bluuebunny/crossref_metadata_2025 huggingface dataset:
First results from Project SUNBIRD: Supernovae UNmasked By Infra-Red Detection
Authors: Kool Erik C. , Ryder Stuart D. , Kankare Erkki , Mattila Seppo
Published: July 2017

A substantial number of core-collapse supernovae (CCSNe) are expected to be hosted by starbursting luminous infrared galaxies (LIRGs). However, so far very few CCSNe have been discovered in LIRGs, most likely as a result of dust extinction and lack of contrast in their typically luminous and complex nuclear regions. We present the first results of Project SUNBIRD (Supernovae UNmasked By InfraRed Detection), where we aim to uncover dust-obscured nuclear supernovae by monitoring over 30 LIRGs, using near-infrared state-of-the-art Laser Guide Star Adaptive Optics (LGSAO) imaging on the Gemini South and Keck telescopes. Such discoveries are vital for determining the fraction of supernovae which will be missed as a result of dust obscuration by current and future optical surveys.
HDUST3 — A chemically realistic, 3-D, NLTE radiative transfer code
Authors: Carciofi Alex C. , Bjorkman Jon E. , Zsargó Janos
Published: July 2017

HDUST is a 3D, NLTE radiative transfer code based on the Monte Carlo method. We report on recent advancements on the code, which is now capable of handling He and other elements in the NLTE regime and in 3D configurations. In this contribution we show initial comparisons with CMFGEN, made with spherical wind models composed of H + He.
Massive pre-main-sequence stars in M17
Authors: Ramírez-Tannus M. C. , Kaper L. , de Koter A. , Tramper F. , Sana H. , Ramírez-Agudelo O. H. , Bik A. , Ellerbroek L. E. , Ochsendorf B. B.
Published: July 2017

We obtained VLT/X-shooter spectra of twelve candidate young massive stars previously selected by Hanson et al. (1997) in the giant Hii region M17. An analysis of their spectra using FASTWIND models (Puls et al. 2005) shows that they span a mass range of 6 - 20 M⊙. We identify the presence of gaseous and dusty disks around six sources based on emission lines in the spectrum and infrared continuum excess.
A multi-wavelength view of NGC 1624-2
Authors: David-Uraz A. , Petit V. , MacInnis R. , Erba C. , Owocki S. P. , Fullerton A. W. , Walborn N. R. , Cohen D. H.
Published: July 2017

Large magnetometric surveys have contributed to the detection of an increasing number of magnetic massive stars, and to the recognition of a population of magnetic massive stellar objects with distinct properties. Among these, NGC 1624-2 possesses the largest magnetic field of any O-type star; such a field confines the stellar wind into a circumstellar magnetosphere, which can be probed using observations at different wavelength regimes. Recent optical and X-ray observations suggest that NGC 1624-2’s magnetosphere is much larger than that of any other magnetic O star. By modeling the variations of UV resonance lines, we can constrain its velocity structure. Furthermore, recent spectropolarimetric observations raise the possibility of a more complex field topology than previously expected. Putting all of these multi-wavelength constraints together will allow us to paint a consistent picture of NGC 1624-2 and its surprising behavior, giving us valuable insight into the very nature of massive star magnetospheres.
Emission-line Diagnostics of Nearby HII Regions Including Supernova Hosts
Authors: Xiao Lin , Eldridge J. J. , Stanway Elizabeth , Galbany L.
Published: July 2017

We present a new model of the optical nebular emission from HII regions by combining the results of the Binary Population and Spectral Synthesis (bpass) code with the photoionization code cloudy (Ferland et al. 1998). We explore a variety of emission-line diagnostics of these star-forming HII regions and examine the effects of metallicity and interacting binary evolution on the nebula emission-line production. We compare the line emission properties of HII regions with model stellar populations, and provide new constraints on their stellar populations and supernova progenitors. We find that models including massive binary stars can successfully match all the observational constraints and provide reasonable age and mass estimation of the HII regions and supernova progenitors.
Resolving the mass loss from red supergiants by high angular resolution
Authors: Ohnaka Keiichi
Published: July 2017

Despite its importance on late stages of the evolution of massive stars, the mass loss from red supergiants (RSGs) is a long-standing problem. To tackle this problem, it is essential to observe the wind acceleration region close to the star with high spatial resolution. While the mass loss from RSGs is often assumed to be spherically symmetric with a monotonically accelerating wind, there is mounting observational evidence that the reality is much more complex. I review the recent progress in high spatial resolution observations of RSGs, encompassing from the circumstellar envelope on rather large spatial scales (~100 stellar radii) to milliarcsecond-resolution aperture-synthesis imaging of the surface and the atmosphere of RSGs with optical and infrared long-baseline interferometers.
Massive infrared clusters in the Milky Way
Authors: Chené André-Nicolas , Ramírez Alegría Sebastian , Borissova Jordanka , Hervé Anthony , Martins Fabrice , Kuhn Michael , Minniti Dante ,   the VVV Science Team
Published: July 2017

Our position in the Milky Way (MW) is both a blessing and a curse. We are nearby to many star clusters, but the dust that is a product of their very existence obscures them. Also, many massive young clusters are expected to be located near, or across the Galactic Center, where the dust extinction is extreme (AV > 15 mag) and can be better penetrated by infrared photons. This paper reviews the discoveries and the study of new MW massive stars and massive clusters made possible by near infrared observations that are part of the VISTA Variables in the Vía Láctea (VVV) survey. It discusses what the studies of their fundamental parameters have taught us.
Properties of the O-type giants and supergiants in 30 Doradus
Authors: Ramírez-Agudelo O. H. ,   VFTS consortium
Published: July 2017

