bluuebunny/crossref_metadata_2025 huggingface dataset:
On the interaction of Taylor length scale size droplets and isotropic turbulence
Authors: Dodd Michael S. , Ferrante Antonino
Published: September 2016

Droplets in turbulent flows behave differently from solid particles, e.g. droplets deform, break up, coalesce and have internal fluid circulation. Our objective is to gain a fundamental understanding of the physical mechanisms of droplet–turbulence interaction. We performed direct numerical simulations (DNS) of 3130 finite-size, non-evaporating droplets of diameter approximately equal to the Taylor length scale and with 5 % droplet volume fraction in decaying isotropic turbulence at initial Taylor-scale Reynolds number $\mathit{Re}_{\unicode[STIX]{x1D706}}=83$. In the droplet-laden cases, we varied one of the following three parameters: the droplet Weber number based on the r.m.s. velocity of turbulence ($0.1\leqslant \mathit{We}_{rms}\leqslant 5$), the droplet- to carrier-fluid density ratio ($1\leqslant \unicode[STIX]{x1D70C}_{d}/\unicode[STIX]{x1D70C}_{c}\leqslant 100$) or the droplet- to carrier-fluid viscosity ratio ($1\leqslant \unicode[STIX]{x1D707}_{d}/\unicode[STIX]{x1D707}_{c}\leqslant 100$). In this work, we derive the turbulence kinetic energy (TKE) equations for the two-fluid, carrier-fluid and droplet-fluid flow. These equations allow us to explain the pathways for TKE exchange between the carrier turbulent flow and the flow inside the droplet. We also explain the role of the interfacial surface energy in the two-fluid TKE equation through the power of the surface tension. Furthermore, we derive the relationship between the power of surface tension and the rate of change of total droplet surface area. This link allows us to explain how droplet deformation, breakup and coalescence play roles in the temporal evolution of TKE. Our DNS results show that increasing $\mathit{We}_{rms}$, $\unicode[STIX]{x1D70C}_{d}/\unicode[STIX]{x1D70C}_{c}$ and $\unicode[STIX]{x1D707}_{d}/\unicode[STIX]{x1D707}_{c}$ increases the decay rate of the two-fluid TKE. The droplets enhance the dissipation rate of TKE by enhancing the local velocity gradients near the droplet interface. The power of the surface tension is a source or sink of the two-fluid TKE depending on the sign of the rate of change of the total droplet surface area. Thus, we show that, through the power of the surface tension, droplet coalescence is a source of TKE and breakup is a sink of TKE. For short times, the power of the surface tension is less than $\pm 5\,\%$ of the dissipation rate. For later times, the power of the surface tension is always a source of TKE, and its magnitude can be up to 50 % of the dissipation rate.
DESAlert: Enabling Real-Time Transient Follow-Up with Dark Energy Survey Data
Authors: Poci A. , Kuehn K. , Abbott T. , Abdalla F. B. , Allam S. , Bauer A.H. , Benoit-Lévy A. , Bertin E. , Brooks D. , Brown P. J. , Buckley-Geer E. , Burke D. L. , Rosell A. Carnero , Kind M. Carrasco , Covarrubias R. , da Costa L. N. , D’Andrea C. B. , DePoy D. L. , Desai S. , Dietrich J. P. , Cunha C. E , Eifler T. F. , Estrada J. , Evrard A. E. , Neto A. Fausti , Finley D. A. , Flaugher B. , Fosalba P. , Frieman J. , Gerdes D. , Gruen D. , Gruendl R. A. , Honscheid K. , James D. , Kuropatkin N. , Lahav O. , Li T. S. , March M. , Marshall J. , Merritt K. W. , Miller C.J. , Nichol R. C. , Nord B. , Ogando R. , Plazas A. A. , Romer A. K. , Roodman A. , Rykoff E. S. , Sako M. , Sanchez E. , Scarpine V. , Schubnell M. , Sevilla I. , Smith C. , Soares-Santos M. , Sobreira F. , Suchyta E. , Swanson M. E. C. , Tarle G. , Thaler J. , Thomas R. C. , Tucker D. , Walker A. R. , Wester W. ,   (The DES Collaboration)
Published: September 2016

The Dark Energy Survey is undertaking an observational programme imaging 1/4 of the southern hemisphere sky with unprecedented photometric accuracy. In the process of observing millions of faint stars and galaxies to constrain the parameters of the dark energy equation of state, the Dark Energy Survey will obtain pre-discovery images of the regions surrounding an estimated 100 gamma-ray bursts over 5 yr. Once gamma-ray bursts are detected by, e.g., the Swift satellite, the DES data will be extremely useful for follow-up observations by the transient astronomy community. We describe a recently-commissioned suite of software that listens continuously for automated notices of gamma-ray burst activity, collates information from archival DES data, and disseminates relevant data products back to the community in near-real-time. Of particular importance are the opportunities that non-public DES data provide for relative photometry of the optical counterparts of gamma-ray bursts, as well as for identifying key characteristics (e.g., photometric redshifts) of potential gamma-ray burst host galaxies. We provide the functional details of the DESAlert software, and its data products, and we show sample results from the application of DESAlert to numerous previously detected gamma-ray bursts, including the possible identification of several heretofore unknown gamma-ray burst hosts.
Early life adversity alters normal sex-dependent developmental dynamics of DNA methylation
Authors: Massart Renaud , Nemoda Zsofia , Suderman Matthew J. , Sutti Sheila , Ruggiero Angela M. , Dettmer Amanda M. , Suomi Stephen J. , Szyf Moshe
Published: September 2016

