bluuebunny/crossref_metadata_2025 huggingface dataset:
Humanitarian Armed Intervention
Authors: Miller Seumas
Published: November 2016

In this chapter it is argued that humanitarian armed intervention in relation to large-scale human rights violations is in some cases morally justified (e.g., the Rwanda genocide), and that intervention is best understood as a collective moral responsibility. Moreover, collective moral responsibility is to be understood as the joint moral responsibility of individual human actors. Here two notions are utilized: multilayered structures of joint actions and joint institutional mechanisms. It is further argued that humanitarian armed intervention can, at least in principle, be morally justified in the case where there is large-scale violation of (basic) positive rights (e.g., subsistence rights). This is the case, even if it is held that a single individual would not be morally justified in using lethal force against someone violating his or her (basic) positive rights. The critical difference is the scale of the rights violations.
Autonomous Weapons and Moral Responsibility
Authors: Miller Seumas
Published: November 2016

In this chapter the question addressed is whether autonomous robotic weapons necessarily compromise the moral responsibility of human combatants and their leaders. In order to answer this question, a novel argument is developed: the moral ramification argument. The conclusion of this argument is that it is highly improbable that the moral jus in bello principles of military necessity, discrimination, and proportionality could ever be programmed into robots. The argument utilizes theoretical descriptions of the key notions of military necessity, and individual and collective moral responsibility. Crucially, it relies on the inability of computers to detect and respond to moral—as opposed to physical—properties.
Annals of Native America
Authors: Townsend Camilla
Published: November 2016

After the Spanish conquest, the Nahuas of colonial Mexico learned the Roman alphabet and used it to transcribe oral performances of traditional histories of their peoples. These texts were called xiuhpohaulli in Nahuatl and are usually referred to as “annals” now. They were produced by indigenous people and for indigenous people, without regard to European interests, and they therefore provide the closest view of pre-Columbian historiography we are ever likely to find. Over the course of the colonial era, the annals changed with the times, but for over one hundred years their flexibility allowed for incorporating the new without obliterating the old. Usually these texts have been assumed to be anonymous, but Camilla Townsend has deduced authorship in the case of most of the key texts, and in so doing, has been able to place them securely in their proper contexts, thus rendering them more legible to modern readers. Each chapter begins with a selection from a key text, then considers who wrote it and why, before finally embarking on an exploration of its meanings.
Old Stories in New Letters (1520s–1550s)
Authors: Townsend Camilla
Published: November 2016

In Central Mexico, the generation in power at the time of the Spanish conquest faced not only a crisis but also a new set of opportunities. Don Alonso Castañeda Chimalpopoca, a chief of Cuauhtinchan whose younger relatives attended the Colegio de Santa Cruz in Tlatelolco, supervised the transcription of his people’s history into the text now known as the Historia Tolteca Chichimeca, while peers of his worked on the Annals of Tlatelolco. They welcomed the use of a phonetic alphabet. In the history they recorded in their texts, the political nature of marriage alliances and warfare are both key elements.
Epilogue
Authors: Townsend Camilla
Published: November 2016

The 1690s saw the production of the most eloquent and expressive set of extant Nahuatl annals. They were written by an indigenous craftsman named don Miguel de los Santos. He was a descendant of Tlaxcalan migrants who helped to found and settle the city of Puebla de los Angeles, and he lived in that city in the glory of its Baroque era. His text demonstrates both a break with the Aztec past as well as remarkable continuities. It describes a Spanish city where descendants of the Nahua elite continue to participate in governance and legal proceedings following old patterns, and yet where at the same time they intermingle regularly with Spaniards and Africans and must adapt themselves accordingly. The form and even the substance of don Miguel’s account follows the traditional xiuhpohualli in some regards, yet at the same time the text introduces emotive content and ways of thinking entirely different from those of the past.
The Concept ofErgon: Towards an Achievement Interpretation of Aristotle’s ‘Function Argument’
Authors: Baker Samuel H.
Published: November 2016

In Nicomachean Ethics 1.7, Aristotle gives a definition of the human good, and he does so by means of the ‘ergon argument’. This chapter clears the way for a new interpretation of this argument by arguing that Aristotle does not think that the ergon of something is always the proper activity (‘function’) of that thing. Though he has a single concept of an ergon, Aristotle identifies the ergon of an X as an activity in some cases but a product in others, depending on the sort of thing the X is — for while the ergon of the eye is seeing, the ergon of a sculptor is a sculpture. This alternative interpretation of Aristotle's concept of an ergon allows the key explanatory middle term of the ergon argument to be what it ought to be: ‘the best achievement of a human’.
Aristotle on Essence and Habitat
Authors: Gelber Jessica
Published: November 2016

