bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancement of high-order harmonic generation in intense laser interactions with solid density plasma by multiple reflections and harmonic amplification
Authors: Zhang Peng , Thomas A. G. R.
Published: April 2015

High order harmonic generation (HHG) from laser solid-density plasma interactions is considered as a promising way to generate bright and ultrashort burst of x-rays. One of the key issues for HHG is the low conversion efficiency due to a power law fall off in harmonic intensity. Here, we explore a possible mechanism for HHG enhancement by reflecting an intense laser pulse multiple times between two plasma surfaces. We find that HHG can be nonlinearly enhanced by orders of magnitude through multiple reflections compared with a single reflection. We argue this enhancement is due to the non-linear combination of the relativistically oscillating plasma mirror and the harmonic-rich pulse generated in preceding reflections. This mechanism should allow moderate power laser systems to efficiently generate coherent, ultrashort bursts of soft x-rays.
Observing and tuning the density distribution of localized states of monolayer graphene oxide by using external electric field
Authors: Gao Yan , Qin Chengbing , Qiao Zhixing , Wang Baotian , Li Weidong , Zhang Guofeng , Chen Ruiyun , Xiao Liantuan , Jia Suotang
Published: April 2015

The density distribution of localized states (DDLS) in monolayer graphene oxide (mGO) was observed and tuned under applied external electric field. The fluorescence anisotropy in mGO basal plane was observed which revealed the inhomogeneous DDLS. The enhanced and/or quenched fluorescence trajectories under electric field demonstrated the tuning of DDLS. Using the first-principles density-functional calculations, we demonstrated that the DDLS tuned by electric field could be attributed to the polarity effect of oxidized sp3 functional groups. The tunable DDLS is beneficial to improve and control the mGO's optoelectronic properties.
Magnetic phase coexistence and metastability caused by the first-order magnetic phase transition in the Heusler compound Mn2PtGa
Authors: Nayak A. K. , Sahoo R. , Salazar Mejia C. , Nicklas M. , Felser C.
Published: April 2015

The Heusler compound Mn2PtGa exhibits a first-order ferrimagnetic (FI) to antiferromagnetic (AFM) phase transition, in contrary to the conventional martensitic structural transition displayed by their close relatives, the Heusler shape-memory alloys. With the help of isofield and isothermal magnetization experiments as well as magnetic relaxation measurements, we exemplify the presence of a magnetic-phase coexistence and a metastable magnetic behavior below the FI-AFM phase transition. Field cooling across the FI-AFM transition leads to a nucleation of a supercooled FI phase below the transition temperature, where the fraction of the supercooled phase depends upon the strength of the cooling field.
Ferromagnetic and paramagnetic magnetization of implanted GaN:Ho,Tb,Sm,Tm films
Authors: Maryško M. , Hejtmánek J. , Laguta V. , Sofer Z. , Sedmidubský D. , Šimek P. , Veselý M. , Mikulics M. , Buchal C. , Macková A. , Malínský P. , Wilhelm R. A.
Published: April 2015

The SQUID magnetic measurements were performed on the GaN films prepared by metal-organic vapour phase epitaxy and implanted by Tb3+, Tm3+, Sm3+, and Ho3+ ions. The sapphire substrate was checked by the electron paramagnetic resonance method which showed a content of Cr3+ and Fe3+ impurities. The samples 5 × 5 mm2 were positioned in the classical straws and within an estimated accuracy of 10−6 emu, no ferromagnetic moment was detected in the temperature region of 2–300 K. The paramagnetic magnetization was studied for parallel and perpendicular orientation. In the case of GaN:Tb sample, at T = 2 K, a pronounced anisotropy with the easy axis perpendicular to the film was observed which can be explained by the lowest quasi-doublet state of the non-Kramers Tb3+ ion. The Weiss temperature deduced from the susceptibility data using the Curie-Weiss (C-W) law was found to depend substantially on the magnetic field.
Evidence of rare backflow and skin-friction critical points in near-wall turbulence using micropillar imaging
Authors: Brücker Ch.
Published: April 2015

The recent discovery of rare backflow events in turbulent boundary layer flows based on the analysis of simulation data has again raised the need of experimental visualizations of wall-shear stress fields in unsteady flows. The localization of critical points, which are thought to strongly correlate with large-scale events in the log-layer, is of importance. Up to now, there is no experimental proof of these rare events and their topological patterns. Their existence in a turbulent boundary-layer flow along a flat plate is shown herein by means of imaging with 2D arrays of flexible micropillars attached at the wall.
Manipulation of exciton and photon lasing in a membrane-type ZnO microcavity
Authors: Lai Ying-Yu , Chen Jee-Wei , Chang Tsu-Chi , Chou Yu-Hsun , Lu Tien-Chang
Published: April 2015

We report on the fabrication and characterization of a membrane-type ZnO microcavity (MC). The ZnO membrane was cut from a single crystalline ZnO substrate by using focused ion beam milling, and was then placed onto a SiO2 substrate by using glass microtweezers. Through changing the pumping regime, manipulation of P-band exciton lasing and whispering-gallery mode (WGM) photon lasing could be easily achieved. P-band exciton lasing was observed only when the pumping laser was focused at the center of the ZnO MC with a small pumping size because of the innate ring-shaped WGM distribution. Furthermore, the lasing threshold of the ZnO MC could be reduced to an order lower by using a larger pumping spot because of the more favorable spatial overlap between the optical gain and WGM.
Thermal boundary resistance at Si/Ge interfaces by molecular dynamics simulation
Authors: Zhan Tianzhuo , Minamoto Satoshi , Xu Yibin , Tanaka Yoshihisa , Kagawa Yutaka
Published: April 2015

