were found. While the majority of states reflected US Centers for Disease Control and Prevention guidance, some states enacted aggressive quarantine policies and movement restrictions, developed unique categorization strategies, and established more frequent monitoring procedures.

Conclusions:

Findings may help public health practitioners and policymakers anticipate what policies could be implemented in response to future infectious disease threats. Furthermore, practitioners and policymakers should assume that some variation in response policies will occur at the state level.
Father's death does not affect growth and maturation but hinders reproduction: evidence from adolescent girls in post-war Estonia
Authors: Hõrak Peeter , Valge Markus
Published: December 2015

The popular concept of predictive–adaptive responses poses that girls growing up without a father present in the family mature and start reproduction earlier because the father's absence is a cue for environmental harshness and uncertainty that favours switching to a precocious life-history strategy. Most studies supporting this concept have been performed in situations where the father's absence is caused by divorce or abandonment. Using a dataset of Estonian adolescent girls who had lost their fathers over the period of World War II, we show that father's death did not affect the rate of pubertal maturation (assessed on the basis of development of breasts and axillary hair) or growth. Father's death did not affect the age of first birth but, contrary to predictions, reduced lifetime reproductive success. Our findings thus do not support the concept of predictive–adaptive responses and suggest that alternative explanations for covariation between fatherlessness and early maturation are required.
Predators modify the evolutionary response of prey to temperature change
Authors: Tseng M. , O'Connor M. I.
Published: December 2015

As climate regimes shift in many ecosystems worldwide, evolution may be a critical process allowing persistence in rapidly changing environments. Organisms regularly interact with other species, yet whether climate-mediated evolution can occur in the context of species interactions is not well understood. We tested whether a species interaction could modify evolutionary responses to temperature. We demonstrate that predation pressure by Dipteran larvae (
Chaoborus americanus
) modified the evolutionary response of a freshwater crustacean (
Daphnia pulex
) to its thermal environment over approximately seven generations in laboratory conditions.
Daphnia
kept at 21°C evolved higher population growth rates than those kept at 18°C, but only in those populations that were also reared with predators. Furthermore, predator-mediated selection resulted in the evolution of elevated
Daphnia
thermal plasticity. This laboratory natural selection experiment demonstrates that biotic interactions can modify evolutionary adaptation to temperature. Understanding the interplay between multiple selective forces can improve predictions of ecological and evolutionary responses of organisms to rapid environmental change.
Sir (Basil) John Mason CB. 18 August 1923 — 6 January 2015
Authors: Browning Keith A.
Published: December 2015

Sir John Mason will be remembered for establishing cloud microphysics as a coherent discipline and for building the Meteorological Office into a leading centre of excellence on the international stage. A charismatic man, he possessed scientific vision, enthusiasm and an inspiring style of lecturing and advocacy that enabled him to recruit good scientists and raise the funds needed to achieve these ends, although his manifest self-belief and forthright manner upset some. He was highly influential within international institutions such as the World Meteorological Organization and nationally as president of many scientific bodies and Senior Vice-President and Treasurer of the Royal Society from 1976 to 1986.
A generative inference framework for analysing patterns of cultural change in sparse population data with evidence for fashion trends in LBK culture
Authors: Kandler Anne , Shennan Stephen
Published: December 2015

Cultural change can be quantified by temporal changes in frequency of different cultural artefacts and it is a central question to identify what underlying cultural transmission processes could have caused the observed frequency changes. Observed changes, however, often describe the dynamics in samples of the population of artefacts, whereas transmission processes act on the whole population. Here we develop a modelling framework aimed at addressing this inference problem. To do so, we firstly generate population structures from which the observed sample could have been drawn randomly and then determine theoretical samples at a later timet2produced under the assumption that changes in frequencies are caused by a specific transmission process. Thereby we also account for the potential effect of time-averaging processes in the generation of the observed sample. Subsequent statistical comparisons (e.g. using Bayesian inference) of the theoretical and observed samples att2can establish which processes could have produced the observed frequency data. In this way, we infer underlying transmission processes directly from available data without any equilibrium assumption. We apply this framework to a dataset describing pottery from settlements of some of the first farmers in Europe (the LBK culture) and conclude that the observed frequency dynamic of different types of decorated pottery is consistent with age-dependent selection, a preference for ‘young’ pottery types which is potentially indicative of fashion trends.
Johann Peter Griess FRS (1829–88): Victorian brewer and synthetic dye chemist
Authors: Yates Edwin , Yates Andrew
Published: December 2015

