bluuebunny/crossref_metadata_2025 huggingface dataset:
Advanced perspective on the synchronized bifunctional activities of P2-type materials to implement an interconnected voltage profile for seawater batteries
Authors: Manikandan Palanisamy , Kishor Koshal , Han Jinhyup , Kim Youngsik
Published: May 2018

Na0.5Co0.5Mn0.5O2 comprising an integrated voltage profile for a seawater battery and showing intercalation–deintercalation and OER/ORR characteristics in comparison with a carbon felt and 20% Pt/C catalyst at 0.1 mA for 5 h.
Atomic-layer-deposited AZO outperforms ITO in high-efficiency polymer solar cells
Authors: Kan Zhipeng , Wang Zhenwei , Firdaus Yuliar , Babics Maxime , Alshareef Husam N. , Beaujuge Pierre M.
Published: May 2018

An aluminum doped zinc oxide electrode grown by atomic layer deposition for polymer solar cells outperforms ITO in high performance PSCs.
Colloidal Ni2−xCoxP nanocrystals for the hydrogen evolution reaction
Authors: Liu Junfeng , Wang Zhenxing , David Jeremy , Llorca Jordi , Li Junshan , Yu Xiaoting , Shavel Alexey , Arbiol Jordi , Meyns Michaela , Cabot Andreu
Published: May 2018

Ni2−xCoxP nanocrystals with controlled composition were produced and demonstrated to show excellent activity toward the hydrogen evolution reaction.
A simple design of fluorescent probes for indirect detection of β-lactamase based on AIE and ESIPT processes
Authors: Peng Lu , Xiao Lu , Ding Yiwen , Xiang Yu , Tong Aijun
Published: May 2018

A fluorescent probe with both AIE and ESIPT characteristics has been developed for β-lactamase based on an indirect approach.
Osteogenesis, vascularization and osseointegration of a bioactive multiphase macroporous scaffold in the treatment of large bone defects
Authors: Chu Linyang , Jiang Guoqiang , Hu Xi-Le , James Tony D. , He Xiao-Peng , Li Yaping , Tang Tingting
Published: May 2018

We report a segmental radial bone defect model used to evaluate the osteogenesis, vascularization and osseointegration of a bioactive multiphase macroporous scaffold with nano-crystal surface microstructures that can release bioactive ions.
Antigen detection with thermosensitive hydrophilicity of poly(N-isopropylacrylamide)-grafted poly(vinyl chloride) fibrous mats
Authors: Guo Jian-Wei , Lin Zhen-Yu , Huang Bohr-Ran , Lu Chien-Hsing , Chen Jem-Kun
Published: May 2018

The static water contact angle of stimuli-responsive fibrous mats is used as a convenient index for rapid antigen detection.
Electric-double-layer transistors for synaptic devices and neuromorphic systems
Authors: He Yongli , Yang Yi , Nie Sha , Liu Rui , Wan Qing
Published: May 2018

This article reviews the recent progress in the field of electric-double-layer transistors for synaptic devices and neuromorphic systems.
Enhanced electrical conductivity and photoconductive properties of Sn-doped Sb2Se3 crystals
Authors: Chen Shuo , Qiao Xvsheng , Zheng Zhuanghao , Cathelinaud Michel , Ma Hongli , Fan Xianping , Zhang Xianghua
Published: May 2018

An effective melt-quenching method is used to synthesize Sn-doped Sb2Se3 crystals with enhanced electrical conductivity and photoconductive properties.
Bioactive nano-metal–organic frameworks as antimicrobials against Gram-positive and Gram-negative bacteria
Authors: Bhardwaj Neha , Pandey Satish K. , Mehta Jyotsana , Bhardwaj Sanjeev K. , Kim Ki-Hyun , Deep Akash
Published: May 2018

More effective antibiotics are needed to overcome the problem of multidrug resistance.
Retraction of rod-like mitochondria during microtubule-dependent transport
Authors: De Rossi María Cecilia , Levi Valeria , Bruno Luciana
Published: May 2018

Molecular motors play relevant roles on the regulation of mitochondria size and shape, essential properties for the cell homeostasis. In this work, we tracked single rod-shaped mitochondria with nanometer precision to explore the performance of microtubule motor teams during processive anterograde and retrograde transport. We analyzed simultaneously the organelle size and verified that mitochondria retracted during retrograde transport with their leading tip moving slower in comparison with the rear tip. In contrast, mitochondria preserved their size during anterograde runs indicating a different performance of plus-end directed teams. These results were interpreted considering the different performance of dynein and kinesin teams and provide valuable information on the collective action of motors during mitochondria transport.
ERCC1 rs11615 polymorphism increases susceptibility to breast cancer: a meta-analysis of 4547 individuals
Authors: Li Bingjie , Shi Xiaoqing , Yuan Yingying , Peng Mengle , Jin Huifang , Qin Dongchun
Published: May 2018

