bluuebunny/crossref_metadata_2025 huggingface dataset:
Limits on quantum gravity effects from Swift short gamma-ray bursts
Authors: Bernardini M. G. , Ghirlanda G. , Campana S. , D’Avanzo P. , Atteia J.-L. , Covino S. , Ghisellini G. , Melandri A. , Piron F. , Salvaterra R. , Tagliaferri G.
Published: October 2017

The delay in arrival times between high and low energy photons from cosmic sources can be used to test the violation of the Lorentz invariance (LIV), predicted by some quantum gravity theories, and to constrain its characteristic energy scale EQG that is of the order of the Planck energy. Gamma-ray bursts (GRBs) and blazars are ideal for this purpose thanks to their broad spectral energy distribution and cosmological distances: at first order approximation, the constraints on EQG are proportional to the photon energy separation and the distance of the source. However, the LIV tiny contribution to the total time delay can be dominated by intrinsic delays related to the physics of the sources: long GRBs typically show a delay between high and low energy photons related to their spectral evolution (spectral lag). Short GRBs have null intrinsic spectral lags and are therefore an ideal tool to measure any LIV effect. We considered a sample of 15 short GRBs with known redshift observed by Swift and we estimate a limit on EQG ≳ 1.5 × 1016 GeV. Our estimate represents an improvement with respect to the limit obtained with a larger (double) sample of long GRBs and is more robust than the estimates on single events because it accounts for the intrinsic delay in a statistical sense.
Post-depositional evolution over a time scale of 1 million years of eastern Mediterranean organic-rich and organic-poor sediments: new insights on the debromination and layer-silicate markers
Authors: Murat Anne , Beaufort Daniel , Hébert Benoît , Baudin François , Bernasconi Stefano Michele , Ducassou Emmanuelle , Lelièvre Céline , Poizot Emmanuel , Mathian Maximilien , Grauby Olivier
Published: October 2017

Organic matter degradation is the engine behind the biogeochemical evolution of sediments during burial. Previous research has shown that eogenesis is the seat of a complex interplay between organic matter, microbes and the most reactive part of inorganic compounds, such as clay minerals. To explore the variability and stability of bromine and clay minerals as geochemical and mineral tracers, we selected an eastern Mediterranean core that has a high degree of stability in the quality and quantity of organic matter through time at a one-million-year scale and great variability in organic matter content at a 10 ky scale. According to the very low maximal burial depth reached by these sediments (the core length is only 36.5 m), physical parameters, such as temperature and pressure, did not significantly influence the evolution of the studied parameters during the burial history. The bulk clay mineralogy of organic-rich and organic-poor sediments is similar all along the investigated core material; smectite predominates over kaolinite. The only identified authigenic minerals are biogenetic framboidal pyrite and manganese oxides. The X-ray data and the chemical compositions of the smectite are characteristic of a montmorillonite which is representative of a detrital Nile source. At a one-million-year scale, the organic matter content has no significant influence on clay eogenesis, and detrital smectite and kaolinite remain unchanged. Bromine is present in marine organic matter as organobromine compounds. During eogenesis, bromine is released from organic matter as bromide ion, resulting in an increase in the bromide concentration in the pore water with depth. Dissolved bromide can be used as a conservative tracer of the debromination of sedimentary organic matter. For the first time, we established that solid-phase BrOrg is a reliable tracer of debromination rates in marine sediments. The rate of debromination depends on the organic matter content. The rate increases from less than 2.3 × 10−4 μmolBrOrg mol.C−1.y−1to 6.3 × 10−4 μmolBrOrg mol.C−1.y−1when TOC varies from 0.17 to 3%. This increase is related to the development of the bacterial population and provides the basis for further investigation of other oceanic basins. For TOC values  >4%, the rate of debromination decreases. We propose that the bioavailability of organic matter is another factor of variability in the debromination rate.
Pattern of Bone Generation after Irradiation in Vascularized Tissue Engineered Constructs
Authors: Fathi Ibrahim , Eltawila Ahmed , Elsherif Ahmad , Elkerm Yasser , Harhaus Leila , Kneser Ulrich , Sakr Mahmoud , Eweida Ahmad
Published: October 2017

Background Regenerative medicine modalities provide promising alternatives to conventional reconstruction techniques but are still deficient after malignant tumor excision or irradiation due to defective vascularization.

Methods We investigated the pattern of bone formation in axially vascularized tissue engineering constructs (AVTECs) after irradiation in a study that mimics the clinical scenario after head and neck cancer. Heterotopic bone generation was induced in a subcutaneously implanted AVTEC in the thigh of six male New Zealand rabbits. The tissue construct was made up of Nanobone (Artoss GmbH; Rostock, Germany) granules mixed with autogenous bone marrow and 80 μL of bone morphogenic protein-2 at a concentration of 1.5 μg/μL. An arteriovenous loop was created microsurgically between the saphenous vessels and implanted in the core of the construct to induce axial vascularization. The constructs were subjected to external beam irradiation on postoperative day 20 with a single dose of 15 Gy. The constructs were removed 20 days after irradiation and subjected to histological and immunohistochemical analysis for vascularization, bone formation, apoptosis, and cellular proliferation.

