bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic response of dry and water-saturated sand systems
Authors: LaJeunesse J. W. , Hankin M. , Kennedy G. B. , Spaulding D. K. , Schumaker M. G. , Neel C. H. , Borg J. P. , Stewart S. T. , Thadhani N. N.
Published: July 2017

The effect of grain size and moisture content on the dynamic macroscopic response of granular geological materials was explored by performing uniaxial planar impact experiments on high purity, Oklahoma #1, sand samples composed of either fine (75–150 μm) or coarse (425–500 μm) grain sizes in either dry or fully water-saturated conditions. Oklahoma #1 sand was chosen for its smooth, quasi-spherical grain shapes, narrow grain size distributions, and nearly pure SiO2 composition (99.8 wt. %). The water-saturated samples were completely saturated ensuring a two-phase mixture with roughly 65% sand and 35% water. Sand samples were dynamically loaded to pressures between 1 and 11 GPa. Three-dimensional meso-scale simulations using an Eulerian hydrocode, CTH, were created to model the response of each sand sample. Multi-phase equations of state were used for both silicon dioxide, which comprised individual sand grains, and water, which surrounded individual grains. Particle velocity profiles measured from the rear surface of the sand, both experimentally and computationally, reveal that fine grain samples have steeper rise characteristics than coarse grain samples and water-saturated samples have an overall much stiffer response than dry samples. The experimentally determined particle velocity vs. shock velocity response of dry sand was linear over this pressure range, with little difference between the two grain sizes investigated. The experimental response for the water saturated sand exhibited a piecewise continuous response with a transition region between particle velocities of 0.6 km s−1 and 0.8 km s−1 and a pressure of 4.5–6 GPa. Hypotheses for the cause of this transition region are drawn based on results of the meso-scale simulations.
An efficient and reliable growth method for epitaxial complex oxide films by molecular beam epitaxy
Authors: Zhang T. W. , Mao Z. W. , Gu Z. B. , Nie Y. F. , Pan X. Q.
Published: July 2017

Transition metal oxide heterostructures and interfaces host a variety of exciting quantum phases and can be grown with atomic-scale precision by utilising the intensity oscillations of in situ reflection high-energy electron diffraction. However, establishing a stable oscillation pattern in the growth calibration of complex oxide films is very challenging and time consuming. Here, we develop a substantially more efficient and reliable growth calibration method for complex oxide films using molecular beam epitaxy.
Nonlinear coupling of kinetic Alfven waves with acoustic waves in a self-gravitating dusty plasma with adiabatic trapping
Authors: Sabeen A. , Masood W. , Qureshi M. N. S. , Shah H. A.
Published: July 2017

In this paper, linear and nonlinear coupling of kinetic Alfven and acoustic waves has been studied in a dusty plasma in the presence of trapping and self-gravitation effects. In this regard, we have derived the linear dispersion relations for positively and negatively coupled dust kinetic Alfven-acoustic waves. Stability analysis of the coupled dust kinetic Alfven-acoustic wave has also been presented. The formation of solitary structures has been investigated following the Sagdeev potential approach by using the two-potential theory. Numerical results show that the solitary structures can be obtained only for sub-Alfvenic regimes in the scenario of space plasmas.
Oscillation of a bubble in a liquid confined in an elastic solid
Authors: Wang Q. X.
Published: July 2017

A simple theoretical model is described for the oscillation of a gas bubble in a liquid in a cavity confined by an elastic solid. The phenomenon occurs in nature and technology but has only recently received attention. The compressibility effects in the continuity equation are shown to be negligible, using dimensional analysis. However, the volume change of the confined liquid has to be considered since the associated pressure variation is large. The variation of the cavity volume is assumed to be proportional to the change of the liquid pressure at the confinement wall. The Rayleigh-Plesset-like equation describing the dynamics of a confined bubble is derived, considering the viscous and surface tension effects. Using the linear stability analysis, we show that the bubble undergoes stable damping oscillation when it is subject to small disturbances. The natural frequency of oscillation is obtained analytically. The theory agrees well with recent experiments. The analyses show that the natural frequency of oscillation for a bubble in an elastic confinement is larger, in order of magnitude, than that in an unbounded liquid. The amplitude and period of oscillation of a transient bubble decrease significantly owing to the presence of a confinement, reaching a steady state in a much longer period and at a larger equilibrium radius. When subject to an acoustic wave, a bubble in a confinement oscillates at smaller amplitude. The effects of the confinement increase with the bulk modulus of the confinement and decrease rapidly with the cavity size but are still significant for a large cavity whose size is an order of magnitude larger than the bubble.
Approaching the intrinsic quality factor limit for micromechanical bulk acoustic resonators using phononic crystal tethers
Authors: Gokhale Vikrant J. , Gorman Jason J.
Published: July 2017

