bluuebunny/crossref_metadata_2025 huggingface dataset:
Extreme multistability: Attractor manipulation and robustness
Authors: Hens Chittaranjan , Dana Syamal K. , Feudel Ulrike
Published: May 2015

The coexistence of infinitely many attractors is called extreme multistability in dynamical systems. In coupled systems, this phenomenon is closely related to partial synchrony and characterized by the emergence of a conserved quantity. We propose a general design of coupling that leads to partial synchronization, which may be a partial complete synchronization or partial antisynchronization and even a mixed state of complete synchronization and antisynchronization in two coupled systems and, thereby reveal the emergence of extreme multistability. The proposed design of coupling has wider options and allows amplification or attenuation of the amplitude of the attractors whenever it is necessary. We demonstrate that this phenomenon is robust to parameter mismatch of the coupled oscillators.
Tuning the optoelectronic properties of amorphous MoOx films by reactive sputtering
Authors: Fernandes Cauduro André L. , Fabrim Zacarias E. , Ahmadpour Mehrad , Fichtner Paulo F. P. , Hassing Søren , Rubahn Horst-Günter , Madsen Morten
Published: May 2015

In this letter, we report on the effect of oxygen partial pressure and sputtering power on amorphous DC-sputtered MoOx films. We observe abrupt changes in the optoelectronic properties of the reported films by increasing the oxygen partial pressure from 1.00 × 10−3 mbar to 1.37 × 10−3 mbar during the sputtering process. A strong impact on the electrical conductivity, varying from 1.6 × 10−5 S/cm to 3.22 S/cm, and on the absorption coefficient in the range of 0.6–3.0 eV is observed for the nearly stoichiometric MoO3.00 and for the sub-stoichiometric MoO2.57 films, respectively, without modifying significantly the microstructure of the studied films. The presence of states within the band gap due to the lack of oxygen is the most probable mechanism for generating a change in electrical conductivity as well as optical absorption in DC-sputtered MoOx. The large tuning range of the optoelectronic properties in these films holds strong promise for their implementation in optoelectronic devices.
Influence of surface charge on the transport characteristics of nanowire-field effect transistors in liquid environments
Authors: Nozaki Daijiro , Kunstmann Jens , Zörgiebel Felix , Cuniberti Gianaurelio
Published: May 2015

One dimensional nanowire field effect transistors (NW-FETs) are a promising platform for sensor applications. The transport characteristics of NW-FETs are strongly modified in liquid environment due to the charging of surface functional groups accompanied with protonation or deprotonation. In order to investigate the influence of surface charges and ionic concentrations on the transport characteristics of Schottky-barrier NW-FETs, we have combined the modified Poisson-Boltzmann theory with the Landauer-Büttiker transport formalism. For a typical device, the model is able to capture the reduction of the sensitivity of NW-FETs in ionic solutions due to the screening from counter ions as well as a local gating from surface functional groups. Our approach allows to model, to investigate, and to optimize realistic Schottky-barrier NW-FET devices in liquid environment.
Extracting magnetic cluster size and its distributions in advanced perpendicular recording media with shrinking grain size using small angle x-ray scattering
Authors: Mehta Virat , Wang Tianhan , Ikeda Yoshihiro , Takano Ken , Terris Bruce D. , Wu Benny , Graves Catherine , Dürr Hermann A. , Scherz Andreas , Stöhr Jo , Hellwig Olav
Published: May 2015

We analyze the magnetic cluster size (MCS) and magnetic cluster size distribution (MCSD) in a variety of perpendicular magnetic recording (PMR) media designs using resonant small angle x-ray scattering at the Co L3 absorption edge. The different PMR media flavors considered here vary in grain size between 7.5 and 9.5 nm as well as in lateral inter-granular exchange strength, which is controlled via the segregant amount. While for high inter-granular exchange, the MCS increases rapidly for grain sizes below 8.5 nm, we show that for increased amount of segregant with less exchange the MCS remains relatively small, even for grain sizes of 7.5 and 8 nm. However, the MCSD still increases sharply when shrinking grains from 8 to 7.5 nm. We show evidence that recording performance such as signal-to-noise-ratio on the spin stand correlates well with the product of magnetic cluster size and magnetic cluster size distribution.
Time constant of defect relaxation in ion-irradiated 3C-SiC
Authors: Wallace J. B. , Bayu Aji L. B. , Shao L. , Kucheyev S. O.
Published: May 2015

Above room temperature, the buildup of radiation damage in SiC is a dynamic process governed by the mobility and interaction of ballistically generated point defects. Here, we study the dynamics of radiation defects in 3C-SiC bombarded at 100 °C with 500 keV Ar ions, with the total ion dose split into a train of equal pulses. Damage–depth profiles are measured by ion channeling for a series of samples irradiated under identical conditions except for different durations of the passive part of the beam cycle. Results reveal an effective defect relaxation time constant of ∼3 ms (for second order kinetics) and a dynamic annealing efficiency of ∼40% for defects in both Si and C sublattices. This demonstrates a crucial role of dynamic annealing at elevated temperatures and provides evidence of the strong coupling of defect accumulation processes in the two sublattices of 3C-SiC.
The dynamics and stability of lubricating oil films during droplet transport by electrowetting in microfluidic devices
Authors: Kleinert Jairus , Srinivasan Vijay , Rival Arnaud , Delattre Cyril , Velev Orlin D. , Pamula Vamsee K.
Published: May 2015