Studies in rodents, nonhuman primates, and humans suggest that epigenetic processes mediate between early life experiences and adult phenotype. However, the normal evolution of epigenetic programs during child development, the effect of sex, and the impact of early life adversity on these trajectories are not well understood. This study mapped the genome-wide DNA methylation changes in CD3+ T lymphocytes from rhesus monkeys from postnatal day 14 through 2 years of age in both males and females and determined the impact of maternal deprivation on the DNA methylation profile. We show here that DNA methylation profiles evolve from birth to adolescence and are sex dependent. DNA methylation changes accompany imposed weaning, attenuating the difference between males and females. Maternal separation at birth alters the normal evolution of DNA methylation profiles and targets genes that are also affected by a later stage maternal separation, that is, weaning. Our results suggest that early life events dynamically interfere with the normal developmental evolution of the DNA methylation profile and that these changes are highly effected by sex.
Contextual adversity, telomere erosion, pubertal development, and health: Two models of accelerated aging, or one?
Authors: Belsky Jay , Shalev Idan
Published: September 2016

Two independent lines of inquiry suggest that growing up under conditions of contextual adversity (e.g., poverty and household chaos) accelerates aging and undermines long-term health. Whereas work addressing the developmental origins of health and disease highlights accelerated-aging effects of contextual adversity on telomere erosion, that informed by an evolutionary analysis of reproductive strategies highlights such effects with regard to pubertal development (in females). That both shorter telomeres early in life and earlier age of menarche are associated with poor health later in life raises the prospect, consistent with evolutionary life-history theory, that these two bodies of theory and research are tapping into the same evolutionary–developmental process whereby longer term health costs are traded off for increased probability of reproducing before dying via a process of accelerated aging. Here we make the case for such a claim, while highlighting biological processes responsible for these effects, as well as unknowns in the epigenetic equation that might instantiate these contextually regulated developmental processes.
Parkinson’s disease psychosis as a serotonin-dopamine imbalance syndrome
Authors: Stahl Stephen M.
Published: September 2016

Parkinson’s disease psychosis (PDP) is theoretically a serotonin-dopamine imbalance syndrome due to disruption of the normal balance between the serotonergic and dopaminergic neurotransmitter systems in key brain circuits.
POLITICAL DELIBERATION UNDER CONDITIONS OF DECEPTION: THE CASE OF BREXIT
Authors: Chappell Sophie Grace
Published: September 2016

Individual deliberations under conditions of serious deception are generally agreed to be invalidated by that deception. So political deliberations under conditions of serious deception should also be agreed to be invalidated. The UK’s referendum on membership of the EU was a flawed process of public deliberation precisely for this reason – that the public debate about the referendum involved serious deception. I raise the question what should be done about such public deceptions, and suggest a restrained form of legal remedy.
A review of fundamental principles for animal models of DOHaD research: an Australian perspective
Authors: Dickinson H. , Moss T. J. , Gatford K. L. , Moritz K. M. , Akison L. , Fullston T. , Hryciw D. H. , Maloney C. A. , Morris M. J. , Wooldridge A. L. , Schjenken J. E. , Robertson S. A. , Waddell B. J. , Mark P. J. , Wyrwoll C. S. , Ellery S. J. , Thornburg K. L. , Muhlhausler B. S. , Morrison J. L.
Published: September 2016

Epidemiology formed the basis of ‘the Barker hypothesis’, the concept of ‘developmental programming’ and today’s discipline of the Developmental Origins of Health and Disease (DOHaD). Animal experimentation provided proof of the underlying concepts, and continues to generate knowledge of underlying mechanisms. Interventions in humans, based on DOHaD principles, will be informed by experiments in animals. As knowledge in this discipline has accumulated, from studies of humans and other animals, the complexity of interactions between genome, environment and epigenetics, has been revealed. The vast nature of programming stimuli and breadth of effects is becoming known. As a result of our accumulating knowledge we now appreciate the impact of many variables that contribute to programmed outcomes. To guide further animal research in this field, the Australia and New Zealand DOHaD society (ANZ DOHaD) Animals Models of DOHaD Research Working Group convened at the 2nd Annual ANZ DOHaD Congress in Melbourne, Australia in April 2015. This review summarizes the contributions of animal research to the understanding of DOHaD, and makes recommendations for the design and conduct of animal experiments to maximize relevance, reproducibility and translation of knowledge into improving health and well-being.
Workplace Ostracism and Its Negative Outcomes
Authors: Zheng Xiaoming , Yang Jun , Ngo Hang-Yue , Liu Xiao-Yu , Jiao Wengjuan
Published: September 2016

Abstract. Workplace ostracism, conceived as to being ignored or excluded by others, has attracted the attention of researchers in recent years. One essential topic in this area is how to reduce or even eliminate the negative consequences of workplace ostracism. Based on conservation of resources (COR) theory, the current study assesses the relationship between workplace ostracism and its negative outcomes, as well as the moderating role played by psychological capital, using data collected from 256 employees in three companies in the northern part of China. The study yields two important findings: (1) workplace ostracism is positively related to intention to leave and (2) psychological capital moderates the effect of workplace ostracism on affective commitment and intention to leave. This paper concludes by discussing the implications of these findings for organizations and employees, along with recommendations for future research.
Deficiency of Parkinson’s disease-related gene Fbxo7 is associated with impaired mitochondrial metabolism by PARP activation
Authors: Delgado-Camprubi Marta , Esteras Noemi , Soutar Marc PM , Plun-Favreau Helene , Abramov Andrey Y
Published: September 2016