We systematically demonstrate that one-dimensional phononic crystal (1-D PnC) tethers can significantly reduce tether loss in micromechanical resonators to a point where the total energy loss is dominated by intrinsic mechanisms, particularly phonon damping. Multiple silicon resonators are designed, fabricated, and tested to provide comparisons in terms of the number of periods in the PnC and the resonance frequency, as well as a comparison with conventional straight-beam tethers. The product of resonance frequency and measured quality factor (f × Q) is the critical figure of merit, as it is inversely related to the total energy dissipation in a resonator. For a wide range of frequencies, devices with PnC tethers consistently demonstrate higher f × Q values than the best conventional straight-beam tether designs. The f × Q product improves with increasing number of PnC periods and at a maximum value of 1.2 × 1013 Hz approaches limiting values set by intrinsic material loss mechanisms.
Oersted-field-induced switching of a ferromagnet on a Si substrate via localized dielectric breakdown of the native SiO2 layer
Authors: Polushkin N. I. , Sapozhnikov M. V. , Gusev N. S. , Vdovichev S. N. , Drozdov M. N.
Published: July 2017

The phenomenon of dielectric breakdown is employed for switching of magnetization in ferromagnetic (FM) metallic layers of Co and CoFe sputtered onto the native oxide (SiO2) of Si substrates of different types. The switching can occur even without applying a bias field under discharging a capacitor through an FM/SiO2/Si sample via electric pads lying on its surface. The switching thresholds and biasing fields (if needed) are found to be much lower in samples based on low-resistivity (∼10 mΩ cm) substrates. It is argued that the discharge induces localized breakdown of the SiO2 layer, and so, the discharge current is able to flow through the Si substrate. This current produces the magnetic (Oersted) field inside the FM layer, which is sufficient for the switching. Such on-chip pulsed magnetic fields generated in FM/SiO2/Si structures can be employed instead of bulky electromagnets for developing magnetic technologies, which would be compatible with Si-based electronics.
Adjustment of diffraction efficiency of polarization holograms in azobenzene polymers films using electric field
Authors: Davidenko N. A. , Davidenko I. I. , Pavlov V. A. , Chuprina N. G. , Tarasenko V. V. , Studzinsky S. L.
Published: July 2017

There have been two effects of the external electric field influence on the diffraction efficiency of reconstructed holograms observed in the films of copolymers 4-[(2-nitrophenyl)diazenyl]phenyl methacrylate with octylmethacrylate, when holographic recording of the plane wave front for parallel and orthogonal orientation of polarization vectors of light beams was performed at room temperature. After recording at exposure with small energies, diffraction efficiency in the electric field formed by corona discharge decreases, while with large exposure energies, it increases. Diffraction efficiency and recording velocity are higher in copolymer with lower softening temperature. The first effect is caused by reorientation of the dipole moments of azobenzene isomer fragments in the electric field, while the growth of diffraction efficiency is explained by the increase in the amplitude of regular geometric relief of the film surface, which appears during formation of the polarization hologram.
Electric and photovoltaic characteristics of a multi-layer ReS2/ReSe2 heterostructure
Authors: Cho Ah-Jin , Namgung Seok Daniel , Kim Hojoong , Kwon Jang-Yeon
Published: July 2017

Among the various unique properties of two-dimensional materials, the ability to form a van der Waals (vdW) heterojunction between them is very valuable, as it offers a superior interface quality without the lattice mismatch problem. In this work, a ReS2/ReSe2 vdW heterostructure was fabricated, and its electrical and photovoltaic behaviors were discovered. The heterojunction showed a gate-tunable diode property with the maximum rectification ratio of 3150. Under illumination, it exhibited a photovoltaic effect with an efficiency of ∼0.5%. This study outlines the potential of Re-based 2D semiconductors and their integration by forming a vdW heterojunction for use in optoelectronic devices.
Precipitation growth of graphene under exfoliated hexagonal boron nitride to form heterostructures on cobalt substrate by molecular beam epitaxy
Authors: Zheng Renjing , Khanaki Alireza , Tian Hao , He Yanwei , Cui Yongtao , Xu Zhongguang , Liu Jianlin
Published: July 2017

Research on graphene/hexagonal boron nitride (h-BN) heterostructures has attracted much attention for band engineering and device performance optimization of graphene. However, the growth of graphene/h-BN heterostructure is still challenging, which usually requires high growth temperature and long growth duration. In this paper, we demonstrate graphene/h-BN heterostructures by growing graphene onto the substrates which consist of exfoliated h-BN flakes on Co thin films using molecular beam epitaxy. The heterostructure samples grown at different temperatures and growth times were characterized by Raman, optical microscopy, atomic force microscopy, microwave impedance microscopy, and scanning tunneling microscopy. It is found that the graphene/h-BN heterostructures were formed by the formation of graphene underneath rather than on top of the h-BN flakes. The growth mechanism is discussed.
Efficient single-photon source based on a deterministically fabricated single quantum dot - microstructure with backside gold mirror
Authors: Fischbach Sarah , Kaganskiy Arsenty , Tauscher Esra Burcu Yarar , Gericke Fabian , Thoma Alexander , Schmidt Ronny , Strittmatter André , Heindel Tobias , Rodt Sven , Reitzenstein Stephan
Published: July 2017