The operation of digital microfluidic devices with water droplets manipulated by electrowetting is critically dependent on the static and dynamic stability and lubrication properties of the oil films that separate the droplets from the solid surfaces. The factors determining the stability of the films and preventing surface fouling in such systems are not yet thoroughly understood and were experimentally investigated in this study. The experiments were performed using a standard digital microfluidic cartridge in which water droplets enclosed in a thin, oil-filled gap were transported over an array of electrodes. Stable, continuous oil films separated the droplets from the surfaces when the droplets were stationary. During droplet transport, capillary waves formed in the films on the electrode surfaces as the oil menisci receded. The waves evolved into dome-shaped oil lenses. Droplet deformation and oil displacement caused the films at the surface opposite the electrode array to transform into dimples of oil trapped over the centers of the droplets. Lower actuation voltages were associated with slower film thinning and formation of fewer, but larger, oil lenses. Lower ac frequencies induced oscillations in the droplets that caused the films to rupture. Films were also destabilized by addition of surfactants to the oil or droplet phases. Such a comprehensive understanding of the oil film behavior will enable more robust electrowetting-actuated lab-on-a-chip devices through prevention of loss of species from droplets and contamination of surfaces at points where films may break.
Effect of an obesity pamphlet on parental perception and knowledge of excess weight in their children: results of a randomised controlled trial
Authors: Rune Karina T. , Mulgrew Kate , Sharman Rachael , Lovell Geoff P.
Published: May 2015

Issues addressed

This study examined the effectiveness of a brief educational intervention in increasing parental knowledge of childhood obesity risk factors and ability to correctly identify their child's weight status.

Methods

Eighty parents were randomly allocated to an experimental group given an obesity pamphlet or a control group given a stress management pamphlet. A survey measured parents' knowledge about risk factors, cause and consequences of childhood obesity, and perception of their child's weight.

Results

Parents with overweight or obese children increased their understanding of childhood obesity immediately after receiving the intervention, but did not differ significantly on perception of their child's weight.

Conclusion

The experimental intervention increased knowledge of health risks associated with childhood obesity in parents of overweight or obese children. Parental perception of their child's weight status did not improve, suggesting that other factors have a role to play.
Evaluating taboo trade-offs in ecosystems services and human well-being
Authors: Daw Tim M. , Coulthard Sarah , Cheung William W. L. , Brown Katrina , Abunge Caroline , Galafassi Diego , Peterson Garry D. , McClanahan Tim R. , Omukoto Johnstone O. , Munyi Lydiah
Published: May 2015

Significance

Environmental management inevitably involves trade-offs among different objectives, values, and stakeholders. Most evaluations of such trade-offs involve monetary valuation or calculation of aggregate production of ecosystem services, which can mask individual winners and losers. We combine a participatory, modeling, and scenarios approach to identify social–ecological trade-offs in a tropical fishery and the implications on well-being of different stakeholders. Such trade-offs are often ignored because losers are marginalized or not represented by quantification, and because the nature of underlying values may result in socially “taboo” trade-offs that pit incommensurable values against one another. A participatory modeling and scenarios approach can increase awareness of such trade-offs, promote discussion of what is socially acceptable, and potentially identify and reduce obstacles to compliance.
Th17 cells give rise to Th1 cells that are required for the pathogenesis of colitis
Authors: Harbour Stacey N. , Maynard Craig L. , Zindl Carlene L. , Schoeb Trenton R. , Weaver Casey T.
Published: May 2015

Significance

The Th17 subset of CD4+T cells are important in the pathogenesis of inflammatory bowel disease (IBD), but the mechanisms of their actions, particularly the role of the development of IFN-γ–producing progeny of Th17 cells (Th1-like cells), are incompletely understood. Here, we show in a mouse model of Th17-driven IBD that transition of Th17 precursors to Th1-like cells is absolutely required for disease, because Th17 cells deficient in IFN-γ fail to induce intestinal inflammation. This transition is dependent on the transcription factors T-bet and, to a lesser extent, Stat4. These findings are relevant for clinical strategies that target IBD and suggest that focusing on both the Th17 and Th1-like arms of disease may be beneficial in therapy design.
Virus-induced translational arrest through 4EBP1/2-dependent decay of 5′-TOP mRNAs restricts viral infection
Authors: Hopkins Kaycie C. , Tartell Michael A. , Herrmann Christin , Hackett Brent A. , Taschuk Frances , Panda Debasis , Menghani Sanjay V. , Sabin Leah R. , Cherry Sara
Published: May 2015

Significance

Rift Valley fever virus (RVFV), a mosquito-transmitted bunyavirus, blocks the two common methods of antiviral translational shutdown, PKR and type I interferon. However, it has previously been shown that RVFV infection halts protein production in infected human cells. Here, we demonstrate that RVFV is restricted by a previously unknown mechanism of antiviral translational shutdown, wherein 5′-terminal oligopyrimidine (5′-TOP) mRNAs encoding the core translational machinery are selectively degraded by the RNA decapping enzyme NUDT16 during RVFV infection, and that this decay is triggered in response to mTOR attenuation via the translational repressor 4EBP1/2 axis. We present a previously unknown mechanism for translational shutdown in response to viral infection and identify mTOR attenuation as a potential therapeutic target against bunyaviral infection.
Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont
Hodgkinia
Authors: Campbell Matthew A. , Van Leuven James T. , Meister Russell C. , Carey Kaitlin M. , Simon Chris , McCutcheon John P.
Published: May 2015

