bluuebunny/crossref_metadata_2025 huggingface dataset:
Hole mobility modulation of solution-processed nickel oxide thin-film transistor based on high-k dielectric
Authors: Liu Ao , Liu Guoxia , Zhu Huihui , Shin Byoungchul , Fortunato Elvira , Martins Rodrigo , Shan Fukai
Published: June 2016

Solution-processed p-type oxide semiconductors have recently attracted increasing interests for the applications in low-cost optoelectronic devices and low-power consumption complementary metal-oxide-semiconductor circuits. In this work, p-type nickel oxide (NiOx) thin films were prepared using low-temperature solution process and integrated as the channel layer in thin-film transistors (TFTs). The electrical properties of NiOx TFTs, together with the characteristics of NiOx thin films, were systematically investigated as a function of annealing temperature. By introducing aqueous high-k aluminum oxide (Al2O3) gate dielectric, the electrical performance of NiOx TFT was improved significantly compared with those based on SiO2 dielectric. Particularly, the hole mobility was found to be 60 times enhancement, quantitatively from 0.07 to 4.4 cm2/V s, which is mainly beneficial from the high areal capacitance of the Al2O3 dielectric and high-quality NiOx/Al2O3 interface. This simple solution-based method for producing p-type oxide TFTs is promising for next-generation oxide-based electronic applications.
Ferroelectricity and ferroelectric resistive switching in sputtered Hf0.5Zr0.5O2 thin films
Authors: Fan Zhen , Xiao Juanxiu , Wang Jingxian , Zhang Lei , Deng Jinyu , Liu Ziyan , Dong Zhili , Wang John , Chen Jingsheng
Published: June 2016

Ferroelectric properties and ferroelectric resistive switching (FE-RS) of sputtered Hf0.5Zr0.5O2 (HZO) thin films were investigated. The HZO films with the orthorhombic phase were obtained without capping or post-deposition annealing. Ferroelectricity was demonstrated by polarization-voltage (P-V) hysteresis loops measured in a positive-up negative-down manner and piezoresponse force microscopy. However, defects such as oxygen vacancies caused the films to become leaky. The observed ferroelectricity and semiconducting characteristics led to the FE-RS effect. The FE-RS effect may be explained by a polarization modulated trap-assisted tunneling model. Our study not only provides a facile route to develop ferroelectric HfO2-based thin films but also explores their potential applications in FE-RS memories.
Formation of blade and slot die coated small molecule multilayers for OLED applications studied theoretically and by XPS depth profiling
Authors: Peters Katharina , Raupp Sebastian , Hummel Helga , Bruns Michael , Scharfer Philip , Schabel Wilhelm
Published: June 2016

Slot die coaters especially designed for low material consumption and doctor blades were used to process small molecule solutions for organic light-emitting diodes (OLEDs). Optimum process parameters were developed for the large-scale coating techniques to generate stable single and multiple layers only a few nanometers thick. Achieving a multilayer architecture for solution-processed OLEDs is the most challenging step. X-ray photoelectron spectroscopy sputter depth profiling was performed to determine defined interfaces between coated organic layers. Commercially available small molecules NPB (N,N’-Di(1-naphthyl)-N,N’-diphenyl-(1,1’-biphenyl)-4,4’-diamine) and BAlq (Bis(8-hdroxy-2methylquinoline)-(4-phenylphenoxy)aluminum), originally developed for vacuum deposition, were used as hole, respectively electron transport material. Defined double-layers were processed with both scalable coating methods using the orthogonal solvent approach. The use of non-orthogonal solvents resulted in complete intermixing of the material. The results are explained by calculations of solubilities and simulating drying and diffusion kinetics of the small molecule solutions.
Mapped orthogonal functions method applied to acoustic waves-based devices
Authors: Lefebvre J. E. , Yu J. G. , Ratolojanahary F. E. , Elmaimouni L. , Xu W. J. , Gryba T.
Published: June 2016

This work presents the modelling of acoustic wave-based devices of various geometries through a mapped orthogonal functions method. A specificity of the method, namely the automatic incorporation of boundary conditions into equations of motion through position-dependent physical constants, is presented in detail. Formulations are given for two classes of problems: (i) problems with guided mode propagation and (ii) problems with stationary waves. The method’s interest is demonstrated by several examples, a seven-layered plate, a 2D rectangular resonator and a 3D cylindrical resonator, showing how it is easy to obtain either dispersion curves and field profiles for devices with guided mode propagation or electrical response for devices with stationary waves. Extensions and possible further developments are also given.
Influence of Acacia tortilis leaf meal-based diet on serum biochemistry, carcass characteristics and internal organs of finishing pigs
Authors: Khanyile M. , Ndou S. P. , Chimonyo M.
Published: June 2016