The German organic chemist Johann Peter Griess (1829–88), who first developed the diazotization of aryl amines (the key reaction in the synthesis of the azo dyes), and a major figure in the formation of the modern dye industry, worked for more than a quarter of a century at the brewery of Samuel Allsopp and Sons in Burton upon Trent, which, owing to the presence of several notable figures and an increase in the scientific approach to brewing, became a significant centre of scientific enquiry in the 1870s and 1880s. Unlike the other Burton brewing chemists, Griess paralleled his work at the brewery with significant contributions to the chemistry of synthetic dyes, managing to keep the two activities separate—to the extent that some of his inventions in dye chemistry were filed as patents on behalf of the German dye company BASF, without the involvement of Allsopp's. This seemingly unlikely situation can be explained partly by the very different attitudes to patent protection in Britain and in Germany combined with an apparent indifference to the significant business opportunity that the presence of a leading dye chemist presented to Allsopp's. Although his work for the brewery remained largely proprietary, Griess's discoveries in dye chemistry were exploited by the German dye industry, which quickly outpaced its British counterpart. One less well-known connection between brewing and synthetic dyes, and one that may further explain Allsopp's attitude, is the use of synthetic dyes in identifying microorganisms—the perennial preoccupation of brewers seeking to maintain yield and quality. Developments of Griess's original work continue to be applied to many areas of science and technology.
Dual functionality of
O
-GlcNAc transferase is required for
Drosophila
development
Authors: Mariappa Daniel , Zheng Xiaowei , Schimpl Marianne , Raimi Olawale , Ferenbach Andrew T. , Müller H.-Arno J. , van Aalten Daan M. F.
Published: December 2015

Post-translational modification of intracellular proteins with
O
-linked
N
-acetylglucosamine (
O
-GlcNAc) catalysed by
O
-GlcNAc transferase (OGT) has been linked to regulation of diverse cellular functions. OGT possesses a C-terminal glycosyltransferase catalytic domain and N-terminal tetratricopeptide repeats that are implicated in protein–protein interactions.
Drosophila
OGT (
Dm
OGT) is encoded by
super sex combs
(
sxc
), mutants of which are pupal lethal. However, it is not clear if this phenotype is caused by reduction of
O
-GlcNAcylation. Here we use a genetic approach to demonstrate that post-pupal
Drosophila
development can proceed with negligible OGT catalysis, while early embryonic development is OGT activity-dependent. Structural and enzymatic comparison between human OGT (hOGT) and
Dm
OGT informed the rational design of
Dm
OGT point mutants with a range of reduced catalytic activities. Strikingly, a severely hypomorphic OGT mutant complements
sxc
pupal lethality. However, the hypomorphic OGT mutant-rescued progeny do not produce F2 adults, because a set of
Hox
genes is de-repressed in F2 embryos, resulting in homeotic phenotypes. Thus, OGT catalytic activity is required up to late pupal stages, while further development proceeds with severely reduced OGT activity.
Heat dissipation during hovering and forward flight in hummingbirds
Authors: Powers Donald R. , Tobalske Bret W. , Wilson J. Keaton , Woods H. Arthur , Corder Keely R.
Published: December 2015

Flying animals generate large amounts of heat, which must be dissipated to avoid overheating. In birds, heat dissipation is complicated by feathers, which cover most body surfaces and retard heat loss. To understand how birds manage heat budgets during flight, it is critical to know how heat moves from the skin to the external environment. Hummingbirds are instructive because they fly at speeds from 0 to more than 12 m s−1, during which they transit from radiative to convective heat loss. We used infrared thermography and particle image velocimetry to test the effects of flight speed on heat loss from specific body regions in flying calliope hummingbirds (Selasphorus calliope). We measured heat flux in a carcass with and without plumage to test the effectiveness of the insulation layer. In flying hummingbirds, the highest thermal gradients occurred in key heat dissipation areas (HDAs) around the eyes, axial region and feet. Eye and axial surface temperatures were 8°C or more above air temperature, and remained relatively constant across speeds suggesting physiological regulation of skin surface temperature. During hovering, birds dangled their feet, which enhanced radiative heat loss. In addition, during hovering, near-body induced airflows from the wings were low except around the feet (approx. 2.5 m s−1), which probably enhanced convective heat loss. Axial HDA and maximum surface temperature exhibited a shallow U-shaped pattern across speeds, revealing a localized relationship with power production in flight in the HDA closest to the primary flight muscles. We conclude that hummingbirds actively alter routes of heat dissipation as a function of flight speed.
Discretization of polynomial vector fields by polarization
Authors: Celledoni Elena , McLachlan Robert I. , McLaren David I. , Owren Brynjulf , Quispel G. R. W.
Published: December 2015

