bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation and prediction of color-tunable organic light-emitting diodes based on carrier/exciton adjusting interlayer
Authors: Liu Shengqiang , Li Jie , Du Chunlei , Yu Junsheng
Published: July 2015

A color tuning index (ICT) parameter for evaluating the color change capability of color-tunable organic light-emitting diodes (CT-OLEDs) was proposed and formulated. And a series of CT-OLEDs, consisting of five different carrier/exciton adjusting interlayers (C/EALs) inserted between two complementary emitting layers, were fabricated and applied to disclose the relationship between ICT and C/EALs. The result showed that the trend of electroluminescence spectra behavior in CT-OLEDs has good accordance with ICT values, indicating that the ICT parameter is feasible for the evaluation of color variation. Meanwhile, by changing energy level and C/EAL thickness, the optimized device with the widest color tuning range was based on N,N′-dicarbazolyl-3,5-benzene C/EAL, exhibiting the highest ICT value of 41.2%. Based on carrier quadratic hopping theory and exciton transfer model, two fitting ICT formulas derived from the highest occupied molecular orbital (HOMO) energy level and triplet energy level were simulated. Finally, a color tuning prediction (CTP) model was developed to deduce the ICT via C/EAL HOMO and triplet energy levels, and verified by the fabricated OLEDs with five different C/EALs. We believe that the CTP model assisted with ICT parameter will be helpful for fabricating high performance CT-OLEDs with a broad range of color tuning.
Negative differential resistance in direct bandgap GeSn p-i-n structures
Authors: Schulte-Braucks C. , Stange D. , von den Driesch N. , Blaeser S. , Ikonic Z. , Hartmann J. M. , Mantl S. , Buca D.
Published: July 2015

Certain GeSn alloys are group IV direct bandgap semiconductors with prospects for electrical and optoelectronical applications. In this letter, we report on the temperature dependence of the electrical characteristics of high Sn-content Ge0.89Sn0.11 p-i-n diodes. NiGeSn contacts were used to minimize the access resistance and ensure compatibility with silicon technology. The major emphasis is placed on the negative differential resistance in which peak to valley current ratios up to 2.3 were obtained. TCAD simulations were performed to identify the origin of the various current contributions, providing evidence for direct band to band tunneling and trap assisted tunneling.
Fast reversible laser-induced crystallization of Sb-rich Zn-Sb-Se phase change material with excellent stability
Authors: Chen Yimin , Wang Guoxiang , Tian Manman , Shen Xiang , Xu Tiefeng , Lu Yegang , Dai Shixun , Nie Qiuhua
Published: July 2015

We present a new reversible phase-change medium Sb-rich Zn-Sb-Se film, which possesses a large difference in both optical and electrical constant. The doped-ZnSb, sub-formed Zn-Se, and exhausted Sb-Se3/2 co-influence the physical properties. Typically, there is ∼105 resistance ratio and ∼14% relative reflectivity change in Zn19Sb45.7Se35.3 film when switched by electricity or laser pulses between amorphous and crystalline states. The higher Tc (∼250°C), larger Ea (∼8.57eV), better 10-yr data retention (∼200.2°C), higher crystallization resistance (∼3 × 103Ω/□ at 300°C-annealled) and relative lower melting temperature (∼550.2°C) are exhibited in Zn19Sb45.7Se35.3 film. Importantly, a short crystalline time (∼80ns at 70mW) of the ideal Zn19Sb45.7Se35.3 film can be obtained without sacrificing room-temperature stability.
Construction of a New ZnII Coordination Polymer for Selective Fluorescence Sensing of CCl4
Authors: Li Jiang-Tao , Dong Yan-Li , Li Jing
Published: July 2015

Solvothermal reactions of Zn(NO3)2·6H2O, H3tci, and biimpy generated a new ZnII coordination polymer namely [Zn3(tci)2(biimpy)]n·2n(DMF) (1 H3tci = tri(2-carboxyethyl)isocyanurate, biimpy = 2,6-bis(1-imdazoly)pyridine, DMF = N,N-dimethylformamide). Single-Crystal X-ray diffraction analysis reveals that compound 1 features a 2-fold interpenetrated 3D pillar-layered framework based on trinuclear [Zn3(COO)6] cluster subunits. Topological analysis reveals that compound 1 represents a 2-fold interpenetrated (3,8)-connected tfz-d topological network with the point symbol of {43}2{46.618.84}. The luminescence properties of compound 1 dispersed in different organic solvents were systematically investigated. The results indicated that compound 1 can be used as a candidate for selective sensing of CCl4 via a luminescence quenching mechanism.
Environmental effects on arsenosugars and arsenolipids in Ectocarpus (Phaeophyta)
Authors: Pétursdóttir Ásta H. , Fletcher Kyle , Gunnlaugsdóttir Helga , Krupp Eva , Küpper Frithjof C. , Feldmann Jörg
Published: July 2015

Environmental context
Arsenolipids, which are present in seaweed, can show high toxicity, emphasising the need for more information on these compounds. We investigated the effects of different stress factors on the arsenic compounds formed by cultures of brown algae, and compared the results with those from field-collected samples. We show that the arsenolipid and arsenosugar profiles differ depending on the experimental conditions, and that a deficiency in phosphate has a direct positive effect on the biosynthesis of arsenic-containing phospholipids.