We present an efficient broadband single-photon source which is fabricated by a flip-chip gold-bonding technique and in-situ electron beam lithography. The device comprises a single InGaAs quantum dot that is centered at the bottom of a monolithic mesa structure and located above a gold mirror for enhanced photon-extraction efficiency. We show a photon-extraction efficiency of ηext=(18±2) % into a numerical aperture of 0.4 and a high suppression of multi-photon events from this source with g(2)(0)=0.015±0.009. Our deterministic device with a backside gold mirror can be combined with electrical contacts and piezo-tuning capabilities in future refinements, which represents an important step towards a spectrally tunable plug-and-play quantum-light source with broadband enhancement for photonic quantum networks.
High-efficiency polarization conversion phase gradient metasurface for wideband anomalous reflection
Authors: Zhang Jiameng , Yang Lan , Li Linpeng , Zhang Tong , Li Haihong , Wang Qingmin , Hao Yanan , Lei Ming , Bi Ke
Published: July 2017

An ultra-wideband polarization conversion metasurface based on S-shaped metallic structure is designed and prepared. The simulation results show that the polarization conversion bandwidth is 14 GHz for linearly polarized normally incident electromagnetic waves and the cross-polarized reflectance is more than 99% in the range of 10.3 GHz–20.5 GHz. On the premise of high reflection efficiency, the reflective phase can be regulated by changing the geometrical parameter of the S-shaped metallic structure. A phase gradient metasurface composed of six periodically arrayed S-shaped unit cells is proposed and further demonstrated both numerically and experimentally. The specular cross-polarization reflection of the phase gradient metasurface is below −10 dB, which shows a good performance on manipulating the direction of the reflected electromagnetic waves.
Light extraction enhancement of AlGaN-based ultraviolet light-emitting diodes by substrate sidewall roughening
Authors: Guo Yanan , Zhang Yun , Yan Jianchang , Xie Haizhong , Liu Lei , Chen Xiang , Hou Mengjun , Qin Zhixin , Wang Junxi , Li Jinmin
Published: July 2017

The effect of sapphire substrate's sidewall roughening on light extraction of AlGaN-based ultraviolet light-emitting diodes (UV LEDs) is investigated. Finite-difference time-domain simulation reveals that a roughening region for effective light extraction enhancement exists on the substrate's sidewall. Roughening outside the effective roughening region will result in undesirable inward photon scattering and absorption. For TM-polarization-dominated deep-UV LEDs, the effective roughening region is from the substrate's backside to the position about L/2 × tan(θc) away from the substrate's front side, where L is the side length of the LED device and θc is the critical angle of total reflection. In the LED device fabrication, picosecond laser dicing is employed to realize roughening layers on the sapphire substrate's sidewalls. The UV LEDs with three roughening layers have 13.2% higher average light output power (LOP) at 20 mA than those with two roughening layers, thanks to the larger roughening area in the effective roughening region. When additional roughening layers beyond the effective roughening region are applied, the LOP decreases as the simulation predicts. Furthermore, the values of leakage current and forward voltage of these LEDs are consistently below 0.2 μA at −10 V and 5.8–6.0 V at 20 mA, respectively, showing no thermal damage to intrinsic diode performance by the laser processing.
Long-term studies of post-fire reproduction in an Australian shrubland and woodland
Authors: Harvey J. M. , Hopkins A. J. M. , Langley M. A. , Gosper C. R. , Williams M. R. , Yates C. J.
Published: July 2017

Identifying appropriate fire-return times is critical for management of temperate southern Australia’s fire-prone shrublands and woodlands. The time to first flowering and peak flowering are useful attributes for understanding how species and vegetation will respond to different fire intervals. Using a plant fire-response trait framework, we investigate patterns of reproduction in south-western Australian kwongan and woodland after prescribed fires with a 30-year longitudinal study, with the aim of identifying appropriate fire intervals. Modelling of post-fire flowering responses of species and aggregating responses into plant functional types showed substantial differences in the time after fire to first and peak flowering. Tests of hypotheses of flowering patterns after fire with different fire-response traits showed that (1) resprouters flower sooner than recruits of non-resprouters, (2) serotinous non-resprouters reach first and peak flowering later than do non-resprouters with soil-stored seed, (3) species in taller strata reach first and peak flowering later than those in lower strata and (4) geophytes flower earlier than other resprouters that lose their aboveground biomass in fire. The most fire interval-sensitive non-resprouting serotinous species take 15–20 years in kwongan to reach peak flowering and in Allocasuarina woodland 25–30 years, providing a working hypothesis for minimum fire intervals in the plant communities under investigation. Our study illustrates the value of long-term ecological studies for informing biodiversity management.
Development of new kabuli large-seeded chickpea materials with resistance to Ascochyta blight
Authors: Gil J. , Castro P. , Millan T. , Madrid E. , Rubio J.
Published: July 2017