The Parkinson’s disease (PD)-related protein F-box only protein 7 (Fbxo7) is the substrate-recognition component of the Skp1-Cullin-F-box protein E3 ubiquitin ligase complex. We have recently shown that PD-associated mutations in Fbxo7 disrupt mitochondrial autophagy (mitophagy), suggesting a role for Fbxo7 in modulating mitochondrial homeostasis. Here we report that Fbxo7 deficiency is associated with reduced cellular NAD+ levels, which results in increased mitochondrial NADH redox index and impaired activity of complex I in the electron transport chain. Under these conditions of compromised respiration, mitochondrial membrane potential and ATP contents are reduced, and cytosolic reactive oxygen species (ROS) production is increased. ROS activates poly (ADP-ribose) polymerase (PARP) activity in Fbxo7-deficient cells. PARP inhibitor restores cellular NAD+ content and redox index and ATP pool, suggesting that PARP overactivation is cause of decreased complex I-driven respiration. These findings bring new insight into the mechanism of Fbxo7 deficiency, emphasising the importance of mitochondrial dysfunction in PD.
Dichotomy of cellular inhibition by small-molecule inhibitors revealed by single-cell analysis
Authors: Vogel Robert M. , Erez Amir , Altan-Bonnet Grégoire
Published: September 2016

Despite progress in drug development, a quantitative and physiological understanding of how small-molecule inhibitors act on cells is lacking. Here, we measure the signalling and proliferative response of individual primary T-lymphocytes to a combination of antigen, cytokine and drug. We uncover two distinct modes of signalling inhibition: digital inhibition (the activated fraction of cells diminishes upon drug treatment, but active cells appear unperturbed), versus analogue inhibition (the activated fraction is unperturbed whereas activation response is diminished). We introduce a computational model of the signalling cascade that accounts for such inhibition dichotomy, and test the model predictions for the phenotypic variability of cellular responses. Finally, we demonstrate that the digital/analogue dichotomy of cellular response as revealed on short (signal transduction) timescales, translates into similar dichotomy on longer (proliferation) timescales. Our single-cell analysis of drug action illustrates the strength of quantitative approaches to translate in vitro pharmacology into functionally relevant cellular settings.
CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion
Authors: Jones Shawn W. , Fast Alan G. , Carlson Ellinor D. , Wiedel Carrissa A. , Au Jennifer , Antoniewicz Maciek R. , Papoutsakis Eleftherios T. , Tracy Bryan P.
Published: September 2016

Maximizing the conversion of biogenic carbon feedstocks into chemicals and fuels is essential for fermentation processes as feedstock costs and processing is commonly the greatest operating expense. Unfortunately, for most fermentations, over one-third of sugar carbon is lost to CO2 due to the decarboxylation of pyruvate to acetyl-CoA and limitations in the reducing power of the bio-feedstock. Here we show that anaerobic, non-photosynthetic mixotrophy, defined as the concurrent utilization of organic (for example, sugars) and inorganic (for example, CO2) substrates in a single organism, can overcome these constraints to increase product yields and reduce overall CO2 emissions. As a proof-of-concept, Clostridium ljungdahlii was engineered to produce acetone and achieved a mass yield 138% of the previous theoretical maximum using a high cell density continuous fermentation process. In addition, when enough reductant (that is, H2) is provided, the fermentation emits no CO2. Finally, we show that mixotrophy is a general trait among acetogens.
Giant superconducting fluctuations in the compensated semimetal FeSe at the BCS–BEC crossover
Authors: Kasahara S. , Yamashita T. , Shi A. , Kobayashi R. , Shimoyama Y. , Watashige T. , Ishida K. , Terashima T. , Wolf T. , Hardy F. , Meingast C. , Löhneysen H. v. , Levchenko A. , Shibauchi T. , Matsuda Y.
Published: September 2016

The physics of the crossover between weak-coupling Bardeen–Cooper–Schrieffer (BCS) and strong-coupling Bose–Einstein condensate (BEC) limits gives a unified framework of quantum-bound (superfluid) states of interacting fermions. This crossover has been studied in the ultracold atomic systems, but is extremely difficult to be realized for electrons in solids. Recently, the superconducting semimetal FeSe with a transition temperature Tc=8.5 K has been found to be deep inside the BCS–BEC crossover regime. Here we report experimental signatures of preformed Cooper pairing in FeSe, whose energy scale is comparable to the Fermi energies. In stark contrast to usual superconductors, large non-linear diamagnetism by far exceeding the standard Gaussian superconducting fluctuations is observed below T*∼20 K, providing thermodynamic evidence for prevailing phase fluctuations of superconductivity. Nuclear magnetic resonance and transport data give evidence of pseudogap formation at ∼T*. The multiband superconductivity along with electron–hole compensation in FeSe may highlight a novel aspect of the BCS–BEC crossover physics.
Dynamic actin cycling through mitochondrial subpopulations locally regulates the fission–fusion balance within mitochondrial networks
Authors: Moore Andrew S. , Wong Yvette C. , Simpson Cory L. , Holzbaur Erika L. F.
Published: September 2016