Abstract
Seaweeds have recently been shown to contain a significant proportion of arsenic in the form of arsenolipids (AsLp). Three strains of the filamentous brown alga Ectocarpus species were grown in the laboratory with different simulations of environmental stress: control conditions (1/2 Provasoli-enriched seawater), low nitrate (30% of the amount of nitrates in the control), low phosphate (30% of the amount of phosphate in the control) and under oxidative stress levels (2mM H2O2). Generally, the major AsLp was an arsenic-containing hydrocarbon, AsHC360 (50–80%), but additionally, several arsenic-containing phospholipids (AsPL) were identified and quantified using high-performance liquid chromatography–inductively coupled plasma mass spectrometry and electrospray ionisation mass spectrometry (HPLC-ICP-MS/ESI-MS). The AsLps in cultures were compared with AsLps in Ectocarpus found in its natural habitat as well as with other brown filamentous algae. The AsLp and arsenosugar profiles differed depending on the experimental conditions. Under low phosphate conditions, a significant reduction of phosphorus-containing arsenosugars was noticed, and a significant increase of phosphate-containing AsLps was found when compared with the controls. Strains grown under oxidative stress showed a significant increase in AsLps as well as clear physiological changes.
Derivation of soil-attribute estimations from legacy soil maps
Authors: Odgers Nathan P. , Holmes Karen W. , Griffin Ted , Liddicoat Craig
Published: July 2015

It is increasingly necessary to apply quantitative techniques to legacy soil polygon maps given that legacy soil maps may be the only source of soil information over large areas. Spatial disaggregation provides a means of extracting information from legacy soil maps and enables us to downscale the original information to produce new soil class maps at finer levels of detail. This is a useful outcome in its own right; however, the disaggregated soil-class coverage can also be used to make digital maps of soil properties with associated estimates of uncertainty. In this work, we take the spatially disaggregated soil-class coverage for all of Western Australia and the agricultural region of South Australia and demonstrate its application in mapping clay content at six depth intervals in the soil profile. Estimates of uncertainty are provided in the form of the 90% prediction interval. The work can be considered an example of harmonisation to a common output specification. The validation results highlighted areas in the landscape and taxonomic spaces where more knowledge of soil properties is necessary.
Is aridity a high-order control on the hydro–geomorphic response of burned landscapes?
Authors: Sheridan Gary J. , Nyman Petter , Langhans Christoph , Cawson Jane , Noske Philip J. , Oono Akiko , Van der Sant Rene , Lane Patrick N. J.
Published: July 2015

Fire can result in hydro–geomorphic changes that are spatially variable and difficult to predict. In this research note we compile 294 infiltration measurements and 10 other soil, catchment runoff and erosion datasets from the eastern Victorian uplands in south-eastern Australia and argue that higher aridity (a function of the long-term mean precipitation and net radiation) is associated with lower post-fire infiltration capacities, increasing the chance of surface runoff and strongly increasing the chance of debris flows. Post-fire debris flows were only observed in the more arid locations within the Victorian uplands, and resulted in erosion rates more than two orders of magnitude greater than non-debris flow processes. We therefore argue that aridity is a high-order control on the magnitude of post-wildfire hydro–geomorphic processes. Aridity is a landscape-scale parameter that is mappable at a high resolution and therefore is a useful predictor of the spatial variability of the magnitude of post-fire hydro–geomorphic responses.
Systematic review of current efforts to quantify the impacts of climate change on undernutrition
Authors: Phalkey Revati K. , Aranda-Jan Clara , Marx Sabrina , Höfle Bernhard , Sauerborn Rainer
Published: July 2015

Significance

The World Health Organization and the Intergovernmental Panel for Climate Change propose undernutrition as the most significant impact of climate change on child health. The question then arises: Where does the empirical evidence to back this claim come from? Current evidence for the impacts of climate on childhood undernutrition draws on a limited number of heterogeneous studies with methodological limitations and is based predominantly on secondary data. Establishing and validating causal pathways among complex confounding factors remain the main challenge in quantifying the climate-attributable fraction of undernutrition. Systematically generating evidence from long-term, high-quality primary data on a range of factors (agricultural, environmental, socioeconomic, and health) at the household level is critical for designing adaptation strategies, particularly for subsistence farmers.
Relation between stability and resilience determines the performance of early warning signals under different environmental drivers
Authors: Dai Lei , Korolev Kirill S. , Gore Jeff
Published: July 2015

Significance

Alternative stable states and critical transitions are widespread in nature and can have profound consequences for conservation, climate changes, and human health. Our current toolbox of early warning signals before critical transitions has seen both successes and failures. Understanding the limitations of these indicators is crucial for application in real-world scenarios. In this study, we explored the population dynamics of laboratory yeast under different forms of environmental deterioration. We found that the performance of early warning signals under different environmental drivers is determined by the underlying relation between stability and resilience. This work presents a framework to evaluate the utility of early warning signals, and it sets a foundation for further studies on how dynamical systems respond to environmental changes.
MALDI mass spectrometry imaging analysis of pituitary adenomas for near-real-time tumor delineation
Authors: Calligaris David , Feldman Daniel R. , Norton Isaiah , Olubiyi Olutayo , Changelian Armen N. , Machaidze Revaz , Vestal Matthew L. , Laws Edward R. , Dunn Ian F. , Santagata Sandro , Agar Nathalie Y. R.
Published: July 2015

Significance

This study presents the use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to detect and delineate pituitary tumors. Using MALDI MSI, it is possible to determine the peptide and protein hormone composition of pituitary tumor resection samples in fewer than 30 min. Surgeons could therefore have access to critical information for surgical decision-making in a near-real-time manner and be able to localize and discriminate pituitary tumor from nonpathological pituitary gland. This study supports the inclusion of MALDI MSI in the clinical workflow for the surgical resection of pituitary tumors, potentially allowing for improved surgical precision and patient outcomes.
Action potentials and amphetamine release antipsychotic drug from dopamine neuron synaptic VMAT vesicles
Authors: Tucker Kristal R. , Block Ethan R. , Levitan Edwin S.
Published: July 2015