Excision repair cross-complementation group 1 (ERCC1), a DNA repair protein, is vital for maintaining genomic fidelity and integrity. Despite the fact that a mounting body of case–control studies has concentrated on investigating the association of the ERCC1 rs11615 polymorphism and breast cancer risk, there is still no consensus on it. We conducted the current meta-analysis of all eligible articles to reach a much more explicit conclusion on this ambiguous association. A total of seven studies involving 2354 breast cancer cases and 2193 controls were elaborately selected for this analysis from the Embase, EBSCO, PubMed, WanFang, and China National Knowledge Infrastructure (CNKI) databases. Pooled odds ratios (ORs) and their 95% confidence intervals (CIs) were estimated in our meta-analysis. We found that the ERCC1 rs11615 polymorphism was significantly associated with breast cancer risk under all genetic models. When excluded, the studies that deviated from Hardy–Weinberg equilibrium (HWE), the pooled results of what remained significantly increase the risk of breast cancer under the allele model (OR = 1.14, 95% CI = 1.02–1.27, P=0.02), heterozygote model (OR = 1.24, 95% CI = 1.06–1.44, P=0.007), and dominant model (OR = 1.21, 95% CI = 1.05–1.41, P=0.01). This increased breast cancer risk was found in Asian population as well as under the heterozygote model (OR = 1.24, 95% CI = 1.05–1.48, P=0.013) and dominant model (OR = 1.20, 95% CI = 1.02–1.42, P=0.03). Our results suggest that the ERCC1 rs11615 polymorphism is associated with breast cancer susceptibility, and in particular, this increased risk of breast cancer existence in Asian population.
Resveratrol enhances matrix biosynthesis of nucleus pulposus cells through activating autophagy via the PI3K/Akt pathway under oxidative damage
Authors: Gao Jinlou , Zhang Qingyun , Song Lin
Published: May 2018

The decrease in nucleus pulposus (NP) matrix production is a classic feature during disc degeneration. Resveratrol (RSV) is reported to play protective effects under many pathological factors.The present study aims to study the effects of RSV on NP matrix homeostasis under oxidative damage and the potential mechanism. Rat NP cells were exposed to H2O2 solution to create an oxidative damage. RSV and the 3-methyladenine (3-MA) were added along with the culture medium to respectively investigate the role of RSV and cellular autophagy. NP matrix synthesis was evaluated by the expression of macromolecules (aggrecan and collagen II) and glycosaminoglycan (GAG) content. Activation of cellular autophagy was assessed by the expression of several molecular markers. Additionally, activity of the PI3K/Akt pathway was also evaluated to study its potential role. Compared with the control group (NP cells treated with H2O2), RSV significantly up-regulated expression of matrix macromolecules (aggrecan and collagen), promoted GAG production, and increased the expression of autophagy-related markers (Beclin-1 and LC-3). Further analysis showed that inhibition of autophagy by 3-MA partly attenuated NP matrix production. Additionally, RSV increased activity of the PI3K/Akt pathway compared with the control NP cells, but it was not affected by the addition of 3-MA. RSV plays a protective role in enhancing NP matrix synthesis under oxidative damage. Mechanistically, activation of the cellular autophagy via the PI3K/Akt pathway may participate in this process. RSV may be an effective drug to attenuate oxidative stress-induced disc degeneration.
Modification of the surface properties of glass-ceramic materials at low-pressure RF plasma stream
Authors: Tovstopyat Alexander , Gafarov Ildar , Galeev Vadim , Azarova Valentina , Golyaeva Anastasia
Published: May 2018

The surface roughness has a huge effect on the mechanical, optical, and electronic properties of materials. In modern optical systems, the specifications for the surface accuracy and smoothness of substrates are becoming even more stringent. Commercially available pre-polished glass-ceramic substrates were treated with the radio frequency (RF) inductively coupled (13.56 MHz) low-pressure plasma to clean the surface of the samples and decrease the roughness. Optical emission spectroscopy was used to investigate the plasma stream parameters and phase-shifted interferometry to investigate the surface of the specimen. In this work, the dependence of RF inductively coupled plasma on macroscopic parameters was investigated with the focus on improving the surfaces. The ion energy, sputtering rate, and homogeneity were investigated. The improvements of the glass-ceramic surfaces from 2.6 to 2.2 Å root mean square by removing the “waste” after the previous operations had been achieved.
Quantum chemical approach for positron annihilation spectra of atoms and molecules beyond plane-wave approximation
Authors: Ikabata Yasuhiro , Aiba Risa , Iwanade Toru , Nishizawa Hiroaki , Wang Feng , Nakai Hiromi
Published: May 2018

We report theoretical calculations of positron-electron annihilation spectra of noble gas atoms and small molecules using the nuclear orbital plus molecular orbital method. Instead of a nuclear wavefunction, the positronic wavefunction is obtained as the solution of the coupled Hartree-Fock or Kohn-Sham equation for a positron and the electrons. The molecular field is included in the positronic Fock operator, which allows an appropriate treatment of the positron-molecule repulsion. The present treatment succeeds in reproducing the Doppler shift, i.e., full width at half maximum (FWHM) of experimentally measured annihilation (γ-ray) spectra for molecules with a mean absolute error less than 10%. The numerical results indicate that the interpretation of the FWHM in terms of a specific molecular orbital is not appropriate.
On the noise optimization of resonant MEMS sensors utilizing vibration mode localization
Authors: Zhao Chun , Pandit Milind , Sobreviela Guillermo , Mustafazade Arif , Du Sijun , Zou Xudong , Seshia Ashwin
Published: May 2018