Mitochondria form interconnected networks that dynamically remodel in response to cellular needs. Using live-cell imaging, we investigate the role of the actin cytoskeleton in regulating mitochondrial fission and fusion. We identify cycling of actin filaments onto and off of subsets of cellular mitochondria. The association of actin filaments with mitochondrial subpopulations is transient; actin quickly disassembles, then reassembles around a distinct subpopulation, efficiently cycling through all cellular mitochondria within 14 min. The focal assembly of actin induces local, Drp1-dependent fragmentation of the mitochondrial network. On actin disassembly, fragmented mitochondria undergo rapid fusion, leading to regional recovery of the tubular mitochondrial network. Cycling requires dynamic actin polymerization and is blocked by inhibitors of both Arp2/3 and formins. We propose that cyclic assembly of actin onto mitochondria modulates the fission/fusion balance, promotes network remodelling and content mixing, and thus may serve as an essential mechanism regulating mitochondrial network homeostasis.
Stille coupling via C–N bond cleavage
Authors: Wang Dong-Yu , Kawahata Masatoshi , Yang Ze-Kun , Miyamoto Kazunori , Komagawa Shinsuke , Yamaguchi Kentaro , Wang Chao , Uchiyama Masanobu
Published: September 2016

Cross-coupling is a fundamental reaction in the synthesis of functional molecules, and has been widely applied, for example, to phenols, anilines, alcohols, amines and their derivatives. Here we report the Ni-catalysed Stille cross-coupling reaction of quaternary ammonium salts via C–N bond cleavage. Aryl/alkyl-trimethylammonium salts [Ar/R–NMe3]+react smoothly with arylstannanes in 1:1 molar ratio in the presence of a catalytic amount of commercially available Ni(cod)2and imidazole ligand together with 3.0 equivalents of CsF, affording the corresponding biaryl with broad functional group compatibility. The reaction pathway, including C–N bond cleavage step, is proposed based on the experimental and computational findings, as well as isolation and single-crystal X-ray diffraction analysis of Ni-containing intermediates. This reaction should be widely applicable for transformation of amines/quaternary ammonium salts into multi-aromatics.
Wideband dynamic microwave frequency identification system using a low-power ultracompact silicon photonic chip
Authors: Burla Maurizio , Wang Xu , Li Ming , Chrostowski Lukas , Azaña José
Published: September 2016

Photonic-based instantaneous frequency measurement (IFM) of unknown microwave signals offers improved flexibility and frequency range as compared with electronic solutions. However, no photonic platform has ever demonstrated the key capability to perform dynamic IFM, as required in real-world applications. In addition, all demonstrations to date employ bulky components or need high optical power for operation. Here we demonstrate an integrated photonic IFM system that can identify frequency-varying signals in a dynamic manner, without any need for fast measurement instrumentation. The system is based on a fully linear, ultracompact system based on a waveguide Bragg grating on silicon, only 65-μm long and operating up to ∼30 GHz with carrier power below 10 mW, significantly outperforming present technologies. These results open a solid path towards identification of dynamically changing signals over tens of GHz bandwidths using a practical, low-cost on-chip implementation for applications from broadband communications to biomedical, astronomy and more.
Treatment with Piribedil and Memantine Reduces Noise-Induced Loss of Inner Hair Cell Synaptic Ribbons
Authors: Altschuler Richard A. , Wys Noel , Prieskorn Diane , Martin Cathy , DeRemer Susan , Bledsoe Sanford , Miller Josef M.
Published: September 2016

Noise overstimulation can induce loss of synaptic ribbons associated with loss of Inner Hair Cell – Auditory Nerve synaptic connections. This study examined if systemic administration of Piribedil, a dopamine agonist that reduces the sound evoked auditory nerve compound action potential and/or Memantine, an NMDA receptor open channel blocker, would reduce noise-induced loss of Inner Hair Cell ribbons. Rats received systemic Memantine and/or Piribedil for 3 days before and 3 days after a 3 hour 4 kHz octave band noise at 117 dB (SPL). At 21 days following the noise there was a 26% and 38% loss of synaptic ribbons in regions 5.5 and 6.5 mm from apex, respectively, elevations in 4-, 8- and 20 kHz tonal ABR thresholds and reduced dynamic output at higher intensities of stimulation. Combined treatment with Piribedil and Memantine produced a significant reduction in the noise-induced loss of ribbons in both regions and changes in ABR sensitivity and dynamic responsiveness. Piribedil alone gave significant reduction in only the 5.5 mm region and Memantine alone did not reach significance in either region. Results identify treatments that could prevent the hearing loss and hearing disorders that result from noise-induced loss of Inner Hair Cell – Auditory Nerve synaptic connections.
Extraintestinal pathogenic Escherichia coli are associated with intestinal inflammation in patients with ulcerative colitis
Authors: Mirsepasi-Lauridsen Hengameh C. , Halkjaer Sofie Ingdam , Mortensen Esben Munk , Lydolph Magnus C. , Nordgaard-Lassen Inge , Krogfelt Karen Angeliki , Petersen Andreas Munk
Published: September 2016

E. coli of the phylogenetic group B2 harbouring Extra intestinal Pathogenic Escherichia coli (ExPEC) genes are frequently seen as colonizers of the intestine in patients with active ulcerative colitis (UC). In this study, we describe the influence of E. coli Nissle (EcN) B2 as add-on treatment to conventional therapies in patients with active UC. For this study one hundred active UC patients were randomized to ciprofloxacin or placebo for 1 week followed by EcN or placebo for 7 weeks. Stool samples were collected at weeks 0, 1, 8, 12, where E. coli were characterized and fecal calprotectin was measured. We showed that in the active UC patient group receiving Placebo/EcN, fewer patients reached remission, in comparison to the patient group receiving Placebo/placebo (p < 0.05). Active UC patients initially colonized with E. coli B2 had increased fecal calprotectin values and Colitis Activity Index scores in comparison to patients colonized with E. coli A and D (p < 0.05*). In conclusion, treatment of UC patients with E. coli Nissle (B2) does not promote clinical remission and active UC patients colonized with E. coli B2 have an increased intestinal inflammation.
PLGA nanoparticle encapsulation reduces toxicity while retaining the therapeutic efficacy of EtNBS-PDT in vitro
Authors: Hung Hsin-I , Klein Oliver J. , Peterson Sam W. , Rokosh Sarah R. , Osseiran Sam , Nowell Nicholas H. , Evans Conor L.
Published: September 2016