Aristotle was aware that living organisms tend to have parts and organs that are particularly well suited for exercising their psychic capacities in certain kinds of environments. Despite that awareness, however, Aristotle never tries to explain this. This chapter argues that the reason we do not find Aristotle addressing the ‘fit’ between organisms and their habitats is that his conception of the essence of a living being already includes those features of the habitat that are implicated in the kind's essential activities and functions. Just as understanding what vision is involves understanding that it is of colour and that it takes place in a transparent medium, all of the vital capacities that comprise the soul or essence of a kind are ones that can only be understood in light of the objects that they are capacities upon which to act and by which to be affected. Consequently, the coordination between a kind of organism and its habitat is no surprise, given that the what-it-is-to-be for any kind of organism is partially constituted by the habitat in which its life is carried out.
Plasma Physics and Fusion Plasma Electrodynamics
Authors: Bers Abraham
Published: November 2016

This book covers collective and single particle dynamics of plasmas for fully ionized as well as partially ionized plasmas. Many aspects of plasma physics in current fusion energy generation research are addressed both in magnetic and inertial confinement plasmas. Linear and nonlinear dynamics in hydrodynamic and kinetic descriptions are exposed so that readers are faced with the simple and complex aspects of the subject in nearly every chapter. The approach of dividing the basic aspects of plasma physics as linear, hydrodynamic descriptions to be covered first and postponing the nonlinear and kinetic description for later is abandoned in this book.
Collisions and collisional transport—III. Weakly-ionized plasmas—Unmagnetized
Authors: Bers Abraham
Published: November 2016

This chapter examines the properties of binary collisions between charged particles and neutrals (molecules) and treating them in weakly-ionized plasmas. Fundamental to low-temperature, weakly-ionized plasma, and their large variety of applications, is the much studied (particularly experimentally) domain of electrical discharges in gases. The chapter describes the basic macroscopic properties of such plasma, with a view toward understanding their experimental realizations. Simple physical descriptions are developed and analyzed for the: transport coefficients of mobility and diffusion for electrons and ions; diffusion eigenmodes in a bounded cavity containing a weakly-ionized plasma; the start-up and maintenance of a HF discharge in a cavity; the effects of space charge that couple electrons and ion diffusions leading to ambipolar; plasma columns controlled by diffusion or in the free-fall regime; and the effects of volume recombination and attachment in the evolution of such plasmas.
Charged-particle motion in electromagnetic fields
Authors: Bers Abraham
Published: November 2016

This chapter presents the charged-particle collisionless motions in electromagnetic (EM) fields, with an emphasis on the motion in weakly-nonuniform B-fields that are time independent. It starts with first analyzing motions in several examples of simple, specific fields, and then turns to examples of motion in slowly-varying, spatially-nonuniform EM fields. This culminates with a presentation of the T.G. Northrop analysis of adiabatic motion which systematically derives all drifts, including those studied separately in the preceding sections. Recent computational results are used to illustrate charged-particle motions in the Earth's dipole magnetic field—both exact trajectories and their guiding-center orbits are shown. The chapter concludes with an analysis of particle motions in HF EM fields and the ponderomotive force on the particles engendered by such fields.
Drift-free cold plasma, unmagnetized—Linear and nonlinear electrodynamics
Authors: Bers Abraham
Published: November 2016

This chapter describes linear, normal modes in the simplest, reduced hydrodynamic, two-fluid (electronion) model of a neutral and unmagnetized drift-free cold plasma. Nonlinear effects that limit this hydrodynamic description at large amplitudes, and which couple the linear modes at small but finite amplitudes, are briefly described and illustrated in each case. A systematic treatment is presented of the stable, linear natural modes—waves—in homogeneous plasmas as described by the two- (or multi-) fluid hydrodynamic model of free-charged particles and Maxwell's equations. Although the hydrodynamic model cannot properly describe the dynamics of plasmas in certain regimes of spatial and temporal variations of the fields, it is the simplest for giving a first exposition of the large variety of possible stable linear modes and their properties, particularly for a plasma immersed in a constant, externally applied magnetic field.
Dynamics with thermal pressures—II. Magnetized plasma
Authors: Bers Abraham
Published: November 2016

This chapter describes the linear natural plasma modes in two different two-fluid, reduced hydrodynamic models that include thermal pressures in each charged-particle species of the plasma. The first model, is one in which the thermal pressure is assumed to be isotropic, as in the previous chapter, and with the same closure via an ad-hoc equation of state. In the second model, the thermal pressure perturbations are allowed to be arbitrarily anisotropic, with a closure that neglects heat flow. The first model can be justified for a collision-dominated plasma, but fails to properly describe FLR effects on the dispersion of HF modes in collisionless (high-temperature) plasmas. The second model on the other hand overcomes some of the limitations of the first model for collisionless plasmas and, for some important modes, is able to exhibit the correct dispersion relation transitions of cold-plasma modes to kinetic modes.
Electrodynamics of linear modes—Conservation relations and perturbation theory
Authors: Bers Abraham
Published: November 2016