In this study, we investigated the temperature dependence and size effect of the thermal boundary resistance at Si/Ge interfaces by non-equilibrium molecular dynamics (MD) simulations using the direct method with the Stillinger-Weber potential. The simulations were performed at four temperatures for two simulation cells of different sizes. The resulting thermal boundary resistance decreased with increasing temperature. The thermal boundary resistance was smaller for the large cell than for the small cell. Furthermore, the MD-predicted values were lower than the diffusion mismatch model (DMM)-predicted values. The phonon density of states (DOS) was calculated for all the cases to examine the underlying nature of the temperature dependence and size effect of thermal boundary resistance. We found that the phonon DOS was modified in the interface regions. The phonon DOS better matched between Si and Ge in the interface region than in the bulk region. Furthermore, in interface Si, the population of low-frequency phonons was found to increase with increasing temperature and cell size. We suggest that the increasing population of low-frequency phonons increased the phonon transmission coefficient at the interface, leading to the temperature dependence and size effect on thermal boundary resistance.
Scientific facilities in Japan struggle on bare-bones schedules
Authors: Feder Toni
Published: April 2015

Reduced running times have scientists worried about their experiments, from student theses to international collaborations.
Bone, implants, and their interfaces
Authors: Grandfield Kathryn
Published: April 2015

Thanks to advances in three-dimensional imaging, researchers are on the verge of understanding why certain synthetic materials adhere to bone and others don’t.
Planning at the neighbourhood scale: localism, dialogic politics, and the modulation of community action
Authors: Parker Gavin , Street Emma
Published: April 2015

This paper builds upon literature examining the foreclosing of community interventions to show how a resident-led anti-road-noise campaign in South East England has been framed, managed, and modulated by authorities. We situate the case within wider debates considering dialogical politics. For advocates, this offers the potential for empowerment through nontraditional forums. Others view such trends, most recently expressed as part of the localism agenda, with suspicion. The paper brings together these literatures to analyse the points at which modulation occurs in the community planning process. We describe the types of countertactics residents deployed to deflect the modulation of their demands, and the events that led to the outcome. We find that community planning offers a space—albeit one that is tightly circumscribed—within which (select) groups can effect change. The paper argues that the detail of neighbourhood-scale actions warrant further attention, especially as governmental enthusiasm for dialogical modes of politics shows no sign of abating.
Integrating dual-purpose wheat and canola into high-rainfall livestock systems in south-eastern Australia. 1. Crop forage and grain yield
Authors: Sprague S. J. , Kirkegaard J. A. , Dove H. , Graham J. M. , McDonald S. E. , Kelman W. M.
Published: April 2015

The development of guidelines for successful dual-purpose (graze and grain) use of wheat and canola in Australia’s high-rainfall zones (HRZ) has mostly emerged from separate wheat- and canola-focused research. Less attention has been placed on the benefits of integrating dual-purpose wheat and canola into pasture-based grazing enterprises. We conducted a farming systems experiment during 2010–11 to evaluate the benefits of integrating wheat and canola as dual-purpose crops into a pasture-based grazing system in Australia’s south-eastern tablelands. We compared forage production and grain yield in three separate crop–livestock systems in which the sheep grazed long-season wheat, winter canola or a combination of these. Initial growth rates were higher in early-autumn-sown canola than wheat in 2010, but were much lower although similar in both crops in 2011. Significant forage was available from both canola (3.1–3.4 t ha–1) and wheat (2.3–2.4 t ha–1) at the onset of grazing, but winter growth rates of wheat were higher than those of canola, leading to increased sheep grazing days (SGD). In the favourable 2010 season, dual-purpose wheat and canola separately provided 2393 and 2095 SGD ha–1, and yielded 5.0 and 1.9 t ha–1 grain, respectively, with an apparent nitrogen limitation in canola. In the drier season of 2011, grazing was reduced to 1455 and 735 SGD ha–1 in wheat and canola, respectively. Wheat yield was reduced from 5.9 to 5.4 t ha–1 grain by grazing, whereas canola yield was unaffected (3.6 t ha–1). In both years, grazing did not affect harvest index or oil content of canola, but harvest index was higher in grazed wheat crops. The yield of wheat and canola crops grazed in sequence did not differ from yield in treatments where animals grazed only a single crop, but the total overall grazing window when crops were grazed sequentially increased by 1054 and 618 SGD ha–1 in wheat, and by 1352 and 1338 SGD ha–1 in canola in 2010 and 2011, respectively. The major benefits of including crops that can be grazed sequentially were the widening of the grazing window and other operational windows (sowing, harvest), along with the rotational benefits for wheat by including canola in the system. Additional benefits to pastures may include eliminating the need to re-sow, because a more productive pasture composition is maintained under lower grazing pressure while stock are on crops, and reduced weed invasion. The commercial availability of new, herbicide-tolerant winter canola varieties provides significant opportunities to underpin the performance of dual-purpose crop sequences on mixed farms in the high-rainfall zone.
Effect of defoliation by grazing or shoot removal on the root growth of field-grown wheat (Triticum aestivum L.)
Authors: Kirkegaard J. A. , Lilley J. M. , Hunt J. R. , Sprague S. J. , Ytting N. K. , Rasmussen I. S. , Graham J. M.
Published: April 2015