Appearance and size of chickpea (Cicer arietinum L.) seeds are key factors for the market in the Mediterranean Basin driven by consumer preferences. Hence, kabuli large seeds are sold on the market at higher price than the desi seeds. In this crop, Ascochyta blight (caused by Ascochyta rabiei (Pass.) Lab.) is a serious disease causing major losses in yield. Thus, developing large-seeded kabuli cultivars resistant to blight would be of great importance to farmers. In this study, the use of transgressive inheritance to select new allelic combinations for seed size was applied to develop new chickpea materials with large seeds and resistance to blight. Crosses between five different advanced lines of kabuli chickpea genotypes with medium–large seed size and resistant to blight were performed. As a results of the selections carried out during 10 successive years, 11 F5:9 lines resistant to blight and with large seed size were selected to be released as future varieties. The markers SCY17590 and CaETR were employed to confirm blight resistance of the material developed.
Whither the paradigm shift? Large wildland fires and the wildfire paradox offer opportunities for a new paradigm of ecological fire management
Authors: Ingalsbee Timothy
Published: July 2017

The growing frequency of large wildland fires has raised awareness of the ‘wildfire paradox’ and the ‘firefighting trap’ that are both rooted in the fire exclusion paradigm. However, a paradigm shift has been unfolding in the wildland fire community that seeks to restore fire ecology processes across broad landscapes. This would involve managing rather than aggressively suppressing large fires. Examples of recent fire science publications demonstrating ‘new paradigm’ thinking or critical questioning of ‘old paradigm’ assumptions are offered as evidence of this shift in thinking. However, integration of fire ecology science is lagging in fire-related policies and legislation, media representations of wildland fires, and conventional management responses to most wildland fires. Sociocultural, political and economic factors are functioning as barriers to change in fire management policies and practices. However, the growing risks, costs and impacts of large wildland fires will continue to highlight the crisis of the dominant fire exclusion paradigm. The general inability to prevent and effectively suppress large wildland fires may be the means to break through these institutional and societal barriers and propel efforts to shift philosophy and practice to a new paradigm of ecological fire management.
Reading into the past
Authors: Fitzmaurice Susan , Robinson Justyna A. , Alexander Marc , Hine Iona C. , Mehl Seth , Dallachy Fraser
Published: July 2017

The Linguistic DNA project investigates concepts in Early Modern England and adopts a bottom-up approach to query whether the key concepts intuited by historians of ideas are manifested in the printed discourse of the time. By applying computational methods and close reading to Early English Books Online, we identify concepts that Early Moderns were discussing, developing and changing. In this article, we discuss the challenge of information retrieval and the negotiation between distant reading and close reading. We present three case studies informed by the project’s three research themes. Research Theme 1 examines historical and social contexts of conceptual change. Research Theme 2 analyses lexical semantic relationships within conceptual structures. Research Theme 3 explores lexicalisation pressure, using categories from the Historical Thesaurus of English.
Relativisation in Dutch diaries, private letters and newspapers (1770–1840)
Authors: Krogull Andreas , Rutten Gijsbert , van der Wal Marijke
Published: July 2017

The paper focuses on three important themes in historical sociolinguistics: (1) the emergence of national language planning in the Netherlands around 1800, (2) the influence of historical prescriptivism on usage, and (3) genre as a crucial factor in explaining variation and change. The case study deals with relativisation, particularly the neuter relative pronoun in eighteenth- and nineteenth-century Dutch. Analysing both internal and external factors, we show that the definiteness of the antecedent does not explain the variation, contrary to what is assumed in the research literature. Likewise, a strong effect of language norms on usage patterns cannot be established. The crucial factor turns out to be genre.
A lost Canadian dialect
Authors: Jankowski Bridget L. , Tagliamonte Sali A.
Published: July 2017

Ottawa Valley English (OVE), a rural regional dialect enclave in Ontario, Canada, is under threat from social change, including urban sprawl and the encroachment of standard Canadian English. Using a trend study with two samples collected 30–35 years apart, we conduct a variationist sociolinguistic analysis of two vernacular features found in many varieties of English, including OVE: verbal -s with third-person plural NP subjects (My eyes is failing), and preterite come (They come here in nineteen-and-seven). The findings have implications for models of dialect “dissipation” and “concentration” (Schilling-Estes & Wolfram 1999). For both variables, internal constraints are concentrating. Verbal -s, however, is dissipating, while preterite come is retained and shows evidence of age-grading.
Bare Nominals in Brazilian Portuguese
Authors: Wall Albert
Published: July 2017