We discuss the stellar and wind properties of 72 presumably single O-type giants, bright giants, and supergiants in the 30 Doradus region. This sample constitutes the largest and most homogeneous sample of such stars ever analyzed and offers the opportunity to test models describing their main-sequence evolution.
The evolution of magnetic fields in hot stars
Authors: Oksala Mary E. , Neiner Coralie , Georgy Cyril , Przybilla Norbert , Keszthelyi Zsolt , Wade Gregg , Mathis Stéphane , Blazère Aurore , Buysschaert Bram
Published: July 2017

Over the last decade, tremendous strides have been achieved in our understanding of magnetism in main sequence hot stars. In particular, the statistical occurrence of their surface magnetism has been established (~10%) and the field origin is now understood to be fossil. However, fundamental questions remain: how do these fossil fields evolve during the post-main sequence phases, and how do they influence the evolution of hot stars from the main sequence to their ultimate demise? Filling the void of known magnetic evolved hot (OBA) stars, studying the evolution of their fossil magnetic fields along stellar evolution, and understanding the impact of these fields on the angular momentum, rotation, mass loss, and evolution of the star itself, is crucial to answering these questions, with far reaching consequences, in particular for the properties of the precursors of supernovae explosions and stellar remnants. In the framework of the BRITE spectropolarimetric survey and LIFE project, we have discovered the first few magnetic hot supergiants. Their longitudinal surface magnetic field is very weak but their configuration resembles those of main sequence hot stars. We present these first observational results and propose to interpret them at first order in the context of magnetic flux conservation as the radius of the star expands with evolution. We then also consider the possible impact of stellar structure changes along evolution.
The outer disk of the classical Be star ψ Per
Authors: Klement Robert , Carciofi Alex C. , Rivinius Thomas , Matthews Lynn D. , Ignace Richard , Bjorkman Jon E. , Vieira Rodrigo G. , Mota Bruno C. , Faes Daniel M. , Štefl Stanislav
Published: July 2017

To this date ψ Per is the only classical Be star that was angularly resolved in radio (by the VLA at λ = 2 cm). Gaussian fit to the azimuthally averaged visibility data indicates a disk size (FWHM) of ~500 stellar radii (Dougherty & Taylor 1992). Recently, we obtained new multi-band cm flux density measurements of ψ Per from the enhanced VLA. We modeled the observed spectral energy distribution (SED) covering the interval from ultraviolet to radio using the Monte Carlo radiative transfer code HDUST (Carciofi & Bjorkman 2006). An SED turndown, that occurs between far-IR and radio wavelengths, is explained by a truncated viscous decretion disk (VDD), although the shallow slope of the radio SED suggests that the disk is not simply cut off, as is assumed in our model. The best-fit size of a truncated disk derived from the modeling of the radio SED is 100+5−15 stellar radii, which is in striking contrast with the result of Dougherty & Taylor (1992). The reasons for this discrepancy are under investigation.
The Massive stellar Population at the Galactic Center
Authors: Najarro Francisco , de la Fuente Diego , Geballe Tom R. , Figer Don F. , Hillier D. John
Published: July 2017

We present results from our ongoing infrared spectroscopic studies of the massive stellar content at the Center of the Milky Way. This region hosts a large number of apparently isolated massive stars as well as three of the most massive resolved young clusters in the Local Group. Our survey seeks to infer the presence of a possible top-heavy recent star formation history and to test massive star formation channels: clusters vs isolation.
Modelling the thermal X-ray emission around the Galactic centre from colliding Wolf-Rayet winds
Authors: Russell Christopher M. P. , Wang Q. Daniel , Cuadra Jorge
Published: July 2017

We compute the thermal X-ray emission from hydrodynamic simulations of the 30 Wolf-Rayet (WR) stars orbiting within a parsec of Sgr A*, with the aim of interpreting the Chandra X-ray observations of this region. The model well reproduces the spectral shape of the observations, indicating that the shocked WR winds are the dominant source of this thermal emission. The model X-ray flux is tied to the strength of the Sgr A* outflow, which clears out hot gas from the vicinity of Sgr A*. A moderate outflow best fits the present-day observations, even though this supermassive black hole (SMBH) outflow ended ~100 yr ago.
The Most Massive Heartbeat: Finding the Pulse of ι Orionis
Authors: Pablo Herbert , Richardson Noel , Fuller Jim , Moffat Anthony F. J. ,   BEST and Ritter Observing team
Published: July 2017

ι Orionis is a massive binary system consisting of O9III + B1 III/IV stars. Though the system has been well studied, much about its fundamental properties have been difficult to determine. In this paper we report on the discovery of the heartbeat phenomenon in ι Orionis making it the most massive heartbeat system currently known. Using this phenomenon we have found empirical values for the masses and radii of both components. Moreover, we report the detection of tidally induced oscillations in an O-type star for the first time. These discoveries open a new avenue for exploring asteroseismology in massive stars.
OWN Survey: a spectroscopic monitoring of Southern Galactic O and WN-type stars
Authors: Barbá Rodolfo H. , Gamen Roberto , Arias Julia I. , Morrell Nidia I.
Published: July 2017