Dietary inclusion of tannin-rich leguminous leaf meals beyond threshold levels can impose toxicity and compromise welfare of pigs. The objective of the study was to determine the response of metabolites, carcass characteristics and internal organs of finishing pigs to Acacia tortilis leaf meal inclusion levels. Thirty Large White × Landrace pigs (61.6 ± 1.23 kg bodyweight) were randomly allotted to six dietary treatments, to give five replicates per treatment. The treatments contained 0, 50, 100, 150, 200 and 250 g/kg of A. tortilis leaf meal and were rendered iso-energetic and iso-nitrogenous. An increase in A. tortilis inclusion was related to an initial increase and then a decrease in feed intake (P < 0.05), weight gain (P < 0.001) and feed conversion ratio (P < 0.05). Serum concentrations of iron and activities of aspartate aminotransferase and alkaline phosphatases increased quadratically (P < 0.001) as A. tortilis leaf meal increased. There was a significant linear increase in alanine aminotransferase activity with leaf meal incremental level. Hepatosomatic index, scaled kidney weight and scaled heart weight increased linearly (P < 0.001) as A. tortilis increased. There was a quadratic increase in the relative weight of lungs (P < 0.001) as leaf meal increased. Although quadratic decreases (P < 0.01) in cold-dressed mass and dressing percentage were observed with incremental levels of A. tortilis leaf meal, there was a linear decrease (P < 0.05) in backfat thickness. It was concluded that serum biochemistry, internal organs and carcass characteristics respond differently to increases in A. tortilis inclusion. The A. tortilis leaf meal can be supplemented in finishing pig diets at low levels before feed efficiency and carcass characteristics are negatively affected.
Influence of climate variability and stocking strategies on greenhouse gas emissions (GHGE), production and profit of a northern Queensland beef cattle herd
Authors: Cullen Brendan R. , MacLeod Neil D. , Scanlan Joe C. , Doran-Browne Natalie
Published: June 2016

Previous studies of greenhouse gas emissions (GHGE) from beef production systems in northern Australia have been based on models of ‘steady-state’ herd structures that do not take into account the considerable inter-annual variation in liveweight gain, reproduction and mortality rates that occurs due to seasonal conditions. Nor do they consider the implications of flexible stocking strategies designed to adapt these production systems to the highly variable climate. The aim of the present study was to quantify the variation in total GHGE (t CO2e) and GHGE intensity (t CO2e/t liveweight sold) for the beef industry in northern Australia when variability in these factors was considered. A combined GRASP–Enterprise modelling platform was used to simulate a breeding–finishing beef cattle property in the Burdekin River region of northern Queensland, using historical climate data from 1982–2011. GHGE was calculated using the method of Australian National Greenhouse Gas Inventory. Five different stocking-rate strategies were simulated with fixed stocking strategies at moderate and high rates, and three flexible stocking strategies where the stocking rate was adjusted annually by up to 5%, 10% or 20%, according to pasture available at the end of the growing season. Variation in total annual GHGE was lowest in the ‘fixed moderate’ (~9.5 ha/adult equivalent (AE)) stocking strategy, ranging from 3799 to 4471 t CO2e, and highest in the ‘fixed high’ strategy (~5.9 ha/AE), which ranged from 3771 to 7636 t CO2e. The ‘fixed moderate’ strategy had the least variation in GHGE intensity (15.7–19.4 t CO2e/t liveweight sold), while the ‘flexible 20’ strategy (up to 20% annual change in AE) had the largest range (10.5–40.8 t CO2e/t liveweight sold). Across the five stocking strategies, the ‘fixed moderate’ stocking-rate strategy had the highest simulated perennial grass percentage and pasture growth, highest average rate of liveweight gain (121 kg/steer), highest average branding percentage (74%) and lowest average breeding-cow mortality rate (3.9%), resulting in the lowest average GHGE intensity (16.9 t CO2e/t liveweight sold). The ‘fixed high’ stocking rate strategy (~5.9 ha/AE) performed the poorest in each of these measures, while the three flexible stocking strategies were intermediate. The ‘fixed moderate’ stocking strategy also yielded the highest average gross margin per AE carried and per hectare. These results highlight the importance of considering the influence of climate variability on stocking-rate management strategies and herd performance when estimating GHGE. The results also support a body of previous work that has recommended the adoption of moderate stocking strategies to enhance the profitability and ecological stability of beef production systems in northern Australia.
Biochar amendment altered the molecular-level composition of native soil organic matter in a temperate forest soil
Authors: Mitchell Perry J. , Simpson André J. , Soong Ronald , Simpson Myrna J.
Published: June 2016

