bluuebunny/crossref_metadata_2025 huggingface dataset:
A tightly coupled non-equilibrium model for inductively coupled radio-frequency plasmas
Authors: Munafò A. , Alfuhaid S. A. , Cambier J.-L. , Panesi M.
Published: October 2015

The objective of the present work is the development of a tightly coupled magneto-hydrodynamic model for inductively coupled radio-frequency plasmas. Non Local Thermodynamic Equilibrium (NLTE) effects are described based on a hybrid State-to-State approach. A multi-temperature formulation is used to account for thermal non-equilibrium between translation of heavy-particles and vibration of molecules. Excited electronic states of atoms are instead treated as separate pseudo-species, allowing for non-Boltzmann distributions of their populations. Free-electrons are assumed Maxwellian at their own temperature. The governing equations for the electro-magnetic field and the gas properties (e.g., chemical composition and temperatures) are written as a coupled system of time-dependent conservation laws. Steady-state solutions are obtained by means of an implicit Finite Volume method. The results obtained in both LTE and NLTE conditions over a broad spectrum of operating conditions demonstrate the robustness of the proposed coupled numerical method. The analysis of chemical composition and temperature distributions along the torch radius shows that: (i) the use of the LTE assumption may lead to an inaccurate prediction of the thermo-chemical state of the gas, and (ii) non-equilibrium phenomena play a significant role close the walls, due to the combined effects of Ohmic heating and macroscopic gradients.
Competition between ices Ih and Ic in homogeneous water freezing
Authors: Zaragoza Alberto , Conde Maria M. , Espinosa Jorge R. , Valeriani Chantal , Vega Carlos , Sanz Eduardo
Published: October 2015

The role of cubic ice, ice Ic, in the nucleation of ice from supercooled water has been widely debated in the past decade. Computer simulations can provide insightful information about the mechanism of ice nucleation at a molecular scale. In this work, we use molecular dynamics to study the competition between ice Ic and hexagonal ice, ice Ih, in the process of ice nucleation. Using a seeding approach, in which classical nucleation theory is combined with simulations of ice clusters embedded in supercooled water, we estimate the nucleation rate of ice for a pathway in which the critical nucleus has an Ic structure. Comparing our results with those previously obtained for ice Ih [Sanz et al., J. Am. Chem. Soc. 135, 15008 (2013)], we conclude that within the accuracy of our calculations both nucleation pathways have the same rate for the studied water models (TIP4P/Ice and TIP4P/2005). We examine in detail the factors that contribute to the nucleation rate and find that the chemical potential difference with the fluid, the attachment rate of particles to the cluster, and the ice-water interfacial free energy are the same within the estimated margin of error for both ice polymorphs. Furthermore, we study the morphology of the ice clusters and conclude that they have a spherical shape.
Determination of discharge parameters via OES at the Linac4 H− ion source
Authors: Briefi S. , Fink D. , Mattei S. , Lettry J. , Fantz U.
Published: October 2015

Optical emission spectroscopy (OES) measurements of the atomic Balmer series and the molecular Fulcher transition have been carried out at the Linac4 ion source in order to determine plasma parameters. As the spectroscopic system was only relatively calibrated, the data evaluation only yielded rough estimates of the plasma parameters (Te ≈ 1.2 eV, ne ≈ 1 × 1019 m−3, and nH/nH2 ≈ 0.5 at standard operational parameters). The analysis of the Fulcher transition revealed a non-thermal “hockey-stick” rotational population of the hydrogen molecules. At varying RF power, the measurements at the on-axis line of sight (LOS) showed a peak in the rotational temperatures between 25 and 40 kW of RF power, whereas a steady decrease with power was observed at a tilted LOS, indicating the presence of strong plasma parameter gradients.
Fluid contact angle on solid surfaces: Role of multiscale surface roughness
Authors: Bottiglione F. , Carbone G. , Persson B. N. J.
Published: October 2015

We present a simple analytical model and an exact numerical study which explain the role of roughness on different length scales for the fluid contact angle on rough solid surfaces. We show that there is no simple relation between the distribution of surface slopes and the fluid contact angle. In particular, surfaces with the same distribution of slopes may exhibit very different contact angles depending on the range of length-scales over which the surfaces have roughness.
An overview of the new test stand for H− ion sources at FNAL
Authors: Sosa A. , Bollinger D. S. , Duel K. , Karns P. R. , Pellico W. , Tan C. Y.
Published: October 2015

A new test stand at Fermi National Accelerator Laboratory (FNAL) is being constructed to carry out experiments to develop and upgrade the present magnetron-type sources of H− ions of up to 80 mA at 35 keV in the context of the Proton Improvement Plan. The aim of this plan is to provide high-power proton beams for the experiments at FNAL. The technical details of the construction and layout of this test stand are presented, along with a prospective set of diagnostics to monitor the sources.
Influence of substrate microcrystallinity on the orientation of laser-induced periodic surface structures
Authors: Nürnberger P. , Reinhardt H. , Kim H-C. , Yang F. , Peppler K. , Janek J. , Hampp N.
Published: October 2015