We summarize the status and results of the OWN Survey, a high-resolution monitoring program of Southern Galactic O- and WN-type stars, after twelve years of observing campaign.
The Young and the Massive: Stars at the upper end of the Initial Mass Function
Authors: Caballero-Nieves Saida M. , Crowther P. A.
Published: July 2017

The upper mass limit of stars remains an open question in astrophysics. Here we discuss observations of the most massive stars (greater than 100 solar masses) in the local universe and how the observations fit in with theoretical predictions. In particular, the Large Magellanic Cloud plays host to numerous very massive stars, making it an ideal template to study the roles that environment, metallicity, and multiplicity play in the formation and evolution of the most massive stars. We will discuss the work that is instrumental in laying the groundwork for interpreting future observations by James Webb of starburst regions in the high redshift universe.
Massive stars, successes and challenges
Authors: Meynet Georges , Maeder André , Georgy Cyril , Ekström Sylvia , Eggenberger Patrick , Barblan Fabio , Song Han Feng
Published: July 2017

We give a brief overview of where we stand with respect to some old and new questions bearing on how massive stars evolve and end their lifetime. We focus on the following key points that are further discussed by other contributions during this conference: convection, mass losses, rotation, magnetic field and multiplicity. For purpose of clarity, each of these processes are discussed on its own but we have to keep in mind that they are all interacting between them offering a large variety of outputs, some of them still to be discovered.
The mass-loss before the end: two luminous blue variables with a collimated stellar wind
Authors: Agliozzo C. , Trigilio C. , Buemi C. , Leto P. , Umana G. , Pignata G. , Phillips N. M. , Nikutta R. , Prieto J. L.
Published: July 2017

We gathered a multiwavelength dataset of two well-known LBVs. We found a complex mass-loss, with evidence of variability, such as has been seen previously. In addition, our data reveal signatures of collimated stellar winds. We propose a new scenario for these two stars where the nebula shaping is influenced by the presence of a companion star and/or fast rotation.
Common envelope: progress and transients
Authors: Ivanova Natalia
Published: July 2017

We review the fundamentals and the recent developments in understanding of common envelope physics. We report specifically on the progress that was made by the consideration of the recombination energy. This energy is found to be responsible for the complete envelope ejection in the case of a prompt binary formation, for the delayed dynamical ejections in the case of a self-regulated spiral-in, and for the steady recombination outflows during the transition between the plunge-in and the self-regulated spiral-in. Due to different ways how the recombination affects the common envelope during fast and slow spiral-ins, the apparent efficiency of the orbital energy use can be different between the two types of spiral-ins by a factor of ten. We also discuss the observational signatures of the common envelope events, their link a new class of astronomical transients, Luminous Red Novae, and to a plausible class of very luminous irregular variables.
HD151018: strong magnetic field in a giant O-type star?
Authors: Rubinho M. S. , Damineli A. , Carciofi A. , Moser D.
Published: July 2017

HD151018 is a normal O-type giant with periodic variability of the wind seen in both spectroscopy and linear polarimetry. The characteristics of the wind emission strongly indicate a magnetically confined wind. This work presents the observational results and an initial modelling of the polarimetric modulation of this star.
Implicit Theories of Ability and Self-Efficacy
Authors: Chen Jason A. , Shane Tutwiler M.
Published: July 2017

Abstract. Our overall goal was to empirically test what we called the “growth mindset as inoculation” hypothesis using a series of latent profile analytical approaches. This inoculation hypothesis, which is consistent with the way in which Dweck and Leggett (1988) described their social cognitive approach, states that believing in the malleability of intelligence serves a protective role against negative motivational and achievement outcomes. Participants were Grade 6 students (n = 504) from a middle school and Grade 10 students (n = 354) from two high schools in the Southeastern part of the United States. Two distinct patterns emerged, which corresponded to a growth mindset profile, and an all moderate profile. Our findings did not completely confirm or disconfirm the inoculation hypothesis – rather, a more nuanced conclusion should be drawn. Although there was evidence that the growth mindset profile evinced more adaptive outcomes compared to the all moderate alternative, which reinforced Dweck and Leggett’s claims, there was no evidence of any profiles with a distinct fixed theory of ability. This was true even when we forced our data to conform to such a model. Results refine Dweck and Leggett’s social cognitive approach to motivation.
Digital spiral object identification using random light
Authors: Yang Zhe , Magaña-Loaiza Omar S , Mirhosseini Mohammad , Zhou Yiyu , Gao Boshen , Gao Lu , Rafsanjani Seyed Mohammad Hashemi , Long Gui-Lu , Boyd Robert W
Published: July 2017

Photons that are entangled or correlated in orbital angular momentum have been extensively used for remote sensing, object identification and imaging. It has recently been demonstrated that intensity fluctuations give rise to the formation of correlations in the orbital angular momentum components and angular positions of random light. Here we demonstrate that the spatial signatures and phase information of an object with rotational symmetries can be identified using classical orbital angular momentum correlations in random light. The Fourier components imprinted in the digital spiral spectrum of the object, as measured through intensity correlations, unveil its spatial and phase information. Sharing similarities with conventional compressive sensing protocols that exploit sparsity to reduce the number of measurements required to reconstruct a signal, our technique allows sensing of an object with fewer measurements than other schemes that use pixel-by-pixel imaging. One remarkable advantage of our technique is that it does not require the preparation of fragile quantum states of light and operates at both low- and high-light levels. In addition, our technique is robust against environmental noise, a fundamental feature of any realistic scheme for remote sensing.
Mechanistic and structural basis for activation of cardiac myosin force production by omecamtiv mecarbil
Authors: Planelles-Herrero Vicente J. , Hartman James J. , Robert-Paganin Julien , Malik Fady I. , Houdusse Anne
Published: July 2017