Over the last three decades, Brazilian Portuguese bare nominals have turned into a hot topic in the cross-linguistic study of nominal syntax and semantics. This contribution is the first comprehensive, book-length treatment of the issue, covering both the long-standing discussion about the adequate analysis of these forms as well as the establishment of a solid empirical basis for future research. The book goes further than previous accounts in also taking into consideration the phonetic-phonological dimension, showing the advantages of a more comprehensive account. The empirical section outlines an innovative approach in which different methods and data types are combined and focuses on the underresearched definite / specific / referential uses and interpretations of bare singulars. The book also addresses the traditional topics in the study of bare nominals – genericity, the mass/count distinction, NP-internal plural agreement, the NP/DP distinction, and syntax-semantics-phonology interface questions – in the light of the new findings.
‘She used his name’: provider trait mindfulness in perinatal death counselling / ‘Ella usó el nombre de él’: mindfulness de los rasgos del proveedor en la terapia por muerte perinatal
Authors: Cacciatore Joanne
Published: July 2017

Millions of babies die of stillbirth every year around the world, yet there is a dearth of research on the helping behaviours of counsellors working with grieving families. Mindfulness-based interventions have been increasingly used, and researched, in vulnerable populations. While many studies have empirically focused on mindfulness as an intervention, very few studies have examined trait mindfulness in providers and its relationship to perceptions of helping. This study is an open-ended inquiry to explore trait, or dispositional, mindfulness in counsellors/therapists as perceived by bereaved parents in the aftermath of perinatal death. Descriptive data are reported, and a thematic analysis that identified and coded recurring and unifying statements was performed on the qualitative response ( n = 94). Findings suggest that trait mindfulness in counsellors/therapists is perceived as helpful and inverse findings were also discovered.
Control of precipitation behaviour of Hastelloy-X through grain boundary engineering
Authors: Wang Xiaoyan , Kurosawa Kentaro , Huang Ming , Lu Xianke , Zhang Dao , Kokawa Hiroyuki , Yan Yinbiao , Yang Sen
Published: July 2017

Grain boundary engineering (GBE) was employed to control the precipitation behaviour of Hastelloy-X alloy. The precipitate characteristics and thermal stability of grain boundary character distribution (GBCD) were investigated by aging at 850°C. M6C carbides and µ phases were observed in the matrix and on grain boundaries, respectively. It revealed that the formation of µ phase was closely related to the grain boundary structure. GBCD effectively suppressed the nucleation and coarsening of µ phases on the grain boundaries. Owing to the Mo depletion in the vicinity of random grain boundary, the formation of the precipitates was inhibited on the adjacent grain boundaries. The thermal stability of the GBE-optimised microstructure was confirmed at 850°C for 720 h without significant microstructural degradation.
Reactome enhanced pathway visualization
Authors: Sidiropoulos Konstantinos , Viteri Guilherme , Sevilla Cristoffer , Jupe Steve , Webber Marissa , Orlic-Milacic Marija , Jassal Bijay , May Bruce , Shamovsky Veronica , Duenas Corina , Rothfels Karen , Matthews Lisa , Song Heeyeon , Stein Lincoln , Haw Robin , D’Eustachio Peter , Ping Peipei , Hermjakob Henning , Fabregat Antonio
Published: July 2017

Motivation

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users’ own research presentations and publications.

Results

For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like ‘mitochondrion’ or ‘receptor’ are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects.

Availability and implementation

http://reactome.org
Do Banks Pass through Credit Expansions to Consumers Who want to Borrow?*
Authors: Agarwal Sumit , Chomsisengphet Souphala , Mahoney Neale , Stroebel Johannes
Published: July 2017

We propose a new approach to studying the pass-through of credit expansion policies that focuses on frictions, such as asymmetric information, that arise in the interaction between banks and borrowers. We decompose the effect of changes in banks’ cost of funds on aggregate borrowing into the product of banks’ marginal propensity to lend (MPL) to borrowers and those borrowers’ marginal propensity to borrow (MPB), aggregated over all borrowers in the economy. We apply our framework by estimating heterogeneous MPBs and MPLs in the U.S. credit card market. Using panel data on 8.5 million credit cards and 743 credit limit regression discontinuities, we find that the MPB is declining in credit score, falling from 59% for consumers with FICO scores below 660 to essentially zero for consumers with FICO scores above 740. We use a simple model of optimal credit limits to show that a bank’s MPL depends on a small number of parameters that can be estimated using our credit limit discontinuities. For the lowest FICO score consumers, higher credit limits sharply reduce profits from lending, limiting banks’ optimal MPL to these consumers. The negative correlation between MPB and MPL reduces the impact of changes in banks’ cost of funds on aggregate household borrowing, and highlights the importance of frictions in bank-borrower interactions for understanding the pass-through of credit expansions.
Sir David John Cameron MacKay FRS. 22 April 1967 — 14 April 2016
Authors: Longair Malcolm , Cates Michael
Published: July 2017