In this letter, we experimentally demonstrate the existence of an optimal operating region in a resonant microelectromechanical systems sensor utilizing the principle of vibration mode localization, to achieve ultra-high resolution amplitude ratio measurements. We have shown analytically that the coupling strength and stiffness mismatch between the two resonators are primary parameters that influence the resolution of the amplitude ratio measurements within such a sensor. Using this optimization strategy, a minimum noise spectral density equivalent to 16 ppb/Hz1∕2 in terms of normalized stiffness perturbation is experimentally demonstrated. This is by far the best resolution achieved in this type of sensor. These results can be used to aid the design of future high resolution sensor employing mode localization.
Novel plasma source for safe beryllium spectral line studies in the presence of beryllium dust
Authors: Stankov B. D. , Vinić M. , Gavrilović Božović M. R. , Ivković M.
Published: May 2018

Plasma source for beryllium spectral line studies in the presence of beryllium dust particles was realised. The guideline during construction was to prevent exposure to formed dust, considering the toxicity of beryllium. Plasma source characterization through determination of optimal working conditions is described. The necessary conditions for Be spectral line appearance and optimal conditions for line shape measurements are found. It is proven experimentally that under these conditions dust appears coincidently with the second current maximum. The electron density measured after discharge current maximum is determined from the peak separation of the hydrogen Balmer beta spectral line, and the electron temperature is determined from the ratios of the relative intensities of Be spectral lines emitted from successive ionized stages of atoms. Maximum values of electron density and temperature are measured to be 9.3 × 1022 m−3 and 16 800 K, respectively. Construction details and testing of the BeO discharge tube in comparison with SiO2 and Al2O3 discharge tubes are also presented in this paper.
Giant magnetostriction effect near onset of spin reorientation in MnBi
Authors: Choi Y. , Ryan P. J. , McGuire M. A. , Sales B. C. , Kim J.-W.
Published: May 2018

In materials undergoing spontaneous symmetry breaking transitions, the emergence of multiple competing order parameters is pervasive. Employing in-field x-ray diffraction, we investigate the temperature and magnetic field dependence of the crystallographic structure of MnBi, elucidating the microscopic interplay between lattices and spin. The hexagonal phase of MnBi undergoes a spin reorientation transition (TSR), whereby the easy axis direction changes from the c axis to the basal plane. Across TSR, an abrupt symmetry change is accompanied by a clear sign change in the magnetostrictive coefficient, revealing that this transition corresponds to the onset of the spin reorientation. In the vicinity of TSR, a significantly larger in-plane magnetostrictive effect is observed, presenting the emergence of an intermediate phase that is highly susceptible to an applied magnetic field. X-ray linear dichroism shows that asymmetric Bi and Mn p orbitals do not play a role in the spin reorientation. This work suggests that the spin reorientation is caused by structural modification rather than changes in the local electronic configuration, providing a strategy for manipulating the magnetic anisotropy by external strain.
Hetonic quartets in a two-layer quasi-geostrophic flow: V-states and stability
Authors: Reinaud J. N. , Sokolovskiy M. A. , Carton X.
Published: May 2018

We investigate families of finite core vortex quartets in mutual equilibrium in a two-layer quasi-geostrophic flow. The finite core solutions stem from known solutions for discrete (singular) vortex quartets. Two vortices lie in the top layer and two vortices lie in the bottom layer. Two vortices have a positive potential vorticity anomaly, while the two others have negative potential vorticity anomaly. The vortex configurations are therefore related to the baroclinic dipoles known in the literature as hetons. Two main branches of solutions exist depending on the arrangement of the vortices: the translating zigzag-shaped hetonic quartets and the rotating zigzag-shaped hetonic quartets. By addressing their linear stability, we show that while the rotating quartets can be unstable over a large range of the parameter space, most translating quartets are stable. This has implications on the longevity of such vortex equilibria in the oceans.
The influence of point defects on the thermal conductivity of AlN crystals
Authors: Rounds Robert , Sarkar Biplab , Alden Dorian , Guo Qiang , Klump Andrew , Hartmann Carsten , Nagashima Toru , Kirste Ronny , Franke Alexander , Bickermann Matthias , Kumagai Yoshinao , Sitar Zlatko , Collazo Ramón
Published: May 2018

The average bulk thermal conductivity of free-standing physical vapor transport and hydride vapor phase epitaxy single crystal AlN samples with different impurity concentrations is analyzed using the 3ω method in the temperature range of 30–325 K. AlN wafers grown by physical vapor transport show significant variation in thermal conductivity at room temperature with values ranging between 268 W/m K and 339 W/m K. AlN crystals grown by hydride vapor phase epitaxy yield values between 298 W/m K and 341 W/m K at room temperature, suggesting that the same fundamental mechanisms limit the thermal conductivity of AlN grown by both techniques. All samples in this work show phonon resonance behavior resulting from incorporated point defects. Samples shown by optical analysis to contain carbon-silicon complexes exhibit higher thermal conductivity above 100 K. Phonon scattering by point defects is determined to be the main limiting factor for thermal conductivity of AlN within the investigated temperature range.
Quantum optical measurement with tripartite entangled photons generated by triple parametric down-conversion
Authors: Cho Minhaeng
Published: May 2018