Comparative genomics from mitochondria, plastids, and mutualistic endosymbiotic bacteria has shown that the stable establishment of a bacterium in a host cell results in genome reduction. Although many highly reduced genomes from endosymbiotic bacteria are stable in gene content and genome structure, organelle genomes are sometimes characterized by dramatic structural diversity. Previous results from
Candidatus
Hodgkinia cicadicola, an endosymbiont of cicadas, revealed that some lineages of this bacterium had split into two new cytologically distinct yet genetically interdependent species. It was hypothesized that the long life cycle of cicadas in part enabled this unusual lineage-splitting event. Here we test this hypothesis by investigating the structure of the
Ca.
Hodgkinia genome in one of the longest-lived cicadas,
Magicicada tredecim
. We show that the
Ca.
Hodgkinia genome from
M. tredecim
has fragmented into multiple new chromosomes or genomes, with at least some remaining partitioned into discrete cells. We also show that this lineage-splitting process has resulted in a complex of
Ca.
Hodgkinia genomes that are 1.1-Mb pairs in length when considered together, an almost 10-fold increase in size from the hypothetical single-genome ancestor. These results parallel some examples of genome fragmentation and expansion in organelles, although the mechanisms that give rise to these extreme genome instabilities are likely different.
Entamoeba
mitosomes play an important role in encystation by association with cholesteryl sulfate synthesis
Authors: Mi-ichi Fumika , Miyamoto Tomofumi , Takao Shouko , Jeelani Ghulam , Hashimoto Tetsuo , Hara Hiromitsu , Nozaki Tomoyoshi , Yoshida Hiroki
Published: May 2015

Significance

Evolution and diversification of organelles is a central topic in biology. Mitochondrion-related organelles (MROs) are highly modified forms of mitochondria found in anaerobic eukaryotes. MROs show a spectrum of functions that are either reduced or modified from those of canonical mitochondria by environmental constraints and evolutionary selection. Hence, elucidation of MRO functions will improve our understanding of organelle evolution and the speciation of eukaryotes. Here, we substantiate a role of the
Entamoeba
mitosome, a type of MRO, by showing that cholesteryl sulfate synthesized through a mitosomal pathway regulates differentiation that is essential for the parasite’s life cycle. These findings support the contribution of an endosymbiont-derived organelle to parasitism, a previously unrecognized concept that casts new light on organelle evolution.
The messenger RNA decapping and recapping pathway in
Trypanosoma
Authors: Ignatochkina Anna V. , Takagi Yuko , Liu Yancheng , Nagata Kyosuke , Ho C. Kiong
Published: May 2015

Significance

The 5′ end of eukaryotic mRNA is capped and methylated to protect mRNA from degradation and enhance protein synthesis. However, the cap can be removed from mRNA by decapping. We identified a recapping enzyme with 5′-monophosphate RNA kinase activity from trypanosome and provide evidence that decapped transcripts can be recapped to regenerate translatable mRNA. The kinase activity is dependent on mRNA leader sequence and is stimulated by hypermethylation found in the trypanosome mRNA. We also identify a trypanosome decapping enzyme that removes cap structure from the mRNA, but is less active on hypermethylated capped mRNA. These results suggest that hypermethylated cap structure can influence certain transcripts to be preferentially decapped or recapped during the parasite life cycle.
Kinetically coupled folding of a single HIV-1 glycoprotein 41 complex in viral membrane fusion and inhibition
Authors: Jiao Junyi , Rebane Aleksander A. , Ma Lu , Gao Ying , Zhang Yongli
Published: May 2015

Significance

Enveloped viruses infect cells via fusion of viral and host cell membranes mediated by highly conserved fusion proteins. HIV-1 glycoprotein 41 (gp41) represents a family of fusion proteins with similar structures and fusion mechanisms. They couple their energetic folding to draw two membranes close for fusion, forming trimers of helical hairpins. Yet, the energy release, force generation, and kinetics associated with folding of these proteins are poorly quantified. We found that gp41 hairpins fold sequentially but in a kinetically coupled manner and that an anti-HIV drug blocked gp41 folding by a new mechanism. As major proteins on viral surfaces, fusion proteins are primary targets for vaccine development and fusion inhibitors to intervene in major infectious diseases such as AIDS, Ebola, and influenza.
Why chloroplasts and mitochondria retain their own genomes and genetic systems: Colocation for redox regulation of gene expression
Authors: Allen John F.
Published: May 2015