Significance

Antipsychotic drugs (APDs) are dopamine (DA) receptor antagonists, whose action has been hypothesized to be affected by acidic trapping in and release by synaptic vesicles. However, acidic trapping of APDs has not been detected directly. Therefore, multiphoton microscopy was used to image an APD directly in living brain slices containing DA neurons. The APD accumulated by acidic trapping, and in the striatum, it was selectively depleted from DA synaptic vesicles by an amphetamine. Action potentials evoked Ca2+-dependent striatal APD depletion, suggesting release by vesicle exocytosis. Therefore, APDs concentrate by acidic trapping in DA synaptic vesicles so that these antagonists will be coreleased with the native transmitter when and where physiological and pharmacological stimuli evoke dopaminergic transmission.
Decadal acidification in the water masses of the Atlantic Ocean
Authors: Ríos Aida F. , Resplandy Laure , García-Ibáñez Maribel I. , Fajar Noelia M. , Velo Anton , Padin Xose A. , Wanninkhof Rik , Steinfeldt Reiner , Rosón Gabriel , Pérez Fiz F.
Published: July 2015

Significance

We provide the first (to our knowledge) observation-based acidification trends in the water masses of the Atlantic basin over the past two decades and compare them with climate model results. Observations and model output confirm that pH changes in surface layers are dominated by the anthropogenic component. In mode and intermediate waters, the anthropogenic and natural components are of the same order of magnitude and sign. Large changes in the natural component of newly formed mode and intermediate waters are associated with latitudinal shifts of these water masses caused by the Southern Annular Mode in the South Atlantic and by changes in the rates of water mass formation in the North Atlantic.
Orthologs of the archaeal isopentenyl phosphate kinase regulate terpenoid production in plants
Authors: Henry Laura K. , Gutensohn Michael , Thomas Suzanne T. , Noel Joseph P. , Dudareva Natalia
Published: July 2015

Significance

Terpenoids, one of the largest and most diverse classes of natural products, are found in all living organisms, where they play essential roles in growth and development, respiration and photosynthesis, and interactions with the environment. We discovered that a functional homolog of isopentenyl phosphate kinase (IPK), originally identified in archaebacteria, is unexpectedly present in plants and functions in their terpenoid metabolic network. Cytosolically localized, IPK phosphorylates isopentenyl phosphate (IP) and its isomer dimethylallyl phosphate (DMAP) to their corresponding diphosphates, IPP and DMAPP, the universal C5 building blocks of all natural terpenoids. IPK enhances terpenoid formation by returning IP/DMAP to the terpenoid biosynthetic network. This metabolite reactivation process offers a new approach for metabolic engineering of economically important terpenoids.
Amber fossils demonstrate deep-time stability of Caribbean lizard communities
Authors: Sherratt Emma , del Rosario Castañeda María , Garwood Russell J. , Mahler D. Luke , Sanger Thomas J. , Herrel Anthony , de Queiroz Kevin , Losos Jonathan B.
Published: July 2015

Significance

An unresolved question in ecology is whether the structure of ecological communities can be stable over very long timescales. Here we describe a wealth of new amber fossils for an ancient radiation of Hispaniolan lizards that, until now, has had a very poor fossil record. These fossils provide an important and previously unavailable perspective on an ecologically well-studied group and indicate that anole lizard communities occurring on Hispaniola 20 Mya were made up of the same types of habitat specialists present in this group today. These data indicate that the ecological processes important in extant anole communities have been operative over long periods of time.
Bayesian chronological analyses consistent with synchronous age of 12,835–12,735 Cal B.P. for Younger Dryas boundary on four continents
Authors: Kennett James P. , Kennett Douglas J. , Culleton Brendan J. , Aura Tortosa J. Emili , Bischoff James L. , Bunch Ted E. , Daniel I. Randolph , Erlandson Jon M. , Ferraro David , Firestone Richard B. , Goodyear Albert C. , Israde-Alcántara Isabel , Johnson John R. , Jordá Pardo Jesús F. , Kimbel David R. , LeCompte Malcolm A. , Lopinot Neal H. , Mahaney William C. , Moore Andrew M. T. , Moore Christopher R. , Ray Jack H. , Stafford Thomas W. , Tankersley Kenneth Barnett , Wittke James H. , Wolbach Wendy S. , West Allen
Published: July 2015

The Younger Dryas impact hypothesis posits that a cosmic impact across much of the Northern Hemisphere deposited the Younger Dryas boundary (YDB) layer, containing peak abundances in a variable assemblage of proxies, including magnetic and glassy impact-related spherules, high-temperature minerals and melt glass, nanodiamonds, carbon spherules, aciniform carbon, platinum, and osmium. Bayesian chronological modeling was applied to 354 dates from 23 stratigraphic sections in 12 countries on four continents to establish a modeled YDB age range for this event of 12,835–12,735 Cal B.P. at 95% probability. This range overlaps that of a peak in extraterrestrial platinum in the Greenland Ice Sheet and of the earliest age of the Younger Dryas climate episode in six proxy records, suggesting a causal connection between the YDB impact event and the Younger Dryas. Two statistical tests indicate that both modeled and unmodeled ages in the 30 records are consistent with synchronous deposition of the YDB layer within the limits of dating uncertainty (∼100 y). The widespread distribution of the YDB layer suggests that it may serve as a datum layer.
Highly permeable artificial water channels that can self-assemble into two-dimensional arrays
Authors: Shen Yue-xiao , Si Wen , Erbakan Mustafa , Decker Karl , De Zorzi Rita , Saboe Patrick O. , Kang You Jung , Majd Sheereen , Butler Peter J. , Walz Thomas , Aksimentiev Aleksei , Hou Jun-li , Kumar Manish
Published: July 2015