Omecamtiv mecarbil is a selective, small-molecule activator of cardiac myosin that is being developed as a potential treatment for heart failure with reduced ejection fraction. Here we determine the crystal structure of cardiac myosin in the pre-powerstroke state, the most relevant state suggested by kinetic studies, both with (2.45 Å) and without (3.10 Å) omecamtiv mecarbil bound. Omecamtiv mecarbil does not change the motor mechanism nor does it influence myosin structure. Instead, omecamtiv mecarbil binds to an allosteric site that stabilizes the lever arm in a primed position resulting in accumulation of cardiac myosin in the primed state prior to onset of cardiac contraction, thus increasing the number of heads that can bind to the actin filament and undergo a powerstroke once the cardiac cycle starts. The mechanism of action of omecamtiv mecarbil also provides insights into uncovering how force is generated by molecular motors.
CLICs-dependent chloride efflux is an essential and proximal upstream event for NLRP3 inflammasome activation
Authors: Tang Tiantian , Lang Xueting , Xu Congfei , Wang Xiaqiong , Gong Tao , Yang Yanqing , Cui Jun , Bai Li , Wang Jun , Jiang Wei , Zhou Rongbin
Published: July 2017

The NLRP3 inflammasome can sense different pathogens or danger signals, and has been reported to be involved in the development of many human diseases. Potassium efflux and mitochondrial damage are both reported to mediate NLRP3 inflammasome activation, but the underlying, orchestrating signaling events are still unclear. Here we show that chloride intracellular channels (CLIC) act downstream of the potassium efflux-mitochondrial reactive oxygen species (ROS) axis to promote NLRP3 inflammasome activation. NLRP3 agonists induce potassium efflux, which causes mitochondrial damage and ROS production. Mitochondrial ROS then induces the translocation of CLICs to the plasma membrane for the induction of chloride efflux to promote NEK7–NLRP3 interaction, inflammasome assembly, caspase-1 activation, and IL-1β secretion. Thus, our results identify CLICs-dependent chloride efflux as an essential and proximal upstream event for NLRP3 activation.
Rationalizing the light-induced phase separation of mixed halide organic–inorganic perovskites
Authors: Draguta Sergiu , Sharia Onise , Yoon Seog Joon , Brennan Michael C. , Morozov Yurii V. , Manser Joseph S. , Kamat Prashant V. , Schneider William F. , Kuno Masaru
Published: July 2017

Mixed halide hybrid perovskites, CH3NH3Pb(I1−x
Br
x
)3, represent good candidates for low-cost, high efficiency photovoltaic, and light-emitting devices. Their band gaps can be tuned from 1.6 to 2.3 eV, by changing the halide anion identity. Unfortunately, mixed halide perovskites undergo phase separation under illumination. This leads to iodide- and bromide-rich domains along with corresponding changes to the material’s optical/electrical response. Here, using combined spectroscopic measurements and theoretical modeling, we quantitatively rationalize all microscopic processes that occur during phase separation. Our model suggests that the driving force behind phase separation is the bandgap reduction of iodide-rich phases. It additionally explains observed non-linear intensity dependencies, as well as self-limited growth of iodide-rich domains. Most importantly, our model reveals that mixed halide perovskites can be stabilized against phase separation by deliberately engineering carrier diffusion lengths and injected carrier densities.
Oscillatory vapour shielding of liquid metal walls in nuclear fusion devices
Authors: van Eden G. G. , Kvon V. , van de Sanden M. C. M. , Morgan T. W.
Published: July 2017

Providing an efficacious plasma facing surface between the extreme plasma heat exhaust and the structural materials of nuclear fusion devices is a major challenge on the road to electricity production by fusion power plants. The performance of solid plasma facing surfaces may become critically reduced over time due to progressing damage accumulation. Liquid metals, however, are now gaining interest in solving the challenge of extreme heat flux hitting the reactor walls. A key advantage of liquid metals is the use of vapour shielding to reduce the plasma exhaust. Here we demonstrate that this phenomenon is oscillatory by nature. The dynamics of a Sn vapour cloud are investigated by exposing liquid Sn targets to H and He plasmas at heat fluxes greater than 5 MW m−2. The observations indicate the presence of a dynamic equilibrium between the plasma and liquid target ruled by recombinatory processes in the plasma, leading to an approximately stable surface temperature.
Pan-urologic cancer genomic subtypes that transcend tissue of origin
Authors: Chen Fengju , Zhang Yiqun , Bossé Dominick , Lalani Aly-Khan A. , Hakimi A. Ari , Hsieh James J. , Choueiri Toni K. , Gibbons Don L. , Ittmann Michael , Creighton Chad J.
Published: July 2017