Parametric down-conversion is a second-order nonlinear optical process annihilating a pump photon and creating a pair of photons in the signal and idler modes. Then, by using two parametric down-converters and introducing a path indistinguishability for the two generated idler modes, a quantum coherence between two conjugate signal beams can be induced. Such a double spontaneous or stimulated parametric down-conversion scheme has been used to demonstrate quantum spectroscopy and imaging with undetected idler photons via measuring one-photon interference between their correlated signal beams. Recently, we considered another quantum optical measurement scheme utilizing W-type tripartite entangled signal photons that can be generated by employing three spontaneous parametric down-conversion crystals and by inducing coherences or path-indistinguishabilities between their correlated idler beams and between quantum vacuum fields. Here, we consider an extended triple stimulated parametric down-conversion scheme for quantum optical measurement of sample properties with undetected idler and photons. Noting the real effect of vacuum field indistinguishability on the fringe visibility as well as the role of zero-point field energy in the interferometry, we show that this scheme is an ideal and efficient way to create a coherent state of W-type entangled signal photons. We anticipate that this scheme would be of critical use in further developing quantum optical measurements in spectroscopy and microscopy with undetected photons.
On observation of position in quantum theory
Authors: Kryukov A.
Published: May 2018

Newtonian and Schrödinger dynamics can be formulated in a physically meaningful way within the same Hilbert space framework. This fact was recently used to discover an unexpected relation between classical and quantum motions that goes beyond the results provided by the Ehrenfest theorem. A formula relating the normal probability distribution and the Born rule was also found. Here the dynamical mechanism responsible for the latter formula is proposed and applied to measurements of macroscopic and microscopic systems. A relationship between the classical Brownian motion and the diffusion of state on the space of states is discovered. The role of measuring devices in quantum theory is investigated in the new framework. It is shown that the so-called collapse of the wave function is not measurement specific and does not require a “concentration” near the eigenstates of the measured observable. Instead, it is explained by the common diffusion of a state over the space of states under interaction with the apparatus and the environment. This in turn provides us with a basic reason for the definite position of macroscopic bodies in space.
Multiple-parameter bifurcation analysis in a Kuramoto model with time delay and distributed shear
Authors: Niu Ben , Zhang Jiaming , Wei Junjie
Published: May 2018

In this paper, time delay effect and distributed shear are considered in the Kuramoto model. On the Ott-Antonsen’s manifold, through analyzing the associated characteristic equation of the reduced functional differential equation, the stability boundary of the incoherent state is derived in multiple-parameter space. Moreover, very rich dynamical behavior such as stability switches inducing synchronization switches can occur in this equation. With the loss of stability, Hopf bifurcating coherent states arise, and the criticality of Hopf bifurcations is determined by applying the normal form theory and the center manifold theorem. On one hand, theoretical analysis indicates that the width of shear distribution and time delay can both eliminate the synchronization then lead the Kuramoto model to incoherence. On the other, time delay can induce several coexisting coherent states. Finally, some numerical simulations are given to support the obtained results where several bifurcation diagrams are drawn, and the effect of time delay and shear is discussed.
Investigation of the relevant kinetic processes in the initial stage of a double-arcing instability in oxygen plasmas
Authors: Mancinelli B. , Prevosto L. , Chamorro J. C. , Minotti F. O. , Kelly H.
Published: May 2018

A numerical investigation of the kinetic processes in the initial (nanosecond range) stage of the double-arcing instability was developed. The plasma-sheath boundary region of an oxygen-operated cutting torch was considered. The energy balance and chemistry processes in the discharge were described. It is shown that the double-arcing instability is a sudden transition from a diffuse (glow-like) discharge to a constricted (arc-like) discharge in the plasma-sheath boundary region arising from a field-emission instability. A critical electric field value of ∼107 V/m was found at the cathodic part of the nozzle wall under the conditions considered. The field-emission instability drives in turn a fast electronic-to-translational energy relaxation mechanism, giving rise to a very fast gas heating rate of at least ∼109 K/s, mainly due to reactions of preliminary dissociation of oxygen molecules via the highly excited electronic state O2(B3Σu−) populated by electron impact. It is expected that this fast oxygen heating rate further stimulates the discharge contraction through the thermal instability mechanism.
Latent disciplinal clashes concerning the batch dissolution of minerals, and their wider implications
Authors: Truesdale Victor W. , Greenwood Jim
Published: May 2018