Environmental contextBiochar amendment in soil can sequester carbon but may also stimulate microbial activity, potentially enhancing soil organic matter degradation. We incubated biochar in a temperate forest soil and characterised the soil organic matter composition using molecular-level biomarker and nuclear magnetic resonance techniques. Biochar amendment altered the native soil organic matter composition and decreased the concentration of easily degradable soil organic matter components.
AbstractBiochar amendment in soil can sequester carbon and improve soil water and nutrient retention, fertility and plant productivity. However, biochar may stimulate microbial activity, leading to priming or accelerated soil organic matter (OM) degradation, which could alter the native soil OM molecular composition. To investigate this, we amended sugar maple wood biochar (pyrolysed at 500°C) at four concentrations (0, 5, 10 and 20 metric tons per hectare) in a temperate forest soil for 32 weeks. Solvent extraction and CuO oxidation were used to characterise free compounds and lignin-derived phenols respectively at 8 week intervals, while base hydrolysis was used to examine plant wax, cutin and suberin components at the end of the incubation. Stimulated soil microbial activity following an adaptation period (16 weeks) resulted in increased inputs of microbial- and plant-derived soil OM components including solvent-extractable short-chain n-alkanols and n-alkanoic acids, long-chain n-alkanes and n-alkanols, and sugars. Degradation parameters for base-hydrolysable cutin- and suberin-derived compounds did not show any significant degradation of these plant biopolymers. Analysis of lignin-derived phenols revealed lower concentrations of extractable phenols and progressive oxidation of syringyl and vanillyl phenols at higher biochar application rates over time. Solution-state 1H nuclear magnetic resonance analysis of base-extractable soil OM after 32 weeks showed a decrease in the proportion of labile OM components such as carbohydrates and peptides and a relative increase in more recalcitrant polymethylene OM constituents in the amended soils. The biochar-mediated shifts in soil OM composition and reduction in labile carbon may reduce soil fertility in biochar-amended systems with long-term amendment.
Jubaland: Somalia’s new security dilemma and state-building efforts
Authors: Mwangi Oscar Gakuo
Published: June 2016

The creation of a buffer state aimed at providing a political and security zone is normally the initiative of powerful states within the region it is being established. Globalization has, however, placed buffer states at the centre of the new security dilemma creating national and transnational security risks that adversely impact on the capacity of neighbouring states to effectively perform their basic functions. The establishment of Somalia’s newest semiautonomous region Jubaland, perceived as Kenya’s buffer zone, has created a new security dilemma for Somalia. This article examines the relationship between the creation of Jubaland and the national and transnational security risks it poses for Somalia’s state capacity building efforts. The mutually related national and transnational security risks examined emanate from the adverse effects of Somali clan/militia conflicts and Kenya Defence Forces operations in Jubaland as part of the African Union Mission in Somalia. These security risks have adversely impacted on state capacity and state autonomy hence hindering the ability of the collapsed Somali state to re-build itself and effectively provide political-military security.
Facilitation of axon regeneration by enhancing mitochondrial transport and rescuing energy deficits
Authors: Zhou Bing , Yu Panpan , Lin Mei-Yao , Sun Tao , Chen Yanmin , Sheng Zu-Hang
Published: June 2016

Although neuronal regeneration is a highly energy-demanding process, axonal mitochondrial transport progressively declines with maturation. Mature neurons typically fail to regenerate after injury, thus raising a fundamental question as to whether mitochondrial transport is necessary to meet enhanced metabolic requirements during regeneration. Here, we reveal that reduced mitochondrial motility and energy deficits in injured axons are intrinsic mechanisms controlling regrowth in mature neurons. Axotomy induces acute mitochondrial depolarization and ATP depletion in injured axons. Thus, mature neuron-associated increases in mitochondria-anchoring protein syntaphilin (SNPH) and decreases in mitochondrial transport cause local energy deficits. Strikingly, enhancing mitochondrial transport via genetic manipulation facilitates regenerative capacity by replenishing healthy mitochondria in injured axons, thereby rescuing energy deficits. An in vivo sciatic nerve crush study further shows that enhanced mitochondrial transport in snph knockout mice accelerates axon regeneration. Understanding deficits in mitochondrial trafficking and energy supply in injured axons of mature neurons benefits development of new strategies to stimulate axon regeneration.
Constructing Space for Dissent in War: The Bombing Restriction Committee, 1941–1945
Authors: Overy Richard
Published: June 2016