Urologic cancers include cancers of the bladder, kidney, prostate, and testes, with common molecular features spanning different types. Here, we show that 1954 urologic cancers can be classified into nine major genomic subtypes, on the basis of multidimensional and comprehensive molecular characterization (including DNA methylation and copy number, and RNA and protein expression). Tissue dominant effects are first removed computationally in order to define these subtypes, which reveal common processes—reflecting in part tumor microenvironmental influences—driving cellular behavior across tumor lineages. Six of the subtypes feature a mixture of represented cancer types as defined by tissue or cell of origin. Differences in patient survival and in the manifestation of specific pathways—including hypoxia, metabolism, NRF2-ARE, Hippo, and immune checkpoint—can further distinguish the subtypes. Immune checkpoint markers and molecular signatures of macrophages and T cell infiltrates are relatively high within distinct subsets of each cancer type studied. The pan-urologic cancer genomic subtypes would facilitate information sharing involving therapeutic implications between tissue-oriented domains.
Construction of ground-state preserving sparse lattice models for predictive materials simulations
Authors: Huang Wenxuan , Urban Alexander , Rong Ziqin , Ding Zhiwei , Luo Chuan , Ceder Gerbrand
Published: July 2017

First-principles based cluster expansion models are the dominant approach in ab initio thermodynamics of crystalline mixtures enabling the prediction of phase diagrams and novel ground states. However, despite recent advances, the construction of accurate models still requires a careful and time-consuming manual parameter tuning process for ground-state preservation, since this property is not guaranteed by default. In this paper, we present a systematic and mathematically sound method to obtain cluster expansion models that are guaranteed to preserve the ground states of their reference data. The method builds on the recently introduced compressive sensing paradigm for cluster expansion and employs quadratic programming to impose constraints on the model parameters. The robustness of our methodology is illustrated for two lithium transition metal oxides with relevance for Li-ion battery cathodes, i.e., Li2x
Fe2(1−x)O2 and Li2x
Ti2(1−x)O2, for which the construction of cluster expansion models with compressive sensing alone has proven to be challenging. We demonstrate that our method not only guarantees ground-state preservation on the set of reference structures used for the model construction, but also show that out-of-sample ground-state preservation up to relatively large supercell size is achievable through a rapidly converging iterative refinement. This method provides a general tool for building robust, compressed and constrained physical models with predictive power.
Rewritable ferroelectric vortex pairs in BiFeO3
Authors: Li Yang , Jin Yaming , Lu Xiaomei , Yang Jan-Chi , Chu Ying-Hao , Huang Fengzhen , Zhu Jinsong , Cheong Sang-Wook
Published: July 2017

Ferroelectric vortex in multiferroic materials has been considered as a promising alternative to current memory cells for the merit of high storage density. However, the formation of regular natural ferroelectric vortex is difficult, restricting the achievement of vortex memory device. Here, we demonstrated the creation of ferroelectric vortex-antivortex pairs in BiFeO3 thin films by using local electric field. The evolution of the polar vortex structure is studied by piezoresponse force microscopy at nanoscale. The results reveal that the patterns and stability of vortex structures are sensitive to the poling position. Consecutive writing and erasing processes cause no influence on the original domain configuration. The Z4 proper coloring vortex-antivortex network is then analyzed by graph theory, which verifies the rationality of artificial vortex-antivortex pairs. This study paves a foundation for artificial regulation of vortex, which provides a possible pathway for the design and realization of non-volatile vortex memory devices and logical devices.
An extended model for culture-dependent heterogenous gene expression and proliferation dynamics in mouse embryonic stem cells
Authors: Godwin Simon , Ward Daniel , Pedone Elisa , Homer Martin , Fletcher Alexander G. , Marucci Lucia
Published: July 2017

During development, pluripotency is a transient state describing a cell’s ability to give rise to all three germ layers and germline. Recent studies have shown that, in vitro, pluripotency is highly dynamic: exogenous stimuli provided to cultures of mouse embryonic stem cells, isolated from pre-implantation blastocysts, significantly affect the spectrum of pluripotency. 2i/LIF, a recently defined serum-free medium, forces mouse embryonic stem cells into a ground-state of pluripotency, while serum/LIF cultures promote the co-existence of ground-like and primed-like mouse embryonic stem cell subpopulations. The latter heterogeneity correlates with temporal fluctuations of pluripotency markers, including the master regulator Nanog, in single cells. We propose a mathematical model of Nanog dynamics in both media, accounting for recent experimental data showing the persistence of a small Nanog Low subpopulation in ground-state pluripotency mouse embryonic stem cell cultures. The model integrates into the core pluripotency Gene Regulatory Network both inhibitors present in 2i/LIF (PD and Chiron), and feedback interactions with genes found to be differentially expressed in the two media. Our simulations and bifurcation analysis show that, in ground-state cultures, Nanog dynamics result from the combination of reduced noise in gene expression and the shift of the system towards a monostable, but still excitable, regulation. Experimental data and agent-based modelling simulations indicate that mouse embryonic stem cell proliferation dynamics vary in the two media, and cannot be reproduced by accounting only for Nanog-dependent cell-cycle regulation. We further demonstrate that both PD and Chiron play a key role in regulating heterogeneity in transcription factor expression and, ultimately, mouse embryonic stem cell fate decision.
Interaction between von Hippel-Lindau Protein and Fatty Acid Synthase Modulates Hypoxia Target Gene Expression
Authors: Sun Wendi , Kato Hiroyuki , Kitajima Shojiro , Lee Kian Leong , Gradin Katarina , Okamoto Takashi , Poellinger Lorenz
Published: July 2017