This chapter presents a unified description of linear electrodynamics of a weakly-dissipative, homogeneous medium entailing arbitrary temporal and spatial dispersion in its dynamics. In an electrodynamic description, one asserts that the “mechanical” field variables (e.g. densities, velocities, pressures, velocity distribution functions, etc.) have been eliminated in favor of the SCF EM-fields. For a plasma, the electrodynamic formulation is based upon the (internal response) susceptibility function which comes from any linearized model dynamics of the plasma. Introducing slowly-varying amplitudes on the electrodynamic fields allows for an expansion of the general space-time convolution-integral constitutive relations and, together with Maxwell's equations, leads to electrodynamic partial differential equations (P.D.E.s), in the slow space-time variables, including the presence of weak dissipation and external sources in the medium. The chapter also offers a dynamic perturbation theory of modes which leads to linear (L) and nonlinear (NL) coupling modes (COM).
Inhomogeneous and bounded plasmas and beams
Authors: Bers Abraham
Published: November 2016

This chapter considers mathematical techniques in the analysis of linear wave propagation and parametric interactions in plasma and beams with spatially-nonuniform (inhomogeneous) equilibria in density and confining magnetic fields. These techniques can help in the modeling and analysis of realistic plasma systems. The chapter gives the simplest description of the modifications of collective modes when the plasma equilibrium is no longer homogeneous in space and/or time, but varies sufficiently slowly so that modes maintain their basic character while changing their propagation. This is accomplished by introducing the techniques of geometric optics and ray tracing for a medium with temporal and spatial dispersion such as a plasma. It also describes techniques for analysis of situations in which the basic collective modes are modified and couple to each other due to inhomogeneity in plasma equilibrium, and concludes with a discussion of variational principles which helps in the analysis of bounded plasmas that are also inhomogeneous.
Kinetic waves and instabilities in magnetized plasmas
Authors: Bers Abraham
Published: November 2016

This chapter looks at the Vlasov–Maxwell system of SCF equations, providing illustrations of the various interesting waves and instabilities in such plasma. They contain detailed analysis of linear WPI resonances and energy exchanges, and linear susceptibility tensors. These illustrations relate the various linearized descriptions of plasma dynamics which were based upon hydrodynamic rather than kinetic model dynamics in SCF. In addition, some of the examples are constructed to reveal the use of basic techniques in the analysis and understanding of plasma electrodynamics—techniques that are developed in other chapters—such as: general instability analysis, (positive and negative) energy and momentum of waves, and coupling of modes.
The Oxford Dictionary of Family Names in Britain and Ireland
Authors: Hanks Patrick , Coates Richard , McClure Peter
Published: November 2016

Over 45,000 entries

This huge new dictionary is the ultimate reference work on family names of the UK, covering English, Scottish, Welsh, Irish, Cornish, and immigrant surnames. It includes every surname that currently has more than 100 bearers, and those that had more than 20 bearers in the 1881 census.

Each entry contains lists of variant spellings of the name, an explanation of its origins (including the etymology), lists of early bearers showing evidence for formation and continuity from the date of formation down to the 19th century, geographical distribution, and, where relevant, genealogical and bibliographical notes, making this a fully comprehensive work on family names.

This authoritative guide also includes an introductory essay explaining the historical background, formation, and typology of surnames and a guide to surnames research and family history research. Additional material also includes a list of published and unpublished lists of surnames from the Middle Ages to the present day.
Impact of Visit-to-Visit Variability in Systolic Blood Pressure on Cardiovascular Outcomes in Korean National Health Insurance Service—National Sample Cohort
Authors: Choi SeongIl , Shin Jinho , Choi Sung Yong , Sung Ki Chul , Ihm Sang Hyun , Kim Kwang-il , Kim Yu-Mi
Published: November 2016

BACKGROUND

Despite an association between visit-to-visit blood pressure (BP) variability (VV-BPV) and cardiovascular (CV) outcomes, many studies performed during the past 4 years have shown conflicting results. This study investigated the impact of VV-BPV on CV outcomes in the Korean National Health Insurance Service (NHIS) database-National Sample Cohort.

METHODS

From the 2002 Korean NHIS database (n = 47,851,928), sample subjects with 3 or more BP measurements (n = 51,811) were divided into 2 groups according to a 10 mm Hg cutoff in the SD of systolic BP (SD-SBP). The CV outcomes of these groups were compared by sensitivity analyses using various sampling methods.

RESULTS

Irrespective of sampling method, subjects with SD-SBPs ≥10 mm Hg had higher rates of CV events or death, nonfatal myocardial infarction (MI) or stroke, and total mortality, but were not associated with CV mortality. The hazard ratios for CV events or death, nonfatal MI or stroke, CV mortality, and total mortality were 1.43 (95% confidence interval [CI], 1.25−1.63, P < 0.01), 1.45 (95% CI, 1.27−1.65, P < 0.01), 1.32 (95% CI, 0.89−1.94, P = 0.17), and 1.18 (95% CI, 1.01−1.38, P = 0.04), respectively.