The research in this paper deals with the angular dependence of the formation of laser-induced periodic surface structures (LIPSS) by linearly polarized nanosecond laser pulses on polycrystalline austenitic stainless steel. Incident angles ranging from 45° to 70° lead to the generation of superimposed merely perpendicular oriented LIPSS on steel as well as on monocrystalline (100) silicon which was used as a reference material. Additional extraordinary orientations of superimposing LIPSS along with significantly different periodicities are found on polycrystalline steel but not on (100) silicon. Electron backscatter diffraction measurements indicate that the expansion of these LIPSS is limited to the grain size and affected by the crystal orientation of the individual grains. Atomic force microscopy imaging shows that LIPSS fringe heights are in good agreement with the theoretically predicted penetration depths of surface plasmon polaritons into stainless steel. These results indicate that optical anisotropies must be taken into account to fully describe the theory of light-matter interaction leading to LIPSS formation.
Coil–globule transition of a polymer involved in excluded-volume interactions with macromolecules
Authors: Odagiri Kenta , Seki Kazuhiko
Published: October 2015

Polymers adopt extended coil and compact globule states according to the balance between entropy and interaction energies. The transition of a polymer between an extended coil state and compact globule state can be induced by changing thermodynamic force such as temperature to alter the energy/entropy balance. Previously, this transition was theoretically studied by taking into account the excluded-volume interaction between monomers of a polymer chain using the partition function. For binary mixtures of a long polymer and short polymers, the coil-globule transition can be induced by changing the concentration of the shorter polymers. Here, we investigate the transition caused by short polymers by generalizing the partition function of the long polymer to include the excluded-volume effect of short polymers. The coil-globule transition is studied as a function of the concentration of mixed polymers by systematically varying Flory’s χ-parameters. We show that the transition is caused by the interplay between the excluded-volume interaction and the dispersion state of short polymers in the solvent. We also reveal that the same results can be obtained by combining the mixing entropy and elastic energy if the volume of a long polymer is properly defined.
Research Update: Plentiful magnetic moments in oxygen deficient SrTiO3
Authors: Lopez-Bezanilla Alejandro , Ganesh P. , Littlewood Peter B.
Published: October 2015

Correlated band theory is employed to investigate the magnetic and electronic properties of different arrangements of oxygen di- and tri-vacancy clusters in SrTiO3. Hole and electron doping of oxygen deficient SrTiO3 yields various degrees of magnetization as a result of the interaction between localized magnetic moments at the defect sites. Different kinds of Ti atomic orbital hybridization are described as a function of the doping level and defect geometry. We find that magnetism in SrTiO3−δ is sensitive to the arrangement of neighbouring vacancy sites, charge carrier density, and vacancy-vacancy interaction. Permanent magnetic moments in the absence of vacancy doping electrons are observed. Our description of the charged clusters of oxygen vacancies widens the previous descriptions of mono- and multi-vacancies and points out the importance of the controlled formation at the atomic level of defects for the realization of transition metal oxide based devices with a desirable magnetic performance.
Polymer segregation under confinement: Influences of macromolecular crowding and the interaction between the polymer and crowders
Authors: Chen Yuhao , Yu Wancheng , Wang Jiajun , Luo Kaifu
Published: October 2015

Entropy driven polymer segregation in confinements as a model for chromosome separation in bacteria has attracted wide attention; however, the effects of macromolecular crowding and the interaction between the binding protein and the newly replicated DNA on the segregation dynamics are not clear. Using Langevin dynamics simulations, we investigate the influences of crowders and the attractive interaction between the polymer and a small number of crowders on segregation of two overlapping polymers under a cylindrical confinement. We find that the segregation time increases with increasing the volume fraction of crowders due to the slower chain diffusion in crowded environments. For a fixed volume fraction of crowders, the segregation time decreases with increasing the size of crowders. Moreover, the attractive interaction between the polymer and a small number of crowders can significantly facilitate the chain segregation. These results are important for understanding the chromosome segregation in living cells.
Ambient CdCl2 treatment on CdS buffer layer for improved performance of Sb2Se3 thin film photovoltaics
Authors: Wang Liang , Luo Miao , Qin Sikai , Liu Xinsheng , Chen Jie , Yang Bo , Leng Meiying , Xue Ding-Jiang , Zhou Ying , Gao Liang , Song Haisheng , Tang Jiang
Published: October 2015

Antimony selenide (Sb2Se3) is appealing as a promising light absorber because of its intrinsically benign grain boundaries, suitable band gap (∼1.1 eV), strong absorption coefficient, and relatively environmentally friendly constituents. Recently, we achieved a certified 5.6% efficiency Sb2Se3 thin film solar cell with the assistance of ambient CdCl2 treatment on the CdS buffer layer. Here, we focused on investigating the underlying mechanism from a combined materials and device physics perspective applying current density-voltage (J-V) fitting analysis, atomic force microscope, X-ray photoelectron spectroscopy, fluorescence, and UV–Vis transmission spectroscopy. Our results indicated that ambient CdCl2 treatment on CdS film not only improved CdS grain size and quality, but also incorporated Cl and more O into the film, both of which can significantly improve the heterojunction quality and device performance of CdS/Sb2Se3 solar cells.
Determination of morphological characteristics of metallic nanoparticles based on modified Maxwell-Garnett fitting of optical responses
Authors: Battie Y. , Resano-Garcia A. , En Naciri A. , Akil S. , Chaoui N.
Published: October 2015