Hypoxia-inducible factors (HIFs) play a central role in the transcriptional response to changes in oxygen availability. Stability of HIFs is regulated by multi-step reactions including recognition by the von Hippel-Lindau tumour suppressor protein (pVHL) in association with an E3 ligase complex. Here we show that pVHL physically interacts with fatty acid synthase (FASN), displacing the E3 ubiquitin ligase complex. This results in HIF-α protein stabilization and activation of HIF target genes even in normoxia such as during adipocyte differentiation. 25-hydroxycholesterol (25-OH), an inhibitor of FASN expression, also inhibited HIF target gene expression in cultured cells and in mouse liver. Clinically, FASN is frequently upregulated in a broad variety of cancers and has been reported to have an oncogenic function. We found that upregulation of FASN correlated with induction of many HIF target genes, notably in a malignant subtype of prostate tumours. Therefore, pVHL-FASN interaction plays a regulatory role for HIFs and their target gene expression.
Phytoextraction of cadmium-contaminated soil and potential of regenerated tobacco biomass for recovery of cadmium
Authors: Yang Yang , Ge Yichen , Zeng Hongyuan , Zhou Xihong , Peng Liang , Zeng Qingru
Published: July 2017

The aim of this study was to estimate the influence of regenerated tobacco on the extraction of Cd from two acidic soils as well as to address the problem of how to deal with contaminated leaves following phytoextraction. Results showed that a coppicing tobacco led to a decline in Cd concentration in regenerated leaves and stalks when plants were grown in pots, but increased concentrations in regenerated lower and middle leaves when plants were grown under field conditions. The highest recorded bioconcentration factors in Chaling and Guanxi soil were 37.53 and 19.21 in lower leaves in the field, respectively. Total Cd extraction efficiency in practice (9.43% for Chaling soil and 6.24% for Guanxi soil) under field conditions confirmed our theoretical calculations (10.0% for Chaling soil and 6.73% for Guanxi soil). Use of a 0.5% hydrochloric acid(HCl) solution was sufficient to reduce Cd (98.4%) in tobacco leaves to permissible levels as required by the Hygienic Standard for Feeds in China (≤0.5 mg kg−1). Regenerated tobacco has the potential to allow cultivation of Cd contaminated farmland to produce animal feed, assist in lowering total Cd content of soil, and allow income generation for farmers.
Selection and characterization of DNA aptamer against glucagon receptor by cell-SELEX
Authors: Wang Guodong , Liu Jun , Chen Ke , Xu Yiling , Liu Bo , Liao Jie , Zhu Lei , Hu Xiaoxiao , Li Jianglin , Pu Ying , Zhong Wen , Fu Ting , Liu Huixia , Tan Weihong
Published: July 2017

Excessive secretion of glucagon, a functional insulin antagonist, significantly contributes to hyperglycemia. Glucagon exerts its physiological functions through activation of the glucagon receptor (GCGR). Inhibition of GCGR activity represents a potential therapeutic approach for reducing excess glucose production in diabetes mellitus. Aptamers are short DNA or RNA oligonucleotides evolved from systematic evolution of ligands by exponential enrichment (SELEX). Here, we have successfully selected a DNA aptamer against GCGR by cell-SELEX, which can specifically bind membrane protein of CHO-GCGR cells with a K
d
of 52.7 ± 5.1 nM. Aptamer-mediated pull-down and gcgr knockdown assay verified that GCGR was the target of aptamer GR-3. Binding analysis revealed that GR-3 could recognize other cells with different affinity according to the level of GCGR protein expressed in these cells. Hepatic tissue imaging suggested that GR-3 could bind the cell membrane of hepatic tissues. With the advantages of small size, high binding affinity, good stability, lack of immunogenicity, and easy synthesis, aptamer GR-3 against GCGR can be a promising tool with the potential to attenuate hyperglycemia in diabetes mellitus.
Auditory environmental context affects visual distance perception
Authors: Etchemendy Pablo E. , Abregú Ezequiel , Calcagno Esteban R. , Eguia Manuel C. , Vechiatti Nilda , Iasi Federico , Vergara Ramiro O.
Published: July 2017

In this article, we show that visual distance perception (VDP) is influenced by the auditory environmental context through reverberation-related cues. We performed two VDP experiments in two dark rooms with extremely different reverberation times: an anechoic chamber and a reverberant room. Subjects assigned to the reverberant room perceived the targets farther than subjects assigned to the anechoic chamber. Also, we found a positive correlation between the maximum perceived distance and the auditorily perceived room size. We next performed a second experiment in which the same subjects of Experiment 1 were interchanged between rooms. We found that subjects preserved the responses from the previous experiment provided they were compatible with the present perception of the environment; if not, perceived distance was biased towards the auditorily perceived boundaries of the room. Results of both experiments show that the auditory environment can influence VDP, presumably through reverberation cues related to the perception of room size.
Transition metal alloying effect on the phosphoric acid adsorption strength of Pt nanoparticles: an experimental and density functional theory study
Authors: Park Hee-Young , Lim Dong-Hee , Yoo Sung Jong , Kim Hyoung-Juhn , Henkensmeier Dirk , Kim Jin Young , Ham Hyung Chul , Jang Jong Hyun
Published: July 2017