CONCLUSIONS

Increased VV-BPV was an independent risk factor for future CV outcomes, independent of mean BP status, even in normotensive subjects and in all subgroups, except females. Similar VV-BPV values in the sensitivity analyses suggest VV-BPV is a reproducible phenomenon, reflecting the various types of intrinsic physiologic properties.
Implicating candidate genes at GWAS signals by leveraging topologically associating domains
Authors: Way Gregory P. , Youngstrom Daniel W. , Hankenson Kurt D. , Greene Casey S. , Grant Struan F. A.
Published: November 2016

Genome wide association studies (GWAS) have contributed significantly to the understanding of complex disease genetics. However, GWAS only report associated signals and do not necessarily identify culprit genes. As most signals occur in non-coding regions of the genome, it is often challenging to assign genomic variants to the underlying causal mechanism(s). Topologically associating domains (TADs) are primarily cell-type independent genomic regions that define interactome boundaries and can aid in the designation of limits within which an association most likely impacts gene function. We describe and validate a computational method that uses the genic content of TADs to discover candidate genes. Our method, called “TAD_Pathways,” performs a Gene Ontology (GO) analysis over genes that reside within TAD boundaries corresponding to GWAS signals for a given trait or disease. We applied our pipeline to the GWAS catalog entries associated with bone mineral density (BMD), identifying ‘Skeletal System Development’ (Benjamini-Hochberg adjustedp=1.02x10−5) as the top ranked pathway. In many cases, our method implicated a gene other than the nearest gene. Our molecular experiments describe a novel example:ACP2, implicated at the canonical ‘ARHGAP1’ locus. We foundACP2to be an important regulator of osteoblast metabolism, whereasARHGAP1was not supported. Our results via the example of BMD demonstrate how basic principles of three-dimensional genome organization can define biologically informed association windows.
Optimization of lag phase shapes the evolution of a bacterial enzyme
Authors: Adkar Bharat V. , Manhart Michael , Bhattacharyya Sanchari , Tian Jian , Musharbash Michael , Shakhnovich Eugene I.
Published: November 2016

Mutations provide the variation that drives evolution, yet their effects on fitness remain poorly understood. Here we explore how mutations in the essential enzyme Adenylate Kinase (Adk) ofE. coliaffect multiple phases of population growth. We introduce a biophysical fitness landscape for these phases, showing how they depend on molecular and cellular properties of Adk. We find that Adk catalytic capacity in the cell (product of activity and abundance) is the major determinant of mutational fitness effects. We show that bacterial lag times are at a well-defined optimum with respect to Adk’s catalytic capacity, while exponential growth rates are only weakly affected by variation in Adk. Direct pairwise competitions between strains show how environmental conditions modulate the outcome of a competition where growth rates and lag times have a tradeoff, altogether shedding light on the multidimensional nature of fitness and its importance in the evolutionary optimization of enzymes.
Persistent neural activity encoding real-time presence of visual stimuli decays along the ventral stream
Authors: Gerber Edden M. , Golan Tal , Knight Robert T. , Deouell Leon Y.
Published: November 2016

Neural populations that encode sensory experience should be persistently active for as long as the experience persists. However, research into visual neural activity has focused almost exclusively on onset-driven responses that cannot account for sustained perception. We used intracranial recordings in humans to determine the degree to which the presence of a visual stimulus is persistently encoded by neural activity. The correspondence between stimulus duration and response duration was strongest in early visual cortex and gradually diminished along the visual hierarchy, such that is was weakest in inferior-temporal category-selective regions. A similar posterior-anterior gradient was found within inferior temporal face-selective regions, with posterior but not anterior sites showing persistent face-selective activity. The results suggest that regions that appear uniform in terms of their category selectivity are dissociated by how they temporally represent a stimulus in support of real-time experience, and delineate a large-scale organizing principle of the ventral visual stream.
Disentangling the Effects of Weather and Density on the Dynamics of a Fungal Pathogen
Authors: Kyle Colin , Goldwyn Eli , Dwyer Greg
Published: November 2016

Nonlinear fitting algorithms have illuminated the role of weather in human diseases, by allowing for robust tests of mechanistic transmission models, but a lack of data has prevented applications to animal diseases. This is important because classical models that neglect weather predict that there will be a host density threshold, below which epidemic intensity will be slight, but models that include weather predict that this threshold will often be obliterated by weather variability. To test the applicability of thresholds to animal diseases, we estimated infection rates of the fungal pathogenEntomophaga maimaigain the gypsy moth, by collecting larvae during epidemics at a range of host densities and weather conditions, and we estimated the pathogen's force of infection, by exposing experimental larvae to the pathogen for 24 h periods in the field. By fitting a range of models to our data, we show that epidemics of this pathogen are best explained by a model that allows for positive effects of both host density and cool, moist weather on transmission, such that weather-only and density-dependence-only models provide vastly poorer explanations for the data. Despite the effects of weather, the combined model shows that the effects of density inE. maimaigaare strong enough to ensure that the density threshold will have important effects on the probability of epidemics. Our work shows that weather and density-dependent transmission can interact in non-intuitive ways, and provides an illustration of the usefulness of nonlinear fitting for understanding animal diseases.
Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis
Authors: Vargas J. , Melero R. , Gómez-Blanco J. , Carazo J. M. , Sorzano C. O. S.
Published: November 2016