A modified effective medium theory (MEMT) is introduced to determine morphological characteristics and the volume fraction of colloidal metallic nanoparticles. By analyzing the optical absorption spectra of gold nanoparticles (NPs), this model is used to determine the distribution of prolate and oblate NPs and to demonstrate the presence of spherical NPs. In addition to interband transition, the model takes into account the longitudinal and transversal surface plasmon resonances. The results predicted by the MEMT theory were found to be in very good agreement with the shape distributions obtained by transmission electron microscopy. We found that fitting optical absorption spectra using MEMT provides a robust tool for measuring the shape and concentration of metallic NPs.
Correlation between cell migration and reactive oxygen species under electric field stimulation
Authors: Wu Shang-Ying , Hou Hsien-San , Sun Yung-Shin , Cheng Ji-Yen , Lo Kai-Yin
Published: October 2015

Cell migration is an essential process involved in the development and maintenance of multicellular organisms. Electric fields (EFs) are one of the many physical and chemical factors known to affect cell migration, a phenomenon termed electrotaxis or galvanotaxis. In this paper, a microfluidics chip was developed to study the migration of cells under different electrical and chemical stimuli. This chip is capable of providing four different strengths of EFs in combination with two different chemicals via one simple set of agar salt bridges and Ag/AgCl electrodes. NIH 3T3 fibroblasts were seeded inside this chip to study their migration and reactive oxygen species (ROS) production in response to different EF strengths and the presence of β-lapachone. We found that both the EF and β-lapachone level increased the cell migration rate and the production of ROS in an EF-strength-dependent manner. A strong linear correlation between the cell migration rate and the amount of intracellular ROS suggests that ROS are an intermediate product by which EF and β-lapachone enhance cell migration. Moreover, an anti-oxidant, α-tocopherol, was found to quench the production of ROS, resulting in a decrease in the migration rate.
Effects of lymphocyte profile on development of EBV-induced lymphoma subtypes in humanized mice
Authors: Lee Eun Kyung , Joo Eun Hye , Song Kyung-A , Choi Bongkum , Kim Miyoung , Kim Seok-Hyung , Kim Sung Joo , Kang Myung-Soo
Published: October 2015

Significance

The mechanism of how Epstein-Barr virus (EBV) contributes to the development of two distinct lymphomas remains unknown. Intriguingly, EBV-associated Hodgkin’s lymphoma was seen exclusively in mice with activated T-cell conditions, whereas EBV-associated non-Hodgkin’s lymphoma was developed in mice with suppressed T-cell conditions, in which immature B cells were predominant at the time of EBV infection. This distinct association provides new insight into the pathogenesis of specific types of EBV-induced lymphomas.
pH homeostasis during coral calcification in a free ocean CO
2
enrichment (FOCE) experiment, Heron Island reef flat, Great Barrier Reef
Authors: Georgiou Lucy , Falter James , Trotter Julie , Kline David I. , Holcomb Michael , Dove Sophie G. , Hoegh-Guldberg Ove , McCulloch Malcolm
Published: October 2015

Significance

In situ free ocean CO
2
enrichment (FOCE) experiments and geochemical analyses (δ
11
B, Sr/Ca) conducted on corals (
Porites cylindrica
) from the highly dynamic Heron Island reef flat of the Great Barrier Reef show that this species exerts strong physiological controls on the pH of their calcifying fluid (pH

cf

). Over an ∼6-mo period, from mid-winter to early summer, we show that these corals maintained their pH

cf

at near constant elevated levels independent of the highly variable temperatures and FOCE-controlled carbonate chemistries to which they were exposed, implying they have a high degree of tolerance to ocean acidification.
Consequences of zygote injection and germline transfer of mutant human mitochondrial DNA in mice
Authors: Yu Hong , Koilkonda Rajeshwari D. , Chou Tsung-Han , Porciatti Vittorio , Mehta Arpit , Hentall Ian D. , Chiodo Vince A. , Boye Sanford L. , Hauswirth William W. , Lewin Alfred S. , Guy John
Published: October 2015

Significance

Therapies for Leber hereditary optic neuropathy (LHON), in common with all disorders caused by mutated mtDNA, are inadequate, in part because of the absence of suitable animal models. To test a potential therapy, we introduced mutant human NADH ubiquinone oxidoreductase subunit 4 DNA directly into mitochondria of mouse zygotes to generate transgenic LHON mice. This mutation in mice caused the hallmark visual loss and optic neuropathy seen in LHON patients. We reversed the blindness by gene therapy with the wild-type allele. To our knowledge, this is the first description of a mouse model with the same genotype and phenotype as the human counterpart disorder. This innovative technology has implications not only for creating mouse models of mutant mtDNA but also for treating the mitochondrial dysfunction with gene therapy.
Resource colimitation governs plant community responses to altered precipitation
Authors: Eskelinen Anu , Harrison Susan P.
Published: October 2015