The effect of alloying with transition metals (Ni, Co, Fe) on the adsorption strength of phosphoric acid on Pt alloy surfaces was investigated using electrochemical analysis and first-principles calculations. Cyclic voltammograms of carbon-supported Pt3M/C (M = Ni, Co, and Fe) electrocatalysts in 0.1 M HClO4 with and without 0.01 M H3PO4 revealed that the phosphoric acid adsorption charge density near the onset potential on the nanoparticle surfaces was decreased by alloying with transition metals in the order Co, Fe, Ni. First-principles calculations based on density functional theory confirmed that the adsorption strength of phosphoric acid was weakened by alloying with transition metals, in the same order as that observed in the electrochemical analysis. The simulation suggested that the weaker phosphoric acid adsorption can be attributed to a lowered density of states near the Fermi level due to alloying with transition metals.
Ecological Effect of Arginine on Oral Microbiota
Authors: Zheng Xin , He Jinzhi , Wang Lin , Zhou Shuangshuang , Peng Xian , Huang Shi , Zheng Liwei , Cheng Lei , Hao Yuqing , Li Jiyao , Xu Jian , Xu Xin , Zhou Xuedong
Published: July 2017

Dental caries is closely associated with the microbial dybiosis between acidogenic/aciduric pathogens and alkali-generating commensal bacteria colonized in the oral cavity. Our recent studies have shown that arginine may represent a promising anti-caries agent by modulating microbial composition in an in vitro consortium. However, the effect of arginine on the oral microbiota has yet to be comprehensively delineated in either clinical cohort or in vitro biofilm models that better represent the microbial diversity of oral cavity. Here, by employing a clinical cohort and a saliva-derived biofilm model, we demonstrated that arginine treatment could favorably modulate the oral microbiota of caries-active individuals. Specifically, treatment with arginine-containing dentifrice normalized the oral microbiota of caries-active individuals similar to that of caries-free controls in terms of microbial structure, abundance of typical species, enzymatic activities of glycolysis and alkali-generation related enzymes and their corresponding transcripts. Moreover, we found that combinatory use of arginine with fluoride could better enrich alkali-generating Streptococcus sanguinis and suppress acidogenic/aciduric Streptococcus mutans, and thus significantly retard the demineralizing capability of saliva-derived oral biofilm. Hence, we propose that fluoride and arginine have a potential synergistic effect in maintaining an eco-friendly oral microbial equilibrium in favor of better caries management.
Niche-specific gene expression in a parasitic nematode; increased expression of immunomodulators in Teladorsagia circumcincta larvae derived from host mucosa
Authors: McNeilly Tom N. , Frew David , Burgess Stewart T. G. , Wright Harry , Bartley David J. , Bartley Yvonne , Nisbet Alasdair J.
Published: July 2017

Metazoan parasites have to survive in many different niches in order to complete their life-cycles. In the absence of reliable methods to manipulate parasite genomes and/or proteomes, identification of the molecules critical for parasite survival within these niches has largely depended on comparative transcriptomic and proteomic analyses of different developmental stages of the parasite; however, changes may reflect differences associated with transition between developmental stages rather than specific adaptations to a particular niche. In this study, we compared the transcriptome of two fourth-stage larval populations of the nematode parasite,Teladorsagia circumcincta, which were of the same developmental stage but differed in their location within the abomasum, being either mucosal-dwelling (MD) or lumen-dwelling (LD). Using RNAseq, we identified 57 transcripts which were significantly differentially expressed between MD and LD larvae. Of these transcripts, the majority (54/57) were up-regulated in MD larvae, one of which encoded for an ShKT-domain containing protein, Tck6, capable of modulating ovine T cell cytokine responses. Other differentially expressed transcripts included homologues of ASP-like proteins, proteases, or excretory-secretory proteins of unknown function. Our study demonstrates the utility of niche- rather than stage-specific analysis of parasite transcriptomes to identify parasite molecules of potential importance for survival within the host.
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins
Authors: Halakou Farideh , Kilic Emel Sen , Cukuroglu Engin , Keskin Ozlem , Gursoy Attila
Published: July 2017

Traditional Protein-Protein Interaction (PPI) networks, which use a node and edge representation, lack some valuable information about the mechanistic details of biological processes. Mapping protein structures to these PPI networks not only provides structural details of each interaction but also helps us to find the mutual exclusive interactions. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different interactions, functions, and downstream signalling. In this study, we proposed a new representation for structural PPI networks inspecting the alternative conformations of proteins. We performed a large-scale study by creating breast cancer metastasis network and equipped it with different conformers of proteins. Our results showed that although 88% of proteins in our network has at least two structures in Protein Data Bank (PDB), only 22% of them have alternative conformations and the remaining proteins have different regions saved in PDB. However, using even this small set of alternative conformations we observed a considerable increase in our protein docking predictions. Our protein-protein interaction predictions increased from 54% to 76% using the alternative conformations. We also showed the benefits of investigating structural data and alternative conformations of proteins through three case studies.
Reaction dynamics of the chimeric channelrhodopsin C1C2
Authors: Hontani Yusaku , Marazzi Marco , Stehfest Katja , Mathes Tilo , van Stokkum Ivo H. M. , Elstner Marcus , Hegemann Peter , Kennis John T. M.
Published: July 2017