Chloroplasts and mitochondria are subcellular bioenergetic organelles with their own genomes and genetic systems. DNA replication and transmission to daughter organelles produces cytoplasmic inheritance of characters associated with primary events in photosynthesis and respiration. The prokaryotic ancestors of chloroplasts and mitochondria were endosymbionts whose genes became copied to the genomes of their cellular hosts. These copies gave rise to nuclear chromosomal genes that encode cytosolic proteins and precursor proteins that are synthesized in the cytosol for import into the organelle into which the endosymbiont evolved. What accounts for the retention of genes for the complete synthesis within chloroplasts and mitochondria of a tiny minority of their protein subunits? One hypothesis is that expression of genes for protein subunits of energy-transducing enzymes must respond to physical environmental change by means of a direct and unconditional regulatory control—control exerted by change in the redox state of the corresponding gene product. This hypothesis proposes that, to preserve function, an entire redox regulatory system has to be retained within its original membrane-bound compartment. Colocation of gene and gene product for redox regulation of gene expression (CoRR) is a hypothesis in agreement with the results of a variety of experiments designed to test it and which seem to have no other satisfactory explanation. Here, I review evidence relating to CoRR and discuss its development, conclusions, and implications. This overview also identifies predictions concerning the results of experiments that may yet prove the hypothesis to be incorrect.
Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria
Authors: Yosef Ido , Manor Miriam , Kiro Ruth , Qimron Udi
Published: May 2015

Significance

Antibiotic resistance of pathogens is a growing concern to human health, reviving interest in phage therapy. This therapy uses phages (natural bacterial enemies) to kill pathogens. However, it encounters many obstacles such as delivery barriers into the tissues and bacterial resistance to phages. Here, we use phages for delivering a programmable DNA nuclease, clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas), to reverse antibiotic resistance and eliminate the transfer of resistance between strains. This approach combines CRISPR-Cas delivery with lytic phage selection of antibiotic-sensitized bacteria. The strategy may reduce the prevalence of antibiotic-resistant bacteria in treated surfaces and on skin of medical personnel, as it uses phages in a unique way that overcomes many of the hurdles encountered by phage therapy.
Pds5 regulators segregate cohesion and condensation pathways in
Saccharomyces cerevisiae
Authors: Tong Kevin , Skibbens Robert V.
Published: May 2015

Significance

Chromosomes are replicated during S phase to produce sister chromatids that remain tethered together by protein complexes termed cohesins. In preparation for mitosis, sister chromatids condense into discrete, compact chromosomes, a process that also requires cohesins. At anaphase onset, cohesins are inactivated, allowing each chromatid to segregate away from its sister and into newly forming daughter cells. The requirement for cohesin in both cohesion and condensation suggests that these pathways are intimately coupled. Here, we identify cohesin regulators through which cohesin functions for the first time can be isolated from one another. These regulations will be critical for elucidating post-translation modifications through which cohesin roles in chromatin metabolism can be studied in isolation.
Rodent reservoirs of future zoonotic diseases
Authors: Han Barbara A. , Schmidt John Paul , Bowden Sarah E. , Drake John M.
Published: May 2015

Significance

Forecasting reservoirs of zoonotic disease is a pressing public health priority. We apply machine learning to datasets describing the biological, ecological, and life history traits of rodents, which collectively carry a disproportionate number of zoonotic pathogens. We identify particular rodent species predicted to be novel zoonotic reservoirs and geographic regions from which new emerging pathogens are most likely to arise. We also describe trait profiles—complexes of biological features—that distinguish reservoirs from nonreservoirs. Generally, the most permissive rodent reservoirs display a fast-paced life history strategy, maximizing near-term fitness by having many altricial young that begin reproduction early and reproduce frequently. These findings may constitute an important lead in guiding the search for novel disease reservoirs in the wild.
Gradual decline in mobility with the adoption of food production in Europe
Authors: Ruff Christopher B. , Holt Brigitte , Niskanen Markku , Sladek Vladimir , Berner Margit , Garofalo Evan , Garvin Heather M. , Hora Martin , Junno Juho-Antti , Schuplerova Eliska , Vilkama Rosa , Whittey Erin
Published: May 2015

Significance

Declining mobility levels following the Pleistocene had profound effects on human demography, social organization, and health, but the exact timing and pace of this critical change are unknown. Here we examine direct evidence for changing mobility levels from limb bone structural characteristics in a large sample of European skeletons spanning the past 30,000 y. Our results show that mobility first declined during the Neolithic, at the onset of food production, but that the decline was gradual, continuing for several thousand years as agriculture intensified. No change in relative limb strength occurred during the past 2,000 y. Thus, the more gracile modern human skeleton is a result of increased sedentism tied to food production, not subsequent mechanization and industrialization.
Cell rejuvenation and social behaviors promoted by LPS exchange in myxobacteria
Authors: Vassallo Christopher , Pathak Darshankumar T. , Cao Pengbo , Zuckerman David M. , Hoiczyk Egbert , Wall Daniel
Published: May 2015

Significance

Social organisms benefit from group behaviors that endow favorable fitness consequences among kin. We describe such a behavior in the bacterium
Myxococcus xanthus
in which damaged members of a population are repaired by their kin by exchange of outer membrane material. This behavior rescues lethal cellular damage, restores antibiotic resistance to a compromised cell membrane, and increases the overall fitness of a heterogeneous population. To our knowledge, we provide the first evidence that a social bacterium can use cell-content sharing to repair damaged siblings, leading to beneficial fitness outcomes for both the donor and recipient.
Laser printing hierarchical structures with the aid of controlled capillary-driven self-assembly
Authors: Hu Yanlei , Lao Zhaoxin , Cumming Benjamin P. , Wu Dong , Li Jiawen , Liang Haiyi , Chu Jiaru , Huang Wenhao , Gu Min
Published: May 2015