David MacKay was a true polymath who made pioneering contributions to information theory, inference and learning algorithms. He was a founder of the modern approach to information theory, combining Bayesian inference with artificial neural network algorithms to allow rational decision making by computer. His major achievements include reliable computation with unreliable hardware, in particular in approaching the Shannon limit using enhancements of Gallager codes. He developed communication systems for the disabled, including the Dasher code which he made freely available. He was the author of the influential book
Sustainable Energy: Without the Hot Air
. In 2009 he was appointed Chief Scientific Advisor to the Department of Energy and Climate Change. From 2003 he was Professor of Natural Philosophy in the Cavendish Laboratory, Cambridge, and in 2013 he was appointed to the first Regius Professorship of Engineering in the Engineering Department of Cambridge University. He was appointed Knight Bachelor in the 2016 New Year's Honours List ‘for services to Scientific Advice in Government and Science Outreach’, but lost his battle with stomach cancer soon afterwards at the age of 48.
Monte Carlo profile confidence intervals for dynamic systems
Authors: Ionides E. L. , Breto C. , Park J. , Smith R. A. , King A. A.
Published: July 2017

Monte Carlo methods to evaluate and maximize the likelihood function enable the construction of confidence intervals and hypothesis tests, facilitating scientific investigation using models for which the likelihood function is intractable. When Monte Carlo error can be made small, by sufficiently exhaustive computation, then the standard theory and practice of likelihood-based inference applies. As datasets become larger, and models more complex, situations arise where no reasonable amount of computation can render Monte Carlo error negligible. We develop profile likelihood methodology to provide frequentist inferences that take into account Monte Carlo uncertainty. We investigate the role of this methodology in facilitating inference for computationally challenging dynamic latent variable models. We present examples arising in the study of infectious disease transmission, demonstrating our methodology for inference on nonlinear dynamic models using genetic sequence data and panel time-series data. We also discuss applicability to nonlinear time-series and spatio-temporal data.
Zebrafish lipid droplets regulate embryonic ATP homeostasis to power early development
Authors: Dutta Asmita , Sinha Deepak Kumar
Published: July 2017

In zebrafish embryos, the maternally supplied pool of ATP is insufficient to power even the earliest of developmental events (0–3 hpf) such as oocyte-to-embryo transition (OET). The embryos generate an additional pulse (2.5 h long) of ATP (1.25–4 hpf) to achieve the embryonic ATP homeostasis. We demonstrate that the additional pulse of ATP is needed for successful execution of OET. The maternally supplied yolk lipids play a crucial role in maintaining the embryonic ATP homeostasis. In this paper, we identify the source and trafficking routes of free fatty acids (FFAs) that feed the mitochondria for synthesis of ATP. Interestingly, neither the maternally supplied pool of yolk-FFA nor the yolk-FACoA (fatty acyl coenzyme A) is used for ATP homeostasis during 0–5 hpf in zebrafish embryos. With the help of lipidomics, we explore the link between lipid droplet (LD)-mediated lipolysis and ATP homeostasis in zebrafish embryos. Until 5 hpf, the embryonic LDs undergo extensive lipolysis that generates FFAs. We demonstrate that these newly synthesized FFAs from LDs are involved in the maintenance of embryonic ATP homeostasis, rather than the FFAs/FACoA present in the yolk. Thus, the LDs are vital embryonic organelles that maintain the ATP homeostasis during early developmental stages (0–5 hpf) in zebrafish embryos. Our study highlights the important roles carried on by the LDs during the early development of the zebrafish embryos.
Waterjet and laser etching: the nonlinear inverse problem
Authors: Bilbao-Guillerna A. , Axinte D. A. , Billingham J. , Cadot G. B. J.
Published: July 2017

In waterjet and laser milling, material is removed from a solid surface in a succession of layers to create a new shape, in a depth-controlled manner. The inverse problem consists of defining the control parameters, in particular, the two-dimensional beam path, to arrive at a prescribed freeform surface. Waterjet milling (WJM) and pulsed laser ablation (PLA) are studied in this paper, since a generic nonlinear material removal model is appropriate for both of these processes. The inverse problem is usually solved for this kind of process by simply controlling dwell time in proportion to the required depth of milling at a sequence of pixels on the surface. However, this approach is only valid when shallow surfaces are etched, since it does not take into account either the footprint of the beam or its overlapping on successive passes. A discrete adjoint algorithm is proposed in this paper to improve the solution. Nonlinear effects and non-straight passes are included in the optimization, while the calculation of the Jacobian matrix does not require large computation times. Several tests are performed to validate the proposed method and the results show that tracking error is reduced typically by a factor of two in comparison to the pixel-by-pixel approach and the classical raster path strategy with straight passes. The tracking error can be as low as 2–5% and 1–2% for WJM and PLA, respectively, depending on the complexity of the target surface.
A frequency quantum interpretation of the surface renewal model of mass transfer
Authors: Mondal Chanchal , Chatterjee Siddharth G.
Published: July 2017