A novel integration method for quadratic vector fields was introduced by Kahan in 1993. Subsequently, it was shown that Kahan's method preserves a (modified) measure and energy when applied to quadratic Hamiltonian vector fields. Here we generalize Kahan's method to cubic resp. higher degree polynomial vector fields and show that the resulting discretization also preserves modified versions of the measure and energy when applied to cubic resp. higher degree polynomial Hamiltonian vector fields.
Slender-body theory for transient heat conduction: theoretical basis, numerical implementation and case studies
Authors: Beckers Koenraad F. , Koch Donald L. , Tester Jefferson W.
Published: December 2015

Slender-body theory (SBT) for transient heat transfer from bodies whose lengths are much larger than their radius into a conductive medium is derived. SBT uses matched asymptotic expansions of inner and outer solutions. An analytical inner solution for heat transfer from a circular cross section is matched to an outer solution obtained using Green’s functions. An efficient numerical implementation is obtained based on a judicious choice of the discrete elements used to represent the body and implementation of the fast multipole method (FMM). The SBT requires a one-dimensional spatial discretization only along the axis of the body in contrast to the three-dimensional discretization for finite-element models. Two case studies, heat transfer from two parallel cylinders and heat transfer from a slinky-coil heat exchanger, are used to show the speed and accuracy of the SBT model and its ability to model interacting slender bodies of finite length and bodies with centreline curvature and internal advective heat flow.
Nonlinear dynamics of wave-groups in random seas: unexpected walls of water in the open ocean
Authors: Adcock Thomas A. A. , Taylor Paul H. , Draper Scott
Published: December 2015

This paper investigates the size and structure of large waves on the open ocean. We investigate how nonlinear physics modifies waves relative to those predicted by a linear model. We run linear random simulations and extract extreme waves and the surrounding sea-state. For each extreme event, we propagate the waves back in time under linear evolution before propagating the wave-field forward using a nonlinear model. The differences between large linear and nonlinear wave-groups are then examined. The general trends are that under nonlinear evolution, relative to linear evolution, there is, on average, little or no extra amplitude in the nonlinear simulations; that there is an increase in the width of the crest of the wave-group and a contraction of large wave-groups in the mean wave direction; that large waves tend to move to the front of a wave-packet meaning that the locally largest wave is relatively bigger than the wave preceding it; and that nonlinearity can increase the duration of extreme wave events. In all these trends, there is considerable scatter, although the effects observed are clear. Our simulations show that nonlinearity does play an important part in the formation of extreme waves on deep water.
Striking cuticular hydrocarbon dimorphism in the mason waspOdynerus spinipesand its possible evolutionary cause (Hymenoptera: Chrysididae, Vespidae)
Authors: Wurdack Mareike , Herbertz Sina , Dowling Daniel , Kroiss Johannes , Strohm Erhard , Baur Hannes , Niehuis Oliver , Schmitt Thomas
Published: December 2015