Significance

We propose a strategy to realize designable hierarchical functional structures via laser printing capillary-assisted self-assembly (LPCS). Ultrafast laser printing is applied for building unit blocks and capillary force is finely tuned as driving force. Diverse structures are successfully fabricated by controlling the spatial arrangements, heights, diameters of pillars, and the evaporation process. The ability of these LPCS structures to selectively trap and release microobjects suggests enormous potential applications in the fields of chemistry, biomedicine, and microfluidic engineering.
Retinal waves regulate afferent terminal targeting in the early visual pathway
Authors: Failor Samuel , Chapman Barbara , Cheng Hwai-Jong
Published: May 2015

Significance

Spontaneous neural activity is known to play a role in the maturation of nascent neural circuitry. Here we show for the first time a role for early spontaneous correlated retinal activity (i.e., retinal waves) in regulating the laminar targeting and functional development of the retinogeniculate pathway in the monocular condition—a condition where intereye competition and eye-specific segregation are not present. These findings demonstrate the importance of intraeye competition in early visual pathway circuit development. Our results provide a revision to the model of retinogeniculate development and to our general understanding of how neural activity guides the establishment of proper connectivity in the developing brain.
Subcortical barrelette-like and barreloid-like structures in the prosimian galago (
Otolemur garnetti
)
Authors: Sawyer Eva Kille , Liao Chia-Chi , Qi Hui-Xin , Balaram Pooja , Matrov Denis , Kaas Jon H.
Published: May 2015

Significance

Nearly all mammals have tactile hairs. Distinct modular representations of the vibrissae within the central nervous system have been found in five mammalian orders (Marsupialia, Carnivora, Eulipotyphla, Lagomorpha, Rodentia). This work documents vibrissae-related modules in a sixth order: Primata. The presence of subcortical barrel-like modules in the prosimian galagos suggests broad similarities in the processing of sensory information among rodents and primates. Additionally, the thalamic “galagounculus” appears to show the representation of the entire body surface with unusual clarity.
Predictive information in a sensory population
Authors: Palmer Stephanie E. , Marre Olivier , Berry Michael J. , Bialek William
Published: May 2015

Significance

Prediction is an essential part of life. However, are we really “good” at making predictions? More specifically, are pieces of our brain close to being optimal predictors? To assess the efficiency of prediction, we need to measure the information that neurons carry about the future of our sensory experiences. We show how to do this, at least in simplified contexts, and find that groups of neurons in the retina indeed are close to maximally efficient at separating predictive information from the nonpredictive background. Efficient coding of predictive information is a principle that can be applied at every stage of neural computation.
GABARAPs regulate PI4P-dependent autophagosome:lysosome fusion
Authors: Wang Hanzhi , Sun Hui-Qiao , Zhu Xiaohui , Zhang Li , Albanesi Joseph , Levine Beth , Yin Helen
Published: May 2015

Significance

Autophagy is an essential homeostatic process that is critically important for maintaining health and that is dysregulated in multiple devastating diseases. The steps in the final stages of autophagy that culminate in autophagosome:lysosome fusion are not well understood. The γ-aminobutyric acid receptor-associated protein (GABARAP) family of Atg8 (autophagy-related 8) proteins has been implicated in autophagosome maturation. Here we report that phosphatidylinositol 4-kinase IIα (PI4KIIα), a lipid kinase that generates phosphatidylinositol 4-phosphate (PI4P) and binds GABARAPs, is recruited to autophagosomes by GABARAPs. Furthermore, PI4P generation by PI4KIIα, but not by PI4KIIIβ, another major mammalian PI4K, promotes autophagosome fusion with lysosomes. Our results establish for the first time to our knowledge that PI4KIIα is a specific downstream effector of GABARAP and that PI4P has a key role in the final stage of autophagy.
AMCase is a crucial regulator of type 2 immune responses to inhaled house dust mites
Authors: Kim Lark Kyun , Morita Rimpei , Kobayashi Yasushi , Eisenbarth Stephanie C. , Lee Chun Geun , Elias Jack , Eynon Elizabeth E. , Flavell Richard A.
Published: May 2015

Significance

Millions of people are affected by asthma and that number is growing. A clear understanding of how the disease develops is lacking. The immune responses to inhaled allergens like house dust mite (HDM) provide much of the basis of asthma. Acidic mammalian chitinase (AMCase) is an enzyme that degrades chitin, a major structural polymer in the exoskeleton of HDM. By the use of a newly generated enzymatically dead AMCase knockin mouse, we found that AMCase enzymatic activity is of critical importance in the control of type 2 immune responses to inhaled HDM. This discovery may help the understanding of the mechanisms that govern the development of chitin-related asthma and allergy and may lead to new therapeutic strategies in these disorders.
Preparation of proteoglycan from salmon nasal cartilage under nondenaturing conditions
Authors: Tatara Yota , Suto Shinichiro , Sasaki Yoshitaka , Endo Masahiko
Published: May 2015

Salmon nasal cartilage was micronized in ethanol using a rotor–stator homogenizer for the high yield of proteoglycan extraction. This procedure also brought about depressing the degradation of proteoglycan and the contamination of collagens. Proteoglycan was extracted by 4 M magnesium chloride and isolated by anion-exchange chromatography. The gel filtration HPLC and the antibody reactivity showed that the core protein was intact.
Possible role of NAD-dependent glyceraldehyde-3-phosphate dehydrogenase in growth promotion of Arabidopsis seedlings by low levels of selenium
Authors: Takeda Toru , Fukui Yuki
Published: May 2015