Significance

This study focuses on the design of highly permeable artificial water channels for the use in membrane-based separation materials. A platform was developed for the systematic characterization of the single-channel water conduction of artificial channels, which is based on permeability measurement by stopped-flow light-scattering experiments and single-molecule counting by fluorescence correlation spectroscopy. With this platform the water conduction of the redesigned peptide-appended pillar[5]arene channels was found to be similar to that of aquaporins, natural water channel proteins, and their synthetic analogs, carbon nanotubes, which is an order of magnitude higher than that of first-generation artificial water channels. The channel can also self-assemble into arrays in membranes, opening the possibility for materials that can be used in engineering applications such as liquid and gas separations.
Divergent responses of Atlantic coastal and oceanic
Synechococcus
to iron limitation
Authors: Mackey Katherine R. M. , Post Anton F. , McIlvin Matthew R. , Cutter Gregory A. , John Seth G. , Saito Mak A.
Published: July 2015

Significance

Conventional knowledge suggests that coastal phytoplankton are less able to adapt to Fe limitation than open ocean species. Here we show that in contrast to the established paradigm, coastal
Synechococcus
from the New England shelf is capable of dynamic, multitiered Fe adaptation that allows it to thrive over a broad range of Fe concentrations by partitioning Fe among different uptake and storage proteins. This protein-based response is beneficial in high nitrogen (N) waters with low and variable Fe:N ratios. An oceanic Atlantic
Synechococcus
isolate lacks this adaptive response, suggesting the small yet significant N cost of retaining Fe response proteins offsets the benefit of Fe adaptability in the southern Sargasso Sea, where N is chronically scarce and Fe:N ratios are high.
Prophylactic and postexposure efficacy of a potent human monoclonal antibody against MERS coronavirus
Authors: Corti Davide , Zhao Jincun , Pedotti Mattia , Simonelli Luca , Agnihothram Sudhakar , Fett Craig , Fernandez-Rodriguez Blanca , Foglierini Mathilde , Agatic Gloria , Vanzetta Fabrizia , Gopal Robin , Langrish Christopher J. , Barrett Nicholas A , Sallusto Federica , Baric Ralph S. , Varani Luca , Zambon Maria , Perlman Stanley , Lanzavecchia Antonio
Published: July 2015

Significance

Middle East Respiratory Syndrome coronavirus (MERS-CoV) causes severe respiratory disease with a high mortality rate. There is no licensed vaccine or antiviral for MERS. Here we isolated for the first time, to our knowledge, a potent MERS-CoV–neutralizing antibody from memory B cells of an infected individual. This antibody binds to a novel site on the viral Spike protein, neutralizes by interfering with the binding to the cellular receptor CD26, and is highly effective both in prophylaxis and in therapy in a relevant mouse model. This antibody can be developed for prophylaxis, for postexposure prophylaxis, or for the treatment of severe MERS-CoV infections.
Activity-dependent BDNF release via endocytic pathways is regulated by synaptotagmin-6 and complexin
Authors: Wong Yu-Hui , Lee Chia-Ming , Xie Wenjun , Cui Bianxiao , Poo Mu-ming
Published: July 2015

Significance

Brain-derived neurotrophic factor (BDNF) is a secreted neurotrophin known to mediate activity-dependent synaptic plasticity. Endogenously synthesized BDNF is normally stored and transported in dense core vesicles and secreted at synapses in response to activity. However, secreted BDNF may also be endocytosed by neurons and transported within neuronal cytoplasm in the form of endosomes. By monitoring the endocytosed BDNF bound to fluorescent quantum dots (BDNF-QDs), we found that endocytosed BDNF-QDs could be preferentially localized to postsynaptic sites in cultured hippocampal neurons and became exocytosed in response to synaptic activity. This synaptic release of endocytic BDNF requires a synaptotagmin isoform distinct from that regulates the secretion of dense core vesicles, and may serve as a source for activity-dependent secretion of synaptic BDNF.
Discrete approach to stochastic parametrization and dimension reduction in nonlinear dynamics
Authors: Chorin Alexandre J. , Lu Fei
Published: July 2015

Significance

Many problems in science are too large and/or too complex to be fully analyzed by standard methods of computation. We present an approach where such problems are treated statistically, and the statistical analysis and the equations actually solved are discrete rather than continuous. We connect our approach to well-known results in statistical physics, and demonstrate its effectiveness in a widely used test problem.
Gating of a mechanosensitive channel due to cellular flows
Authors: Pak On Shun , Young Y.-N. , Marple Gary R. , Veerapaneni Shravan , Stone Howard A.
Published: July 2015