Photodynamic therapy regimens, which use light-activated molecules known as photosensitizers, are highly selective against many malignancies and can bypass certain challenging therapeutic resistance mechanisms. Photosensitizers such as the small cationic molecule EtNBS (5-ethylamino-9-diethyl-aminobenzo[a]phenothiazinium chloride) have proven potent against cancer cells that reside within acidic and hypoxic tumour microenvironments. At higher doses, however, these photosensitizers induce “dark toxicity” through light-independent mechanisms. In this study, we evaluated the use of nanoparticle encapsulation to overcome this limitation. Interestingly, encapsulation of the compound within poly(lactic-co-glycolic acid) (PLGA) nanoparticles (PLGA-EtNBS) was found to significantly reduce EtNBS dark toxicity while completely retaining the molecule’s cytotoxicity in both normoxic and hypoxic conditions. This dual effect can be attributed to the mechanism of release: EtNBS remains encapsulated until external light irradiation, which stimulates an oxygen-independent, radical-mediated process that degrades the PLGA nanoparticles and releases the molecule. As these PLGA-encapsulated EtNBS nanoparticles are capable of penetrating deeply into the hypoxic and acidic cores of 3D spheroid cultures, they may enable the safe and efficacious treatment of otherwise unresponsive tumour regions.
In low protein diets, microRNA-19b regulates urea synthesis by targeting SIRT5
Authors: Sun Rui-Ping , Xi Qian-Yun , Sun Jia-Jie , Cheng Xiao , Zhu Yan-Ling , Ye Ding-Ze , Chen Ting , Wei Li-Min , Ye Rui-Song , Jiang Qing-Yan , Zhang Yong-Liang
Published: September 2016

Ammonia detoxification, which takes place via the hepatic urea cycle, is essential for nitrogen homeostasis and physiological well-being. It has been reported that a reduction in dietary protein reduces urea nitrogen. MicroRNAs (miRNAs) are major regulatory non-coding RNAs that have significant effects on several metabolic pathways; however, little is known on whether miRNAs regulate hepatic urea synthesis. The objective of this study was to assess the miRNA expression profile in a low protein diet and identify miRNAs involved in the regulation of the hepatic urea cycle using a porcine model. Weaned 28-days old piglets were fed a corn-soybean normal protein diet (NP) or a corn-soybean low protein diet (LP) for 30 d. Hepatic and blood samples were collected, and the miRNA expression profile was assessed by sequencing and qRT-PCR. Furthermore, we evaluated the possible role of miR-19b in urea synthesis regulation. There were 25 differentially expressed miRNAs between the NP and LP groups. Six of these miRNAs were predicted to be involved in urea cycle metabolism. MiR-19b negatively regulated urea synthesis by targeting SIRT5, which is a positive regulator of CPS1, the rate limiting enzyme in the urea cycle. Our study presented a novel explanation of ureagenesis regulation by miRNAs.
Correction: Corrigendum: Autophagy-associated alpha-arrestin signaling is required for conidiogenous cell development in Magnaporthe oryzae
Authors: Dong Bo , Xu Xiaojin , Chen Guoqing , Zhang Dandan , Tang Mingzhi , Xu Fei , Liu Xiaohong , Wang Hua , Zhou Bo
Published: September 2016

Scientific Reports 6: Article number: 30963; published online: 08 August 2016; updated: 30 September 2016 This Article contains a typographical error in the Acknowledgements section. “We would also like to thank Li Xe and Xijiao Song (Zhejiang Academy of Agricultural Sciences, Hangzhou, China) for technical assistance on the confocal microscopic analysis”.
Plastic microfibre ingestion by deep-sea organisms
Authors: Taylor M. L. , Gwinnett C. , Robinson L. F. , Woodall L. C.
Published: September 2016

Plastic waste is a distinctive indicator of the world-wide impact of anthropogenic activities. Both macro- and micro-plastics are found in the ocean, but as yet little is known about their ultimate fate and their impact on marine ecosystems. In this study we present the first evidence that microplastics are already becoming integrated into deep-water organisms. By examining organisms that live on the deep-sea floor we show that plastic microfibres are ingested and internalised by members of at least three major phyla with different feeding mechanisms. These results demonstrate that, despite its remote location, the deep sea and its fragile habitats are already being exposed to human waste to the extent that diverse organisms are ingesting microplastics.
The domesticated brain: genetics of brain mass and brain structure in an avian species
Authors: Henriksen R. , Johnsson M. , Andersson L. , Jensen P. , Wright D.
Published: September 2016

As brain size usually increases with body size it has been assumed that the two are tightly constrained and evolutionary studies have therefore often been based on relative brain size (i.e. brain size proportional to body size) rather than absolute brain size. The process of domestication offers an excellent opportunity to disentangle the linkage between body and brain mass due to the extreme selection for increased body mass that has occurred. By breeding an intercross between domestic chicken and their wild progenitor, we address this relationship by simultaneously mapping the genes that control inter-population variation in brain mass and body mass. Loci controlling variation in brain mass and body mass have separate genetic architectures and are therefore not directly constrained. Genetic mapping of brain regions indicates that domestication has led to a larger body mass and to a lesser extent a larger absolute brain mass in chickens, mainly due to enlargement of the cerebellum. Domestication has traditionally been linked to brain mass regression, based on measurements of relative brain mass, which confounds the large body mass augmentation due to domestication. Our results refute this concept in the chicken.
Proton Conducting Graphene Oxide/Chitosan Composite Electrolytes as Gate Dielectrics for New-Concept Devices
Authors: Feng Ping , Du Peifu , Wan Changjin , Shi Yi , Wan Qing
Published: September 2016