Significance

Understanding how and why communities vary in their responses to climatic change is critical for global biodiversity conservation. In a 5-y experimental study of a heterogeneous grassland system, we found that the most nutrient-limited communities were relatively insensitive to alterations in rainfall, but that this insensitivity could be reversed by nutrient addition, leading to greatly enhanced productivity, near-complete species turnover, and accelerated diversity loss. Species with slow-growing, resource-conserving traits were especially vulnerable to decline. These results highlight that the ecological principle of colimitation by water and nutrients can lead to powerful predictions about climate change impacts on natural communities.
Bubble nucleation and migration in a lead–iron hydr(oxide) core–shell nanoparticle
Authors: Niu Kaiyang , Frolov Timofey , Xin Huolin L. , Wang Junling , Asta Mark , Zheng Haimei
Published: October 2015

Significance

An understanding of gas bubble formation in a solid and the materials’ responses at the nanoscale is of technological importance. Tracking nanobubble evolution in a solid during chemical reactions involving a solid, a gas, and a liquid is rarely achieved. Here, we show a breakthrough in materials characterization by monitoring gas bubble nucleation and migration and the associated strain evolution in a lead–iron hydroxide core–shell nanoparticle during dehydration reaction using liquid cell transmission electron microscopy. We found strain coupling can be used to remove gas bubbles from nanostructures, which sheds light on strategies for nanomaterials engineering and novel materials synthetic routes.
Epithelial estrogen receptor 1 intrinsically mediates squamous differentiation in the mouse vagina
Authors: Miyagawa Shinichi , Iguchi Taisen
Published: October 2015

Significance

Estrogen regulation of tissue homeostasis, particularly the regulation of cell proliferation and differentiation in female reproductive organs, is interesting both in its basic biology and in several disease models and cancer biology. Using an epithelial estrogen receptor 1 (
Esr1
) conditional knockout mouse model, we showed that vaginal epithelial cells lacking ESR1 failed to activate growth factor signaling and remained undifferentiated and in a proliferative state throughout the epithelium. Thus, epithelial ESR1 mediates the switch between cell proliferation and squamous cell differentiation, demonstrating unique roles of ESR1 in the female reproductive tract.
Direct link between metabolic regulation and the heat-shock response through the transcriptional regulator PGC-1α
Authors: Minsky Neri , Roeder Robert G.
Published: October 2015

Significance

In recent years an extensive effort has been made to elucidate the molecular pathways involved in metabolic signaling. Our study shows, surprisingly, a direct link between metabolic regulation and the heat-shock response, a highly conserved transcriptional program that is activated in the presence of various environmental stresses. Specifically, we demonstrate that peroxisome proliferator-activated receptor γ coactivator 1α, a critical and well-established inducible transcriptional coactivator of metabolic genes, acts as a direct transcriptional repressor of heat-shock factor 1, a key regulator of the heat-shock/stress response and a factor more recently demonstrated to be necessary for cancer initiation and survival. Thus, our findings have possible implications both for our understanding of the full scope of metabolically regulated target genes in vivo and, conceivably, for therapeutics.
Discovery of progenitor cell signatures by time-series synexpression analysis during
Drosophila
embryonic cell immortalization
Authors: Dequéant Mary-Lee , Fagegaltier Delphine , Hu Yanhui , Spirohn Kerstin , Simcox Amanda , Hannon Gregory J. , Perrimon Norbert
Published: October 2015

Significance

Cell line derivation is a complex process and a major challenge outside of mammalian systems. Here we take an unbiased genomic approach to characterize a
Drosophila
embryonic culture system allowing the efficient derivation of cell lines of still unknown origins. We reveal that commonly immortalized cells are related to adult muscle precursors (AMPs), a stem cell-like population contributing to adult muscles and sharing properties with vertebrate satellite cells. Remarkably, the cells retain the ability to differentiate terminally in vitro. We also confirm in vivo a previously unidentified regulator of AMP proliferation predicted by our analysis. Our study reveals the potential of this genetically controlled progenitor culture system to provide key missing resources to the
Drosophila
toolbox for cell-based assays.
A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling
Authors: Patterson Heide Christine , Gerbeth Carolin , Thiru Prathapan , Vögtle Nora F. , Knoll Marko , Shahsafaei Aliakbar , Samocha Kaitlin E. , Huang Cher X. , Harden Mark Michael , Song Rui , Chen Cynthia , Kao Jennifer , Shi Jiahai , Salmon Wendy , Shaul Yoav D. , Stokes Matthew P. , Silva Jeffrey C. , Bell George W. , MacArthur Daniel G. , Ruland Jürgen , Meisinger Chris , Lodish Harvey F.
Published: October 2015

Significance

Both the mitochondrial respiratory chain and reactive oxygen species (ROS) control numerous physiological and pathological cellular responses. ROS such as hydrogen peroxide (H2O2) are thought to initiate signaling by broadly and nonspecifically redox-modifying signaling molecules, suggesting that H2O2signaling may be distinct from other signal transduction pathways. Here, we provide evidence suggesting that H2O2signaling is under control of what appears to be a typical signal transduction cascade that connects the respiratory chain to the mitochondrial intermembrane space-localized conserved Syk pathway and results in a focused signaling response in diverse cell types. The results thus reveal a mechanism that allows the respiratory chain to communicate with the remainder of the cell in response to ROS.
First Record of Pughead Deformity in Blue Catfish
Authors: Schmitt Joseph D. , Orth Donald J.
Published: October 2015