Results The vascularized constructs showed homogenous vascularization and bone formation both in their central and peripheral regions. Although vascularity, proliferation, and apoptosis were similar between central and peripheral regions of the constructs, significantly more bone was formed in the central regions of the constructs.

Conclusion The study shows for the first time the pattern of bone formation in AVTECs after irradiation using doses comparable to those applied after head and neck cancer. Axial vascularization probably enhances the osteoinductive properties in the central regions of AVTECs after irradiation.
Nutritional Counseling Promotes Changes in the Dietary Habits of Overweight and Obese Adolescents with Polycystic Ovary Syndrome
Authors: Carolo Adriana Lúcia , Mendes Maria Célia , Rosa e Silva Ana Carolina Japur de Sá , Vieira Carolina Sales , Silva de Sá Marcos Felipe , Ferriani Rui Alberto , Reis Rosana Maria dos
Published: October 2017

Objective To evaluate the effects of nutritional counseling on the dietary habits and anthropometric parameters of overweight and obese adolescents with polycystic ovary syndrome (PCOS).

Methods This was a prospective, longitudinal and auto-controlled study. Thirty adolescents aged 13–19 years-old, diagnosed with PCOS received nutritional counseling and were followed-up for 6 months. After the follow-up period, the results were evaluated through body weight, body mass index (BMI) and waist circumference (WC).

Results Sixty-percent of the adolescents adhered to the nutritional counseling and, of these, 50% lost weight. Adolescents who lost weight changed their dietary habits by adopting hypocaloric diets and eating more meals per day, as per nutritional counseling. The waist circumference (WC) decreased significantly, although the body weight decreased non-significantly after adoption of a hypocaloric diet.

Conclusion Although there was no significant weight loss, there was a considerable reduction in the WC associated with hypocaloric diets and with eating a greater number of meals per day.
Effect of Kyphoplasty in the Treatment of Osteoporotic Vertebral Fractures Compared to Vertebroplasty – Overview of Systematic Reviews
Authors: Botelho Ricardo , Diniz Juliete , Sousa Ulysses , Mudo Marcelo , Oliveira Matheus
Published: October 2017

Introduction Vertebroplasty and kyphoplasty are possible options for vertebral augmentation after osteoporotic fractures. Both are percutaneous techniques with specific advantages and disadvantages. Our aim is to compare the clinical and radiological results of these two procedures.

Methods An overview of published systematic reviews in the literature on the effects of kyphoplasty compared with vertebroplasty was performed.

Results After short and long follow-up, the kyphoplasty group had lower pain scores on the visual analogue scale (VAS), lower scores in the Oswestry Disability index (ODI), greater restoration of the vertebral body height and lower kyphosis angle in the immediate postoperative period. There was less leakage of cement to the vertebral canal and extraspinal spaces.

Conclusions Compared with vertebroplasty, kyphoplasty achieved better results in pain relief, quality of life, correction of spinal deformity and lower risk of cement leakage.
Measuring impact in the humanities: Learning from accountability and economics in a contemporary history of cultural value
Authors: Bulaitis Zoe
Published: October 2017

This article addresses the future of research assessment within higher education in the UK from a humanities perspective. Recent changes to policy (such as The Browne Report 2010 and the 2014 REF) indicates that humanities research is increasingly required to provide quantifiable or commercial results in order to attain value. Although research assessment exercises have been a formal part of UK higher education since the first Research Assessment Exercise (RAE) in 1986, the last 6 years have seen a significant change in how research is valued within the academy. Specifically, this paper responds to the increasing prioritisation of 'impact' measurement in research assessment criteria. The article situates recent changes in higher education within a historical context of cultural policymaking in the UK from the 1980s to the present day. Such an undertaking highlights the specific challenges and nuances within the shift towards 'impact'. Firstly, this paper details how public cultural institutions (such as museums and art galleries) became subject to practises of economisation and social accountability as a result of 1980s cultural policy. A rich field of literature from museology and arts management provides valuable sources and testimonies that should be considered in the future of the academic humanities. Secondly, this paper considers the implications of the creative industries upon the perception of knowledge production since the 1990s. Following this specific history of cultural assessment mechanisms in the UK, this article concludes by demonstrating that neither the adoption of a purely economic approach nor a refusal of accountability will serve the humanities. Whilst there is a wealth of social science research that explores valuation methods and assessment culture there is a lack of humanities research within this vital debate. This article presents a response from a humanities perspective. As a result, this contribution raises awareness of the urgent need for humanities scholars to engage in these emerging and significant debates concerning the future of research assessment in the UK.
The visual essay and the place of artistic research in the humanities
Authors: Roes Remco , Pint Kris
Published: October 2017