Single Particle Analysis using cryo-electron microscopy is a structural biology technique to capture the three-dimensional conformation of biological macromolecules. The projection images used to construct the 3D density map are characterized by a very low signal-to-noise ratio to minimize radiation damage in the samples. As a consequence, the 3D alignment process is a challenging and error prone task and this job usually determines the success or failure of the macromolecule reconstruction. In this work, we present a soft-alignment validation approach, which can quantify the alignment precision and accuracy as well as the data homogeneity of the single particles when they are confronted with the resultant reconstructed 3DEM map. We have also applied this method to data homogeneity analysis and particle pruning, improving the data quality and as a consequence the final map resolution.
Chimeras Link to Tandem Repeats and Transposable Elements in Tetraploid Hybrid Fish
Authors: Ye Lihai , Tang Xiaojun , Chen Yiyi , Ren Li , Hu Fangzhou , Wang Shi , Wen Ming , Zhang Chun , Tao Ming , Zhao Rurong , Yao Zhanzhou , Liu Shaojun
Published: November 2016

The formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species and therefore it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents. Among the 68 genetic chimeras, 44 (64.71%) are linked to tandem repeats (TRs) and 23 (33.82%) are linked to transposable elements (TEs). The chimeras linked to TRs are related to slipped-strand mispairing and double-strand break repair while the chimeras linked to TEs are benefit from the intervention of recombinases. In addition, TRs and TEs are linked not only with the recombinations, but also with the insertions/deletions of DNA segments. We conclude that DNA chimeras accompanied by TRs and TEs coordinate a balance between the sub-genomes derived from the parents which reduces the genomic shock effects and favors the evolutionary and adaptive capacity of the allotetraploidization. It is the first report on the relationship between formation of the DNA chimeras and TRs and TEs in the polyploid animals.
Upstream trophic structure modulates downstream community dynamics via resource subsidies
Authors: Harvey Eric , Gounand Isabelle , Little Chelsea , Fronhofer Emanuel A. , Altermatt Florian
Published: November 2016

In many natural systems, the physical structure of the landscape dictates the flow of resources. Despite mounting evidence that communities’ dynamics can be indirectly coupled by reciprocal among-ecosystem resource flows, our understanding of how directional resource flows might indirectly link biological communities is limited. We here propose that differences in community structure upstream should lead to different downstream dynamics, even in the absence of dispersal. We report an experimental test of the effect of upstream community structure on downstream community dynamics in a simplified but highly controlled setting, using protist microcosms. We implemented directional flows of resources, without dispersal, from a standard resource pool into upstream communities of contrasting interaction structure and then to further downstream communities of either one or two trophic levels. Our results demonstrate that different types of species interactions in upstream habitats may lead to different population sizes and levels of biomass in these upstream habitats. This, in turn, leads to varying levels of detritus transfer (dead biomass) to the downstream communities, thus influencing their population densities and trophic interactions in predictable ways. Our results suggest that the structure of species interactions in directionally structured ecosystems can be a key mediator of alterations to downstream habitats. Alterations to upstream habitats can thus cascade down to downstream communities, even without dispersal.
Electroceutical disinfection strategies impair the motility of pathogenicPseudomonas aeruginosaandEscherichia coli
Authors: Doxsee Kristina , Berthelot Ryan , Neethirajan Suresh
Published: November 2016

Electrotaxis or galvanotaxis refers to the migration pattern of cells induced in response to electrical potential. Although it has been extensively studied in mammalian cells, electrotaxis has not been explored in detail in bacterial cells; information regarding the impact of current on pathogenic bacteria is severely lacking. Therefore, we designed a series of single and multi-cue experiments to assess the impact of varying currents on bacterial motility dynamics in pathogenic multi-drug resistant (MDR) strains ofPseudomonas aeruginosaandEscherichia coliusing a microfluidic platform. Motility plays key roles in bacterial migration and the colonization of surfaces during the formation of biofilms, which are inherently recalcitrant to removal and resistant to traditional disinfection strategies (e.g. antibiotics). Use of the microfluidic platform allows for exposure to current, which can be supplied at a range that is biocidal to bacteria, yet physiologically safe in humans (single cue). This system also allows for multi-cue experiments where acetic acid, a relatively safe compound with anti-fouling/antimicrobial properties, can be combined with current to enhance disinfection. These strategies may offer substantial therapeutic benefits, specifically for the treatment of biofilm infections, such as those found in the wound environment. Furthermore, microfluidic systems have been successfully used to model the unique microfluidic dynamics present in the wound environment, suggesting that these investigations could be extended to more complex biological systems. Our results showed that the application of current in combination with acetic acid has profound inhibitory effects on MDR strains ofP. aeruginosaandE. coli, even with brief applications. Specifically,E. colimotility dynamics and cell survival were significantly impaired starting at a concentration of 125 μA DC and 0.31% acetic acid, whileP. aeruginosawas impaired at 70 μA and 0.31% acetic acid. As these strains are relevant wound pathogens, it is likely that this strategy would be effective against similar strainsin vivoand could represent a new approach to hasten wound healing.
Visualizing adenosine to inosine RNA editing in single mammalian cells
Authors: Mellis Ian A. , Gupte Rohit K. , Raj Arjun , Rouhanifard Sara H.
Published: November 2016