Environmental contextMineral dissolution kinetics are important to understand natural processes including those increasingly used to store waste carbon dioxide and highly radio-active nuclides, and those involved in the amelioration of climate change and sea-level rise. We highlight a mistake made in the fundamental science that has retarded progress in the field for over 40 years. Its removal suggests improved ways to approach dissolution studies.
AbstractMineral dissolution kinetics are fundamental to biogeochemistry, and to the application of science to reduce the deleterious effects of humanity’s waste products, e.g. CO2 and radio-nuclides. However, a mistake made in the selection of the rate equation appropriate for use at the macro-scale of the aquatic environment has stymied growth in major aspects of the subject for some 40 years. This paper identifies the mistake, shows how it represents a latent disciplinal clash between two rate equations, and explores the misunderstandings that resulted from it. The paper also briefly explores other disciplinal clashes. Using the example of calcite dissolution, the paper also shows how the phenomenon of ‘non-ideal’ dissolution, which is prevalent in alumino-silicate mineral dissolution, as well as with calcite, has obscured the clash. The paper provides new information on plausible mechanisms, the absence of which has contributed to the problem. Finally, it argues that disciplinal clashes need to be minimised so that a rigorous description of dissolution at the large scale can be matched to findings at the atomic, or near-atomic, scale.
Corrigendum to: Influence of climatic factors on variation in the Normalised Difference Vegetation Index in Mongolian Plateau grasslands
Authors: Cao Xu-Juan , Gao Qing-Zhu , Hasbagan Ganjurjav , Liang Yan , Li Wen-Han , Hu Guo-Zheng
Published: May 2018

Climate change will affect how the Normalised Difference Vegetation Index (NDVI), which is correlated with climate factors, varies in space and over time. The Mongolian Plateau is an arid and semi-arid area, 64% covered by grassland, which is extremely sensitive to climate change. Its climate has shown a warming and drying trend at both annual and seasonal scales. We analysed NDVI and climate variation characteristics and the relationships between them for Mongolian Plateau grasslands from 1981 to 2013. The results showed spatial and temporal differences in the variation of NDVI. Precipitation showed the strongest correlation with NDVI (43% of plateau area correlated with total annual precipitation and 44% with total precipitation in the growing season, from May to September), followed by potential evapotranspiration (27% annual, and 30% growing season), temperature (7% annual, 16% growing season) and cloud cover (10% annual, 12% growing season). These findings confirm that moisture is the most important limiting factor for grassland vegetation growth on the Mongolian Plateau. Changes in land use help to explain variations in NDVI in 40% of the plateau, where no correlation with climate factors was found. Our results indicate that vegetation primary productivity will decrease if warming and drying trends continue but decreases will be less substantial if further warming, predicted as highly likely, is not accompanied by further drying, for which predictions are less certain. Continuing spatial and temporal variability can be expected, including as a result of land use changes.
Response of ecosystem functions to climate change and implications for sustainable development on the Inner Mongolian Plateau
Authors: Hu Guozheng , Davies Jocelyn , Gao Qingzhu , Liang Cunzhu
Published: May 2018

The responses of ecosystem functions in Inner Mongolian grasslands to climate change have implications for ecosystem services and sustainable development. Research published in two previous Special Issues of The Rangeland Journal shows that recent climate change added to overgrazing and other factors caused increased degradation of Inner Mongolian rangelands whereas on the Qinghai-Tibetan Plateau, climate change tended to ameliorate the impacts of overgrazing. Recent climate change on the Mongolian Plateau involved warming with increasingly variable annual precipitation and decreased summer rainfall. Future climate projections are different, involving modest increases in precipitation and further climate warming. Research published in the current Special Issue shows that precipitation is the climate factor that has the most substantial impact on ecosystem functions in this region and is positively correlated with plant species diversity, ecosystem carbon exchange and Normalised Difference Vegetation Index. Increased flows of provisioning and regulating ecosystem services are expected with future climate change indicating that its impacts will be positive in this region. However, spatial heterogeneity in the environments and climates of Inner Mongolia highlights the risk of over-generalising from local-scale studies and indicates the value of increased attention to meta-analysis and regional scale models. The enhanced flows of ecosystem services from climate change may support sustainable development by promoting recovery of degraded grasslands with flow-on benefits for livelihoods and the regional economy. However, realising these potential benefits will depend on sound landscape management and addressing the risk of herders increasing livestock numbers to take advantage of the extra forage available. Investment in education is important to improve local capacity to adapt rangeland management to climate change, as are policies and strategies that integrate social, economic and ecological considerations and are tailored to specific regions. Gaps in understanding that could be addressed through further research on ecosystem functions include; belowground carbon exchange processes; the impact of increased variability in precipitation; and the impact of different management practices under changed climates.
Support for the value 5/2 for the spin glass lower critical dimension at zero magnetic field
Authors: Maiorano Andrea , Parisi Giorgio
Published: May 2018

Significance

Glassy systems at low temperature may stay in many equilibrium configurations quite different from one another. An important quantity is the (free) energy difference for going from an equilibrium configuration to another one: Its properties dominate the dynamics at large times. The analytic computation of these differences is notoriously difficult. For spin glasses a clean computation can be done, using uncontrolled approximations. Here we use numerical simulations to show that this theory predicts the correct properties of the differences in three and four dimensions. The same theory predicts also that the spin glass transition disappears at dimensions 5/2 and our verification of the predictions of the theory brings support to this result.
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria
Authors: Belliveau Nathan M. , Barnes Stephanie L. , Ireland William T. , Jones Daniel L. , Sweredoski Michael J. , Moradian Annie , Hess Sonja , Kinney Justin B. , Phillips Rob
Published: May 2018