What could be the place of artistic research in current contemporary scholarship in the humanities? The following essay addresses this question while using as a case study a collaborative artistic project undertaken by two artists, Remco Roes (Belgium) and Alis Garlick (Australia). We argue that the recent integration of arts into academia requires a hybrid discourse, which has to be distinguished both from the artwork itself and from more conventional forms of academic research. This hybrid discourse explores the whole continuum of possible ways to address our existential relationship with the environment: ranging from aesthetic, multi-sensorial, associative, affective, spatial and visual modes of ‘knowledge’ to more discursive, analytical, contextualised ones. Here, we set out to defend the visual essay as a useful tool to explore the non-conceptual, yet meaningful bodily aspects of human culture, both in the still developing field of artistic research and in more established fields of research. It is a genre that enables us to articulate this knowledge, as a transformative process of meaning-making, supplementing other modes of inquiry in the humanities.
Spatial and temporal variations in resilience to tropical cyclones along the United States coastline as determined by the multi-hazard hurricane impact level model
Authors: Pilkington Stephanie , Mahmoud Hussam
Published: October 2017

The United States coastline, where over 50% the population lives, is vulnerable to hurricanes along the East and Gulf coasts. However, the question remains as to whether these two areas are equally resilient to a landfalling hurricane. In addition, while it is assumed that improvements in building codes, infrastructure protections, and changing policy over the past century have been effective in reducing the impacts to a community from historically extreme hurricane events, such an assumption is still to be validated. Here, a multi-hazard artificial neural network model is used to address these questions. The Hurricane Impact Level Model is the first prediction model to utilize machine-learning techniques (artificial neural networks) to established complex connections between all meteorological factors (wind, pressure, storm surge, and precipitation resulting in inland flooding) of a tropical cyclone and how those interact with the location of landfall to produce a certain level of economic damage. This model allows for a more all-encompassing assessment of how the impacts of tropical cyclones vary along the coastline. The Hurricane Impact Level Model was trained with historical tropical cyclone events from 1998 to present day, resulting in established locational associations to modern relevant building codes and mitigation practices. Simulating the meteorological factors from historical events allows for a new assessment of economic impact changes due to infrastructure improvements and policy adaptations over time. In essence, if Hurricane Sandy hit Florida instead of New York, it would have a lower economic impact due to lower population density and more stringent building codes, which the artificial neural network has associated with the latitudes and longitudes within the state of Florida. If the Galveston hurricane were to hit today, the seawall would not succeed in lowering the economic impact to the Texas coastline. Over the years, significant effort has been put in to improving the resiliency of the United States coastline, mainly in the southern states, but it has not been enough to counteract the effects of population growth within coastal counties.
'No spoilers, please': the crux of illustrating the explained Gothic without explaining the mystery
Authors: Schwertfeger Susanne
Published: October 2017

Besides the story itself, illustrations add an extra layer to how a text is perceived. As related to the Gothic novel, this visual attribute and its specific issues have been hardly addressed. This article focuses on a special aspect of the complicated relationship between the literary and the visual Gothic. How can the Gothic atmosphere be translated from the experience of reading (as an establishing and successive act) into an experience of viewing (which, in the case of these illustrations, is not consecutive but almost isolated and selective)? The article concentrates on a certain dilemma that especially occurs for those stories that can be labeled as explained Gothic, in which no actual ghosts or demons haunt the scene, but banditti or other quite human villains do. The characters in the diegesis as well as the readers were for most of the story unaware of the true nature of the described phenomenon. Therefore, how could this phenomenon be visualized to generate interest (as a selling point) and somehow stay true to the source without giving away the ending at the same time? First, this article offers close readings of various illustrations for Ann Radcliffe’s Gothic Novel The Mysteries of Udolpho (1794), in which the artists had to struggle with the depiction of the most famous episode of Emily St. Aubert’s attempts to lift the infamous black veil. It identifies three opposing strategies of how this predicament was solved. The aesthetic of reception is used to further analyze those approaches. The article then argues that the strategies are distinguished by the handling of the mystery and understanding of the concept of the explained Gothic in general. Finally, it reconstructs the assumed readership for those different editions and their preferences of the visual Gothic.
On the elementals and their qualities in David Foster Wallace’s Derivative Sport in Tornado Alley
Authors: Kozin Alexander
Published: October 2017

This article addresses the phenomenological concept of the ‘world’, the ancient Greek notion of the ‘elementals’ as well as their empirically accessible derivatives (‘qualities’). These concepts are examined from the philosophical perspective, with David Foster Wallace’s essay Derivative Sport in Tornado Alley serving as an illustration. The purpose of the examination is to show how the world communicates itself through its basic structures and their qualities to a child who is engaged in play. The works of Edmund Husserl, Martin Heidegger, and the Presocratics assist this study with a methodological framework. The provisional findings include the significance of the elementals (fire, water, earth, and air) for the perception of the world and its structures, as well as the role of ‘wind,’ which is presented as a quality of the elemental ‘air’ and, in a different interpretation, as a divinity. The collusion between a mortal and wind, with sky and earth forming the background for this relationship, produces unique circumstances for playing tennis in a place, which constantly challenges this activity. The notions of ‘childhood’ and ‘nostalgia’ are also touched upon, albeit in a cursive manner. This study is designed to show advantages of employing phenomenology and ancient Greek philosophy for the humanities in general and specifically for the analysis of contemporary literature.
Angular filter refractometry analysis using simulated annealing
Authors: Angland P. , Haberberger D. , Ivancic S. T. , Froula D. H.
Published: October 2017