New-concept devices featuring the characteristics of ultralow operation voltages and low fabrication cost have received increasing attention recently because they can supplement traditional Si-based electronics. Also, organic/inorganic composite systems can offer an attractive strategy to combine the merits of organic and inorganic materials into promising electronic devices. In this report, solution-processed graphene oxide/chitosan composite film was found to be an excellent proton conducting electrolyte with a high specific capacitance of ~3.2 μF/cm2 at 1.0 Hz and it was used to fabricate multi-gate electric double layer transistors. Dual-gate AND logic operation and two-terminal diode operation were realized in a single device. A two-terminal synaptic device was proposed and some important synaptic behaviors were emulated, which is interesting for neuromorphic systems.
Erratum: Shear-mediated contributions to the effective properties of soft acoustic metamaterials including negative index
Authors: Forrester Derek Michael , Pinfield Valerie J.
Published: September 2016

Scientific Reports 5: Article number: 18562; published online: 21 December 2015; updated: 30 September 2016 In this Article, the values of two inequalities have been omitted in the Results section during typesetting. ‘‘For silica particles in water, we examine the long wavelength condition both inside and outside the particles | k C a | ≪ 1, | k′ C a | ≪ but consider the region in which shear effects are known to be significant, | k S a | ≈ 1.
High-mechanical-frequency characteristics of optomechanical crystal cavity with coupling waveguide
Authors: Huang Zhilei , Cui Kaiyu , Bai Guoren , Feng Xue , Liu Fang , Zhang Wei , Huang Yidong
Published: September 2016

Optomechanical crystals have attracted great attention recently for their ability to realize strong photon-phonon interaction in cavity optomechanical systems. By far, the operation of cavity optomechanical systems with high mechanical frequency has to employ tapered fibres or one-sided waveguides with circulators to couple the light into and out of the cavities, which hinders their on-chip applications. Here, we demonstrate larger-centre-hole nanobeam structures with on-chip transmission-coupling waveguide. The measured mechanical frequency is up to 4.47 GHz, with a high mechanical Q-factor of 1.4 × 103 in the ambient environment. The corresponding optomechanical coupling rate is calculated and measured to be 836 kHz and 1.2 MHz, respectively, while the effective mass is estimated to be 136 fg. With the transmission waveguide coupled structure and a small footprint of 3.4 μm2, this simple cavity can be directly used as functional components or integrated with other on-chip devices in future practical applications.
Simultaneous Quantification of Serum Nonesterified and Esterified Fatty Acids as Potential Biomarkers to Differentiate Benign Lung Diseases from Lung Cancer
Authors: Ren Junling , Zhang Dan , Liu Yujie , Zhang Ruiqing , Fang Huiling , Guo Shuai , Zhou Dan , Zhang Mo , Xu Yupin , Qiu Ling , Li Zhili
Published: September 2016

In this study, we have employed graphene oxide as a matrix to simultaneously and directly quantify serum nonesterified and esterified fatty acids (FAs) using matrix-assisted laser/desorption ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR MS). Twelve serum nonesterified FAs combined with their individual esterified FAs (i.e., C16:0, C16:1, C18:0, C18:1, C18:2, C18:3, C20:2, C20:3, C20:4, C20:5, C22:5, and C22:6) were quantified based on their calibration curves with the correlation coefficients of >0.99, along with the analytical time of <1 min each sample. As a result, serum levels of twelve total FAs (TFAs) in 1440 serum samples from 487 healthy controls (HCs), 479 patients with benign lung diseases (BLDs) and 474 patients with lung cancer (LC) were determined. Statistical analysis indicated that significantly increased levels of C16:0, C16:1, C18:0, C18:1, C18:3, C20:3, and C22:6 and decreased levels of C20:5 were observed in LC patients compared with BLDs. Receiver operating characteristic (ROC) analysis revealed that panel a (C18:2, C20:3, C20:4, C20:5, C22:5, and C22:6), panel b (C18:0, C20:4, C20:5, and C22:6), and panel c (C16:1, C18:0, C18:1, C20:3, and C22:6) have exhibited good diagnostic ability to differentiate BLDs from LC relative to clinical uses of tumor markers (CEA and Cyfra 21-1).
Widespread DNA hypomethylation and differential gene expression in Turner syndrome
Authors: Trolle Christian , Nielsen Morten Muhlig , Skakkebæk Anne , Lamy Philippe , Vang Søren , Hedegaard Jakob , Nordentoft Iver , Ørntoft Torben Falck , Pedersen Jakob Skou , Gravholt Claus Højbjerg
Published: September 2016