Significance

Organisms must constantly make regulatory decisions in response to a change in cellular state or environment. However, while the catalog of genomes expands rapidly, we remain ignorant about how the genes in these genomes are regulated. Here, we show how a massively parallel reporter assay, Sort-Seq, and information-theoretic modeling can be used to identify regulatory sequences. We then use chromatography and mass spectrometry to identify the regulatory proteins that bind these sequences. The approach results in quantitative base pair-resolution models of promoter mechanism and was shown in both well-characterized and unannotated promoters inEscherichia coli. Given the generality of the approach, it opens up the possibility of quantitatively dissecting the mechanisms of promoter function in a wide range of bacteria.
Calcium, conformational selection, and redox-active tyrosine YZ in the photosynthetic oxygen-evolving cluster
Authors: Guo Zhanjun , He Jiayuan , Barry Bridgette A.
Published: May 2018

Significance

Photosynthetic water oxidation provides oxygen and maintains aerobic life on earth. The Mn
4
CaO
5
cluster is the catalytic site for this reaction in Photosystem II. During water oxidation, a redox-active tyrosine, YZ, is oxidized and reduced in a proton-coupled electron transfer reaction (PCET). We provide spectroscopic evidence that the essential calcium ion interacts with YZ in its radical and singlet states. In addition, multiple conformational states of the YZ radical/singlet are identified. Calcium is shown to select for a PCET reaction in a subset of these states. Conformational targeting could be a key to control of the PCET pathway and may occur in other enzymes, such as ribonucleotide reductase, which use tyrosine as a PCET cofactor.
Quantum oscillations in a biaxial pair density wave state
Authors: Norman M. R. , Davis J. C. Séamus
Published: May 2018

Significance

At higher temperatures, and in high magnetic fields at low temperatures, an extraordinary and unidentified electronic phase, dubbed the “pseudogap,” appears in lightly hole-doped cuprates. At high fields and low temperatures, the pseudogap phase supports quantum oscillations that have resisted quantitative theoretical explanation since their discovery, and it also exhibits an unidentified density wave state. Although the latter has typically been referred to as a “charge” density wave because of the observed charge density modulations, theory indicates that it could actually be an electron-pair density wave (PDW) state. Here we demonstrate theoretically that a biaxial PDW state with 8
a
periodicity may provide a compelling quantitative explanation for much of the observed quantum oscillation data.
Invasion biology: searching for predictions and prevention, and avoiding lost causes.
Authors: Cassey P. , García-Díaz P. , Lockwood J. L. , Blackburn T. M.
Published: May 2018

The introduction and establishment of alien species is one of the many profound influences of ongoing anthropogenic global environmental change. Invasion biology has emerged as the interdisciplinary study of the patterns, processes and consequences of the redistribution of biodiversity across all environments and spatio-temporal scales. The modern discipline hinges on the knowledge that biological invasions cannot be defined and studied solely by their final outcome of establishing alien species but rather as a sequential series of stages, or barriers, that all alien species transit: the 'invasion pathway'. Some of the most important influences for a species transiting these sequential stages (i.e. transport, introduction, establishment and spread) are event-level effects, which vary independently of species and location, such as the number of individuals released in any given location (propagule pressure). The number of studies of biological invasions has increased exponentially over the past two decades, and we now have a significant body of research on different aspects of the invasion process. In particular, the hierarchical nature of the invasion pathway has lent itself strongly to modern statistical methods in hierarchical modelling. Now, the science behind invasive species management must continue to develop innovative ways of using this accumulated knowledge for delivering actionable management procedures.
The hierarchy-of-hypotheses approach.
Authors: Heger T. , Jeschke J. M.
Published: May 2018

Reviewing empirical evidence for major hypotheses in ecology is connected to two methodological challenges. First, all available empirical tests for a given hypothesis should be identified, collected and organized. This can be difficult due to divergent formulations of the hypothesis in the literature and divergent empirical approaches to address it. Second, the entire body of available data should be used to systematically assess the overall level of support of the hypothesis. Many approaches (e.g. formal meta-analyses) typically use only a fraction of the available data, often because of inconsistencies in the data. In this chapter, we show how the new hierarchy-of-hypotheses (HoH) approach can be used to overcome these challenges.
Hierarchy of hypotheses or hierarchy of predictions? Clarifying key concepts in ecological research.
Authors: Farji-Brener A. G. , Amador-Vargas S.
Published: May 2018

Hypotheses and predictions are the core of scientific research, and are fundamentally different. Nonetheless, predictions are constantly confused with hypotheses in the scientific literature. The hypothetic-deductive method starts with a question to which potential explanations - hypotheses - are proposed. Each hypothesis has expected outcomes - predictions - that are deduced assuming the hypothesis was true. In this chapter, we point out that the hierarchy-of-hypotheses (HoH) approach is confusing the terms hypothesis and prediction, and further explain why the so-called sub-hypotheses of the HoH approach are in fact predictions. We also propose an alternative approach inspired by the HoH approach to help arrange predictions by their potential to disprove the hypothesis.
Mapping theoretical and evidential landscapes in ecological science: Levins' virtue trade-off and the hierarchy-of-hypotheses approach.
Authors: Griesemer J.
Published: May 2018