The prevailing view of the British public’s response to the RAF bomber offensive during the Second World War suggests that there was widespread and even enthusiastic support for the bombing aside from a small number of prominent individuals, chiefly the writer Vera Brittain and the Bishop of Chichester, George Bell. This article challenges the view that there was little overt dissent over the bombing campaign by looking at the origins, activity and impact of the Bombing Restriction Committee, the title given in 1942 to the Committee for the Abolition of Night Bombing founded in August 1941. The Committee undertook a wide range of activity in protest first against night-bombing, and then more generally against the RAF’s shift to area bombing in 1941–2. The article examines the network of supporters that the committee developed and the nature and extent of its propaganda, and addresses the question of why the protest against a major aspect of British strategy was allowed to continue throughout the war without serious interference. The result suggests that the ideal of a ‘democratic consensus’ in Britain was not realised on this issue; instead it can be argued that official tolerance for protest demonstrated more clearly Britain’s democratic credentials, while it allowed the Committee to keep alive the evolving humanitarian concern of sections of pre-war British society, and to sustain those concerns on into the nuclear age.
Implementation and performance of FDPS: a framework for developing parallel particle simulation codes
Authors: Iwasawa Masaki , Tanikawa Ataru , Hosono Natsuki , Nitadori Keigo , Muranushi Takayuki , Makino Junichiro
Published: June 2016

We present the basic idea, implementation, measured performance, and performance model of FDPS (Framework for Developing Particle Simulators). FDPS is an application-development framework which helps researchers to develop simulation programs using particle methods for large-scale distributed-memory parallel supercomputers. A particle-based simulation program for distributed-memory parallel computers needs to perform domain decomposition, exchange of particles which are not in the domain of each computing node, and gathering of the particle information in other nodes which are necessary for interaction calculation. Also, even if distributed-memory parallel computers are not used, in order to reduce the amount of computation, algorithms such as the Barnes–Hut tree algorithm or the Fast Multipole Method should be used in the case of long-range interactions. For short-range interactions, some methods to limit the calculation to neighbor particles are required. FDPS provides all of these functions which are necessary for efficient parallel execution of particle-based simulations as “templates,” which are independent of the actual data structure of particles and the functional form of the particle–particle interaction. By using FDPS, researchers can write their programs with the amount of work necessary to write a simple, sequential and unoptimized program of O(N2) calculation cost, and yet the program, once compiled with FDPS, will run efficiently on large-scale parallel supercomputers. A simple gravitational N-body program can be written in around 120 lines. We report the actual performance of these programs and the performance model. The weak scaling performance is very good, and almost linear speed-up was obtained for up to the full system of the K computer. The minimum calculation time per timestep is in the range of 30 ms (N = 107) to 300 ms (N = 109). These are currently limited by the time for the calculation of the domain decomposition and communication necessary for the interaction calculation. We discuss how we can overcome these bottlenecks.
Evidence for cohesin sliding along budding yeast chromosomes
Authors: Ocampo-Hafalla Maria , Muñoz Sofía , Samora Catarina P. , Uhlmann Frank
Published: June 2016

The ring-shaped cohesin complex is thought to topologically hold sister chromatids together from their synthesis in S phase until chromosome segregation in mitosis. How cohesin stably binds to chromosomes for extended periods, without impeding other chromosomal processes that also require access to the DNA, is poorly understood. Budding yeast cohesin is loaded onto DNA by the Scc2–Scc4 cohesin loader at centromeres and promoters of active genes, from where cohesin translocates to more permanent places of residence at transcription termination sites. Here we show that, at theGAL2andMET17loci, pre-existing cohesin is pushed downstream along the DNA in response to transcriptional gene activation, apparently without need for intermittent dissociation or reloading. We observe translocation intermediates and find that the distribution of most chromosomal cohesin is shaped by transcription. Our observations support a model in which cohesin is able to slide laterally along chromosomes while maintaining topological contact with DNA. In this way, stable cohesin binding to DNA and enduring sister chromatid cohesion become compatible with simultaneous underlying chromosomal activities, including but maybe not limited to transcription.
Connecting caddisworm silk structure and mechanical properties: combined infrared spectroscopy and mechanical analysis
Authors: Ashton Nicholas N. , Pan Huaizhong , Stewart Russell J.
Published: June 2016

The underwater silk of an aquatic casemaking caddisfly larvae (
Hesperophylax occidentalis)
is viscoelastic, and displays distinct yield behaviour, large strain cycle hysteresis and near complete recovery of its initial strength and stiffness when unloaded. Yield followed by a stress plateau has been attributed to sequential rupture of serial Ca
2+
-cross-linked phosphoserine (pS) β-domains. Spontaneous recovery has been attributed to refolding of the Ca
2+
/pS domains powered by an elastic network. In this study, native Ca
2+
ions were exchanged with other metal ions, followed by combined mechanical and FTIR analysis to probe the contribution of pS/metal ion complexes to silk mechanical properties. After exchange of Ca
2+
with Na
+
, the fibres are soft elastomers and the infrared spectra are consistent with C
v3
symmetry of the –