Pugheaded fish exhibit anomalous bone structure, often characterized by a steep, bulging forehead and incomplete closure of the mouth. While the pughead deformity has been observed in many species of fish, thescientific literature contains no documented instances of pugheadedness in Blue Catfish Ictalurus furcatus. Pugheadedness is rare, particularly in tidal systems, and most recorded instances have been based on single specimens. We captured several pugheaded Blue Catfish (N = 18) in the tidal Rappahannock River in eastern Virginia, a tributary of the Chesapeake Bay. While Blue Catfish sampling was extensive in the James, Pamunkey, and Mattaponi rivers (N = 4,357 fish at 163 sites), pugheaded specimens were encountered at only six sampling sites within the upper tidal zone of the Rappahannock River, an area known to be susceptible to summertime hypoxia. We encountered pugheaded individuals at a higher rate than reported in most published studies, ranging between 1.89% and 3.68%, much higher than rates detected in other tidal systems. Pugheaded specimens had significantly lower relative weights than nonpugheaded specimens, indicating that this deformity may affect their ability to forage. Hypoxia, pollutants, and genetic anomalies are all explored as potential drivers of high deformity rates within the Rappahannock River.
Exploring Crowded Trophic Niche Space in a Novel Reservoir Fish Assemblage: How Many is Too Many?
Authors: Winters Lisa K. , Budy Phaedra
Published: October 2015

In highly managed reservoir systems, species interactions within novel fish assemblages can be difficult to predict. In high‐elevation Scofield Reservoir in Utah the unintentional introduction of Utah Chub Gila atraria and subsequent population expansion prompted a shift from stocking exclusively Rainbow Trout Oncorhynchus mykiss to include tiger trout (female Brown Trout Salmo trutta × male Brook Trout Salvelinus fontinalis) and Bonneville Cutthroat Trout O. clarkii utah, which composed a novel suite of top predators and potential competitors. We examined the interspecific interactions among Scofield Reservoir piscivores using a multifaceted approach including gut analyses, stable isotopes, and gape limitation. Large Cutthroat Trout consumed 50–100% Utah Chub and tiger trout consumed 45–80%. In contrast, small and large Rainbow Trout consumed primarily invertebrate prey and exhibited significant overlap with small tiger trout, Cutthroat Trout, and Utah Chub. Large Cutthroat Trout and tiger trout occupy a top piscivore trophic niche and are more littoral, while Rainbow Trout occupy an omnivore niche space and are more pelagic. Both Cutthroat and tiger trout varied in niche space with respect to size‐class, demonstrating an ontogenetic shift to piscivory at approximately 350 mm TL. Cutthroat Trout and tiger trout are capable of consuming prey up to 50% of their own size, which is larger than predicted based on their theoretical gape limit. Because it appears food resources (Utah Chub) are not limited, and performance metrics are high, competition is unlikely between Cutthroat Trout and tiger trout. In contrast, apparent survival of Rainbow Trout has recently declined significantly, potentially due to shared food resources with Utah Chub or negative behavioral interactions with other members of the community. Collectively, this research aids in understanding biotic interactions within a top‐heavy and novel fish community and assists towards developing and implementing suitable management strategies to control nuisance species.
Fictive Layering and Inversion in the Paintings of Ali-Akbar Sadeghi
Authors: Foroutan Aida
Published: October 2015

In Iran surrealism is spoken of by artists and critics as a living element in art, long after its popularity in Europe and North America has waned. This article explores key features of the work of one of the most prolific contemporary Iranian artists, Ali-Akbar Sadeghi. While Sadeghi says that he thinks of himself as a “surrealist,” his work is distinguished from many self-professed surrealists in Iran: whereas the latter are concerned with representing metaphysical, even mystical, meanings, Sadeghi sees his art as a kind of intellectual exercise, presenting a dramatic theater in which the viewer engages in epistemological interrogation. Though Sadeghi’s paintings are full of apparent references to surrealist themes and tropes from the past, here it is argued that his work is not so much a storehouse of surrealist content as a series of puzzles for the viewer to solve.
SAM68 is a physiological regulator of SMN2 splicing in spinal muscular atrophy
Authors: Pagliarini Vittoria , Pelosi Laura , Bustamante Maria Blaire , Nobili Annalisa , Berardinelli Maria Grazia , D’Amelio Marcello , Musarò Antonio , Sette Claudio
Published: October 2015

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by loss of motor neurons in patients with null mutations in the SMN1 gene. The almost identical SMN2 gene is unable to compensate for this deficiency because of the skipping of exon 7 during pre–messenger RNA (mRNA) processing. Although several splicing factors can modulate SMN2 splicing in vitro, the physiological regulators of this disease-causing event are unknown. We found that knockout of the splicing factor SAM68 partially rescued body weight and viability of SMAΔ7 mice. Ablation of SAM68 function promoted SMN2 splicing and expression in SMAΔ7 mice, correlating with amelioration of SMA-related defects in motor neurons and skeletal muscles. Mechanistically, SAM68 binds to SMN2 pre-mRNA, favoring recruitment of the splicing repressor hnRNP A1 and interfering with that of U2AF65 at the 3′ splice site of exon 7. These findings identify SAM68 as the first physiological regulator of SMN2 splicing in an SMA mouse model.
Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis
Authors: Viny Aaron D. , Ott Christopher J. , Spitzer Barbara , Rivas Martin , Meydan Cem , Papalexi Efthymia , Yelin Dana , Shank Kaitlyn , Reyes Jaime , Chiu April , Romin Yevgeniy , Boyko Vitaly , Thota Swapna , Maciejewski Jaroslaw P. , Melnick Ari , Bradner James E. , Levine Ross L.
Published: October 2015