According to Richard Levins, there is no single, best all-purpose model in ecology, nor can useful models simultaneously maximize theoretical virtues of generality, realism and precision (Levins, 1966, 1968a,b). A 'virtue trade-off' must be made if models are to be useful for understanding, explanation, prediction or control. Recently, large-scale data synthesis projects have aimed to systematically review many empirical studies to evaluate major hypotheses. A specific version of systematic review called the 'hierarchy-of-hypotheses' approach has been proposed (Jeschke et al., 2012; Heger and Jeschke, 2014; and Chapter 2, this volume). I argue that investigation of the patchwork of models organized by Levins' theoretical 'virtue space' and discovery of robust theorems across a theoretical landscape could be enhanced by recent efforts to manage evidential complexity in a patchwork of empirical studies by the hierarchy-of-hypotheses approach.
A hierarchy of hypotheses or a network of models.
Authors: Scheiner S. M. , Fox G. A.
Published: May 2018

Many different explanations for biological invasions have been proposed, yet there is little evidence that any of them are general. Invasion biologists are increasingly favouring a multicausal outlook rather than seeking single explanations of invasions, or seeking to identify a list of characteristics of invasive species. The time is ripe for systematization of ideas in invasion biology. The hierarchy-of-hypotheses (HoH) framework proposed by Jeschke and Heger thus comes at an opportune moment but we believe that it must be modified substantially to be useful. A principal problem is the notion that science proceeds simply by testing hypotheses, which neglects the roles of models (the source of hypotheses) and of the broader constitutive theories that give rise to models. Accepting or rejecting hypotheses seems to us a doomed approach for complex phenomena like invasions, in which multiple causes are likely to account for the differences between invading and native populations. This multicausality also means that explanations for invasions are not likely to be strictly hierarchical. Finally, the criteria proposed for retaining hypotheses in the HoH - support by a majority of empirical studies - is ad hoc and beset by severe statistical problems. We argue that examination of a network of models - rather than a hierarchy of hypotheses - is needed to move the field forward.
The hierarchy-of-hypotheses approach updated - a toolbox for structuring and analysing theory, research and evidence.
Authors: Heger T. , Jeschke J. M.
Published: May 2018

In Chapters 3, 4 and 5, three groups of authors have commented on the hierarchy-of-hypotheses (HoH) approach as introduced in Chapter 2. Here, we make suggestions on how to account for the issues raised in Chapters 3-5, whilst also considering several comments by other colleagues that we received during discussions or in response to our presentations on this topic. We focus on five issues and address each in a separate section of this chapter. In the concluding section, we suggest treating the HoH approach as a toolbox; we describe its core as well as an array of modules that can be chosen.
Invasional meltdown hypothesis.
Authors: Braga R. R. , Gómez Aparicio L. , Heger T. , Vitule J. R. S. , Jeschke J. M.
Published: May 2018

Positive interactions among species can be central for community structure and ecosystem functioning. Given the current scenario of species invasions worldwide, the question arises how non-native species will interact in the new environment. Such reasoning has led to the invasional meltdown hypothesis (IM) which states that non-native species facilitate one another's invasion, increasing their likelihood of survival, ecological impact and possibly the magnitude of their impact. However, given the importance of antagonistic interactions in natural communities, it is not yet known to what extent these facilitative effects of non-native species occur. We used the hierarchy-of-hypotheses (HoH) approach to differentiate key aspects of IM and link empirical studies to specific sub-hypotheses of the overall hypothesis. Evidence related to IM was gathered by assessing citations of Simberloff and Von Holle (1999) who first defined it. Our HoH was categorized by the type of interaction among non-native species (e.g. facilitation, mutualism and multi-species interactions), ecological level of evidence and the outcome of the interaction for each non-native species (i.e. response variable measured in the study). We additionally looked for taxonomic and geographic variability. On the basis of the 208 relevant studies we found, the broad hypothesis and the majority of sub-hypotheses indicate that positive interactions among non-natives are happening more frequently than negative ones. Thus, IM is broadly supported by currently available studies. Evidence against IM relates to sub-hypotheses involving reciprocal interactions (e.g. competition between non-native species). We suggest that future research focuses on controlled experimental setups aiming at elucidating the community- or ecosystem-level effects of non-native species interactions, especially for reciprocal interactions.
Enemy release hypothesis.
Authors: Heger T. , Jeschke J. M.
Published: May 2018