Angular filter refractometry (AFR) is a novel technique used to characterize the density profiles of laser-produced, long-scale-length plasmas [Haberberger et al., Phys. Plasmas 21, 056304 (2014)]. A new method of analysis for AFR images was developed using an annealing algorithm to iteratively converge upon a solution. A synthetic AFR image is constructed by a user-defined density profile described by eight parameters, and the algorithm systematically alters the parameters until the comparison is optimized. The optimization and statistical uncertainty calculation is based on the minimization of the χ2 test statistic. The algorithm was successfully applied to experimental data of plasma expanding from a flat, laser-irradiated target, resulting in an average uncertainty in the density profile of 5%–20% in the region of interest.
Near omni-conductors and insulators: Alternant hydrocarbons in the SSP model of ballistic conduction
Authors: Fowler Patrick W. , Sciriha Irene , Borg Martha , Seville Victoria E. , Pickup Barry T.
Published: October 2017

Within the source-and-sink-potential model, a complete characterisation is obtained for the conduction behaviour of alternant π-conjugated hydrocarbons (conjugated hydrocarbons without odd cycles). In this model, an omni-conductor has a molecular graph that conducts at the Fermi level irrespective of the choice of connection vertices. Likewise, an omni-insulator is a molecular graph that fails to conduct for any choice of connections. We give a comprehensive classification of possible combinations of omni-conducting and omni-insulating behaviour for molecular graphs, ranked by nullity (number of non-bonding orbitals). Alternant hydrocarbons are those that have bipartite molecular graphs; they cannot be full omni-conductors or full omni-insulators but may conduct or insulate within well-defined subsets of vertices (unsaturated carbon centres). This leads to the definition of “near omni-conductors” and “near omni-insulators.” Of 81 conceivable classes of conduction behaviour for alternants, only 14 are realisable. Of these, nine are realised by more than one chemical graph. For example, conduction of all Kekulean benzenoids (nanographenes) is described by just two classes. In particular, the catafused benzenoids (benzenoids in which no carbon atom belongs to three hexagons) conduct when connected to leads via one starred and one unstarred atom, and otherwise insulate, corresponding to conduction type CII in the near-omni classification scheme.
Comprehensive electrical analysis of metal/Al2O3/O-terminated diamond capacitance
Authors: Pham T. T. , Maréchal A. , Muret P. , Eon D. , Gheeraert E. , Rouger N. , Pernot J.
Published: October 2017

Metal oxide semiconductor capacitors were fabricated using p-type oxygen-terminated (001) diamond and Al2O3 deposited by atomic layer deposition at two different temperatures 250 °C and 380 °C. Current voltage I(V), capacitance voltage C(V), and capacitance frequency C(f) measurements were performed and analyzed for frequencies ranging from 1 Hz to 1 MHz and temperatures from 160 K to 360 K. A complete model for the Metal-Oxide-Semiconductor Capacitors electrostatics, leakage current mechanisms through the oxide into the semiconductor and small a.c. signal equivalent circuit of the device is proposed and discussed. Interface states densities are then evaluated in the range of 1012eV−1cm−2. The strong Fermi level pinning is demonstrated to be induced by the combined effects of the leakage current through the oxide and the presence of diamond/oxide interface states.
Effect of TiO2 nanoparticles on the ion mobilities in transformer oil-based nanofluid
Authors: Lv Yuzhen , Du Qian , Wang Lei , Sun Qian , Huang Meng , Li Chengrong , Qi Bo
Published: October 2017

TiO2 nanoparticles with an average diameter of 6 nm were synthesized and well dispersed in transformer oil to prepare nanofluids (NFs). Influence of nanoparticles on the ion migration property of NFs was investigated via reversal polarity method under different applied electric fields and temperatures. It was found that the ion mobility in TiO2 nanofluid is increased to 4 times of that in pure oil (PO) under the electric field of 5 kV/m, and then decreased abruptly and keeps around one tenth of ion mobility in PO from 50 to 150 kV/m. While the case in PO keeps almost constant throughout the applied fields. The results of the conductivity and ion characteristics of PO and NFs reveal that the presence of nanoparticles can reduce the diameter of impurity ions by shrinking hydrated solvated shell and greatly enhance their mobility at low electric fields. With the increasing of electric stress, the charged nanoparticles become the major conduction contributor and drift slowly due to the higher viscous resistance from oil molecules.
Synchronization of a micromechanical oscillator in different regimes of electromechanical nonlinearity
Authors: Taheri-Tehrani P. , Defoort M. , Horsley D. A.
Published: October 2017