Dual-purpose crops for grazing and grain production can be highly profitable, provided grazing does not cause significant loss of grain yield. In many plants, defoliation causes a transient reduction in the allocation of resources to stem and root growth and remobilisation of soluble resources to re-establish leaf area rapidly. In Australia, the usual autumn and winter period of defoliation for grazed crops, May–July, coincides with a phase of near-linear root depth penetration in ungrazed crops, and the crop recovery period after grazing occurs during stem elongation, when grain number and yield potential are determined. However, few studies have investigated the potential impact of crop defoliation through grazing on root growth of wheat in the field. We investigated the effect of defoliation by grazing or shoot removal on the root growth of wheat crops in four field experiments in south-eastern Australia in which the timing, frequency and intensity of defoliation varied. Despite significant impacts of defoliation on aboveground biomass (50–90% reduction) and grain yield (10–43% reduction) in all experiments, we found little evidence of effects on the rate of root penetration or final rooting depth. A notable exception was observed in one experiment when defoliation commenced very early (four-leaf stage, Zadoks growth stage Z14) in a repeatedly defoliated crop, reducing rooting depth from 1.65 to 1.35 m. The only other measured impact on roots was in an early-sown winter wheat crop grazed by sheep for 3 months (6 June–3 September), in which root length density was reduced by ~50% in surface layers above 1.0 m depth, but there was no impact on maximum root depth or root length density at 1.0–2.0 m depth. Our results suggest that grazing has little impact on the rooting depth of wheat unless it occurs very early and repeatedly, when plants are allocating significant resources to establish the primary roots. However, there may be some reduction in the density of roots in surface layers during recovery after long-term grazing, presumably associated with reduced proliferation of the nodal root system. We conclude that most significant yield penalties due to grazing relate to impacts on the assimilation of aboveground resources, rather than to reduced water or nutrient acquisition by roots.
Free Zn2+ determination in natural freshwaters of the Pyrenees: towards on-site measurements with AGNES
Authors: Parat Corinne , Authier Laurent , Castetbon Alain , Aguilar David , Companys Encarna , Puy Jaume , Galceran Josep , Potin-Gautier Martine
Published: April 2015

Environmental context Knowledge of the speciation of metals, especially of the free metal ion concentration, is essential to understand the fate of these elements in rivers and their effects on living organisms. On-site analyses are preferred for these measurements as they allow problems associated with sample transportation and preservation to be avoided. In this context, an on-site methodology based on an electrochemical method and screen-printed sensors has been developed in the laboratory and validated on site. Abstract An on-site methodology has been developed for the direct determination of free Zn2+ with AGNES (Absence of Gradients and Nernstian Equilibrium Stripping) in freshwaters. This implementation includes: (i) the use of screen-printed electrodes, which provide good limits of detection and easy transportation and deployment; (ii) no need for sample purging; (iii) a calibration in a synthetic river solution that reproduces the speciation changes of the natural samples well and allows oxygen interference to be minimised; (iv) the addition of a background electrolyte up to 0.01molL–1 in both the calibration and freshwater samples; (v) chemical stripping chronopotentiometry as the quantification stage of AGNES. This procedure minimises the effects of working at low ionic strength and in the presence of dissolved oxygen. In the laboratory, the methodology was checked with different natural samples taken from rivers Garonne, Gave de Cauterets and Gave de Pau in the Pyrenees. Results appeared in good agreement with theoretical estimations computed from Visual Minteq. On-site measurements were performed for the first time with AGNES in the Gave de Cauterets in Soulom (France) and the results were corroborated with purged measurements performed in the laboratory.
Variability in the growth, feeding and condition of barramundi (Lates calcarifer Bloch) in a northern Australian coastal river and impoundment
Authors: Russell D. J. , Thomson F. E. , Thuesen P. A. , Power T. N. , Mayer R. J.
Published: April 2015

Lates calcarifer supports important fisheries throughout tropical Australia. Community-driven fish stocking has resulted in the creation of impoundment fisheries and supplemental stocking of selected wild riverine populations. Using predominantly tag–recapture methods, condition assessment and stomach flushing techniques, this study compared the growth of stocked and wild L. calcarifer in a tropical Australian river (Johnstone River) and stocked fish in a nearby impoundment (Lake Tinaroo). Growth of L. calcarifer in the Johnstone River appeared resource-limited, with juvenile fish in its lower freshwater reaches feeding mainly on small aytid shrimp and limited quantities of fish. Growth was probably greatest in estuarine and coastal areas than in the lower freshwater river. Fish in Lake Tinaroo, where prey availability was greater, grew faster than either wild or stocked fish in the lower freshwater areas of the Johnstone River. Growth of L. calcarifer was highly seasonal with marked declines in the cooler months. This was reflected in both stomach fullness and the percentage of fish with empty stomachs but the condition of L. calcarifer was similar across most sites. In areas where food resources appear stretched, adverse effects on resident L. calcarifer populations and their attendant prey species should be minimised through cessation of, or more conservative, stocking practices.
River metabolism and carbon dynamics in response to flooding in a lowland river
Authors: Cook Robert A. , Gawne Ben , Petrie Rochelle , Baldwin Darren S. , Rees Gavin N. , Nielsen Daryl L. , Ning Nathan S. P.
Published: April 2015