Significance

Mechanosensitive (MS) channels are membrane proteins that can be gated by membrane tension, and they play major roles in mechanosensation and mechanotransduction in cells. As a step in understanding the dynamics of a MS channel in membranes exposed to fluid flows, a multiscale continuum model is constructed to address how a MS channel in a vesicle membrane can be gated by flow-generated stresses in two physiological flows: planar shear flow and pressure-driven flow across a constriction channel. We demonstrate the opening/closing of a MS channel as a function of the flow strength and physical parameters. Our numerical results also suggest the possibility of utilizing fluid flows to deliver macromolecules (e.g., drugs) by gating MS channels reconstituted in liposomes in microfluidic platforms.
Generation of knock-in primary human T cells using Cas9 ribonucleoproteins
Authors: Schumann Kathrin , Lin Steven , Boyer Eric , Simeonov Dimitre R. , Subramaniam Meena , Gate Rachel E. , Haliburton Genevieve E. , Ye Chun J. , Bluestone Jeffrey A. , Doudna Jennifer A. , Marson Alexander
Published: July 2015

Significance

T-cell genome engineering holds great promise for cancer immunotherapies and cell-based therapies for HIV, primary immune deficiencies, and autoimmune diseases, but genetic manipulation of human T cells has been inefficient. We achieved efficient genome editing by delivering Cas9 protein pre-assembled with guide RNAs. These active Cas9 ribonucleoproteins (RNPs) enabled successful Cas9-mediated homology-directed repair in primary human T cells. Cas9 RNPs provide a programmable tool to replace specific nucleotide sequences in the genome of mature immune cells—a longstanding goal in the field. These studies establish Cas9 RNP technology for diverse experimental and therapeutic genome engineering applications in primary human T cells.
Demographics of Shovelnose Sturgeon in the Lower Wabash River, Illinois
Authors: Nepal KC Vaskar , Colombo Robert E. , Frankland Leslie D.
Published: July 2015

With the closure of commercial fishing for Shovelnose Sturgeon Scaphirhynchus platorynchus in most reaches of the Mississippi and Missouri rivers, harvest may increase in other rivers. We studied the demographics of a commercially exploited Shovelnose Sturgeon population in the lower 322 km of the Wabash River, Illinois. During 2000–2013, 10,734 Shovelnose Sturgeon were captured by using DC and AC electrofishing, gill nets, hoop nets, trotlines, and benthic trawls. Of the captured individuals, 399 fish were recaptured. Electrofishing CPUE was the highest reported in any study on Shovelnose Sturgeon. Captured fish ranged between 61 and 909 mm FL (mean = 662 mm; median = 671 mm), but few fish were smaller than 500 mm. Although the fish were in good condition (mean relative weight = 89.9), there was a decreasing trend in mean condition over time. Shovelnose Sturgeon ranged in age from 0 to 25 years; 90% of the fish were between age 8 and age 19. Fish were fully recruited to the sampling gear at age 10; total annual mortality for fish older than 10 years was 20.6%. An empirical growth rate of 2.67 mm/year was observed for fish larger than 635 mm, with several individuals showing negative growth. The sex ratio was slightly skewed toward males (2.18 males : 1 female). The Shovelnose Sturgeon population in the lower Wabash River was generally healthy and stable and had characteristics comparable to those of the upper Wabash River population, with slow growth, large sizes, good condition, and low mortality.

Received December 19, 2014; acceptedMay 11, 2015
Lrrk regulates the dynamic profile of dendritic Golgi outposts through the golgin Lava lamp
Authors: Lin Chin-Hsien , Li Hsun , Lee Yi-Nan , Cheng Ying-Ju , Wu Ruey-Meei , Chien Cheng-Ting
Published: July 2015

Constructing the dendritic arbor of neurons requires dynamic movements of Golgi outposts (GOPs), the prominent component in the dendritic secretory pathway. GOPs move toward dendritic ends (anterograde) or cell bodies (retrograde), whereas most of them remain stationary. Here, we show that Leucine-rich repeat kinase (Lrrk), the Drosophila melanogaster homologue of Parkinson’s disease–associated Lrrk2, regulates GOP dynamics in dendrites. Lrrk localized at stationary GOPs in dendrites and suppressed GOP movement. In Lrrk loss-of-function mutants, anterograde movement of GOPs was enhanced, whereas Lrrk overexpression increased the pool size of stationary GOPs. Lrrk interacted with the golgin Lava lamp and inhibited the interaction between Lva and dynein heavy chain, thus disrupting the recruitment of dynein to Golgi membranes. Whereas overexpression of kinase-dead Lrrk caused dominant-negative effects on GOP dynamics, overexpression of the human LRRK2 mutant G2019S with augmented kinase activity promoted retrograde movement. Our study reveals a pathogenic pathway for LRRK2 mutations causing dendrite degeneration.
SNAREs support atlastin-mediated homotypic ER fusion in Saccharomyces cerevisiae
Authors: Lee Miriam , Ko Young-Joon , Moon Yeojin , Han Minsoo , Kim Hyung-Wook , Lee Sung Haeng , Kang KyeongJin , Jun Youngsoo
Published: July 2015

Dynamin-like GTPases of the atlastin family are thought to mediate homotypic endoplasmic reticulum (ER) membrane fusion; however, the underlying mechanism remains largely unclear. Here, we developed a simple and quantitative in vitro assay using isolated yeast microsomes for measuring yeast atlastin Sey1p-dependent ER fusion. Using this assay, we found that the ER SNAREs Sec22p and Sec20p were required for Sey1p-mediated ER fusion. Consistently, ER fusion was significantly reduced by inhibition of Sec18p and Sec17p, which regulate SNARE-mediated membrane fusion. The involvement of SNAREs in Sey1p-dependent ER fusion was further supported by the physical interaction of Sey1p with Sec22p and Ufe1p, another ER SNARE. Furthermore, our estimation of the concentration of Sey1p on isolated microsomes, together with the lack of fusion between Sey1p proteoliposomes even with a 25-fold excess of the physiological concentration of Sey1p, suggests that Sey1p requires additional factors to support ER fusion in vivo. Collectively, our data strongly suggest that SNARE-mediated membrane fusion is involved in atlastin-initiated homotypic ER fusion.
Actin hotspots blaze a trail along axons
Authors: Short Ben
Published: July 2015