In this letter, we investigate the dynamics of injection-locking a nonlinear micromechanical oscillator operating in different regimes of electromechanical nonlinearity to an external tone generated by a secondary oscillator. The micromechanical oscillator exhibits a combination of mechanical and electrostatic nonlinearities that were tuned using a bias voltage to adjust the relative importance of third-order and fifth-order stiffness nonlinearities. While it is well-known that third-order stiffness (Duffing) nonlinearity results in a synchronization range that increases with an oscillator's amplitude, little is known about the impact of other nonlinearities. We show that when using Duffing nonlinearity cancellation, higher order nonlinearities dominate, the synchronization range is smaller but has a greater rate-of-increase with oscillation amplitude. When both mechanical stiffness-hardening and electrostatic stiffness-softening nonlinearities are present, the frequency response follows an “s-curve” and, unlike the other conditions, the synchronization range does not increase monotonically with amplitude but instead reaches a minimum when both nonlinearities have similar magnitude. We develop a nonlinear resonator model and show that this model achieves good quantitative prediction of the measured synchronization range in all nonlinear operating regimes studied.
Vibrationally resolved electronic spectra including vibrational pre-excitation: Theory and application to VIPER spectroscopy
Authors: von Cosel Jan , Cerezo Javier , Kern-Michler Daniela , Neumann Carsten , van Wilderen Luuk J. G. W. , Bredenbeck Jens , Santoro Fabrizio , Burghardt Irene
Published: October 2017

Vibrationally resolved electronic absorption spectra including the effect of vibrational pre-excitation are computed in order to interpret and predict vibronic transitions that are probed in the Vibrationally Promoted Electronic Resonance (VIPER) experiment [L. J. G. W. van Wilderen et al., Angew. Chem., Int. Ed. 53, 2667 (2014)]. To this end, we employ time-independent and time-dependent methods based on the evaluation of Franck-Condon overlap integrals and Fourier transformation of time-domain wavepacket autocorrelation functions, respectively. The time-independent approach uses a generalized version of the FCclasses method [F. Santoro et al., J. Chem. Phys. 126, 084509 (2007)]. In the time-dependent approach, autocorrelation functions are obtained by wavepacket propagation and by the evaluation of analytic expressions, within the harmonic approximation including Duschinsky rotation effects. For several medium-sized polyatomic systems, it is shown that selective pre-excitation of particular vibrational modes leads to a redshift of the low-frequency edge of the electronic absorption spectrum, which is a prerequisite for the VIPER experiment. This effect is typically most pronounced upon excitation of modes that are significantly displaced during the electronic transition, such as ring distortion modes within an aromatic π-system. Theoretical predictions as to which modes show the strongest VIPER effect are found to be in excellent agreement with experiment.
Self-assembled nanotextures impart broadband transparency to glass windows and solar cell encapsulants
Authors: Liapis Andreas C. , Rahman Atikur , Black Charles T.
Published: October 2017

Most optoelectronic components and consumer display devices require glass or plastic covers for protection against the environment. Optical reflections from these encapsulation layers can degrade the device performance or lessen the user experience. Here, we use a highly scalable self-assembly based approach to texture glass surfaces at the nanoscale, reducing reflections by such an extent so as to make the glass essentially invisible. Our nanotextures provide broadband antireflection spanning visible and infrared wavelengths (450–2500 nm) that is effective even at large angles of incidence. This technology can be used to improve the performance of photovoltaic devices by eliminating reflection losses, which can be as much as 8% for glass encapsulated cells. In contrast, solar cells encapsulated with nanotextured glass generate the same photocurrent as when operated without a cover. Ultra-transparent windows having surface nanotextures on both sides can withstand three times more optical fluence than commercial broadband antireflection coatings, making them useful for pulsed laser applications.
Analytic continuation of Wolynes theory into the Marcus inverted regime
Authors: Lawrence Joseph E. , Manolopoulos David E.
Published: October 2017

The Wolynes theory of electronically nonadiabatic reaction rates [P. G. Wolynes, J. Chem. Phys. 87, 6559 (1987)] is based on a saddle point approximation to the time integral of a reactive flux autocorrelation function in the nonadiabatic (golden rule) limit. The dominant saddle point is on the imaginary time axis at tsp=iλspℏ, and provided λsp lies in the range −β/2≤λsp≤β/2, it is straightforward to evaluate the rate constant using information obtained from an imaginary time path integral calculation. However, if λsp lies outside this range, as it does in the Marcus inverted regime, the path integral diverges. This has led to claims in the literature that Wolynes theory cannot describe the correct behaviour in the inverted regime. Here we show how the imaginary time correlation function obtained from a path integral calculation can be analytically continued to λsp<−β/2, and the continuation used to evaluate the rate in the inverted regime. Comparison with exact golden rule results for a spin-boson model and a more demanding (asymmetric and anharmonic) model of electronic predissociation shows that the theory is just as accurate in the inverted regime as it is in the normal regime.
Temperature Dependence of Mineral Solubility in Water. Part I. Alkaline and Alkaline Earth Chlorides
Authors: Krumgalz B. S.
Published: October 2017