Cleptoparasitic wasps and bees smuggle their eggs into the nest of a host organism. Here the larvae of the cleptoparasite feed upon the food provision intended for the offspring of the host. As cleptoparasitism incurs a loss of fitness for the host organism (offspring of the host fail to develop), hosts of cleptoparasites are expected to exploit cues that alert them to potential cleptoparasite infestation. Cuticular hydrocarbons (CHCs) could serve as such cues, as insects inevitably leave traces of them behind when entering a nest. By mimicking the host's CHC profile, cleptoparasites can conceal their presence and evade detection by their host. Previous studies have provided evidence of cleptoparasites mimicking their host's CHC profile. However, the impact of this strategy on the evolution of the host's CHC profile has remained unexplored. Here, we present results from our investigation of a host–cleptoparasite system consisting of a single mason wasp species that serves syntopically as the host to three cuckoo wasp species. We found that the spiny mason wasp (Odynerus spinipes) is able to express two substantially different CHC profiles, each of which is seemingly mimicked by a cleptoparasitic cuckoo wasp (i.e.Chrysis mediataandPseudospinolia neglecta). The CHC profile of the third cuckoo wasp (Chrysis viridula), a species not expected to benefit from mimicking its host's CHC profile because of its particular oviposition strategy, differs from the two CHC profiles of its host. Our results corroborate the idea that the similarity of the CHC profiles between cleptoparasitic cuckoo wasps and their hosts are the result of chemical mimicry. They further suggest that cleptoparasites may represent a hitherto unappreciated force that drives the evolution of their hosts' CHCs.
The evolutionary convergence of avian lifestyles and their constrained coevolution with species' ecological niche
Authors: Laiolo Paola , Seoane Javier , Illera Juan Carlos , Bastianelli Giulia , Carrascal Luis María , Obeso José Ramón
Published: December 2015

The fit between life histories and ecological niche is a paradigm of phenotypic evolution, also widely used to explain patterns of species co-occurrence. By analysing the lifestyles of a sympatric avian assemblage, we show that species' solutions to environmental problems are not unbound. We identify a life-history continuum structured on the cost of reproduction along a temperature gradient, as well as habitat-driven parental behaviour. However, environmental fit and trait convergence are limited by niche filling and by within-species variability of niche traits, which is greater than variability of life histories. Phylogeny, allometry and trade-offs are other important constraints: lifetime reproductive investment is tightly bound to body size, and the optimal allocation to reproduction for a given size is not established by niche characteristics but by trade-offs with survival. Life histories thus keep pace with habitat and climate, but under the limitations imposed by metabolism, trade-offs among traits and species' realized niche.
Are flies kind to kin? The role of intra- and inter-sexual relatedness in mediating reproductive conflict
Authors: Martin Emily S. , Long Tristan A. F.
Published: December 2015

As individual success often comes at the expense of others, interactions between the members of a species are frequently antagonistic, especially in the context of reproduction. In theory, this conflict may be reduced in magnitude when kin interact, as cooperative behaviour between relatives can result in increased inclusive fitness. Recent tests of the potential role of cooperative behaviour between brothers in
Drosophila melanogaster
have proved to be both exciting and controversial. We set out to replicate these experiments, which have profound implications for the study of kin selection and sexual conflict, and to expand upon them by also examining the potential role of kinship between males and females in reproductive interactions. While we did observe reduced fighting and courtship effort between competing brothers, contrary to previous studies we did not detect any fitness benefit to females as a result of the modification of male antagonistic behaviours. Furthermore, we did not observe any differential treatment of females by their brothers, as would be expected if the intensity of sexual conflict was mediated by kin selection. In the light of these results, we propose an alternative explanation for observed differences in male–male conflict and provide preliminary empirical support for this hypothesis.
Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria
Authors: Puttick Mark N. , Thomas Gavin H.
Published: December 2015

Most of life is extinct, so incorporating some fossil evidence into analyses of macroevolution is typically seen as necessary to understand the diversification of life and patterns of morphological evolution. Here we test the effects of inclusion of fossils in a study of the body size evolution of afrotherian mammals, a clade that includes the elephants, sea cows and elephant shrews. We find that the inclusion of fossil tips has little impact on analyses of body mass evolution; from a small ancestral size (approx. 100 g), there is a shift in rate and an increase in mass leading to the larger-bodied Paenungulata and Tubulidentata, regardless of whether fossils are included or excluded from analyses. For Afrotheria, the inclusion of fossils and morphological character data affect phylogenetic topology, but these differences have little impact upon patterns of body mass evolution and these body mass evolutionary patterns are consistent with the fossil record. The largest differences between our analyses result from the evolutionary model, not the addition of fossils. For some clades, extant-only analyses may be reliable to reconstruct body mass evolution, but the addition of fossils and careful model selection is likely to increase confidence and accuracy of reconstructed macroevolutionary patterns.
Intrinsic and realized generation intervals in infectious-disease transmission
Authors: Champredon David , Dushoff Jonathan
Published: December 2015