We explored functional significance of selenium (Se) in Arabidopsis physiology. Se at very low concentrations in cultivation exerted a considerable positive effect on Arabidopsis growth with no indication of oxidative stress, whereas Se at higher concentrations significantly suppressed the growth and brought serious oxidative damage. Respiration, ATP levels, and the activity of NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (NAD-GAPDH) were enhanced in Arabidopsis grown in the medium containing 1.0 μM Se. Addition of an inhibitor of glutathione (GSH) synthesis to the medium abolished both of the Se-dependent growth promotion and NAD-GAPDH up-regulation. Assay of NAD-GAPDH purified from seedlings subjected to Se interventions raised the possibility of a direct connection between the activity of this enzyme and Arabidopsis growth. These results reveal that trace amounts of Se accelerate Arabidopsis growth, and suggest that this pro-growth effect of Se arises enhancing mitochondrial performance in a GSH-dependent manner, in which NAD-GAPDH may serve as a key regulator.
The Msd1–Wdr8–Pkl1 complex anchors microtubule minus ends to fission yeast spindle pole bodies
Authors: Yukawa Masashi , Ikebe Chiho , Toda Takashi
Published: May 2015

The minus ends of spindle microtubules are anchored to a microtubule-organizing center. The conserved Msd1/SSX2IP proteins are localized to the spindle pole body (SPB) and the centrosome in fission yeast and humans, respectively, and play a critical role in microtubule anchoring. In this paper, we show that fission yeast Msd1 forms a ternary complex with another conserved protein, Wdr8, and the minus end–directed Pkl1/kinesin-14. Individual deletion mutants displayed the identical spindle-protrusion phenotypes. Msd1 and Wdr8 were delivered by Pkl1 to mitotic SPBs, where Pkl1 was tethered through Msd1–Wdr8. The spindle-anchoring defect imposed by msd1/wdr8/pkl1 deletions was suppressed by a mutation of the plus end–directed Cut7/kinesin-5, which was shown to be mutual. Intriguingly, Pkl1 motor activity was not required for its anchoring role once targeted to the SPB. Therefore, spindle anchoring through Msd1–Wdr8–Pkl1 is crucial for balancing the Cut7/kinesin-5–mediated outward force at the SPB. Our analysis provides mechanistic insight into the spatiotemporal regulation of two opposing kinesins to ensure mitotic spindle bipolarity.
Ltc1 is an ER-localized sterol transporter and a component of ER–mitochondria and ER–vacuole contacts
Authors: Murley Andrew , Sarsam Reta D. , Toulmay Alexandre , Yamada Justin , Prinz William A. , Nunnari Jodi
Published: May 2015

Organelle contact sites perform fundamental functions in cells, including lipid and ion homeostasis, membrane dynamics, and signaling. Using a forward proteomics approach in yeast, we identified new ER–mitochondria and ER–vacuole contacts specified by an uncharacterized protein, Ylr072w. Ylr072w is a conserved protein with GRAM and VASt domains that selectively transports sterols and is thus termed Ltc1, for Lipid transfer at contact site 1. Ltc1 localized to ER–mitochondria and ER–vacuole contacts via the mitochondrial import receptors Tom70/71 and the vacuolar protein Vac8, respectively. At mitochondria, Ltc1 was required for cell viability in the absence of Mdm34, a subunit of the ER–mitochondria encounter structure. At vacuoles, Ltc1 was required for sterol-enriched membrane domain formation in response to stress. Increasing the proportion of Ltc1 at vacuoles was sufficient to induce sterol-enriched vacuolar domains without stress. Thus, our data support a model in which Ltc1 is a sterol-dependent regulator of organelle and cellular homeostasis via its dual localization to ER–mitochondria and ER–vacuole contact sites.
BAFF activation of the ERK5 MAP kinase pathway regulates B cell survival
Authors: Jacque Emilie , Schweighoffer Edina , Tybulewicz Victor L.J. , Ley Steven C.
Published: May 2015

B cell activating factor (BAFF) stimulation of the BAFF receptor (BAFF-R) is essential for the homeostatic survival of mature B cells. Earlier in vitro experiments with inhibitors that block MEK 1 and 2 suggested that activation of ERK 1 and 2 MAP kinases is required for BAFF-R to promote B cell survival. However, these inhibitors are now known to also inhibit MEK5, which activates the related MAP kinase ERK5. In the present study, we demonstrated that BAFF-induced B cell survival was actually independent of ERK1/2 activation but required ERK5 activation. Consistent with this, we showed that conditional deletion of ERK5 in B cells led to a pronounced global reduction in mature B2 B cell numbers, which correlated with impaired survival of ERK5-deficient B cells after BAFF stimulation. ERK5 was required for optimal BAFF up-regulation of Mcl1 and Bcl2a1, which are prosurvival members of the Bcl-2 family. However, ERK5 deficiency did not alter BAFF activation of the PI3-kinase–Akt or NF-κB signaling pathways, which are also important for BAFF to promote mature B cell survival. Our study reveals a critical role for the MEK5-ERK5 MAP kinase signaling pathway in BAFF-induced mature B cell survival and homeostatic maintenance of B2 cell numbers.
Geometric Satake, Springer correspondence, and small representations II
Authors: Achar Pramod , Henderson Anthony , Riche Simon
Published: May 2015