Conversion of adenosine bases to inosine in RNA is a frequent type of RNA editing, but important details about its biology, including subcellular localization, remain unknown due to a lack of imaging tools. We developed an RNA FISH strategy we called inoFISH that enables us to directly visualize and quantify adenosine-to-inosine edited transcriptsin situ. Applying this tool to three edited transcripts (GRIA2, EIF2AK2 and NUP43), we found that editing of these transcripts is not correlated with nuclear localization nor paraspeckle association, and that NUP43 exhibits constant editing rates between single cells while the rates for GRIA2 vary.
Shared characteristics underpinning C4leaf maturation derived from analysis of multiple C3and C4species ofFlaveria
Authors: Kümpers Britta M.C. , Burgess Steven J. , Reyna-Llorens Ivan , Smith-Unna Richard , Boursnell Chris , Hibberd Julian M.
Published: November 2016

Most terrestrial plants use C3photosynthesis to fix carbon. In multiple plant lineages a modified system known as C4photosynthesis has evolved. To better understand the molecular patterns associated with induction of C4photosynthesis the genusFlaveriathat contains C3and C4species was used. A base to tip maturation gradient of leaf anatomy was defined, and RNA sequencing was undertaken along this gradient for two C3and two C4Flaveriaspecies. Key C4traits including vein density, mesophyll and bundle sheath cross-sectional area, chloroplast ultrastructure, and abundance of transcripts encoding proteins of C4photosynthesis were quantified. Candidate genes underlying each of these C4characteristics were identified. Principal Components Analysis indicated that leaf maturation and then photosynthetic pathway were responsible for the greatest amount of variation in transcript abundance. Photosynthesis genes were over-represented for a prolonged period in the C4species. Through comparison with publically available datasets we identify a small number of transcriptional regulators that have been up-regulated in diverse C4species. The analysis identifies similar patterns of expression in independent C4lineages and so indicates that the complex C4pathway is associated with parallel as well as convergent evolution.

Highlight

We identify transcription factors that show conserved patterns of expression in multiple 29 C4species, both within the Flaveria genus, but also in more distantly related C4plants.
Coupled enhancer and coding sequence evolution of a homeobox gene shaped leaf diversity
Authors: Vuolo Francesco , Mentink Remco A. , Hajheidari Mohsen , Bailey C. Donovan , Filatov Dmitry A. , Tsiantis Miltos
Published: November 2016

Here we investigate mechanisms underlying the diversification of biological forms using crucifer leaf shape as an example. We show that evolution of an enhancer element in the homeobox gene REDUCED COMPLEXITY (RCO) altered leaf shape by changing gene expression from the distal leaf blade to its base. A single amino acid substitution evolved together with this regulatory change, which reduced RCO protein stability, preventing pleiotropic effects caused by its altered gene expression. We detected hallmarks of positive selection in these evolved regulatory and coding sequence variants and showed that modulating RCO activity can improve plant physiological performance. Therefore, interplay between enhancer and coding sequence evolution created a potentially adaptive path for morphological evolution.
Orientational order of liquids and glassesviafluctuation diffraction
Authors: Martin Andrew V.
Published: November 2016

Liquids, glasses and other amorphous matter lack long-range order, which makes them notoriously difficult to study. Local atomic order is partially revealed by measuring the distribution of pairwise atomic distances, but this measurement is insensitive to orientational order and unable to provide a complete picture of diverse amorphous phenomena, such as supercooling and the glass transition. Fluctuation scattering with electrons and X-rays is able provide this orientational sensitivity, but it is difficult to obtain clear structural interpretations of fluctuation data. Here we show that the interpretation of fluctuation diffraction data can be simplified by converting it into a real-space angular distribution function. We calculate this function from simulated diffraction of amorphous nickel, generated with a classical molecular dynamics simulation of the quenching of a high temperature liquid state. We compare the results of the amorphous case to the initial liquid state and to the ideal f.c.c. lattice structure of nickel. We show that the extracted angular distributions are rich in information about orientational order and bond angles. The diffraction fluctuations are potentially measurable with electron sources and also with the brightest X-ray sources, like X-ray free-electron lasers.
Shade tolerance and the functional trait: demography relationship in temperate and boreal forests
Authors: Ameztegui Aitor , Paquette Alain , Shipley Bill , Heym Michael , Messier Christian , Gravel Dominique
Published: November 2016

Despite being instrumental in forest ecology, the definition and nature of shade tolerance are complex and not beyond controversy. Moreover, the role it plays in the trait–demography relationship remains unclear.

Here, we hypothesize that shade tolerance can be achieved by alternative combinations of traits depending on the species' functional group (evergreen vs. deciduous species) and that its ability to explain the array of traits involved in demography will also vary between these two groups.

We used dimension reduction to identify the main trait spectra for 48 tree species, including 23 evergreens and 25 deciduous – dispersed across 21 genera and 13 families. We assessed the relationship between functional traits, shade tolerance, and demographic performance at high and low light using structural equation modelling.