Lowland riverine–floodplain systems often have significant but irregular inputs of allochthonous carbon. However, the importance of this carbon to riverine systems remains poorly understood. We assessed open water dissolved organic carbon (DOC) concentrations, metabolism and biofilm stable isotope (δ13C) signatures, upstream and downstream of an extensive floodplain forest on the Murray River, Australia, before and after a flood event. Prior to flooding, all sites had similar concentrations of DOC, rates of metabolism and biofilm δ13C signatures. During the flood DOC concentration increased up to three-fold downstream of the forest, gross primary production (GPP) increased at all sites, but community respiration (CR) increased only at the downstream sites, resulting in decreased in NPP downstream and a slight increase upstream. Biofilm δ13C signatures became depleted by between 4 and 7‰ downstream of the forest during the flood, reflecting a rapid incorporation of allochthonous carbon into the biofilm. These results indicate that flooding led to a substantial increase to the energy budget of the Murray River through the provisioning of large quantities of allochthonous carbon and that terrestrial carbon was processed within the river biofilms. Allochthonous carbon assimilation within biofilms during flooding provides a potential pathway for allochthonous carbon to be incorporated into the metazoan foodweb.
Epigenetic pattern changes in prenatal female Sprague-Dawley rats following exposure to androgen
Authors: Xia Yanjie , Shen Shanmei , Zhang Xinlin , Deng Zhantao , Xiang Zou , Wang Hongwei , Yi Long , Gao Qian , Wang Yong
Published: April 2015

Androgen excess is generally considered to be one of the major characteristics of polycystic ovary syndrome (PCOS). Evidence from both clinical research and animal studies has revealed that this syndrome may have fetal origins, with epigenetics being proposed as the underlying mechanism. Our PCOS rat model induced by prenatal administration of 3 mg testosterone from Embryonic Day (E) 16 to E19 showed polycystic ovaries, irregular oestrous cycles and endocrine disorders in adulthood. The methylation status of 16, 8 and 4 cytosine–phosphate–guanine (CpG) sites in the promoter regions of the androgen receptor (Ar), cytochrome P450 family 11, subfamily A, polypeptide 1 (Cyp11a1) and cytochrome P450, family 17, subfamily A, polypeptide 1 (Cyp17a1) genes, respectively, were measured by pyrosequencing. We identified three hypomethylated sites (CpG +58, +65 and +150) in Ar and one hypomethylated site (CpG +1016) in Cyp11a1 in peripheral blood cells of prenatally androgenised (PNA) rats. In ovarian tissue, five CpG sites of Ar (CpG +87, +91, +93, +98, +150) and one single CpG site in Cyp11a1 (CpG +953) were significantly hypomethylated in PNA rats, but the modified methylation of these two genes may not be sufficient to significantly alter levels of gene expression. Furthermore, tissue-specific methylation analysis revealed that both Ar and Cyp11a1 exhibited significant hypomethylation in testis in contrast with ovary and blood. PNA may lead to methylation pattern changes and the development of PCOS, but further studies are required to reveal causal relationships.
Estrogen receptor α inhibitor activates the unfolded protein response, blocks protein synthesis, and induces tumor regression
Authors: Andruska Neal D. , Zheng Xiaobin , Yang Xujuan , Mao Chengjian , Cherian Mathew M. , Mahapatra Lily , Helferich William G. , Shapiro David J.
Published: April 2015

Significance

Late-stage estrogen receptor α (ERα)-positive breast and ovarian cancers exhibit many regulatory alterations and therefore resist therapy. Our novel ERα inhibitor, BHPI, stops growth and often kills drug-resistant ERα
+
cancer cells and induces rapid and substantial tumor regression in a mouse model of human breast cancer. BHPI distorts a normally protective estrogen–ERα-mediated activation of the unfolded protein response (UPR) and elicits sustained UPR activation. The UPR cannot be deactivated because BHPI, acting at a second site, inhibits production of proteins that normally help turn it off. This persistent activation converts the UPR from protective to lethal. Targeting therapy-resistant ERα-positive cancer cells by converting the UPR from cytoprotective to cytotoxic may hold significant therapeutic promise.
Phosphorylation of PCNA by EGFR inhibits mismatch repair and promotes misincorporation during DNA synthesis
Authors: Ortega Janice , Li Jessie Y. , Lee Sanghee , Tong Dan , Gu Liya , Li Guo-Min
Published: April 2015

Significance

DNA replication accuracy is critical for genetic stability and is ensured by high-fidelity replicative DNA polymerases and the mismatch repair (MMR) system, both of which are regulated by the proliferating cell nuclear antigen (PCNA). Dysfunction of either system leads to genome instability and cancer development. Interestingly, many types of cancers have no obvious defects in either system, but they display increased mutation frequency during development. The underlying mechanism is unknown. We demonstrate here that PCNA tyrosine phosphorylation by epidermal growth factor receptor (EGFR) inhibits MMR and promotes misincorporation during DNA synthesis. This study therefore discovers a novel mechanism promoting genome instability and explains why progression of many cancer types is associated with EGFR overexpression and/or activation.
Dido mutations trigger perinatal death and generate brain abnormalities and behavioral alterations in surviving adult mice
Authors: Villares Ricardo , Gutiérrez Julio , Fütterer Agnes , Trachana Varvara , Gutiérrez del Burgo Fernando , Martínez-A Carlos
Published: April 2015