Adults with 45,X monosomy (Turner syndrome) reflect a surviving minority since more than 99% of fetuses with 45,X monosomy die in utero. In adulthood 45,X monosomy is associated with increased morbidity and mortality, although strikingly heterogeneous with some individuals left untouched while others suffer from cardiovascular disease, autoimmune disease and infertility. The present study investigates the leukocyte DNAmethylation profile by using the 450K-Illumina Infinium assay and the leukocyte RNA-expression profile in 45,X monosomy compared with karyotypically normal female and male controls. We present results illustrating that genome wide X-chromosome RNA-expression profile, autosomal DNA-methylation profile and the X-chromosome methylation profile clearly distinguish Turner syndrome from controls. Our results reveal genome wide hypomethylation with most differentially methylated positions showing a medium level of methylation. Contrary to previous studies, applying a single loci specific analysis at well-defined DNA loci, our results indicate that the hypomethylation extend to repetitive elements. We describe novel candidate genes that could be involved in comorbidity in TS and explain congenital urinary malformations (PRKX), premature ovarian failure (KDM6A) and aortic aneurysm formation (ZFYVE9 and TIMP1).
Unique magnetostriction of Fe68.8Pd31.2 attributable to twinning
Authors: Steiner Jake , Lisfi Abdellah , Kakeshita Tomoyuki , Fukuda Takashi , Wuttig Manfred
Published: September 2016

Fe68.8Pd31.2 exhibits an anomalously large magnetostriction of ~400 ppm at room temperature as well as linear, isotropic and hysteresis free magnetization behavior. This near perfectly reversible magnetic response is attributable to the presence of a large number of premartensitic magnetoelastic twin clusters present in the system made possible through the elastic softening that occurs near a martensitic transformation temperature of 252 K. It is proposed that the twin clusters in the material reduce both internal elastic and magnetic energy, causing the elastic and magnetic behavior of the material to be intimately linked. In such a framework, the anisotropy energy becomes extremely low causing the material to bear no crystalline dependence on magnetization and application of a magnetic field causes simultaneous magnetic and twin domain movement which relaxes the system.
Nebivolol Ameliorates Cardiac NLRP3 Inflammasome Activation in a Juvenile-Adolescent Animal Model of Diet-Induced Obesity
Authors: Xie Qihai , Wei Tong , Huang Chenglin , Liu Penghao , Sun Mengwei , Shen Weili , Gao Pingjin
Published: September 2016

NLRP3 is involved in obesity-induced cardiac remodeling and dysfunction. In this study, we evaluated whether the cardiac protective effects of nebivolol relied on attenuating NLRP3 activation in a juvenile-adolescent animal model of diet-induced obesity. Weaning male Sprague-Dawley rats were fed with either a standard chow diet (ND) or a high-fat diet (HFD) for 8 weeks. The obese rats were subsequently subdivided into three groups: 1) HFD control group; 2) HFD with low-dose nebivolol (5 mg/kg/d); 3) HFD with high-dose nebivolol (10 mg/kg/d). Treatment with nebivolol prevented HFD-induced obesity associated excess cardiac lipid accumulation as well as myocardial mitochondrial dysfunction. Nebivolol attenuated pro-inflammatory cytokines secretion and NLRP3 inflammasome activation in myocardium of obese rats. In parallel, nebivolol treatment of obese animals increased cardiac β3-AR expression, reversing the reduction of endothelial nitric oxide synthase (eNOS). In vitro, nebivolol treatment of palmitate-incubated H9C2 cells suppressed autophagy, restored mitochondrial biogenesis, leading to decreased mitochondrial reactive oxygen species (mtROS) generation and suppressed NLRP3 inflammasome activation. Meanwhile the presence of shRNA against β3-AR or against eNOS deteriorated the protective effects of nebivolol. These data suggest the beneficial effect of nebivolol on myocardial lipotoxicity contributing to inhibiting NLRP3 inflammasome activation possibly via improved mitochondrial dysfunction.
Single-cell analysis reveals IGF-1 potentiation of inhibition of the TGF-β/Smad pathway of fibrosis in human keratocytes in vitro
Authors: Sarenac Tomislav , Trapecar Martin , Gradisnik Lidija , Rupnik Marjan Slak , Pahor Dusica
Published: September 2016

Corneal wound healing is often affected by TGF-β–mediated fibrosis and scar formation. Guided fibrosis with IGF-1 and antifibrotic substances might maintain corneal transparency. Primary human corneal keratocytes under serum-free conditions were used as a model of corneal stromal wounding, with markers of corneal fibrosis and opacity studied under TGF-β2 stimulation. Single-cell imaging flow cytometry was used to determine nuclearization of Smad3 and intracellular fluorescence intensity of Smad7 and the corneal crystallin aldehyde dehydrogenase 3A1. Extracellular matrix proteoglycans keratocan and biglycan were quantified using ELISAs. On the TGF-β2 background, the keratocytes were treated with IGF-1 and suberoylanilidehydroxamic acid (SAHA) or halofuginone ± IGF-1. IGF-1 alone decreased Smad3 nuclearization and increased aldehyde dehydrogenase 3A1 expression, with favorable extracellular matrix proteoglycan composition. SAHA induced higher Smad7 levels and inhibited translocation of Smad3 to the nucleus, also when combined with IGF-1. Immunofluorescence showed that myofibroblast transdifferentiation is attenuated and appearance of fibroblasts is favored by IGF-1 alone and in combination with the antifibrotic substances. The TGF-β/Smad pathway of fibrosis and opacity was inhibited by IGF-1 and further with SAHA in particular and with halofuginone. IGF-1 is thus a valid aid to antifibrotic treatment, with potential for effective and transparent corneal wound healing.
Volitional exaggeration of body size through fundamental and formant frequency modulation in humans
Authors: Pisanski Katarzyna , Mora Emanuel C. , Pisanski Annette , Reby David , Sorokowski Piotr , Frackowiak Tomasz , Feinberg David R.
Published: September 2016