For a split reductive group scheme

G
ˇ

\check G

over a commutative ring

k
\Bbbk

with Weyl group

W
W

, there is an important functor
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="sans-serif upper R sans-serif e sans-serif p left-parenthesis ModifyingAbove upper G With ˇ comma double-struck k right-parenthesis right-arrow sans-serif upper R sans-serif e sans-serif p left-parenthesis upper W comma double-struck k right-parenthesis">

R
e
p

(

G
ˇ

,
k
)
→

R
e
p

(
W
,
k
)

{\mathsf {Rep}}(\check G,\Bbbk )\to {\mathsf {Rep}}(W,\Bbbk )

defined by taking the zero weight space. We prove that the restriction of this functor to the subcategory of small representations has an alternative geometric description, in terms of the affine Grassmannian and the nilpotent cone of the Langlands dual group

G
G

. The translation from representation theory to geometry is via the Satake equivalence and the Springer correspondence. This generalizes the result for the

k
=

C

\Bbbk =\mathbb {C}

case proved by the first two authors, and also provides a better explanation than in the earlier paper, since the current proof is uniform across all types.
Associations of Reducing Sedentary Time With Vascular Function and Insulin Sensitivity in Older Sedentary Adults
Authors: Suboc Tisha B. , Knabel Daniel , Strath Scott J. , Dharmashankar Kodlipet , Coulliard Allison , Malik Mobin , Haak Kristoph , Widlansky Michael E.
Published: May 2015

BACKGROUND

We previously reported increased moderate-intensity (3–6 metabolic equivalents (METs)) physical activity (PA) reverses aging-associated vascular endothelial dysfunction, a surrogate marker of cardiovascular risk. Whether reductions in sedentary time alone contribute to this improvement is unknown.

METHODS

Data from 96 adults (aged ≥50 years) enrolled in a randomized control trial evaluating a 12-week intervention to increase PA in sedentary individuals were analyzed. Amount and intensity of activity were measured pre- and post-intervention by step count and accelerometry. Subjects were divided into 3 categories based on change in sedentary activity (<1. 5 METs): (i) ≥5% reduction in sedentary time, (ii) 0–4.99% reduction, and (iii) increase sedentary time. Vascular endothelial function was measured by brachial artery flow-mediated dilation (FMD%) pre- and post-intervention.

RESULTS

Sedentary time decreased overall ( P = 0.001), with a 101-minute decrease in category 1 ( N = 27, P < 0.001), a 42-minute decrease in category 2 ( N = 29, P = 0.003), and a 44-minute increase in category 3 ( N = 40, P = 0.02). While FMD% increased in the entire study population ( P = 0.008) over 12 weeks, no differences were observed between the categories ( P = 0.73). In category 1, FMD% improvement was associated achievement of ≥20 minutes/day of moderate intensity PA in bouts ≥ 10 minutes in length.

CONCLUSIONS

Reductions of up to 100 minutes of sedentary time per day over 12 weeks was not significantly associated with improved vascular endothelial function in older adults. FMD% was significantly higher among those with lower sedentary behavior and concomitant moderate-intensity PA of ≥20 minutes/day in bouts.
TRAL: tandem repeat annotation library
Authors: Schaper Elke , Korsunsky Alexander , Pečerska Jūlija , Messina Antonio , Murri Riccardo , Stockinger Heinz , Zoller Stefan , Xenarios Ioannis , Anisimova Maria
Published: May 2015

Motivation: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results.

Results: We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly.

Availability and implementation: TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral.

Contact:  elke.schaper@isb-sib.ch
IMSEQ—a fast and error aware approach to immunogenetic sequence analysis
Authors: Kuchenbecker Leon , Nienen Mikalai , Hecht Jochen , Neumann Avidan U. , Babel Nina , Reinert Knut , Robinson Peter N.
Published: May 2015

Motivation: Recombined T- and B-cell receptor repertoires are increasingly being studied using next generation sequencing (NGS) in order to interrogate the repertoire composition as well as changes in the distribution of receptor clones under different physiological and disease states. This type of analysis requires efficient and unambiguous clonotype assignment to a large number of NGS read sequences, including the identification of the incorporated V and J gene segments and the CDR3 sequence. Current tools have deficits with respect to performance, accuracy and documentation of their underlying algorithms and usage.

Results: We present IMSEQ, a method to derive clonotype repertoires from NGS data with sophisticated routines for handling errors stemming from PCR and sequencing artefacts. The application can handle different kinds of input data originating from single- or paired-end sequencing in different configurations and is generic regarding the species and gene of interest. We have carefully evaluated our method with simulated and real world data and show that IMSEQ is superior to other tools with respect to its clonotyping as well as standalone error correction and runtime performance.

Availability and implementation: IMSEQ was implemented in C++ using the SeqAn library for efficient sequence analysis. It is freely available under the GPLv2 open source license and can be downloaded at www.imtools.org.