Significance

The primary cilium is an organelle protruding from most postmitotic vertebrate cells. A growing body of data supports the crucial role of primary cilia in developmental signaling pathways. Recent studies describe the main stages in ciliogenesis at the morphological level and components of some of the mechanisms involved, including the selective acetylation of tubulin. How this acetylation is modulated in cilia nonetheless remains poorly understood. Here we show that the death inducer-obliterator (
dido
) gene product, which regulates histone deacetylase 6 deacetylase activity, is necessary for orofacial development in the mouse embryo and influences brain patterning and neuromuscular activity. Mice deficient in dido function present neonatal mortality and various ciliopathies including cleft palate and hydrocephalus, as well as hippocampal and commissural dysplasia.
Sleep- and wake-dependent changes in neuronal activity and reactivity demonstrated in fly neurons using in vivo calcium imaging
Authors: Bushey Daniel , Tononi Giulio , Cirelli Chiara
Published: April 2015

Significance

Sleep in fruit flies shares all the essential features of mammalian sleep. Here, by using in vivo calcium imaging, we show for the first time, to our knowledge, that neuronal activity and reactivity decline during sleep and increase during wake simultaneously in many cells of the fly brain. Furthermore, we show that long wake reduces baseline and evoked neural activity and causes neurons to respond inconsistently to stimuli. The latter finding is reminiscent of the phenomenon of “local sleep in wake” described in rats, in which single cortical neurons unpredictably go “offline” during extended wake, leading to performance errors. Thus, these findings open the way to use
Drosophila
to study the molecular mechanisms underlying the cognitive deficits caused by sleep loss.
Loose coupling in the bacterial flagellar motor
Authors: Boschert Ryan , Adler Frederick R. , Blair David F.
Published: April 2015

Significance

Many species of bacteria swim using rotating helical propellers called flagella. Flagellar rotary motors obtain energy from the transmembrane gradient of ions (either H
+
or Na
+
). Physiological properties of the motor have been studied for more than 40 y and have led to the longstanding view that the motor is tightly coupled, meaning that each revolution is associated with the movement of a fixed number of ions across the membrane. Simulations described here indicate that this may not be the case: A loosely coupled mechanism can explain all of the observations that have been taken to indicate tight coupling, as well as some measurements that are more difficult to account for within the tight-coupling framework.
Revealing the hidden networks of interaction in mobile animal groups allows prediction of complex behavioral contagion
Authors: Rosenthal Sara Brin , Twomey Colin R. , Hartnett Andrew T. , Wu Hai Shan , Couzin Iain D.
Published: April 2015

Significance

We know little about the nature of the evolved interaction networks that give rise to the rapid coordinated collective response exhibited by many group-living organisms. Here, we study collective evasion in schooling fish using computational techniques to reconstruct the scene from the perspective of the organisms themselves. This method allows us to establish how the complex social scene is translated into behavioral response at the level of individuals and to visualize, and analyze, the resulting complex communication network as behavioral change spreads rapidly through groups. Thus, we can map, for any moment in time, the extent to which each individual is socially influential during collective evasion and predict the magnitude of such behavioral epidemics before they actually occur.
Targeting diverse protein–protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold
Authors: Checco James W. , Kreitler Dale F. , Thomas Nicole C. , Belair David G. , Rettko Nicholas J. , Murphy William L. , Forest Katrina T. , Gellman Samuel H.
Published: April 2015

Significance

Medium-sized peptides that bind tightly to a specific partner protein can be biomedically useful. However, conventional peptides, comprised exclusively of the 20 proteinogenic α-amino acid residues, are rapidly degraded in vivo by protease enzymes. We have developed a strategy that delivers protein-binding peptides that contain β-amino acid residues in addition to α-residues. The unnatural “α/β-peptide” backbone substantially diminishes susceptibility to proteolytic degradation relative to conventional peptides. Starting from a well-known family of conventional peptides that bind to diverse protein targets, we designed three sets of α/β-peptides that bind to three specific protein partners with high affinity and selectivity. These results suggest a general strategy for creating protease-resistant protein-targeting agents for diagnostic and therapeutic applications.
Plant nanobionic materials with a giant temperature response mediated by pectin-Ca
2+
Authors: Di Giacomo Raffaele , Daraio Chiara , Maresca Bruno
Published: April 2015

Significance

We present a bionic material made of plant cells and carbon nanotubes (CNTs) that exhibits record high temperature sensitivity. This material outperforms by ∼2 orders of magnitude the best man-made materials. The basic mechanism governing this response is the ionic conductivity in the egg-box structure of the pectin backbone, which interconnects cellulose microfibrils in the plant cell wall. The use of CNTs allows the bioelectrical property found in living plants to persist after cell death and stabilizes the response of the dried cells at high temperatures.
Extreme rainfall activity in the Australian tropics reflects changes in the El Niño/Southern Oscillation over the last two millennia
Authors: Denniston Rhawn F. , Villarini Gabriele , Gonzales Angelique N. , Wyrwoll Karl-Heinz , Polyak Victor J. , Ummenhofer Caroline C. , Lachniet Matthew S. , Wanamaker Alan D. , Humphreys William F. , Woods David , Cugley John
Published: April 2015