A database of alkaline and alkaline earth chloride solubilities in water at various temperatures was created using data from more than 670 publications over about the last two centuries. Statistical critical evaluations of the created database were produced since there were enough independent data sources to justify such evaluations. The reliable experimental data were adequately described by polynomial expressions over various temperature ranges. Using the Pitzer approach for ionic activity and osmotic coefficients, the thermodynamic solubility products for the discussed minerals have been calculated at various temperature intervals and also represented by polynomial expressions. The solubility products calculated in the current study yield excellent agreement between the predicted and experimental mineral solubility values in natural waters over a wide range of temperature and ionic solution matrices.
Analysis and observation of moving domain fronts in a ring of coupled electronic self-oscillators
Authors: English L. Q. , Zampetaki A. , Kevrekidis P. G. , Skowronski K. , Fritz C. B. , Abdoulkary Saidou
Published: October 2017

In this work, we consider a ring of coupled electronic (Wien-bridge) oscillators from a perspective combining modeling, simulation, and experimental observation. Following up on earlier work characterizing the pairwise interaction of Wien-bridge oscillators by Kuramoto–Sakaguchi phase dynamics, we develop a lattice model for a chain thereof, featuring an exponentially decaying spatial kernel. We find that for certain values of the Sakaguchi parameter α, states of traveling phase-domain fronts involving the coexistence of two clearly separated regions of distinct dynamical behavior, can establish themselves in the ring lattice. Experiments and simulations show that stationary coexistence domains of synchronization only manifest themselves with the introduction of a local impurity; here an incoherent cluster of oscillators can arise reminiscent of the chimera states in a range of systems with homogeneous oscillators and suitable nonlocal interactions between them.
Estimating mobility using sparse data: Application to human genetic variation
Authors: Loog Liisa , Mirazón Lahr Marta , Kovacevic Mirna , Manica Andrea , Eriksson Anders , Thomas Mark G.
Published: October 2017

Significance

Migratory activity is a critical factor in shaping processes of biological and cultural change through time. We introduce a method to estimate changes in underlying migratory activity that can be applied to genetic, morphological, or cultural data and is well-suited to samples that are sparsely distributed in space and through time. By applying this method to ancient genome data, we infer a number of changes in human mobility in Western Eurasia, including higher mobility in pre- than post-Last Glacial Maximum hunter–gatherers, and oscillations in Holocene mobility with peaks centering on the Neolithic transition and the beginnings of the Bronze Age and the Late Iron Age.
Nasal airflow simulations suggest convergent adaptation in Neanderthals and modern humans
Authors: de Azevedo S. , González M. F. , Cintas C. , Ramallo V. , Quinto-Sánchez M. , Márquez F. , Hünemeier T. , Paschetta C. , Ruderman A. , Navarro P. , Pazos B. A. , Silva de Cerqueira C. C. , Velan O. , Ramírez-Rozzi F. , Calvo N. , Castro H. G. , Paz R. R. , González-José R.
Published: October 2017

Significance

Due to its role in humidifying and warming the air before it reaches the lungs, adaptations in the internal nasal anatomy are suspected to have been essential for modern humans and Neanderthals during the settlement of Eurasian harsh landscapes. Unfortunately, the lack of soft-tissue evidence in the fossil record precludes any study of Neanderthal respiratory performance. Here, we use warping techniques to reconstruct a generic Neanderthal nose, computational fluid dynamics simulations to compare the respiratory performance on both species, and evolutionary analyses to detect signals of selection. We report striking differences on fluid residence times under cold/dry climatic conditions. Different from previously suggested, our results indicate that both species would have achieved an advantageous species-specific respiratory performance in cold climates.
Rewriting nature’s assembly manual for a ssRNA virus
Authors: Patel Nikesh , Wroblewski Emma , Leonov German , Phillips Simon E. V. , Tuma Roman , Twarock Reidun , Stockley Peter G.
Published: October 2017

Significance

Viruses composed of a shell of coat proteins enclosing ssRNA genomes are among the simplest biological entities. Their lifecycles include a range of processes, such as specific genome encapsidation and efficient capsid self-assembly. Until recently, these were not linked, but we have shown that many viruses in this class encode multiple, degenerate RNA sequence/structure motifs that bind cognate coat proteins collectively. This simultaneously ensures specific genome packaging and efficient virion assembly via an RNA-encoded instruction manual. Here we extract essential features of this manual in a viral RNA genome, creating a synthetic sequence with an assembly substrate superior to the natural equivalent. Such RNAs have the potential for efficient production of stable virus-like particle vaccines and/or gene/drug delivery vehicles.
DsbA-L prevents obesity-induced inflammation and insulin resistance by suppressing the mtDNA release-activated cGAS-cGAMP-STING pathway
Authors: Bai Juli , Cervantes Christopher , Liu Juan , He Sijia , Zhou Haiyan , Zhang Bilin , Cai Huan , Yin Dongqing , Hu Derong , Li Zhi , Chen Hongzhi , Gao Xiaoli , Wang Fang , O’Connor Jason C. , Xu Yong , Liu Meilian , Dong Lily Q. , Liu Feng
Published: October 2017