Cohesin complex members have recently been identified as putative tumor suppressors in hematologic and epithelial malignancies. The cohesin complex guides chromosome segregation; however, cohesin mutant leukemias do not show genomic instability. We hypothesized that reduced cohesin function alters chromatin structure and disrupts cis-regulatory architecture of hematopoietic progenitors. We investigated the consequences of Smc3 deletion in normal and malignant hematopoiesis. Biallelic Smc3 loss induced bone marrow aplasia with premature sister chromatid separation and revealed an absolute requirement for cohesin in hematopoietic stem cell (HSC) function. In contrast, Smc3 haploinsufficiency increased self-renewal in vitro and in vivo, including competitive transplantation. Smc3 haploinsufficiency reduced coordinated transcriptional output, including reduced expression of transcription factors and other genes associated with lineage commitment. Smc3 haploinsufficiency cooperated with Flt3-ITD to induce acute leukemia in vivo, with potentiated Stat5 signaling and altered nucleolar topology. These data establish a dose dependency for cohesin in regulating chromatin structure and HSC function.
Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms
Authors: Mullenders Jasper , Aranda-Orgilles Beatriz , Lhoumaud Priscillia , Keller Matthew , Pae Juhee , Wang Kun , Kayembe Clarisse , Rocha Pedro P. , Raviram Ramya , Gong Yixiao , Premsrirut Prem K. , Tsirigos Aristotelis , Bonneau Richard , Skok Jane A. , Cimmino Luisa , Hoehn Daniela , Aifantis Iannis
Published: October 2015

The cohesin complex (consisting of Rad21, Smc1a, Smc3, and Stag2 proteins) is critically important for proper sister chromatid separation during mitosis. Mutations in the cohesin complex were recently identified in a variety of human malignancies including acute myeloid leukemia (AML). To address the potential tumor-suppressive function of cohesin in vivo, we generated a series of shRNA mouse models in which endogenous cohesin can be silenced inducibly. Notably, silencing of cohesin complex members did not have a deleterious effect on cell viability. Furthermore, knockdown of cohesin led to gain of replating capacity of mouse hematopoietic progenitor cells. However, cohesin silencing in vivo rapidly altered stem cells homeostasis and myelopoiesis. Likewise, we found widespread changes in chromatin accessibility and expression of genes involved in myelomonocytic maturation and differentiation. Finally, aged cohesin knockdown mice developed a clinical picture closely resembling myeloproliferative disorders/neoplasms (MPNs), including varying degrees of extramedullary hematopoiesis (myeloid metaplasia) and splenomegaly. Our results represent the first successful demonstration of a tumor suppressor function for the cohesin complex, while also confirming that cohesin mutations occur as an early event in leukemogenesis, facilitating the potential development of a myeloid malignancy.
Hyper-luminous dust-obscured galaxies discovered by the Hyper Suprime-Cam on Subaru and WISE
Authors: Toba Yoshiki , Nagao Tohru , Strauss Michael A. , Aoki Kentaro , Goto Tomotsugu , Imanishi Masatoshi , Kawaguchi Toshihiro , Terashima Yuichi , Ueda Yoshihiro , Bosch James , Bundy Kevin , Doi Yoshiyuki , Inami Hanae , Komiyama Yutaka , Lupton Robert H. , Matsuhara Hideo , Matsuoka Yoshiki , Miyazaki Satoshi , Morokuma Tomoki , Nakata Fumiaki , Oi Nagisa , Onoue Masafusa , Oyabu Shinki , Price Paul , Tait Philip J. , Takata Tadafumi , Tanaka Manobu M. , Terai Tsuyoshi , Turner Edwin L. , Uchida Tomohisa , Usuda Tomonori , Utsumi Yousuke , Yamada Yoshihiko , Wang Shiang-Yu
Published: October 2015

We present the photometric properties of a sample of infrared (IR) bright dust-obscured galaxies (DOGs). Combining wide and deep optical images obtained with the Hyper Suprime-Cam on the Subaru Telescope and all-sky mid-IR (MIR) images taken with Wide-Field Infrared Survey Explorer, we discovered 48 DOGs with i − Ks > 1.2 and i − [22] > 7.0, where i, Ks, and [22] represent AB magnitude in the i-band, Ks-band, and 22 μm, respectively, in the GAMA 14 hr field (∼ 9 deg2). Among these objects, 31 (∼ 65%) show power-law spectral energy distributions (SEDs) in the near-IR (NIR) and MIR regime, while the remainder show an NIR bump in their SEDs. Assuming that the redshift distribution for our DOGs sample is Gaussian, with mean and sigma z = 1.99 ± 0.45, we calculated their total IR luminosity using an empirical relation between 22 μm luminosity and total IR luminosity. The average value of the total IR luminosity is (3.5 ± 1.1) × 1013 L⊙, which classifies them as hyper-luminous infrared galaxies. We also derived the total IR luminosity function (LF) and IR luminosity density (LD) for a flux-limited subsample of 18 DOGs with 22 μm flux greater than 3.0 mJy and with i-band magnitude brighter than 24 AB magnitude. The derived space density for this subsample is log ϕ = −6.59 ± 0.11 [Mpc−3]. The IR LF for DOGs including data obtained from the literature is fitted well by a double-power law. The derived lower limit for the IR LD for our sample is ρIR ∼ 3.8 × 107 [L⊙ Mpc−3] and its contributions to the total IR LD, IR LD of all ultra-luminous infrared galaxies, and that of all DOGs are > 3%, > 9%, and > 15%, respectively.
Methanol observation of IRAS 19312+1950: A possible new type of class I methanol maser
Authors: Nakashima Jun-ichi , Sobolev Andrej M. , Salii Svetlana V. , Zhang Yong , Yung Bosco H. K. , Deguchi Shuji
Published: October 2015