Significance

Variations in tropical cyclone (TC) activity are poorly known prior to the twentieth century, complicating our ability to understand how cyclogenesis responds to different climate states. We used stalagmites to develop a near-annual record of cave flooding from the central Australian tropics, where TCs are responsible for the majority of extreme rainfall events. Our 2,200-year time series reveals shifts in the mean number of storms through time, similar to TC variability from the North Atlantic. This finding is consistent with modern relationships between El Niño/Southern Oscillation (ENSO) and cyclogenesis, as well as with the reconstructed state of ENSO over the past two millennia, suggesting that changes between La Niña- and El Niño-dominated periods drove multicentennial shifts in TC activity in both basins.
Mechanisms for low-frequency variability of summer Arctic sea ice extent
Authors: Zhang Rong
Published: April 2015

Significance

The observed decline in summer Arctic sea ice has often been attributed, in large part, to the increase in greenhouse gases. However, the contributions from internal low-frequency variability in the climate system are not well understood. Here a multiple regression model is developed for the first time, to the author’s knowledge, to quantify the contributions of three key predictors on the internal low-frequency variability of summer Arctic sea ice extent. If the ocean heat transport into the Arctic were to weaken in the near future due to internal variability, there might be a hiatus in the decline of September Arctic sea ice, and a delay in attaining a summer ice-free Arctic. This plausible scenario with broad ecological and economic impacts should not be ignored.
Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity
Authors: Mertz Tony M. , Sharma Sushma , Chabes Andrei , Shcherbakova Polina V.
Published: April 2015

Significance

Mutations affecting replicative DNA polymerases δ (Polδ) and ε (Polε) are linked to sporadic and hereditary colorectal cancer and sporadic endometrial cancer in humans. How these mutations promote the genome instability and tumorigenesis is unclear. Here, we deciphered the mechanism of mutagenesis caused by the colon cancer-associated variant Polδ-R696W in a yeast model. It is a previously unappreciated pathway in which erroneous DNA synthesis by Polδ-R696W induces checkpoint-dependent expansion of dNTP pools. The increase in dNTP levels, in turn, causes further dramatic reduction in the fidelity of Polδ-R696W, resulting in more errors and continuous activation of the signaling cascade that keeps the dNTP pools expanded, thus forming a “vicious circle.” This phenomenon may provide insight into the processes shaping the genomes of hypermutated human cancers.
ATP binding to the pseudokinase domain of JAK2 is critical for pathogenic activation
Authors: Hammarén Henrik M. , Ungureanu Daniela , Grisouard Jean , Skoda Radek C. , Hubbard Stevan R. , Silvennoinen Olli
Published: April 2015

Significance

Mutations in the JAK pseudokinase domain are bona fide oncogenic drivers that underlie many myeloproliferative and autoimmune diseases in humans. TheJAK2V617F mutation is responsible for ∼95% of polycythemia vera and ∼60% of primary myelofibrosis and essential thrombocytosis cases. Currently, developed JAK2 tyrosine kinase inhibitors have not been able to eradicate disease caused by mutated JAK2. The data presented here show that alteration of the ATP binding site of the pseudokinase domain has the potential to suppress JAK hyperactivation caused by pathogenic mutations, with minimal effects on wild-type JAK, thus establishing the ATP binding site of the pseudokinase domain as a potential pharmacological target.
Juvenile hormone-activated phospholipase C pathway enhances transcriptional activation by the methoprene-tolerant protein
Authors: Liu Pengcheng , Peng Hong-Juan , Zhu Jinsong
Published: April 2015

Significance

Juvenile hormone (JH) controls many key processes during insect life cycles. Some of the effects of JH are mediated by a membrane-associated mechanism. In other circumstances, an intracellular JH receptor, methoprene-tolerant protein (MET), is activated upon binding of JH and directly regulates the expression of JH target genes. Here we use adult female mosquitoes as an example to demonstrate that both mechanisms are interconnected to coordinate hormonal responses. Our results indicate that the phospholipase C pathway is activated shortly after hormone exposure. Activation of this pathway induces phosphorylation of MET and profoundly increases the ability of MET to bind to JH target. This study establishes the link between the membrane-initiated JH signaling and the MET-mediated genomic action of JH.
Molecular cartography of the human skin surface in 3D
Authors: Bouslimani Amina , Porto Carla , Rath Christopher M. , Wang Mingxun , Guo Yurong , Gonzalez Antonio , Berg-Lyon Donna , Ackermann Gail , Moeller Christensen Gitte Julie , Nakatsuji Teruaki , Zhang Lingjuan , Borkowski Andrew W. , Meehan Michael J. , Dorrestein Kathleen , Gallo Richard L. , Bandeira Nuno , Knight Rob , Alexandrov Theodore , Dorrestein Pieter C.
Published: April 2015

Significance

The paper describes the implementation of an approach to study the chemical makeup of human skin surface and correlate it to the microbes that live in the skin. We provide the translation of molecular information in high-spatial resolution 3D to understand the body distribution of skin molecules and bacteria. In addition, we use integrative analysis to interpret, at a molecular level, the large scale of data obtained from human skin samples. Correlations between molecules and microbes can be obtained to further gain insights into the chemical milieu in which these different microbial communities live.
Ideal probe single-molecule experiments reveal the intrinsic dynamic heterogeneity of a supercooled liquid
Authors: Paeng Keewook , Park Heungman , Hoang Dat Tien , Kaufman Laura J.
Published: April 2015