The surface of a turbulent liquid is visualized as consisting of a large number of chaotic eddies or liquid elements. Assuming that surface elements of a particular age have renewal frequencies that are integral multiples of a fundamental frequency quantum, and further assuming that the renewal frequency distribution is of the Boltzmann type, performing a population balance for these elements leads to the Danckwerts surface age distribution. The basic quantum is what has been traditionally called the rate of surface renewal. The Higbie surface age distribution follows if the renewal frequency distribution of such elements is assumed to be continuous. Four age distributions, which reflect different start-up conditions of the absorption process, are then used to analyse transient physical gas absorption into a large volume of liquid, assuming negligible gas-side mass-transfer resistance. The first two are different versions of the Danckwerts model, the third one is based on the uniform and Higbie distributions, while the fourth one is a mixed distribution. For the four cases, theoretical expressions are derived for the rates of gas absorption and dissolved-gas transfer to the bulk liquid. Under transient conditions, these two rates are not equal and have an inverse relationship. However, with the progress of absorption towards steady state, they approach one another. Assuming steady-state conditions, the conventional one-parameter Danckwerts age distribution is generalized to a two-parameter age distribution. Like the two-parameter logarithmic normal distribution, this distribution can also capture the bell-shaped nature of the distribution of the ages of surface elements observed experimentally in air–sea gas and heat exchange. Estimates of the liquid-side mass-transfer coefficient made using these two distributions for the absorption of hydrogen and oxygen in water are very close to one another and are comparable to experimental values reported in the literature.
Chromium oxide coatings with the potential for eliminating the risk of chromium ion release in orthopaedic implants
Authors: Oje A. M. , Ogwu A. A.
Published: July 2017

Chromium oxide coatings prepared by radiofrequency reactive magnetron sputtering on stainless steel substrates were exposed to Ringer's physiological solution and tested for their electrochemical corrosion stability using an open circuit potential measurement, potentiodynamic polarization, electrochemical impedance spectroscopy and Mott–Schottky analysis. The coatings were found to be predominantly Cr2O3, based on the observation of the dominance ofA1gand Egsymmetric modes in our Raman spectroscopic investigation and the Euvibrational modes in our Fourier transform infrared spectroscopic measurements on the coatings. We investigated for the presence of chromium ions in Ringer's solution after all of the above electrochemical tests using atomic absorption spectroscopy, without finding a trace of chromium ions at the ppm level for coatings tested under open circuit and at the lower potentials implants are likely to experience in the human body. The coatings were further exposed to Ringer's solution for one month and tested for adhesion strength changes, and we found that they retained substantial adhesion to the substrates. We expect this finding to be significant for future orthopaedic implants where chromium ion release is still a major challenge.
Population patterns in World’s administrative units
Authors: Fontanelli Oscar , Miramontes Pedro , Cocho Germinal , Li Wentian
Published: July 2017

Whereas there has been an extended discussion concerning city population distribution, little has been said about that of administrative divisions. In this work, we investigate the population distribution of second-level administrative units of 150 countries and territories and propose the discrete generalized beta distribution (DGBD) rank-size function to describe the data. After testing the balance between the goodness of fit and number of parameters of this function compared with a power law, which is the most common model for city population, the DGBD is a good statistical model for 96% of our datasets and preferred over a power law in almost every case. Moreover, the DGBD is preferred over a power law for fitting country population data, which can be seen as the zeroth-level administrative unit. We present a computational toy model to simulate the formation of administrative divisions in one dimension and give numerical evidence that the DGBD arises from a particular case of this model. This model, along with the fitting of the DGBD, proves adequate in reproducing and describing local unit evolution and its effect on the population distribution.
Ant queens increase their reproductive efforts after pathogen infection
Authors: Giehr Julia , Grasse Anna V. , Cremer Sylvia , Heinze Jürgen , Schrempf Alexandra
Published: July 2017

Infections with potentially lethal pathogens may negatively affect an individual's lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the antCardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens ofC. obscuriorreact to infection with the entomopathogenic fungusMetarhizium brunneumby an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect.
The physical environment mediates male harm and its effect on selection in females
Authors: Yun Li , Chen Patrick J. , Singh Amardeep , Agrawal Aneil F. , Rundle Howard D.
Published: July 2017