Study identifies a dynamic cytoskeletal network that delivers actin to presynaptic boutons.
Functional IRF3 deficiency in a patient with herpes simplex encephalitis
Authors: Andersen Line Lykke , Mørk Nanna , Reinert Line S. , Kofod-Olsen Emil , Narita Ryo , Jørgensen Sofie E. , Skipper Kristian A. , Höning Klara , Gad Hans Henrik , Østergaard Lars , Ørntoft Torben F. , Hornung Veit , Paludan Søren R. , Mikkelsen Jacob Giehm , Fujita Takashi , Christiansen Mette , Hartmann Rune , Mogensen Trine H.
Published: July 2015

Herpes simplex encephalitis (HSE) in children has previously been linked to defects in type I interferon (IFN) production downstream of Toll-like receptor 3. Here, we describe a novel genetic etiology of HSE by identifying a heterozygous loss-of-function mutation in the IFN regulatory factor 3 (IRF3) gene, leading to autosomal dominant (AD) IRF3 deficiency by haploinsufficiency, in an adolescent female patient with HSE. IRF3 is activated by most pattern recognition receptors recognizing viral infections and plays an essential role in induction of type I IFN. The identified IRF3 R285Q amino acid substitution results in impaired IFN responses to HSV-1 infection and particularly impairs signaling through the TLR3–TRIF pathway. In addition, the R285Q mutant of IRF3 fails to become phosphorylated at S386 and undergo dimerization, and thus has impaired ability to activate transcription. Finally, transduction with WT IRF3 rescues the ability of patient fibroblasts to express IFN in response to HSV-1 infection. The identification of IRF3 deficiency in HSE provides the first description of a defect in an IFN-regulating transcription factor conferring increased susceptibility to a viral infection in the CNS in humans.
The era of stereotactic body radiotherapy for spinal metastases and the multidisciplinary management of complex cases
Authors: Kumar Rachit , Nater Anick , Hashmi Ahmed , Myrehaug Sten , Lee Young , Ma Lijun , Redmond Kristin , Lo Simon S. , Chang Eric L. , Yee Albert , Fisher Charles G. , Fehlings Michael G. , Sahgal Arjun
Published: July 2015

Spinal metastases are increasingly becoming a focus of attention with respect to treating with locally “ablative” intent, as opposed to locally “palliative” intent. This is due to increasing survival rates among patients with metastatic disease, early detection as a result of increasing availability of spinal MRI, the recognition of the oligometastatic state as a distinct sub-group of favorable metastatic patients and the advent of stereotactic body radiotherapy (SBRT). Although conventionally fractionated radiation therapy has been utilized for decades, the rates of complete pain relief and local control for complex tumors are sub-optimal. SBRT has the advantage of delivering high total doses in few fractions (typically, 24 Gy in 1 or 2 fractions to 30–45 Gy in 5 fractions) that can be considered “ablative”. With mature clinical experience emerging among early adopters, we are realizing beyond efficacy the limitations of spine SBRT. In particular, toxicities such as vertebral compression fracture, and epidural disease progression as the most common pattern of local tumor progression. As a result, the multidisciplinary evaluation of cases prior to SBRT is emphasized with the intent to identify patients who could benefit from surgical stabilization or down-staging of epidural disease. The purpose of this review is to provide an overview of the current literature with respect to outcomes, technical details for safe delivery, patient selection criteria, common and uncommon side effects of therapy, and the increasing use of minimally invasive surgical techniques that can improve both safety and local control.
Environmental Conditions Affect Botrytis cinerea Infection of Mature Grape Berries More Than the Strain or Transposon Genotype
Authors: Ciliberti Nicola , Fermaud Marc , Roudet Jean , Rossi Vittorio
Published: July 2015

Effects of environment, Botrytis cinerea strain, and their interaction on the infection of mature grape berries were investigated. The combined effect of temperature (T) of 15, 20, 25, and 30°C and relative humidity (RH) of 65, 80, 90, and 100% was studied by inoculating berries with mycelium plugs. Regardless of the T, no disease occurred at 65% RH, and both disease incidence and severity increased with increasing RH. The combined effect of T (5 to 30°C) and wetness duration (WD) of 3, 6, 12, 24, and 36 h was studied by inoculating berries with conidia. At WD of 36 h, disease incidence was approximately 75% of affected berries at 20 or 25°C, 50% at 15°C, and 30 to 20% at 30 and 10°C; no infection occurred at 5°C. Under favorable conditions (100% RH or 36 h of WD) and unfavorable conditions (65% RH or 3 h of WD), berry wounding did not significantly affect disease incidence; under moderately favorable conditions (80% RH or 6 to 12 h of WD), disease incidence was approximately 1.5 to 5 times higher in wounded than in intact berries. Our data collectively showed that (i) T and RH or WD were more important than strain for mature berry infection by either mycelium or conidia and (ii) the effect of the environment on the different strains was similar. Two equations were developed describing the combined effect of T and RH, or T and WD, on disease incidence following inoculation by mycelium (R2 = 0.99) or conidia (R2 = 0.96), respectively. These equations may be useful in the development of models used to predict and control Botrytis bunch rot during berry ripening.
Graded metascreens to enable a new degree of nanoscale light management
Authors: Mohammadi Estakhri Nasim , Argyropoulos Christos , Alù Andrea
Published: July 2015