groups. Multivalent metal ions decreased the –

symmetry and the symmetric stretching modes (
v
s
) split in a manner characteristic of ordered phosphate compounds, such as phosphate minerals and lamellar bilayers of phosphatidic acid lipids. Integrated intensities of the
v
s
bands, indicative of the metal ion's effect on transition dipole moment of the P–O bonds, and thereby the strength of the phosphate metal complex, increased in the order: Na
+
< Mg
2+
< Sr
2+
< Ba
2+
< Ca
2+
< Eu
3+
< La
3+
< Zn
2+
< Fe
2+
. With a subset of the metal ion series, the initial stiffness and yield stress of metal ion-exchanged fibres increased in the same order:

establishing the link between phosphate transition dipole moments and silk fibre strength.
Effects on a Landau-type system for a neutral particle with no permanent electric dipole moment subject to the Kratzer potential in a rotating frame
Authors: Oliveira Abinael B. , Bakke Knut
Published: June 2016

The behaviour of a neutral particle (atom, molecule) with an induced electric dipole moment in a region with a uniform effective magnetic field under the influence of the Kratzer potential (Kratzer 1920Z. Phys.3, 289–307. (doi:10.1007/BF01327754)), and rotating effects is analysed. It is shown that the degeneracy of the Landau-type levels is broken and the angular frequency of the system acquires a new contribution that stems from the rotation effects. Moreover, in the search for bound state solutions, it is shown that the possible values of this angular frequency of the system are determined by the quantum numbers associated with the radial modes and the angular momentum, the angular velocity of the rotating frame and by the parameters associated with the Kratzer potential.
Waveform information from quantum mechanical entropy
Authors: Funkhouser Scott , Suski William , Winn Andrew
Published: June 2016

Although the entropy of a given signal-type waveform is technically zero, it is nonetheless desirable to use entropic measures to quantify the associated information. Several such prescriptions have been advanced in the literature but none are generally successful. Here, we report that the Fourier-conjugated ‘total entropy’ associated with quantum-mechanical probabilistic amplitude functions (PAFs) is a meaningful measure of information in non-probabilistic real waveforms, with either the waveform itself or its (normalized) analytic representation acting in the role of the PAF. Detailed numerical calculations are presented for both adaptations, showing the expected informatic behaviours in a variety of rudimentary scenarios. Particularly noteworthy are the sensitivity to the degree of randomness in a sequence of pulses and potential for detection of weak signals.
Dynamical emergence of Markovianity in local time scheme
Authors: Jeknić-Dugić J. , Arsenijević M. , Dugić M.
Published: June 2016

Recently we pointed out the so-called local time scheme as a novel approach to quantum foundations that solves the preferred pointer-basis problem. In this paper, we introduce and analyse in depth a rather non-standard dynamical map that is imposed by the scheme. On the one hand, the map does not allow for introducing a properly defined generator of the evolution nor does it represent a quantum channel. On the other hand, the map is linear, positive, trace preserving and unital as well as completely positive, but is not divisible and therefore non-Markovian. Nevertheless, we provide quantitative criteria for dynamical emergence of time-coarse-grained Markovianity, for exact dynamics of an open system, as well as for operationally defined approximation of a closed or open many-particle system. A closed system never reaches a steady state, whereas an open system may reach a unique steady state given by the Lüders–von Neumann formula; where the smaller the open system, the faster a steady state is attained. These generic findings extend the standard open quantum systems theory and substantially tackle certain cosmological issues.
Axial–transversal coupling in the free nonlinear vibrations of Timoshenko beams with arbitrary slenderness and axial boundary conditions
Authors: Lenci Stefano , Rega Giuseppe
Published: June 2016

The nonlinear free oscillations of a straight planar Timoshenko beam are investigated analytically by means of the asymptotic development method. Attention is focused for the first time, to the best of our knowledge, on the nonlinear coupling between the axial and the transversal oscillations of the beam, which are decoupled in the linear regime. The existence of coupled and uncoupled motion is discussed. Furthermore, the softening versus hardening nature of the backbone curves is investigated in depth. The results are summarized by means of behaviour charts that illustrate the different possible classes of motion in the parameter space. New, and partially unexpected, phenomena, such as the changing of the nonlinear behaviour from softening to hardening by adding/removing the axial vibrations, are highlighted.
Splitting of the neutral mechanical plane depends on the length of the multi-layer structure of flexible electronics
Authors: Li Shuang , Su Yewang , Li Rui
Published: June 2016