Significance

Activation of the cGAMP-cGAS-STING pathway has recently been shown to mediate virus- or bacteria-induced activation of the innate immune response. Here we report that this pathway also plays an important role in obesity-induced inflammation and metabolic dysfunction, beyond its well-characterized roles in innate immune surveillance. We have also identified adipose disulfide-bond A oxidoreductase-like protein as a key regulator of mitochondrial integrity and function, which protects mice from obesity-induced inflammation and insulin resistance by suppressing mtDNA release-induced activation of the cGAS-cGAMP-STING pathway. Our study suggests that targeting the cGAS-cGAMP-STING pathway in adipose tissue may be an effective approach to ameliorating obesity-induced chronic inflammation and its associated metabolic diseases.
Inhibition of curli assembly and
Escherichia coli
biofilm formation by the human systemic amyloid precursor transthyretin
Authors: Jain Neha , Ådén Jörgen , Nagamatsu Kanna , Evans Margery L. , Li Xinyi , McMichael Brennan , Ivanova Magdalena I. , Almqvist Fredrik , Buxbaum Joel N. , Chapman Matthew R.
Published: October 2017

Significance

Functional amyloids, like curli, contribute to biofilm development by uropathogenic
Escherichia coli
and other Gram-negative bacteria. Biofilms allow pathogens to subvert immune defenses and antibiotic treatments. Therefore, strategies to interrupt bacterial biofilm formation are urgently required. Here, we discovered that human transthyretin potently inhibits biofilm formation by
E. coli
and
Bacillus subtilis
. Transthyretin inhibits biofilm formation by preventing curli proteins from adopting the functional amyloid state that supports biofilm development. To our knowledge, this report of amyloid-dependent biofilm inhibition by a human protein with no significant bactericidal or bacteriostatic activity is unique. The observations indicate that a conformational relationship relevant to a set of specific protein–protein interactions, independent of primary sequence, can be functional across biological kingdoms.
Interplay of hemilability and redox activity in models of hydrogenase active sites
Authors: Ding Shengda , Ghosh Pokhraj , Darensbourg Marcetta Y. , Hall Michael B.
Published: October 2017

Significance

Segmentation of the bimetallic electrocatalysts under investigation into a metallodithiolate, bidentate S-donor ligand, and a receiver metal is effective for understanding the proton and electron uptake in H
2
-evolution reactions. Coexisting actor/reaction-involved ligands, i.e., electron-buffering NO and hemilabile, chelating metallodithiolate, subtly cooperate to control electrocatalytic H
2
-production mechanisms. Two mechanisms emerge in a single catalyst to yield H
2
: protonation of a hydride or reductive elimination from a metal dihydride. A Lewis acid–base pair appears by cleaving the hemilabile thiolate from the metal and serves as the reactive centers to process electrons and protons; a protonation or a reduction on the Lewis pair modulates their electron densities and protects these reactive centers from converting back to a dative bond.
Role of the nucleotidyl cyclase helical domain in catalytically active dimer formation
Authors: Vercellino Irene , Rezabkova Lenka , Olieric Vincent , Polyhach Yevhen , Weinert Tobias , Kammerer Richard A. , Jeschke Gunnar , Korkhov Volodymyr M.
Published: October 2017

Significance

Adenylyl and guanylyl cyclases are at the core of cellular signaling. Although the molecular mechanisms of the reactions catalyzed by these enzymes are well established, their structures and biophysical properties remain only partially characterized. Here, we report the structure of the cytosolic domain of a mycobacterial adenylyl cyclase Cya, an evolutionary ancestor of mammalian membrane adenylyl cyclases. The structure reveals the helical domain, a highly conserved structural element that links the catalytic and transmembrane portions of Cya. We show how helical domains bring together the catalytic domains to form functionally active dimers. Our data suggest that the disease-linked mutations in human nucleotidyl cyclases may disrupt the correct assembly of the helical domain, preventing the formation of an active dimeric enzyme.
Radiocarbon test for demographic events in written and oral history
Authors: Edinborough Kevan , Porčić Marko , Martindale Andrew , Brown Thomas Jay , Supernant Kisha , Ames Kenneth M.
Published: October 2017

Significance

Indigenous oral traditions remain a very controversial source of historical knowledge in Western scientific, humanistic, and legal traditions. Likewise, demographic models using radiocarbon-based simulation methods are controversial. We rigorously test the historicity of indigenous Tsimshian oral records (
adawx
) using an extended simulation-based method. Our methodology is able to detect short-duration (1–2 centuries) demographic events. First, we successfully test the methodology against a simulated radiocarbon dataset for the catastrophic European Black Death/bubonic plague (
Yersinia pestis
). Second, we test the Tsimshian
adawx
accounts of an occupational hiatus in their territorial heartland ca. 1,500–1,000 years ago. We are unable to disconfirm the oral accounts. This represents the first formal test of indigenous oral traditions using modern radiocarbon modeling techniques.
Contaminants of emerging concern affect
Trichoplusia ni
growth and development on artificial diets and a key host plant
Authors: Pennington Marcus J. , Rothman Jason A. , Dudley Stacia L. , Jones Michael B. , McFrederick Quinn S. , Gan Jay , Trumble John T.
Published: October 2017