The generation interval is the interval between the time when an individual is infected by an infector and the time when this infector was infected. Its distribution underpins estimates of the reproductive number and hence informs public health strategies. Empirical generation-interval distributions are often derived from contact-tracing data. But linking observed generation intervals to the underlying generation interval required for modelling purposes is surprisingly not straightforward, and misspecifications can lead to incorrect estimates of the reproductive number, with the potential to misguide interventions to stop or slow an epidemic. Here, we clarify the theoretical framework for three conceptually different generation-interval distributions: the ‘intrinsic’ one typically used in mathematical models and the ‘forward’ and ‘backward’ ones typically observed from contact-tracing data, looking, respectively, forward or backward in time. We explain how the relationship between these distributions changes as an epidemic progresses and discuss how empirical generation-interval data can be used to correctly inform mathematical models.
Interactions among bacterial strains and fluke genotypes shape virulence of co-infection
Authors: Louhi Katja-Riikka , Sundberg Lotta-Riina , Jokela Jukka , Karvonen Anssi
Published: December 2015

Most studies of virulence of infection focus on pairwise host–parasite interactions. However, hosts are almost universally co-infected by several parasite strains and/or genotypes of the same or different species. While theory predicts that co-infection favours more virulent parasite genotypes through intensified competition for host resources, knowledge of the effects of genotype by genotype (G × G) interactions between unrelated parasite species on virulence of co-infection is limited. Here, we tested such a relationship by challenging rainbow trout with replicated bacterial strains and fluke genotypes both singly and in all possible pairwise combinations. We found that virulence (host mortality) was higher in co-infections compared with single infections. Importantly, we also found that the overall virulence was dependent on the genetic identity of the co-infecting partners so that the outcome of co-infection could not be predicted from the respective virulence of single infections. Our results imply that G × G interactions among co-infecting parasites may significantly affect host health, add to variance in parasite fitness and thus influence evolutionary dynamics and ecology of disease in unexpected ways.
Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment withEscherichia coli
Authors: Lenski Richard E. , Wiser Michael J. , Ribeck Noah , Blount Zachary D. , Nahum Joshua R. , Morris J. Jeffrey , Zaman Luis , Turner Caroline B. , Wade Brian D. , Maddamsetti Rohan , Burmeister Alita R. , Baird Elizabeth J. , Bundy Jay , Grant Nkrumah A. , Card Kyle J. , Rowles Maia , Weatherspoon Kiyana , Papoulis Spiridon E. , Sullivan Rachel , Clark Colleen , Mulka Joseph S. , Hajela Neerja
Published: December 2015

Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories ofEscherichia colipopulations over 50 000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10 000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely—or at least for a long time—even in a constant environment.
A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population
Authors: Prentice Honor C. , Li Yuan , Lönn Mikael , Tunlid Anders , Ghatnekar Lena
Published: December 2015

Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population.Festuca ovinais polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extraPgiClocus having been acquired horizontally from the distantly related grass genusPoa.We investigated variation atPgiCin samples ofF. ovinafrom a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions ofF. ovinaindividuals carrying the additionalPgiClocus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that thePgiCtransgene contributes, together with the unlinked ‘native’PgiClocus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats.
Emergent Patterns from Probabilistic Generalisations of Lateral Activation and Inhibition
Authors: Willis Lisa , Kabla Alexandre
Published: December 2015

The combination of laterally activating and inhibiting feedbacks is well known to spontaneously generate spatial organisation. It was introduced by Gierer and Meinhardt as an extension of Turing’s great insight, that two reacting and diffusing chemicals can spontaneously drive spatial morphogenesisper se. In this study, we develop an accessible nonlinear and discrete probabilistic model to study simple generalisations of lateral activation and inhibition. By doing so, we identify novel modes of morphogenesis beyond the familiar Turing-type modes; notably, beyond stripes, hexagonal nets, pores, and labyrinths, we identify labyrinthine highways, Kagome lattices, gyrating labyrinths, and multi-colour travelling waves and spirals. The results are discussed within the context of Turing’s original motivating interest: the mechanisms which underpin the morphogenesis of living organisms.
Independent evolution of ab- and adaxial stomatal density enables adaptation
Authors: Muir Christopher David , Conesa Miquel Àngel , Galmés Jeroni
Published: December 2015