Optical metasurfaces, typically referred to as two-dimensional metamaterials, are arrays of engineered subwavelength inclusions suitably designed to tailor the light properties, including amplitude, phase and polarization state, over deeply subwavelength scales. By exploiting anomalous localized interactions of surface elements with optical waves, metasurfaces can go beyond the functionalities offered by conventional diffractive optical gratings. The innate simplicity of implementation and the distinct underlying physics of their wave–matter interaction distinguish metasurfaces from three-dimensional metamaterials and provide a valuable means of moulding optical waves in the desired manner. Here, we introduce a general approach based on the electromagnetic equivalence principle to develop and synthesize graded, non-periodic metasurfaces to generate arbitrarily prescribed distributions of electromagnetic waves. Graded metasurfaces are realized with a single layer of spatially modulated, electrically polarizable nanoparticles, tailoring the scattering response of the surface with nanoscale resolutions. We discuss promising applications based on the proposed local wave management technique, including the design of ultrathin optical carpet cloaks, alignment-free polarization beam splitters and a novel approach to enable broadband light absorption enhancement in thin-film solar cells. This concept opens up a practical route towards efficient planarized optical structures with potential impact on the integrated nanophotonic technology.
A new look at the transformation electromagnetics approach for some real-world applications
Authors: Mittra Raj , Zhou Yuda
Published: July 2015

In this paper, we present an alternative approach to addressing the problem of designing a number of practical ‘microwave’ devices such as blankets serving as absorbers for radar targets, flat lenses and reflectarrays.
Experiments on cloaking in optics, thermodynamics and mechanics
Authors: Kadic Muamer , Bückmann Tiemo , Schittny Robert , Wegener Martin
Published: July 2015

Spatial coordinate transformations can be used to transform boundaries, material parameters or discrete lattices. We discuss fundamental constraints in regard to cloaking and review our corresponding experiments in optics, thermodynamics and mechanics. For example, we emphasize three-dimensional broadband visible-frequency carpet cloaking, transient thermal cloaking, three-dimensional omnidirectional macroscopic broadband cloaking for diffuse light throughout the entire visible range, cloaking for flexural waves in thin plates and three-dimensional elasto-static core–shell cloaking using pentamode mechanical metamaterials.
Watching surface waves in phononic crystals
Authors: Wright Oliver B. , Matsuda Osamu
Published: July 2015

In this paper, we review results obtained by ultrafast imaging of gigahertz surface acoustic waves in surface phononic crystals with one- and two-dimensional periodicities. By use of quasi-point-source optical excitation, we show how, from a series of images that form a movie of the travelling waves, the dispersion relation of the acoustic modes, their corresponding mode patterns and the position and widths of phonon stop bands can be obtained by temporal and spatio-temporal Fourier analysis. We further demonstrate how one can follow the temporal evolution of phononic eigenstates in k-space using data from phononic-crystal waveguides as an example.
Spatial transformations: from fundamentals to applications
Authors: Foster Robert , Grant Patrick , Hao Yang , Hibbins Alastair , Philbin Thomas , Sambles Roy
Published: July 2015

This paper forms the introduction to this themed issue of
Philosophical Transactions of the Royal Society A
on ‘Spatial transformations’, arising from the Royal Society Scientific Discussion Meeting held in January 2015. The paper begins with a review of the concepts and history of spatial transformations, followed by a discussion of the contributions from the papers in this themed issue. A summary of the advantages and current limitations of spatial transformations concludes the paper, with the key challenges identified at the Scientific Discussion Meeting also given.
Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons
Authors: Zhuang Lingping , Liu Yang , Wang Lin , Wang Wanpeng , Shao Zongze
Published: July 2015

A Gram-stain-negative, motile, rod-shaped, orange-pigmented bacterium able to degrade polycyclic aromatic hydrocarbons was isolated from deep-sea sediment of the Atlantic Ocean and subjected to a polyphasic taxonomic study. The strain, designated s21-N3T, could grow at 4–37 °C (optimum 28 °C), at pH 5–10 (optimum pH 7–8) and with 1–7 % (w/v) NaCl (optimum 2–3 %). Strain s21-N3T was positive for nitrate reduction, denitrification, aesculin hydrolysis, oxidase and catalase, but negative for indole production and urease. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain s21-N3T formed a distinct branch within the genus Erythrobacter, sharing high similarities with three closely related strains, Erythrobacter marinus HWDM-33T (98.67 %), ‘Erythrobacter luteus’ KA37 (97.80 %) and Erythrobacter gangjinensis K7-2T (97.59 %). The similarities between strain s21-N3T and other type strains of recognized species within the genus Erythrobacter ranged from 95.00 to 96.47 %. The digital DNA–DNA hybridization values and average nucleotide identity (ANI) values between strain s21-N3T and the three closely related strains Erythrobacter marinus HWDM-33T, ‘Erythrobacter luteus’ KA37 and Erythrobacter gangjinensis K7-2T were 18.60, 18.00 and 18.50 % and 74.24, 72.49 and 72.54 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1ω7c/ω6c) and summed feature 3 (C16 : 1ω7c/ω6c). The respiratory lipoquinone was identified as Q-10. The major polar lipids comprised sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The G+C content of the chromosomal DNA was determined to be 58.18 mol%. The combined genotypic and phenotypic distinctiveness demonstrated that strain s21-N3T represents a novel species of the genus Erythrobacter, for which the name Erythrobacter atlanticus sp. nov. is proposed, with the type strain s21-N3T ( = MCCC 1A00519T = KCTC 42697T).
Salininema proteolyticum gen. nov., sp. nov., a halophilic rare actinomycete isolated from wetland soil, and emended description of the family Glycomycetaceae
Authors: Moshtaghi Nikou Mahdi , Ramezani Mohaddaseh , Ali Amoozegar Mohammad , Rasouli Mehrnoush , Abolhassan Shahzadeh Fazeli Seyed , Schumann Peter , de la Haba Rafael R. , Ventosa Antonio
Published: July 2015