Channelrhodopsin (ChR) is a key protein of the optogenetic toolkit. C1C2, a functional chimeric protein of Chlamydomonas reinhardtii ChR1 and ChR2, is the only ChR whose crystal structure has been solved, and thus uniquely suitable for structure-based analysis. We report C1C2 photoreaction dynamics with ultrafast transient absorption and multi-pulse spectroscopy combined with target analysis and structure-based hybrid quantum mechanics/molecular mechanics calculations. Two relaxation pathways exist on the excited (S1) state through two conical intersections CI1 and CI2, that are reached via clockwise and counter-clockwise rotations: (i) the C13=C14 isomerization path with 450 fs via CI1 and (ii) a relaxation path to the initial ground state with 2.0 ps and 11 ps via CI2, depending on the hydrogen-bonding network, hence indicating active-site structural heterogeneity. The presence of the additional conical intersection CI2 rationalizes the relatively low quantum yield of photoisomerization (30 ± 3%), reported here. Furthermore, we show the photoreaction dynamics from picoseconds to seconds, characterizing the complete photocycle of C1C2.
Scalable and Transfer-Free Fabrication of MoS2/SiO2 Hybrid Nanophotonic Cavity Arrays with Quality Factors Exceeding 4000
Authors: Hammer Sebastian , Mangold H. Moritz , Nguyen Ariana E. , Martinez-Ta Dominic , Naghibi Alvillar Sahar , Bartels Ludwig , Krenner Hubert J.
Published: July 2017

We report the fully-scalable fabrication of a large array of hybrid molybdenum disulfide (MoS2) - silicon dioxide (SiO2) one-dimensional, free-standing photonic-crystal cavities capable of enhancement of the MoS2 photoluminescence at the narrow cavity resonance. We demonstrate continuous tunability of the cavity resonance wavelength across the entire emission band of MoS2 simply by variation of the photonic crystal periodicity. Device fabrication started by substrate-scale growth of MoS2 using chemical vapor deposition (CVD) on non-birefringent thermal oxide on a silicon wafer; it was followed by lithographic fabrication of a photonic crystal nanocavity array on the same substrate at more than 50% yield of functional devices. Our cavities exhibit three dominant modes with measured linewidths less than 0.2 nm, corresponding to quality factors exceeding 4000. All experimental findings are found to be in excellent agreement with finite difference time domain (FDTD) simulations. CVD MoS2 provides scalable access to a direct band gap, inorganic, stable and efficient emitter material for on-chip photonics without the need for epitaxy and is at CMOS compatible processing parameters even for back-end-of-line integration; our findings suggest feasibility of cavity based line-narrowing in MoS2-based on-chip devices as it is required for instance for frequency-multiplexed operation in on-chip optical communication and sensing.
High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales
Authors: Erwin Patrick M. , Rhodes Ryan G. , Kiser Kevin B. , Keenan-Bateman Tiffany F. , McLellan William A. , Pabst D. Ann
Published: July 2017

Mammals host diverse bacterial and archaeal symbiont communities (i.e. microbiomes) that play important roles in digestive and immune system functioning, yet cetacean microbiomes remain largely unexplored, in part due to sample collection difficulties. Here, fecal samples from stranded pygmy (Kogia breviceps) and dwarf (K.sima) sperm whales were used to characterize the gut microbiomes of two closely-related species with similar diets. 16S rRNA gene sequencing revealed diverse microbial communities in kogiid whales dominated by Firmicutes and Bacteroidetes. Core symbiont taxa were affiliated with phylogenetic lineages capable of fermentative metabolism and sulfate respiration, indicating potential symbiont contributions to energy acquisition during prey digestion. The diversity and phylum-level composition of kogiid microbiomes differed from those previously reported in toothed whales, which exhibited low diversity communities dominated by Proteobacteria and Actinobacteria. Community structure analyses revealed distinct gut microbiomes inK.brevicepsandK.sima, driven by differential relative abundances of shared taxa, and unique microbiomes in kogiid hosts compared to other toothed and baleen whales, driven by differences in symbiont membership. These results provide insight into the diversity, composition and structure of kogiid gut microbiomes and indicate that host identity plays an important role in structuring cetacean microbiomes, even at fine-scale taxonomic levels.
TIA1 is a gender-specific disease modifier of a mild mouse model of spinal muscular atrophy
Authors: Howell Matthew D. , Ottesen Eric W. , Singh Natalia N. , Anderson Rachel L. , Seo Joonbae , Sivanesan Senthilkumar , Whitley Elizabeth M. , Singh Ravindra N.
Published: July 2017

Spinal muscular atrophy (SMA) is caused by deletions or mutations of Survival Motor Neuron 1 (SMN1) gene. The nearly identical SMN2 cannot compensate for SMN1 loss due to exon 7 skipping. The allele C (C+/+) mouse recapitulates a mild SMA-like phenotype and offers an ideal system to monitor the role of disease-modifying factors over a long time. T-cell-restricted intracellular antigen 1 (TIA1) regulates SMN exon 7 splicing. TIA1 is reported to be downregulated in obese patients, although it is not known if the effect is gender-specific. We show that female Tia1-knockout (Tia1−/−) mice gain significant body weight (BW) during early postnatal development. We next examined the effect of Tia1 deletion in novel C+/+/Tia1−/− mice. Underscoring the opposing effects of Tia1 deletion and low SMN level on BW gain, both C+/+ and C+/+/Tia1−/− females showed similar BW gain trajectory at all time points during our study. We observed early tail necrosis in C+/+/Tia1−/− females but not in males. We show enhanced impairment of male reproductive organ development and exacerbation of the C+/+/Tia1−/− testis transcriptome. Our findings implicate a protein factor as a gender-specific modifier of a mild mouse model of SMA.