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact:  lkuchenb@inf.fu-berlin.de or peter.robinson@charite.de
Between Classicism and Modernity: Éric Rohmer on Urban Change
Authors: Schmid Marion
Published: May 2015

A director at the crossroads of the arts, Éric Rohmer took a keen interest in the urban transformations France underwent in the course of the twentieth century, in particular the post-war
villes nouvelles
project launched by the Gaullist government in 1965. In a programmatic article on the relationship between cinema and architecture, followed by a series of television documentaries from the 1960s and 1970s, as well as two feature films —
Les Nuits de la pleine lune
(1984) and
L
'
Ami de mon amie
(1987) — the director interrogates the new types of urban living proposed by progressive architects and town planners. Focusing on the intersection between his theoretical writings, his little-known documentaries, and his fictional work, this article assesses Rohmer's ambivalent attitude towards modern architecture in the wider context of the tension between classicism and modernity evidenced in his aesthetics and creative practice. As cautious of the functional modernism of a Le Corbusier as he is of postmodern housing schemes, the director offers a probing reflection on the relationship between the built environment and lived experience, framed by a broader questioning of cinema's place among its more established sister arts.
Galaxy pairs in the Sloan Digital Sky Survey – XII. The fuelling mechanism of low-excitation radio-loud AGN
Authors: Ellison Sara L. , Patton David R. , Hickox Ryan C.
Published: May 2015

We investigate whether the fuelling of low-excitation radio galaxies (LERGs) is linked to major galaxy interactions. Our study utilizes a sample of 10 800 spectroscopic galaxy pairs and 97 post-mergers selected from the Sloan Digital Sky Survey with matches to multiwavelength data sets. The LERG fraction amongst interacting galaxies is a factor of 3.5 higher than that of a control sample matched in local galaxy density, redshift and stellar mass. However, the LERG excess in pairs does not depend on projected separation and remains elevated out to at least 500 $h_{70}^{-1}$ kpc, suggesting that major mergers are not their main fuelling channel. In order to identify the primary fuelling mechanism of LERGs, we compile samples of control galaxies that are matched in various host galaxy and environmental properties. The LERG excess is reduced, but not completely removed, when halo mass or D4000 are included in the matching parameters. However, when bothMhalo and D4000 are matched, there is no LERG excess and the 1.4 GHz luminosities (which trace jet mechanical power) are consistent between the pairs and control. In contrast, the excess of optical and mid-IR selected active galactic nuclei (AGN) in galaxy pairs is unchanged when the additional matching parameters are implemented. Our results suggest that whilst major interactions may trigger optically and mid-IR selected AGN, the gas which fuels the LERGs has two secular origins: one associated with the large-scale environment, such as accretion from the surrounding medium or minor mergers, plus an internal stellar mechanism, such as winds from evolved stars.
Children With Anorectal Malformations, Hirschsprung Disease, and Their Siblings
Authors: Hartman Esther E. , Oort Frans J. , Aronson Daniel C. , van der Steeg Alida F.W. , Heij Hugo A. , van Heurn Ernest , Madern Gerard C. , van der Zee David C. , de Blaauw Ivo , van Dijk A. , Sprangers Mirjam A.G.
Published: May 2015

Objectives:

The aim of the present study was to compare parent proxy reports with that of self‐reports of children with anorectal malformations (ARMs) or Hirschsprung disease (HD) and healthy siblings and thereafter was examine whether these comparisons differed between patients and their siblings.

Methods:

Parents (n = 98) of either children with ARM (n = 44) or HD (n = 54) and a healthy sibling (n = 98) recruited from the 6 Dutch pediatric surgical centers and from the ARM and HD patient societies were included in this cross‐sectional multilevel study. Agreement between child self‐reports and parent proxy reports was compared through mean differences and through (intraclass) correlations. We conducted multilevel analyses to take dependencies between assessments within families into account.

Results:

All of the children (children with ARM or HD and their siblings) reported more pain and symptoms than their parents reported. We also found that only children with ARM or HD reported less positive emotions than their parents. Furthermore, higher correlations were found between parent proxy reports and patient‐self reports than between parent proxy reports and sibling self‐reports on cognitive functioning and social interaction.

Conclusions:

Parents tend to overestimate the physical functioning of both their ill and healthy children, and overestimate the emotional functioning of only their children with ARM or HD. Furthermore, children with ARM or HD and parents agree more on health‐related quality of life domains than healthy children and parents.
Hepatitis D in Children
Authors: Xue Megan M. , Glenn Jeffrey S. , Leung Daniel H.
Published: May 2015

Hepatitis D virus (HDV) is an uncommon, defective, single‐stranded circular RNA virus that is dependent on the hepatitis B virus’ surface antigen envelope proteins for transmission. It is highly pathogenic and associated with high rates of progression to cirrhosis and associated complications. HDV continues to ravage endemic parts of Asia and Europe, and its prevalence in the United States, although low, has not decreased in frequency, despite universal hepatitis B virus vaccination, because of lack of testing and underrecognition. There are few reports on the prevalence and characteristics of HDV infection in the pediatric population. We present 2 patients with HDV infection at our institution; both were from eastern Europe and were treated with pegylated interferon‐α. The present standard of care treatment for HDV yields suboptimal results, but insights into the virology of hepatitis D are stimulating the search for novel therapeutic approaches, particularly the development of prenylation inhibitors and viral entry inhibitors.