A Gram-stain-positive actinobacterial strain, Miq-4T, was isolated from soil around Meighan wetland in the centre of Iran. Strain Miq-4T was strictly aerobic, catalase- and oxidase-positive. The isolate grew in the presence of 3–15 % (w/v) NaCl, at 20–40 °C and pH 6.0–11.0. The optimum NaCl, temperature and pH for growth were 7.0 %, 30 °C and 7.0–8.5, respectively. The cell wall of strain Miq-4T contained meso-diaminopimelic acid as the diamino acid and glucose and ribose as the whole-cell sugars. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Strain Miq-4T synthesized cellular fatty acids of anteiso- and iso-branched types, including anteiso-C17 : 0, anteiso- C15 : 0 and iso-C16 : 0, and the major respiratory quinone was MK-9(H4). The G+C content of the genomic DNA was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and characteristic patterns of 16S rRNA gene signature nucleotides revealed that strain Miq-4T belongs to the family Glycomycetaceae and showed the closest phylogenetic similarity with Haloglycomyces albus YIM 92370T (94.1 % 16S rRNA gene sequence similarity). On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain Miq-4T represents a novel species of a new genus in the family Glycomycetaceae, for which the name Salininema proteoliyticum gen. nov., sp. nov. is proposed. The type strain of the type species is Miq-4T ( = IBRC-M 10908T = LMG 28391T). An emended description of the family Glycomycetaceae is also proposed in order to include features of the new genus.
Self-organized patterning and morphogenesis in embryonic epithelia from antagonistic signals and fiber networks
Authors: Cummings F.W. , Lu Kai
Published: July 2015

A number of universals can be observed in the developing embryos of all phyla. An attempt is made here to describe some of these with a simple model, one consisting of two mutually repelling regions of gene patterning produced by signaling pathways, two acting at each growth phase. The diffusion of ligands is short range, nearest or near neighbors, but the transcription patterns extend over many cellular diameters. The universals discussed are: gastrulation, formation of a blastopore, patterning of stem cells as surrounding compartments (propagating anew with each growth phase, to the adult), the origin of bilaterality, the prevalence of segmentation, and the general ability to regenerate and duplicate. The origin of organ sizes are determined by the parameters of the signaling pathways involved, independent of cell sizes or numbers. The important fiber mesh, or fiber network that can also extend over many cell diameters is also briefly discussed, and is seen as a partner with the signaling pathways in the overall patterning.
A spatio-temporal model for spontaneous thrombus formation in cerebral aneurysms
Authors: Malaspinas Orestis , Turjman Alexis , Ribeiro de Sousa Daniel , Garcia-Cardena Guillermo , Raes Martine , Nguyen Phuc-Thien Thomas , Zhang Yue , Courbebaisse Guy , Lelubre Christophe , Zouaoui Boudjeltia Karim , Chopard Bastien
Published: July 2015

We propose a new numerical model to describe thrombus formation in cerebral aneurysms. This model combines CFD simulations with a set of bio-mechanical processes identified as being the most important to describe the phenomena at a large space and time scales. The hypotheses of the model are based on in vitro experiments and clinical observations. We document that we can reproduce very well the shape and volume of patient specific thrombus segmented in giant aneurysms.
Long-term natural selection affects patterns of neutral divergence on the X chromosome more than the autosomes
Authors: Narang Pooja , Wilson Sayres Melissa A.
Published: July 2015

Natural selection reduces neutral population genetic diversity near coding regions of the genome because recombination has not had time to unlink selected alleles from nearby neutral regions. For ten sub-species of great apes, including human, we show that long-term selection affects estimates of divergence on the X differently from the autosomes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes, resulting in increasing ratios of X/A divergence in putatively neutral regions. Similarly, divergence is reduced more on the X chromosome in neutral regions near conserved regulatory elements than on the autosomes. Consequently estimates of male mutation bias, which rely on comparing neutral divergence between the X and autosomes, are twice as high in neutral regions near genes versus far from genes. Our results suggest filters for putatively neutral genomic regions differ between the X and autosomes.
GOTHiC, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C data
Authors: Mifsud Borbala , Martincorena Inigo , Darbo Elodie , Sugar Robert , Schoenfelder Stefan , Fraser Peter , Luscombe Nicholas M.
Published: July 2015

1.

Hi-C is one of the main methods for investigating spatial co-localisation of DNA in the nucleus. However, the raw sequencing data obtained from Hi-C experiments suffer from large biases and spurious contacts, making it difficult to identify true interactions. Existing methods use complex models to account for biases and do not provide a significance threshold for detecting interactions. Here we introduce a simple binomial probabilistic model that resolves complex biases and distinguishes between true and false interactions. The model corrects biases of known and unknown origin and yields a p-value for each interaction, providing a reliable threshold based on significance. We demonstrate this experimentally by testing the method against a random ligation dataset. Our method outperforms previous methods and provides a statistical framework for further data analysis, such as comparisons of Hi-C interactions between different conditions. GOTHiC is available as a BioConductor package (http://www.bioconductor.org/packages/release/bioc/html/GOTHiC.html).