The dimensions found corresponded to the trait spectra previously observed in the literature and were significantly related to measures of demography. However, our results support the existence of a divergence between evergreen and deciduous species in the way shade tolerance relates to the demography of species along light gradients.

We show that shade tolerance can be attained through different combination of traits depending on the functional and geographical context, and thus, its utilization as a predictor of forest dynamics and species coexistence requires previous knowledge on the role it plays in the demographic performance of the species under study.

A lay summary is available for this article.
Does movement behaviour predict population densities? A test with 25 butterfly species
Authors: Schultz Cheryl B. , Pe'er B. Guy , Damiani Christine , Brown Leone , Crone Elizabeth E.
Published: November 2016

Diffusion, which approximates a correlated random walk, has been used by ecologists to describe movement, and forms the basis for many theoretical models. However, it is often criticized as too simple a model to describe animal movement in real populations.

We test a key prediction of diffusion models, namely, that animals should be more abundant in land cover classes through which they move more slowly. This relationship between density and diffusion has rarely been tested across multiple species within a given landscape.

We estimated diffusion rates and corresponding densities of 25 Israeli butterfly species from flight path data and visual surveys. The data were collected across 19 sites in heterogeneous landscapes with four land cover classes: semi‐natural habitat, olive groves, wheat fields and field margins.

As expected from theory, species tended to have higher densities in land cover classes through which they moved more slowly and lower densities in land cover classes through which they moved more quickly. Two components of movement (move length and turning angle) were not associated with density, nor was expected net squared displacement. Move time, however, was associated with density, and animals spent more time per move step in areas with higher density.

The broad association we document between movement behaviour and density suggests that diffusion is a good first approximation of movement in butterflies. Moreover, our analyses demonstrate that dispersal is not a species‐invariant trait, but rather one that depends on landscape context. Thus, land cover classes with high diffusion rates are likely to have low densities and be effective conduits for movement.
Co‐parenting conversation process: a qualitative study of Chinese Singaporean parents
Authors: Sim Charles T. K.
Published: November 2016

Although co‐parenting in two‐parent families has been an increasingly important area of research, little is known about the co‐parenting conversation as a crucial aspect of co‐parenting. This study used grounded theory methodology to explore how Chinese Singaporean parents perceive their co‐parenting conversations in light of the influence of their families of origin. Interviews were conducted with mothers and fathers in sixteen families. Findings revealed a central category, ‘conversations along the co‐parenting journey’, and two main categories, ‘conversations that connect and collaborate in co‐parenting’, and ‘conversations on family heritage and practices’. A substantive theory of co‐parenting conversation process was generated from the synthesis of the findings. This study serves as the foundation for future research in co‐parenting conversation, and its implications for clinicians and researchers are presented and discussed.

Practitioner Points

The typology of co‐parenting conversation can serve as a common language of communication for family practitioners, clinicians, and researchers working with parents of young children

The scheme of co‐parenting conversation process, and the classification for decision‐making conversations, can provide a working framework to consider how, when, and where to intervene in therapy for parents dealing with co‐parenting issues

Co‐parenting intentionality is potentially important in addressing family‐of‐origin issues in co‐parenting therapy sessions
Trait Anger, Physical Aggression, and Violent Offending in Antisocial and Borderline Personality Disorders
Authors: Kolla Nathan J. , Meyer Jeffrey H. , Bagby R. Michael , Brijmohan Amanda
Published: November 2016

Antisocial personality disorder (ASPD) and borderline personality disorder (BPD) are common conditions in forensic settings that present high rates of violence. Personality traits related to the five‐factor model personality domains of neuroticism and agreeableness have shown a relationship with physical aggression in nonclinical and general psychiatric samples. The aim of the present investigation was to examine the association of these personality traits with violence and aggression in ASPD and BPD. Results revealed that trait anger/hostility predicted self‐reported physical aggression in 47 ASPD and BPD subjects (β = 0.5, p = 0.03) and number of violent convictions in a subsample of the ASPD participants (β = 0.2, p = 0.009). These preliminary results suggest that high anger and hostility are associated with physical aggression in BPD and ASPD. Application of validated, self‐report personality measures could provide useful and easily accessible information to supplement clinical risk assessment of violence in these conditions.
Self‐Strangulation Through A Sphygmomanometer: An Uncommon Suicide
Authors: Lo Pinto Sara , Tacchella Tiziana , Fossati Francesca , Bonsignore Alessandro , Ventura Francesco
Published: November 2016