We report the result of a systematic methanol observation toward IRAS 19312+1950. The properties of the SiO, H2O, and OH masers of this object are consistent with those of mass-losing evolved stars, but some other properties are difficult to explain in the standard scheme of stellar evolution in its late stage. Interestingly, a tentative detection of radio methanol lines was suggested toward this object by a previous observation. To date, there are no confirmed detections of methanol emission towards evolved stars, so investigation of this possible detection is important to better understand the circumstellar physical/chemical environment of IRAS 19312+1950. In this study, we systematically observed multiple methanol lines of IRAS 19312+1950 in the λ = 3 mm, 7 mm, and 13 mm bands, and detected six lines including four thermal lines and two class I maser lines. We derived basic physical parameters, including kinetic temperature and relative abundances, by fitting a radiative transfer model. According to the derived excitation temperature and line profiles, a spherically expanding outflow lying at the center of the nebulosity is excluded from the possibilities for methanol emission regions. The detection of class I methanol maser emission suggests that a shock region is involved in the system of IRAS 19312+1950. If the central star of IRAS 19312+1950 is an evolved star as suggested in the past, the class I maser detected in the present observation is the first case detected in an interaction region between an evolved star outflow and ambient molecular gas.
Evolution and dynamics of a solar active prominence
Authors: Magara Tetsuya
Published: October 2015

The life of a solar active prominence, one of the most remarkable objects on the Sun, is full of dynamics; after first appearing on the Sun, the prominence continuously evolves with various internal motions and eventually produces a global eruption toward interplanetary space. Here we report that the whole life of an active prominence is successfully reproduced by performing as long-term a magnetohydrodynamic simulation of a magnetized prominence plasma as was ever done. The simulation reveals underlying dynamic processes that give rise to observed properties of an active prominence: invisible subsurface flows self-consistently produce the cancellation of magnetic flux observed in the photosphere, while observed but somewhat counterintuitive strong upflows are driven against gravity by enhanced gas pressure gradient force along a magnetic field line locally standing vertical. The most highlighted dynamic event, transition into an eruptive phase, occurs as a natural consequence of the self-consistent evolution of a prominence plasma interacting with a magnetic field, which is obtained by seamlessly reproducing dynamic processes involved in the formation and eruption of an active prominence.
Host Phenology and Leaf Effects on Susceptibility of California Bay Laurel toPhytophthora ramorum
Authors: Johnston Steven F. , Cohen Michael F. , Torok Tamas , Meentemeyer Ross K. , Rank Nathan E.
Published: October 2015

Spread of the plant pathogen Phytophthora ramorum, causal agent of the forest disease sudden oak death, is driven by a few competent hosts that support spore production from foliar lesions. The relationship between traits of a principal foliar host, California bay laurel (Umbellularia californica), and susceptibility to P. ramorum infection were investigated with multiple P. ramorum isolates and leaves collected from multiple trees in leaf-droplet assays. We examined whether susceptibility varies with season, leaf age, or inoculum position. Bay laurel susceptibility was highest during spring and summer and lowest in winter. Older leaves (>1 year) were more susceptible than younger ones (8 to 11 months). Susceptibility was greater at leaf tips and edges than the middle of the leaf. Leaf surfaces wiped with 70% ethanol were more susceptible to P. ramorum infection than untreated leaf surfaces. Our results indicate that seasonal changes in susceptibility of U. californica significantly influence P. ramorum infection levels. Thus, in addition to environmental variables such as temperature and moisture, variability in host plant susceptibility contributes to disease establishment of P. ramorum.
Insights into low-latitude cloud feedbacks from high-resolution models
Authors: Bretherton Christopher S.
Published: October 2015