Recent experiments indicate that male preferential harassment of high-quality females reduces the variance in female fitness, thereby weakening natural selection through females and hampering adaptation and purging. We propose that this phenomenon, which results from a combination of male choice and male-induced harm, should be mediated by the physical environment in which intersexual interactions occur. UsingDrosophila melanogaster, we examined intersexual interactions in small and simple (standard fly vials) versus slightly more realistic (small cages with spatial structure) environments. We show that in these more realistic environments, sexual interactions are less frequent, are no longer biased towards high-quality females, and that overall male harm is reduced. Next, we examine the selective advantage of high- over low-quality females while manipulating the opportunity for male choice. Male choice weakens the viability advantage of high-quality females in the simple environment, consistent with previous work, but strengthens selection on females in the more realistic environment. Laboratory studies in simple environments have strongly shaped our understanding of sexual conflict but may provide biased insight. Our results suggest that the physical environment plays a key role in the evolutionary consequences of sexual interactions and ultimately the alignment of natural and sexual selection.
Exposure to the leaf litter microbiome of healthy adults protects seedlings from pathogen damage
Authors: Christian Natalie , Herre Edward Allen , Mejia Luis C. , Clay Keith
Published: July 2017

It is increasingly recognized that microbiota affect host health and physiology. However, it is unclear what factors shape microbiome community assembly in nature, and how microbiome assembly can be manipulated to improve host health. All plant leaves host foliar endophytic fungi, which make up a diverse, environmentally acquired fungal microbiota. Here, we experimentally manipulated assembly of the cacao tree (
Theobroma cacao
) fungal microbiome in nature and tested the effect of assembly outcome on host health. Using next-generation sequencing, as well as culture-based methods coupled with Sanger sequencing, we found that manipulating leaf litter exposure and location within the forest canopy significantly altered microbiome composition in cacao. Exposing cacao seedlings to leaf litter from healthy conspecific adults enriched the seedling microbiome with
Colletotrichum tropicale
, a fungal endophyte known to enhance pathogen resistance of cacao seedlings by upregulating host defensive pathways. As a result, seedlings exposed to healthy conspecific litter experienced reduced pathogen damage. Our results link processes that affect the assembly and composition of microbiome communities to their functional consequences for host success, and have broad implications for understanding plant–microbe interactions. Deliberate manipulation of the plant–fungal microbiome also has potentially important applications for cacao production and other agricultural systems in general.
Tracheophyte genomes keep track of the deep evolution of theCaulimoviridae
Authors: Diop Seydina , Geering Andrew D.W. , Alfama-Depauw Françoise , Loaec Mikaël , Teycheney Pierre-Yves , Maumus Florian
Published: July 2017

Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. TheCaulimoviridaeis the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants. Evidence is provided that almost every vascular plant (tracheophyte), including the most primitive taxa (clubmosses, ferns and gymnosperms) contains caulimovirid EVEs, many of which represent previously unrecognized evolutionary branches. In angiosperms, EVEs from at least one and as many as five different caulimovirid genera were frequently detected, and florendoviruses were the most widely distributed, followed by petuviruses. From the analysis of the distribution of different caulimovirid genera within different plant species, we propose a working evolutionary scenario in which this family of viruses emerged at latest during Devonian era (approx. 320 million years ago) followed by vertical transmission and by several cross-division host swaps.
Single nucleus analysis of the chromatin landscape in mouse forebrain development
Authors: Preissl Sebastian , Fang Rongxin , Zhao Yuan , Raviram Ramya , Zhang Yanxiao , Sos Brandon C. , Huang Hui , Gorkin David U. , Afzal Veena , Dickel Diane E. , Kuan Samantha , Visel Axel , Pennacchio Len A. , Zhang Kun , Ren Bing
Published: July 2017

Genome-wide analysis of chromatin accessibility in primary tissues has uncovered millions of candidate regulatory sequences in the human and mouse genomes1–4. However, the heterogeneity of biological samples used in previous studies has prevented a precise understanding of the dynamic chromatin landscape in specific cell types. Here, we show that analysis of the transposase-accessible-chromatin in single nuclei isolated from frozen tissue samples can resolve cellular heterogeneity and delineate transcriptional regulatory sequences in the constituent cell types. Our strategy is based on a combinatorial barcoding assisted single cell assay for transposase-accessible chromatin5and is optimized for nuclei from flash-frozen primary tissue samples (snATAC-seq). We used this method to examine the mouse forebrain at seven development stages and in adults. From snATAC-seq profiles of more than 15,000 high quality nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell-types in foetal and adult forebrains. We further define cell-type specificcisregulatory sequences and infer potential master transcriptional regulators of each cell population. Our results demonstrate the feasibility of a general approach for identifying cell-type-specificcisregulatory sequences in heterogeneous tissue samples, and provide a rich resource for understanding forebrain development in mammals.