Suicide by asphyxia is quite a common event in forensic practice and may be implemented in different ways. The authors report a unique case of a 16‐year‐old youth who committed suicide by means of a standard mercury sphygmomanometer. This manner of suicide has never been described in the literature reviewed. A complete forensic investigation led to the conclusion that the cause of death was mechanical asphyxia, ascribed to self‐strangulation by means of an atypical item. The victim suffered from attention‐deficit/hyperactivity disorder (ADHD) syndrome and was assisted by support teachers. He had a solitary and depressive personality. The exceptional nature of this case suggests that sphygmomanometers may be regarded as possible means of self‐strangulation. The case also highlights the importance of managing patients with psychiatric or cognitive disorders; indeed, particular caution is required to keep them away from objects that, although apparently harmless, can become lethal.
Engineering Mycobacterium smegmatis for testosterone production
Authors: Fernández‐Cabezón Lorena , Galán Beatriz , García José L.
Published: November 2016

A new biotechnological process for the production of testosterone (TS) has been developed to turn the model strain Mycobacterium smegmatis suitable for TS production to compete with the current chemical synthesis procedures. We have cloned and overexpressed two genes encoding microbial 17β‐hydroxysteroid: NADP 17‐oxidoreductase, from the bacterium Comamonas testosteroni and from the fungus Cochliobolus lunatus. The host strains were M. smegmatis wild type and a genetic engineered androst‐4‐ene‐3,17‐dione (AD) producing mutant. The performances of the four recombinant bacterial strains have been tested both in growing and resting‐cell conditions using natural sterols and AD as substrates respectively. These strains were able to produce TS from sterols or AD with high yields. This work represents a proof of concept of the possibilities that offers this model bacterium for the production of pharmaceutical steroids using metabolic engineering approaches.
Microbial synthesis of a novel terpolyester P(LA‐co‐3HB‐co‐3HP) from low‐cost substrates
Authors: Ren Yilin , Meng Dechuan , Wu Linping , Chen Jinchun , Wu Qiong , Chen Guo‐Qiang
Published: November 2016

Polylactide (PLA) is a bio‐based plastic commonly synthesized by chemical catalytic reaction using lactic acid (LA) as a substrate. Here, novel LA‐containing terpolyesters, namely, P[LA‐co‐3‐hydroxybutyrate (3HB)‐co‐3‐hydroxypropionate (3HP)], short as PLBP, were successfully synthesized for the first time by a recombinant Escherichia coli harbouring polyhydroxyalkanoate (PHA) synthase from Pseudomonas stutzeri (PhaC1Ps) with 4‐point mutations at E130D, S325T, S477G and Q481K, and 3‐hydroxypropionyl‐CoA (3HP‐CoA) synthesis pathway from glycerol, 3‐hydroxybutyryl‐CoA (3HB‐CoA) as well as lactyl‐CoA (LA‐CoA) pathways from glucose. Combining these pathways with the PHA synthase mutant phaC1Ps (E130D S325T S477G Q481K), the random terpolyester P(LA‐co‐3HB‐co‐3HP), or PLBP, was structurally confirmed by nuclear magnetic resonance to consist of 2 mol% LA, 90 mol% 3HB, and 8 mol% 3HP respectively. Remarkably, the PLBP terpolyester was produced from low‐cost sustainable glycerol and glucose. Monomer ratios of PLBP could be regulated by ratios of glycerol to glucose. Other terpolyester thermal and mechanical properties can be manipulated by adjusting the monomer ratios. More PLBP applications are to be expected.
Depositional Controls on the Ichnology of Ordovician Wave‐dominated Marine Facies: New Evidence from the Shirgesht Formation, Central Iran
Authors: BAYET‐GOLL Aram , MYROW Paul M. , ACEÑOLAZA Guillermo F. , MOUSSAVI‐HARAMI Reza , MAHBOUBI Asadollah
Published: November 2016

The Lower Ordovician Shirgesht Formation in central Iran is composed of siliciclastic and carbonate rocks deposited in diverse coastal and marine shelfal environments (tidal flat, lagoon, shoreface, offshore‐shelf and carbonate ramp). Five facies associations contain diverse ichnofossil assemblages that show distinct proximal to distal trends formed in a wide range of physical‐chemical conditions. The ethological groups of trace fossils in the Shirgesht Formation reflect a gradient of depositional stress conditions across a wave‐influenced shoreline and shelf. Deposits of wave‐influenced environments make up a significant component of the geological record of shallow marine settings, and the ability to determine paleoenvironments in detail in such successions is critical for reconstruction of depositional histories and sequence‐stratigraphic interpretation.

The Cruziana ichnofacies of the study shows highly diverse suites that record the establishment of a benthic community under stable conditions and a long‐term colonization window. The Skolithos ichnofacies recognized is a low diversity opportunistic ichnocommunity suite that resulted from colonization after tempestite deposition in a stressed environment. The strata record an onshore to offshore replacement of the Cruziana ichnofacies (with abundant feeding traces of deposit‐feeders) by the Skolithos ichnofacies (dominated by suspension‐feeders and predators). A transitional zone between the two ichnofacies coincides with the offshore‐transition/distal lower‐surface deposits. The distribution of ichnofacies, the diversity and range of ethological characteristics reflected by the ichnogenera, and the wide range of wave‐dominated coastal facies demonstrate the potential to use individual trace fossils and ichnofacies for significantly refined palaeoenvironmental analysis of wave‐dominated coastal settings, particularly in Ordovician successions.