Multi-layer structures with soft (compliant) interlayers have been widely used in flexible electronics and photonics as an effective design for reducing interactions among the hard (stiff) layers and thus avoiding the premature failure of an entire device. The analytic model for bending of such a structure has not been well established due to its complex mechanical behaviour. Here, we present a rational analytic model, without any parameter fitting, to study the bending of a multi-layer structure on a cylinder, which is often regarded as an important approach to mechanical reliability testing of flexible electronics and photonics. For the first time, our model quantitatively reveals that, as the key for accurate strain control, the splitting of the neutral mechanical plane depends not only on the relative thickness of the middle layer, but also on the length-to-thickness ratio of the multi-layer structure. The model accurately captures the key quantities, including the axial strains in the top and bottom layers, the shear strain in the middle layer and the locations of the neutral mechanical planes of the top and bottom layers. The effects of the length of the multi-layer and the thickness of the middle layer are elaborated. This work is very useful for the design of multi-layer structure-based flexible electronics and photonics.
Edge bending wave on a thin elastic plate resting on a Winkler foundation
Authors: Kaplunov J. , Prikazchikov D. A. , Rogerson G. A.
Published: June 2016

This paper is concerned with elucidation of the general properties of the bending edge wave in a thin linearly elastic plate that is supported by a Winkler foundation. A homogeneous wave of arbitrary profile is considered, and represented in terms of a single harmonic function. This serves as the basis for derivation of an explicit asymptotic model, containing an elliptic equation governing the decay away from the edge, together with a parabolic equation at the edge, corresponding to beam-like behaviour. The model extracts the contribution of the edge wave from the overall dynamic response of the plate, providing significant simplification for analysis of the localized near-edge wave field.
Amplifiers and the origin of animal signals
Authors: Bogaardt Laurens , Johnstone Rufus A.
Published: June 2016

In 1989, Hasson introduced the concept of an ‘amplifier’ within animal communication. This display reduces errors in the assessment of traits for which there is direct selection and renders differences in quality among animals more obvious. Amplifiers can evolve to fixation via the benefit they confer on high-quality animals. However, they also impose a cost on low-quality animals by revealing their lower quality, potentially leading these to refrain from amplifying. Hence, it was suggested that, if the level of amplification correlates with quality, direct choice for the amplifying display might emerge. Using the framework of signal detection theory, this article shows that, if the use of an amplifier is observable, direct choice for the amplifying display can indeed evolve. Consequently, low-quality animals may choose to amplify to some extent as well, even though this reveals their lower quality. In effect, the amplifier evolves to become a signal in its own right. We show that, as amplifiers can evolve without direct female choice and are likely to become correlated with male quality, selection for quality-dependent amplification provides a simple explanation for the origin of reliable signals in the absence of pre-existing preferences.
Colour change on different body regions provides thermal and signalling advantages in bearded dragon lizards
Authors: Smith Kathleen R. , Cadena Viviana , Endler John A. , Porter Warren P. , Kearney Michael R. , Stuart-Fox Devi
Published: June 2016

Many terrestrial ectotherms are capable of rapid colour change, yet it is unclear how these animals accommodate the multiple functions of colour, particularly camouflage, communication and thermoregulation, especially when functions require very different colours. Thermal benefits of colour change depend on an animal's absorptance of solar energy in both UV–visible (300–700 nm) and near-infrared (NIR; 700–2600 nm) wavelengths, yet colour research has focused almost exclusively on the former. Here, we show that wild-caught bearded dragon lizards (Pogona vitticeps) exhibit substantial UV–visible and NIR skin reflectance change in response to temperature for dorsal but not ventral (throat and upper chest) body regions. By contrast, lizards showed the greatest temperature-independent colour change on the beard and upper chest during social interactions and as a result of circadian colour change. Biophysical simulations of heat transfer predicted that the maximum temperature-dependent change in dorsal reflectivity could reduce the time taken to reach active body temperature by an average of 22 min per active day, saving 85 h of basking time throughout the activity season. Our results confirm that colour change may serve a thermoregulatory function, and competing thermoregulation and signalling requirements may be met by partitioning colour change to different body regions in different circumstances.
Origins of food crops connect countries worldwide
Authors: Khoury Colin K. , Achicanoy Harold A. , Bjorkman Anne D. , Navarro-Racines Carlos , Guarino Luigi , Flores-Palacios Ximena , Engels Johannes M. M. , Wiersema John H. , Dempewolf Hannes , Sotelo Steven , Ramírez-Villegas Julian , Castañeda-Álvarez Nora P. , Fowler Cary , Jarvis Andy , Rieseberg Loren H. , Struik Paul C.
Published: June 2016

Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.
Efficient cardinality estimation for k-mers in large DNA sequencing data sets
Authors: Irber Luiz C. , Brown C. Titus
Published: June 2016

We present an open implementation of the HyperLogLog cardinality estimation sketch for counting fixed-length substrings of DNA strings (“k-mers”).