Significance

Supercooled liquids are believed to exhibit spatially heterogeneous dynamics, where molecular mobility within a given spatial region may differ from that of a neighboring region, potentially by orders of magnitude. If supercooled liquids are ergodic, such that the spatial average of all regions with distinct dynamics equals the time average of a given region, these regions of distinct dynamics must interchange over time. With an appropriate probe, similar in size and mobility to the host, single-molecule measurements can provide direct access to these spatial and temporal variations. Here, such a probe is used, revealing how relaxation dynamics are distributed in time and space and directly demonstrating ergodicity of a prototypical glass former down to the glass transition temperature.
Diversity partitioning during the Cambrian radiation
Authors: Na Lin , Kiessling Wolfgang
Published: April 2015

Significance

Many mechanisms of the Cambrian Explosion have been proposed, but rigorous quantitative analyses of biodiversity dynamics are scarce, although they may shed light on important factors. Using a comprehensive database and sampling standardization, we dissect global diversity patterns. The trajectories of within-community, between-community, and global diversity during the main phase of the Cambrian radiation revealed a low-competition model, which was probably governed by niche contraction and the increase of predation at local scales. At continental scales, the increase of beta diversity was controlled by the high rate of community turnover among adjacent continents. This finding supports the general importance of plate tectonics in large-scale diversifications.
Molecular recognition of human ephrinB2 cell surface receptor by an emergent African henipavirus
Authors: Lee Benhur , Pernet Olivier , Ahmed Asim A. , Zeltina Antra , Beaty Shannon M. , Bowden Thomas A.
Published: April 2015

Significance

African henipaviruses (HNVs) may be responsible for the misdiagnosis of encephalitis-associated outbreaks of malaria. Host-cell infection by an African HNV relies on the initial interaction between a virally encoded surface glycoprotein and a host-cell receptor. Here, we provide a structural description of how a bat-borne Ghanaian HNV hijacks human ephrinB2 to facilitate cross-species transmission. We demonstrate that, although the Ghanian HNV is sequence dissimilar (<30% sequence identity) and displays a receptor-binding scaffold that differs significantly in structure to pathogenic HNV relatives from Asia, it adopts a nearly identical primary ephrinB2 binding mode. These data provide a molecular-level explanation for previously observed spillover of African HNVs into human populations.
Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells
Authors: Hayashi Yohei , Caboni Laura , Das Debanu , Yumoto Fumiaki , Clayton Thomas , Deller Marc C. , Nguyen Phuong , Farr Carol L. , Chiu Hsiu-Ju , Miller Mitchell D. , Elsliger Marc-André , Deacon Ashley M. , Godzik Adam , Lesley Scott A. , Tomoda Kiichiro , Conklin Bruce R. , Wilson Ian A. , Yamanaka Shinya , Fletterick Robert J.
Published: April 2015

Significance

Maintenance and reprogramming of pluripotency are among the most important issues in stem cell biology and regenerative medicine. Pluripotency is governed by several key transcription factors regulating transcription of other factors. Among these, regulation of
OCT4
transcription by NANOG (from Irish myth-ology Tír na nÓg) is a critical interaction. We present here the crystal structure of human NANOG homeodomain in complex with the
OCT4
promoter DNA and, through a series of ration-ally designed mutations, we identify key functional residues in the protein–DNA interaction, protein stability, and maintenance of mouse ESC self-renewal. Furthermore, we describe a mutation, NANOG L122A, which enhances DNA binding affinity, protein stability, mouse ESC self-renewal, and reprogramming into ground state from primed state pluripotency.
Gα
i1
and Gα
i3
regulate macrophage polarization by forming a complex containing CD14 and Gab1
Authors: Li Xianjing , Wang Duowei , Chen Zhen , Lu Ermei , Wang Zhuo , Duan Jingjing , Tian Wei , Wang Yun , You Linjun , Zou Yulian , Cheng Yan , Zhu Qingyi , Wan Xiaojian , Xi Tao , Jiang Meisheng , Han Yuyuan , Cao Cong , Birnbaumer Lutz , Chu Wen-Ming , Yang Yong
Published: April 2015

Significance

In this study, we demonstrate that guanine nucleotide-binding protein G(i) subunit alpha-1 and alpha-3 (Gα
i1/3
) regulate the downstream signaling pathways of Toll-like receptor 4 (TLR4). We show that Gα
i1/3
form complexes containing the pattern recognition receptor (PRR) CD14 and growth factor receptor binding 2 (Grb2)-associated binding protein (Gab1), which are required for activation of PI3K-Akt signaling and NF-κB activation. Besides, Gα
i1/3
act at both the plasma membrane and the endosome levels and are involved in TLR4 endocytosis. Furthermore, Gα
i1/3
participated in the induction of M1 polarization of macrophages, and their decreased expression contributed to LPS tolerance. Thus, Gα
i1/3
are important in controlling inflammation.
Decoding stimulus features in primate somatosensory cortex during perceptual categorization
Authors: Alvarez Manuel , Zainos Antonio , Romo Ranulfo
Published: April 2015

Significance

A key step in studying perceptual categorization mechanisms is to understand how neurons from early sensory cortices encode the relevant features categorized of a sensory stimulus and how they relate to it. We studied the encoding capacities of primary somatosensory cortex (S1) neurons while trained monkeys categorized only one sensory feature of a vibrotactile stimulus: frequency, amplitude, or duration. The results suggest a hierarchical encoding scheme in S1: from neurons that encode all sensory features of the vibrotactile stimulus to neurons that encode only one sensory feature. Sensory feature encoding in S1 could serve downstream networks for constructing perceptual categorization.
Tectal microcircuit generating visual selection commands on gaze-controlling neurons
Authors: Kardamakis Andreas A. , Saitoh Kazuya , Grillner Sten
Published: April 2015