Several mammalian species scale their voice fundamental frequency (F0) and formant frequencies in competitive and mating contexts, reducing vocal tract and laryngeal allometry thereby exaggerating apparent body size. Although humans’ rare capacity to volitionally modulate these same frequencies is thought to subserve articulated speech, the potential function of voice frequency modulation in human nonverbal communication remains largely unexplored. Here, the voices of 167 men and women from Canada, Cuba, and Poland were recorded in a baseline condition and while volitionally imitating a physically small and large body size. Modulation of F0, formant spacing (∆F), and apparent vocal tract length (VTL) were measured using Praat. Our results indicate that men and women spontaneously and systemically increased VTL and decreased F0 to imitate a large body size, and reduced VTL and increased F0 to imitate small size. These voice modulations did not differ substantially across cultures, indicating potentially universal sound-size correspondences or anatomical and biomechanical constraints on voice modulation. In each culture, men generally modulated their voices (particularly formants) more than did women. This latter finding could help to explain sexual dimorphism in F0 and formants that is currently unaccounted for by sexual dimorphism in human vocal anatomy and body size.
Erratum: Sensitivity of density-dependent threshold to species composition in arthropod aggregates
Authors: Broly Pierre , Ectors Quentin , Decuyper Geoffrey , Nicolis Stamatios C. , Deneubourg Jean-Louis
Published: September 2016

Scientific Reports 6: Article number: 32576; published online: 31 August 2016; updated: 30 September 2016 The original version of this Article contained errors in the spelling of the authors Pierre Broly, Quentin Ectors, Geoffrey Decuyper & Jean-Louis Deneubourg which were incorrectly given as Broly Pierre, Ectors Quentin, Decuyper Geoffrey & Deneubourg Jean-Louis respectively.
Allochthonous carbon is a major regulator to bacterial growth and community composition in subarctic freshwaters
Authors: Roiha Toni , Peura Sari , Cusson Mathieu , Rautio Milla
Published: September 2016

In the subarctic region, climate warming and permafrost thaw are leading to emergence of ponds and to an increase in mobility of catchment carbon. As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. By sampling different subarctic water bodies for a one complete year we show how terrestrial and algal carbon compounds vary in a range of freshwaters and how differential organic carbon quality is linked to bacterial metabolism and community composition. We show that terrestrial drainage and associated nutrients supported higher bacterial growth in ponds and river mouths that were influenced by fresh terrestrial carbon than in large lakes with carbon from algal production. Bacterial diversity, however, was lower at sites influenced by terrestrial carbon inputs. Bacterial community composition was highly variable among different water bodies and especially influenced by concentrations of dissolved organic carbon (DOC), fulvic acids, proteins and nutrients. Furthermore, a distinct preference was found for terrestrial vs. algal carbon among certain bacterial tribes. The results highlight the contribution of the numerous ponds to cycling of terrestrial carbon in the changing subarctic and arctic regions.
Identification of DNA methylation changes associated with disease progression in subchondral bone with site-matched cartilage in knee osteoarthritis
Authors: Zhang Yanfei , Fukui Naoshi , Yahata Mitsunori , Katsuragawa Yozo , Tashiro Toshiyuki , Ikegawa Shiro , Lee Ming Ta Michael
Published: September 2016

Subchondral bone plays a key role in the development of osteoarthritis, however, epigenetics of subchondral bone has not been extensively studied. In this study, we examined the genome-wide DNA methylation profiles of subchondral bone from three regions on tibial plateau representing disease progression using HumanMethylation450 BeadChip to identify progression associated DNA methylation alterations. Significant differential methylated probes (DMPs) and differential methylated genes (DMGs) were identified in the intermediate and late stages and during the transition from intermediate to late stage of OA in the subchondral bone. Over half of the DMPs were hyper-methylated. Genes associated with OA and bone remodeling were identified. DMGs were enriched in morphogenesis and development of skeletal system and HOX transcription factors. Comparison of DMGs identified in subchondral bone and site-matched cartilage indicated that DNA methylation changes occurred earlier in subchondral bone and identified different methylation patterns at the late stage of OA. However, shared DMPs, DMGs and common pathways that implicated the tissue reparation were also identified. Methylation is one key mechanism to regulate the crosstalk between cartilage and subchondral bone.
Neural Stem Cell Tumorigenicity and Biodistribution Assessment for Phase I Clinical Trial in Parkinson’s Disease
Authors: Garitaonandia Ibon , Gonzalez Rodolfo , Christiansen-Weber Trudy , Abramihina Tatiana , Poustovoitov Maxim , Noskov Alexander , Sherman Glenn , Semechkin Andrey , Snyder Evan , Kern Russell
Published: September 2016

Human pluripotent stem cells (PSC) have the potential to revolutionize regenerative medicine. However undifferentiated PSC can form tumors and strict quality control measures and safety studies must be conducted before clinical translation. Here we describe preclinical tumorigenicity and biodistribution safety studies that were required by the US Food and Drug Administration (FDA) and Australian Therapeutic Goods Administration (TGA) prior to conducting a Phase I clinical trial evaluating the safety and tolerability of human parthenogenetic stem cell derived neural stem cells ISC-hpNSC for treating Parkinson’s disease (ClinicalTrials.gov Identifier NCT02452723). To mitigate the risk of having residual PSC in the final ISC-hpNSC population, we conducted sensitive in vitro assays using flow cytometry and qRT-PCR analyses and in vivo assays to determine acute toxicity, tumorigenicity and biodistribution. The results from these safety studies show the lack of residual undifferentiated PSC, negligible tumorigenic potential by ISC-hpNSC and provide additional assurance to their clinical application.