The HyperLogLog sketch implementation is in C++ with a Python interface, and is distributed as part of the khmer software package. khmer is freely available fromhttps://github.com/dib-lab/khmerunder a BSD License. The features presented here are included in version 1.4 and later.
Daisy-chain gene drives for the alteration of local populations
Authors: Noble Charleston , Min John , Olejarz Jason , Buchthal Joanna , Chavez Alejandro , Smidler Andrea L. , DeBenedictis Erika A. , Church George M. , Nowak Martin A. , Esvelt Kevin M.
Published: June 2016

RNA-guided gene drive elements could address many ecological problems by altering the traits of wild organisms, but the likelihood of global spread tremendously complicates ethical development and use. Here we detail a localized form of CRISPR-based gene drive composed of genetic elements arranged in a daisy-chain such that each element drives the next. “Daisy drive” systems can duplicate any effect achievable using an equivalent global drive system, but their capacity to spread is limited by the successive loss of non-driving elements from the base of the chain. Releasing daisy drive organisms constituting a small fraction of the local wild population can drive a useful genetic element to local fixation for a wide range of fitness parameters without resulting in global spread. We additionally report numerous highly active guide RNA sequences sharing minimal homology that may enable evolutionary stable daisy drive as well as global CRISPR-based gene drive. Daisy drives could simplify decision-making and promote ethical use by enabling local communities to decide whether, when, and how to alter local ecosystems.

Author’s Summary

‘Global’ gene drive systems based on CRISPR are likely to spread to every population of the target species, hampering safe and ethical use. ‘Daisy drive’ systems offer a way to alter the traits of only local populations in a temporary manner. Because they can exactly duplicate the activity of any global CRISPR-based drive at a local level, daisy drives may enable safe field trials and empower local communities to make decisions concerning their own shared environments.

For more details and an animation intended for a general audience, see the summary atSculpting Evolution.
A Common Class of Transcripts with 5′-Intron Depletion, Distinct Early Coding Sequence Features, and N1-Methyladenosine Modification
Authors: Cenik Can , Chua Hon Nian , Singh Guramrit , Akef Abdalla , Snyder Michael P , Palazzo Alexander F. , Moore Melissa J , Roth Frederick P
Published: June 2016

Introns are found in 5’ untranslated regions (5’UTRs) for 35% of all human transcripts. These 5’UTR introns are not randomly distributed: genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5’UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5’UTR intron status, we developed a classifier that can predict 5’UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with5’ proximal-intron-minus-like-coding regions (“5IM” transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5’ cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the Exon Junction Complex (EJC) at non-canonical 5’ proximal positions. Finally, N1-methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5’ proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N1-methyladenosines in the early coding region, and enrichment for non-canonical binding by the Exon Junction Complex.
Uplift and erosion of genomic islands with standing genetic variation
Authors: Hether Tyler D.
Published: June 2016

Details of the processes that generate biological diversity have long been of interest to evolutionary biologists. A common theme in nature is diversification via divergent selection with gene flow. Empirical studies on this topic find variable genetic differentiation throughout the genome, that genetic differentiation is non-randomly distributed, and that loci of adaptive significance are often found clustered together within “genomic islands of divergence”. Theoretical models based on new mutations show how these genomic islands can arise and grow as a result of a complex interaction of various evolutionary and genic processes. In the current study, I ask if such genomic islands can alternatively arise from divergent selection from standing genetic variation and I tested this using a simple two locus model of selection. There are numerous ways in which standing genetic variation can be partitioned (e.g., between alleles, between loci, and between populations) and I tested which of these scenarios can give rise to an island pattern compared to no genomic differentiation or complete genomic differentiation. I found that divergent selection, even without reciprocal gene exchange between populations, following a bout of admixture can relatively quickly produce an island pattern. Moreover, I found two pathways in which islands can form from divergence from standing variation: 1) through the build up of islands and 2) through the breakdown of larger, genome-wide differentiation. Lastly, similar to new mutation theory, I found that the frequency of recombination is an important determinant of island formation from standing genetic variation such that mating behavior of a species (e.g., facultative or obligate sexual) can impact the likelihood of island formation.
Enhanced pre-frontal functional-structural networks to support behavioural deficits after traumatic brain injury
Authors: Diez Ibai , Drijkoningen David , Stramaglia Sebastiano , Bonifazi Paolo , Marinazzo Daniele , Gooijers Jolien , Swinnen Stephan P. , Cortes Jesus M.
Published: June 2016