Are organisms free to reach their adaptive optima or constrained by hard-wired developmental programs? Recent evidence suggests that the arrangement of stomata on abaxial (lower) and adaxial (upper) leaf surfaces may be an important adaptation in plants, but stomatal traits on each surface likely share developmental pathways that could hamper evolution. We reviewed the quantitative genetics of stomatal density to look for loci that (1) affected ab- or adaxial density independently or (2) pleiotropically affected stomatal density on both surfaces. We also used phylogenetic comparative methods to test for independent versus correlated evolution of stomatal traits (density, size, and pore index) on each surface from 14 amphistomatous wild tomato taxa (Solanum; Solanaceae). Naturally occurring and laboratory-induced genetic variation alters stomatal density on one surface without affecting the other, indicating that development does not strongly constrain the spectrum of available mutations. Among wild tomato taxa, traits most closely related to function (stomatal pore index and density) evolved independently on each surface, whereas stomatal size was constrained by correlated evolution. Genetics and phylogenetics demonstrate mostly independent evolution of stomatal function on each leaf surface, facilitating largely unfettered access to fitness optima.
Event Extraction from Biomedical Literature
Authors: M.A. Basher Abdur Rahman , Purdy Alexander S. , Birol Inanç
Published: December 2015

The breadth and scope of the biomedical literature hinders a timely and thorough comprehension of its content. PubMed, the leading repository for biomedical literature, currently holds over 26 million records, and is growing at a rate of over 1.2 million records per year, with about 300 records added daily that mention ‘cancer’ in the title or abstract. Natural language processing (NLP) can assist in accessing and interpreting this massive volume of literature, including its quality NLP approaches to the automatic extraction of biomedical entities and relationships may assist the development of explanatory models that can comprehensively scan and summarize biomedical articles for end users. Users can also formulate structured queries against these entities, and their interactions, to mine the latest developments in related areas of interest. In this article, we explore the latest advances in automated event extraction methods in the biomedical domain, focusing primarily on tools participated in the Biomedical NLP (BioNLP) Shared Task (ST) competitions. We review the leading BioNLP methods, summarize their results, and their innovative contributions in this field.
A Multiscale Framework for Deconstructing the Ecosystem Physical Template of High-Altitudes Lakes
Authors: Zaharescu Dragos G. , Hooda Peter S. , Burghelea Carmen I. , Palanca-Soler Antonio
Published: December 2015

An ecosystem is generally sustained by a set of integrated physical elements forming a functional landscape unit – ecotope, which supplies nutrients, microclimate, and exchanges matter and energy with the wider environment. To better predict environmental change effects on ecosystems, particularly in critically sensitive regions such as high altitudes, it is imperative to recognise how their natural landscape heterogeneity works at different scales to shape habitats and sustain biotic communities prior to major changes.

We conducted a comprehensive survey of catchment physical, geological and ecological properties of 380 high altitude lakes and ponds in the axial Pyrenees at a variety of scales, in order to formulate and test an integrated model encompassing major flows and interactions that drive lake ecosystems.

Three composite drivers encompassed most of the variability in lake catchment characteristics. In order of total percentage of variance explained they were: (i) hydrology/hydrodynamics-responsible for type and discharge of inlets/outlets, and for water body size; (ii) bedrock geomorphology, summarizing geology, slope and fractal order-all dictating vegetation cover of catchment slope and lake shore, and the presence of aquatic vegetation; and, (iii) topography, i.e. catchment formation type-driving lakes connectivity, and the presence of summer snow deposits. While driver (i) appeared to be local, (ii) and (iii) showed gradient changes along altitude and latitude. These three drivers differentiated several lake ecotopes based on their landscape similarities. The three-driver model was successfully tested on a riparian vegetation composition dataset, further illustrating the validity and fundamental nature of the concept.

The findings inform on the relative contribution of scale-dependent catchment physical elements to lake ecotope and ecosystem formation in high altitude lakes, which should be considered in any assessment of potentially major deleterious effects due to environmental/climate change.

Abstract Figure

Lake Bassia at 2275m a.s.l. in the Pyrenees National Park, France, is one of the millions of remote high altitude lakes worldwide whose catchments are likely to experience severe effects due to climate change. Photo credit: Antonio Palanca-Soler.