Significance

Neurons in the optic tectum are involved in stimulus selection and also control gaze reorientation. This study relies on an in vitro preparation that allows visual activation of the retina while providing accessibility for whole-cell recordings from specific cells that control gaze action. We show the tectal (collicular in mammals) GABAergic interneurons generate rivalry between visual areas and that tectal gaze-controlling cells integrate this inhibition along with local retinal excitation to form stimulus selection commands that will move the eyes and head, and may also contribute to edge detection. We propose that this subcortical visuomotor circuit is phylogenetically conserved throughout vertebrate evolution.
Spontaneous dynamics and wild design in green roofs
Authors: Lundholm Jeremy T.
Published: April 2015

Green roofs and other constructed environments represent novel ecosystems, yet have potential to contribute to biodiversity conservation goals. Constructed ecosystems are intentionally managed to produce specific services, and thus could be viewed as highly artificial or controlled. Yet all constructed ecosystems exhibit spontaneous dynamics, as community structure changes due to internal or external ecological processes. While all green roofs have some element of design and human control over ecological trajectories, the level of ongoing management can vary greatly. I discuss “wildness” as a characteristic of green roofs in response to their spontaneous dynamics after initial setup, and their potential to provide ecosystem services related to human psychological well-being, aesthetics and habitat for biodiversity. This approach suggests new design possibilities in interaction with spontaneous ecosystem dynamics and highlights a need for greater ecological understanding of green roof systems.
Values in Science: The Case of Scientific Collaboration
Authors: Rolin Kristina
Published: April 2015

Much of the literature on values in science is limited in its perspective because it focuses on the role of values in individual scientists’ decision making, thereby ignoring the context of scientific collaboration. I examine the epistemic structure of scientific collaboration and argue that it gives rise to two arguments showing that moral and social values can legitimately play a role in scientists’ decision to accept something as scientific knowledge. In the case of scientific collaboration some moral and social values are properly understood to be extrinsic epistemic values, that is, values that promote the attainment of scientific knowledge.
On the structure of almost Einstein manifolds
Authors: Tian Gang , Wang Bing
Published: April 2015

In this paper, we study the structure of the limit space of a sequence of almost Einstein manifolds, which are generalizations of Einstein manifolds. Roughly speaking, such manifolds are the initial manifolds of some normalized Ricci flows whose scalar curvatures are almost constants over space-time in the

L
1

L^1

-sense, and Ricci curvatures are bounded from below at the initial time. Under the non-collapsed condition, we show that the limit space of a sequence of almost Einstein manifolds has most properties which are known for the limit space of Einstein manifolds. As applications, we can apply our structure results to study the properties of Kähler manifolds.
Sub-MeV band observation of a hard burst from AXP 1E 1547.0−5408 with the Suzaku Wide-band All-sky Monitor
Authors: Yasuda Tetsuya , Iwakiri Wataru B. , Tashiro Makoto S. , Terada Yukikatsu , Kouzu Tomomi , Enoto Teruaki , Nakagawa Yujin E. , Bamba Aya , Urata Yuji , Yamaoka Kazutaka , Ohno Masanori , Shibata Shinpei , Makishima Kazuo
Published: April 2015

The 2.1-s anomalous X-ray pulsar 1E 1547.0−5408 exhibited an X-ray outburst on 2009 January 22, emitting a large number of short bursts. The wide-band all-sky monitor (WAM) on-board Suzaku detected at least 254 bursts in the 160 keV–6.2 MeV band over the period of January 22 00:57–17:02 UT from the direction of 1E 1547.0−5408. One of these bursts, which occurred at 06:45:13, produced the brightest fluence in the 0.5–6.2 MeV range, with an averaged 0.16–6.2 MeV flux and extrapolated 25 keV–2 MeV fluence of about 1 × 10−5 erg cm−2 s−1 and about 3 × 10−4 erg cm−2, respectively. After pile-up corrections, the time-resolved WAM spectra of this burst were well-fitted in the 0.16–6.2 MeV range by two-component models; specifically, a blackbody plus an optically thin thermal bremsstrahlung or a combination of a blackbody and a power-law component with an exponential cut-off. These results are compared with previous works reporting the persistent emission and weaker short bursts followed by the same outburst.
Applications of computational models to better understand microvascular remodelling: a focus on biomechanical integration across scales
Authors: Murfee Walter L. , Sweat Richard S. , Tsubota Ken-ichi , Gabhann Feilim Mac , Khismatullin Damir , Peirce Shayn M.
Published: April 2015

Microvascular network remodelling is a common denominator for multiple pathologies and involves both angiogenesis, defined as the sprouting of new capillaries, and network patterning associated with the organization and connectivity of existing vessels. Much of what we know about microvascular remodelling at the network, cellular and molecular scales has been derived from reductionist biological experiments, yet what happens when the experiments provide incomplete (or only qualitative) information? This review will emphasize the value of applying computational approaches to advance our understanding of the underlying mechanisms and effects of microvascular remodelling. Examples of individual computational models applied to each of the scales will highlight the potential of answering specific questions that cannot be answered using typical biological experimentation alone. Looking into the future, we will also identify the needs and challenges associated with integrating computational models across scales.