Significance

Rising temperatures, drought, and growing human populations are increasing demand for reclaimed wastewater for agricultural use. However, wastewater often contains biologically active, pseudopersistent pharmaceuticals, even after passage through a water treatment facility. We determined that the biology, life histories, and microbial communities of an agricultural pest insect were altered when reared on artificial diets or plants irrigated by these chemicals. In this study, pharmaceuticals translocated through plants have been shown to negatively affect the biology of an agriculturally important insect. The responses to these pharmaceuticals could have implications for integrating pest management practices and for understanding the effects of reclaimed water on agricultural ecosystems that are critical for the sustainability of our food supply.
Facephenes and rainbows: Causal evidence for functional and anatomical specificity of face and color processing in the human brain
Authors: Schalk Gerwin , Kapeller Christoph , Guger Christoph , Ogawa Hiroshi , Hiroshima Satoru , Lafer-Sousa Rosa , Saygin Zeynep M. , Kamada Kyousuke , Kanwisher Nancy
Published: October 2017

Significance

Are some regions of the human brain exclusively engaged in a single specific mental process? Here we test this question in a neurosurgery patient implanted with electrodes for clinical reasons. When electrically stimulated in the fusiform face area while viewing objects, the patient reported illusory faces while the objects remained unchanged. When stimulated in nearby color-preferring sites, he reported seeing rainbows. The fact that stimulation of face-selective sites affected only face percepts and stimulation of color-preferring sites affected only color percepts, in both cases independent of the object being viewed, supports the view that some regions of cortex are indeed exclusively causally engaged in a single mental process and highlights the risks entailed in standard interpretations of neural decoding results.
Probing and manipulating intracellular membrane traffic by microinjection of artificial vesicles
Authors: Koike Seiichi , Jahn Reinhard
Published: October 2017

Significance

In eukaryotic cells, membranous organelles exchange trafficking vesicles that bud from the precursor and are transported to the target membrane where they fuse. Many of the required proteins are known. Moreover, some steps such as budding and fusion have been reconstituted using artificial membranes and a minimalistic set of proteins. However, it is not known whether these vesicles are functional in the complex environment of a cell. Here, we have introduced such artificial vesicles into living cells and find that only few components are needed for function in membrane traffic, with all other factors recruited from the cytoplasm. Thus, eukaryotic cells have a remarkable capacity for self-organization that can be exploited for targeting tags to specific regions in the cell.
Active site voltage clamp fluorometry of the sodium glucose cotransporter hSGLT1
Authors: Gorraitz Edurne , Hirayama Bruce A. , Paz Aviv , Wright Ernest M. , Loo Donald D. F.
Published: October 2017

Significance

Site-directed fluorometry was used to understand conformational changes of the Na
+
/glucose symporter. SGLT1 functions by a mechanism where the substrate-binding site alternates between the two faces of the membrane, but little is known about the underlying conformational changes. Rhodamines were covalently inserted into the substrate cavity, and changes of fluorescence were measured in real time with the opening and closing of the outer gate as SGLT1 was driven between inward and outward conformations using voltage jumps. Structural modeling indicated that the quenching with gating opening was due to an increased solvation of rhodamine and an increase in polar residues lining the wall of the cavity. This experimental approach will lead to a better understanding of the mechanism of membrane transport.
Molecular basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1
Authors: Alblova Miroslava , Smidova Aneta , Docekal Vojtech , Vesely Jan , Herman Petr , Obsilova Veronika , Obsil Tomas
Published: October 2017

Significance

14-3-3 proteins are conserved scaffolding proteins expressed in all eukaryotic cells, where they regulate the function of several hundreds of partner proteins by constraining their conformation. Yeast neutral trehalases (Nth), enzymes responsible for the hydrolysis of trehalose, compared with trehalases from other organisms, possess distinct structure and regulation involving phosphorylation followed by binding to 14-3-3. Here we present the crystal structures of yeast Nth1 and its complex with the 14-3-3 protein and propose a molecular mechanism in which 14-3-3 activates Nth1 by stabilizing the flexible part of its active site. Comparison of the 14-3-3:Nth1 complex structure with those of other 14-3-3 complexes suggests the highly conserved nature of 14-3-3 affects the structures of many client proteins.
Dynamics of cell transformation in culture and its significance for tumor development in animals
Authors: Rubin Harry
Published: October 2017

Significance

Growth of NIH 3T3 cells in an optimized medium produced transformed foci after reaching confluence in the absence of treatment with carcinogens or transfection with tumor DNA. Dynamic experiments showed the first response of the crowded cells was gradual population-wide increases in saturation density followed by transformed foci. The latter produced malignant tumors when injected into mice. The field of cells around the foci became increasingly susceptible to transformation. Analysis of the data revealed that transformation was driven by epigenetic selection of cell populations that grew well at high densities rather than genetic instability. That conclusion is reinforced by two other methods of selection, one at low cell density in low serum concentration and the other by suspension in agar.