The enemy release hypothesis is a prominent explanation for invasion success. It is, however, a complex multi-faceted hypothesis and has multiple sub-hypotheses. Empirical tests of the enemy release hypothesis therefore often address very different questions. For this reason, we previously applied the hierarchy-of-hypotheses (HoH) approach to analyse the level of evidence for the enemy release hypothesis and its sub-hypotheses, taking into account this variety of formulations and research questions. This chapter provides an update and extension of that analysis by including recently published evidence and implementing some of the suggestions made in Chapters 3 to 6, this volume, concerning the HoH approach. In detail, we: (i) re-organized the HoH, now separating research approaches from working hypotheses; (ii) displayed results including bar charts in order to avoid a classification of the level of evidence for the different hypotheses; and (iii) tested the robustness of our results based on the precision of the tests (estimated as number of replicates), their generality (using number of focal species as a proxy), realism (i.e. whether they were conducted in the lab, an enclosure or in the field) and their general approach (observation or experiment). We found relatively strong support for the enemy release hypothesis in studies looking at release in the sense of reduced enemy pressure. However, this is not paralleled by strong evidence for enhanced performance. Support for the enemy release hypothesis differs according to which question is asked. It is highest if species in their native vs introduced range are compared and lowest if invasive aliens are compared to non-invasive aliens. There is a comparatively high level of supporting evidence if specialist enemies are considered. From these findings, we conclude that future studies should focus on testing whether invaders show enhanced performance if released from specialist enemies - an underexplored research question so far. Our robustness analysis indicates that empirical results are influenced by the generality (estimated by the number of focal species) and realism (estimated by the number of replicates) of studies addressing the enemy release hypothesis. We suggest that future studies in the context of enemy release should preferentially be done in the field rather than in the lab and use more than ten focal alien species.
Tens rule.
Authors: Jeschke J. M. , Pyšek P.
Published: May 2018

The tens rule became a popular invasion hypothesis in the 1990s and is still widely used today, even though empirical support has been mixed from the beginning and the number of studies questioning it has been increasing in the past decade. Also, the rule is not based on a model or other defensible concept or argument. Here we divide the tens rule into two more specific sub-hypotheses: the invasion tens rule and the impact tens rule, where the former predicts that about 10% of species successfully take consecutive steps of the invasion process, and the latter that about 10% of established non-native species and about 1% of all introduced non-native species cause significant detrimental impacts. A quantitative metaanalysis of 102 empirical tests of the tens rule from 65 publications shows no support for this hypothesis. Looking at the invasion tens rule and comparing different taxonomic groups, about 25% of non-native plants and invertebrates, and about 50% of non-native vertebrates are on average successful in taking consecutive steps of the invasion process. We thus suggest replacing the invasion tens rule by two taxon-dependent hypotheses: the 50% invasion rule for vertebrates and the 25% invasion rule for other organisms, particularly plants and invertebrates. The impact tens rule is not supported by currently available evidence, either, and more data are needed before a reasonable alternative hypothesis can be formulated. In a nutshell, we suggest abandoning the tens rule and using the 50% invasion rule for vertebrates and the 25% invasion rule for other organisms. These hypotheses provide new standards that are supported by currently available data and against which future data can be tested.
Darwin's naturalization and limiting similarity hypotheses.
Authors: Jeschke J. M. , Erhard F.
Published: May 2018

Darwin's naturalization hypothesis (DN) and the limiting similarity hypothesis (LS) are topically similar: DN posits that the invasion success of non-native species is higher in areas that are poor in closely related species than in areas that are rich in closely related species; LS says that the invasion success of non-native species is high if they strongly differ from native species and low if they are similar to native species. We performed systematic reviews for both DN and LS, and divided these into sub-hypotheses using the hierarchy-of-hypotheses (HoH) approach. For DN, we thereby considered if studies used phylogenies to assess relatedness of native and non-native species or if they did so by using taxonomic groups (e.g. the number of native species in the same genus as the non-native species). We found that studies using phylogenies usually support DN, whereas those using taxonomic groups typically question DN. We divided the limiting similarity hypothesis into subhypotheses according to how functional similarity was assessed between native and non-native species. This hypothesis was largely empirically supported. Both DN and LS, however, have basically only been addressed in terrestrial habitats, and limiting similarity hypothesis only for plants, thus studies in other habitats and for other taxonomic groups are needed to test the general validity of both hypotheses. Due to their similarity, these hypotheses can be seen as sub-hypotheses of an overarching limiting similarity hypothesis sensu lato.
Solution to the Bagaryatskii and Isaichev ferrite–cementite orientation relationship problem
Authors: Bhadeshia H. K. D. H.
Published: May 2018

The Bagaryatskii and Isaichev orientation relationships between cementite and ferrite are closely related but not identical. They cannot easily be distinguished using ordinary electron diffraction methods and precise methods indicate that the Bargaryatski orientation does not exist. The issue is important when considering the mechanism by which cementite forms during the tempering of martensite or the formation of lower bainite, where the iron and substitutional solutes are unable to diffuse during the course of precipitation. It is demonstrated here that just one of the orientation relationships is consistent with the mechanism of precipitation at low temperatures, and is associated with much smaller deformations than the other.
Material flow and void defect formation in friction stir welding of aluminium alloys
Authors: Zeng X. H. , Xue P. , Wang D. , Ni D. R. , Xiao B. L. , Wang K. S. , Ma Z. Y.
Published: May 2018

An ingenious experimental programme by combining artificially thickened oxide layer as marker material and ‘stop-action’ welding were used to study the material flow and defect formation in friction stir welding of aluminium alloys. The results showed that material flow around the pin on the advancing side (AS) was severer than that on the retreating side (RS) and the fastest velocity of material flow in the middle stir zone (SZ) was 43.9 mm s−1. Moreover, the material under the RS shoulder included extruded metal only and the material under the AS shoulder included extruded and rotated metal. Lastly, instantaneous void occurrence and insufficient inflow material were reasons for the preferential formation of void defects in the top SZ on the AS.