Traumatic brain injury (TBI) affects its structural connectivity, triggering the re-organization of structural-functional circuits in a manner that remains poorly understood. We studied the re-organization of brain networks after TBI, taking advantage of a computational method based on magnetic resonance imaging (MRI) including diffusion-weighted imaging in combination with functional resting state data obtained from the blood-oxygenation-level-dependent T2*signal. We enrolled young participants who had suffered moderate to severe TBI (N=14, age 13.14 ± 3.25 years), comparing them to young typically developing control participants (N=27, age 15.04 ± 2.26 years). We found increased functional and structural connectivity within a cortico-subcortical network in TBI patient’s brains that involved prefrontal cortex, anterior cingulate gyrus, orbital gyrus and caudate nucleus. In comparison to control participants, TBI patients increased functional connectivity from prefrontal regions towards two different networks: 1) a subcortical network including part of the motor network, basal ganglia, cerebellum, hippocampus, amygdala, posterior cingulum and precuneus; and 2) a task-positive network, involving regions of the dorsal attention system together with the dorsolateral and ventrolateral prefrontal regions. We also found the increased prefrontal activation in TBI patients was correlated with some behavioural indices, such as the amount of body sway, whereby patients with worse balance activated frontal regions more strongly. The enhanced prefrontal activation found in TBI patients may provide the structural scaffold for stronger cognitive control of certain behavioural functions, consistent with the observation that various motor tasks are performed less automatically following TBI and that more cognitive control is associated with such actions.
Estimating the functional impact of INDELs in transcription factor binding sites: a genome-wide landscape
Authors: Eickhardt Esben , Als Thomas Damm , Grove Jakob , Boerglum Anders Dupont , Lescai Francesco
Published: June 2016

Background

Variants in transcription factor binding sites (TFBSs) may have important regulatory effects, as they have the potential to alter transcription factor (TF) binding affinities and thereby affecting gene expression. With recent advances in sequencing technologies the number of variants identified in TFBSs has increased, hence understanding their role is of significant interest when interpreting next generation sequencing data. Current methods have two major limitations: they are limited to predicting the functional impact of single nucleotide variants (SNVs) and often rely on additional experimental data, laborious and expensive to acquire. We propose a purely bioinformatic method that addresses these two limitations while providing comparable results.

Results

Our method uses position weight matrices and a sliding window approach, in order to account for the sequence context of variants, and scores the consequences of both SNVs and INDELs in TFBSs. We tested the accuracy of our method in two different ways. Firstly, we compared it to a recent method based on DNase I hypersensitive sites sequencing (DHS-seq) data designed to predict the effects of SNVs: we found a significant correlation of our score both with their DHS-seq data and their prediction model. Secondly, we called INDELs on publicly available DHS-seq data from ENCODE, and found our score to represent well the experimental data. We concluded that our method is reliable and we used it to describe the landscape of variation in TFBSs in the human genome, by scoring all variants in the 1000 Genomes Project Phase 3. Surprisingly, we found that most insertions have neutral effects on binding sites, while deletions, as expected, were found to have the most severe TFBS-scores. We identified four categories of variants based on their TFBS-scores and tested them for enrichment of variants classified as pathogenic, benign and protective in ClinVar: we found that the variants with the most negative TFBS-scores have the most significant enrichment for pathogenic variants.

Conclusions

Our method addresses key shortcomings of currently available bioinformatic tools in predicting the effects of INDELs in TFBSs, and provides an unprecedented window into the genome-wide landscape of INDELs, their predicted influences on TF binding, and potential relevance for human diseases. We thus offer an additional tool to help prioritising non-coding variants in sequencing studies.
Snapshots of a shrinking partner: Genome reduction inSerratia symbiotica
Authors: Manzano-Marín Alejandro , Latorre Amparo
Published: June 2016

Genome reduction is pervasive among maternally-inherited endosymbiotic organisms, from bacteriocyte- to gut-associated ones. This genome erosion is a step-wise process in which once free-living organisms evolve to become obligate associates, thereby losing non-essential or redundant genes/functions.Serratia symbiotica(Gammaproteobacteria), a secondary endosymbiont present in many aphids (Hemiptera: Aphididae), displays various characteristics that make it a good model organism for studying genome reduction. While some strains are of facultative nature, others have established co-obligate associations with their respective aphid host and its primary endosymbiont (Buchnera). Furthermore, the different strains hold genomes of contrasting sizes and features, and have strikingly disparate cell shapes, sizes, and tissue tropism. Finally, genomes from closely related free-livingSerratia marcescensare also available. In this study, we describe in detail the genome reduction process (from free-living to reduced obligate endosymbiont) undergone byS. symbiotica, and relate it to the stages of integration to the symbiotic system the different strains find themselves in. We establish that the genome reduction patterns observed inS. symbioticafollow those from other dwindling genomes, thus proving to be a good model for the study of the genome reduction process within a single bacterial taxon evolving in a similar biological niche (aphid-Buchnera).