Cloud feedbacks are a leading source of uncertainty in the climate sensitivity simulated by global climate models (GCMs). Low-latitude boundary-layer and cumulus cloud regimes are particularly problematic, because they are sustained by tight interactions between clouds and unresolved turbulent circulations. Turbulence-resolving models better simulate such cloud regimes and support the GCM consensus that they contribute to positive global cloud feedbacks. Large-eddy simulations using sub-100 m grid spacings over small computational domains elucidate marine boundary-layer cloud response to greenhouse warming. Four observationally supported mechanisms contribute: ‘thermodynamic’ cloudiness reduction from warming of the atmosphere–ocean column, ‘radiative’ cloudiness reduction from CO
2
- and H
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O-induced increase in atmospheric emissivity aloft, ‘stability-induced’ cloud increase from increased lower tropospheric stratification, and ‘dynamical’ cloudiness increase from reduced subsidence. The cloudiness reduction mechanisms typically dominate, giving positive shortwave cloud feedback. Cloud-resolving models with horizontal grid spacings of a few kilometres illuminate how cumulonimbus cloud systems affect climate feedbacks. Limited-area simulations and superparameterized GCMs show upward shift and slight reduction of cloud cover in a warmer climate, implying positive cloud feedbacks. A global cloud-resolving model suggests tropical cirrus increases in a warmer climate, producing positive longwave cloud feedback, but results are sensitive to subgrid turbulence and ice microphysics schemes.
Atmospheric and oceanic impacts of Antarctic glaciation across the Eocene–Oligocene transition
Authors: Kennedy A. T. , Farnsworth A. , Lunt D. J. , Lear C. H. , Markwick P. J.
Published: October 2015

The glaciation of Antarctica at the Eocene–Oligocene transition (approx. 34 million years ago) was a major shift in the Earth’s climate system, but the mechanisms that caused the glaciation, and its effects, remain highly debated. A number of recent studies have used coupled atmosphere–ocean climate models to assess the climatic effects of Antarctic glacial inception, with often contrasting results. Here, using the HadCM3L model, we show that the global atmosphere and ocean response to growth of the Antarctic ice sheet is sensitive to subtle variations in palaeogeography, using two reconstructions representing Eocene and Oligocene geological stages. The earlier stage (Eocene; Priabonian), which has a relatively constricted Tasman Seaway, shows a major increase in sea surface temperature over the Pacific sector of the Southern Ocean in response to the ice sheet. This response does not occur for the later stage (Oligocene; Rupelian), which has a more open Tasman Seaway. This difference in temperature response is attributed to reorganization of ocean currents between the stages. Following ice sheet expansion in the earlier stage, the large Ross Sea gyre circulation decreases in size. Stronger zonal flow through the Tasman Seaway allows salinities to increase in the Ross Sea, deep-water formation initiates and multiple feedbacks then occur amplifying the temperature response. This is potentially a model-dependent result, but it highlights the sensitive nature of model simulations to subtle variations in palaeogeography, and highlights the need for coupled ice sheet–climate simulations to properly represent and investigate feedback processes acting on these time scales.
Carbon cycle feedbacks and future climate change
Authors: Friedlingstein Pierre
Published: October 2015

Climate and carbon cycle are tightly coupled on many timescales, from interannual to multi-millennial timescales. Observations always evidence a positive feedback, warming leading to release of carbon to the atmosphere; however, the processes at play differ depending on the timescales. State-of-the-art Earth System Models now represent these climate-carbon cycle feedbacks, always simulating a positive feedback over the twentieth and twenty-first centuries, although with substantial uncertainty. Recent studies now help to reduce this uncertainty. First, on short timescales, El Niño years record larger than average atmospheric CO2growth rate, with tropical land ecosystems being the main drivers. These climate-carbon cycle anomalies can be used as emerging constraint on the tropical land carbon response to future climate change. Second, centennial variability found in last millennium records can be used to constrain the overall global carbon cycle response to climatic excursions. These independent methods point to climate-carbon cycle feedback at the low-end of the Earth System Models range, indicating that these models overestimate the carbon cycle sensitivity to climate change. These new findings also help to attribute the historical land and ocean carbon sinks to increase in atmospheric CO2and climate change.
What does global mean temperature tell us about local climate?
Authors: Sutton Rowan , Suckling Emma , Hawkins Ed
Published: October 2015

The subject of climate feedbacks focuses attention on global mean surface air temperature (GMST) as the key metric of climate change. But what does knowledge of past and future GMST tell us about the climate of specific regions? In the context of the ongoing UNFCCC process, this is an important question for policy-makers as well as for scientists. The answer depends on many factors, including the mechanisms causing changes, the timescale of the changes, and the variables and regions of interest. This paper provides a review and analysis of the relationship between changes in GMST and changes in local climate, first in observational records and then in a range of climate model simulations, which are used to interpret the observations. The focus is on decadal timescales, which are of particular interest in relation to recent and near-future anthropogenic climate change. It is shown that GMST primarily provides information about forced responses, but that understanding and quantifying internal variability is essential to projecting climate and climate impacts on regional-to-local scales. The relationship between local forced responses and GMST is often linear but may be nonlinear, and can be greatly complicated by competition between different forcing factors. Climate projections are limited not only by uncertainties in the signal of climate change but also by uncertainties in the characteristics of real-world internal variability. Finally, it is shown that the relationship between GMST and local climate provides a simple approach to climate change detection, and a useful guide to attribution studies.
The $10 trillion value of better information about the transient climate response
Authors: Hope Chris
Published: October 2015

How much is better information about climate change worth? Here, I use PAGE09, a probabilistic integrated assessment model, to find the optimal paths of CO
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emissions over time and to calculate the value of better information about one aspect of climate change, the transient climate response (TCR). Approximately halving the uncertainty range for TCR has a net present value of about $10.3 trillion (year 2005 US$) if accomplished in time for emissions to be adjusted in 2020, falling to $9.7 trillion if accomplished by 2030. Probabilistic integrated assessment modelling is the only method we have for making estimates like these for the value of better information about the science and impacts of climate change.