bluuebunny/crossref_metadata_2025 huggingface dataset:
New-generation of cryogenic sapphire microwave oscillators for space, metrology, and scientific applications
Authors: Giordano Vincent , Grop Serge , Dubois Benoît , Bourgeois Pierre-Yves , Kersalé Yann , Haye Gregory , Dolgovskiy Vladimir , Bucalovic Nikola , Di Domenico Gianni , Schilt Stéphane , Chauvin Jacques , Valat David , Rubiola Enrico
Published: August 2012

This article reports on the characterization of cryogenic sapphire oscillators (CSOs), and on the first test of a CSO in a real field installation, where ultimate frequency stability and continuous operation are critical issues, with no survey. Thanks to low-vibration liquid-He cryocooler design, Internet monitoring, and a significant effort of engineering, these oscillators could bridge the gap from an experiment to a fully reliable machine. The cryocooler needs scheduled maintenance every 2 years, which is usual for these devices. The direct comparison of two CSOs demonstrates a frequency stability of 5 × 10−16 for 30 s ⩽ τ ⩽ 300 s integration time, and 4.5 × 10−15 at 1 day (1 × 10−14 typical). Two prototypes are fully operational, codenamed ELISA and ULISS. ELISA has been permanently installed the new deep space antenna station of the European Space Agency in Malargüe, Argentina, in May 2012. ULISS is a transportable version of ELISA, modified to fit in a small van (8.5 m2 footprint). Installation requires a few hours manpower and 1 day of operation to attain full stability. ULISS, intended for off-site experiments and as a technology demonstrator, and has successfully completed two long-distance travels.
Kinetic analysis of image sticking with adsorption and desorption of ions to a surface of an alignment layer
Authors: Mizusaki Masanobu , Miyashita Tetsuya , Uchida Tatsuo
Published: August 2012

Generation of residual direct current (DC) voltage (VrDC) induces a serious image sticking of liquid crystal (LC) displays. VrDC is generated with the ions in a LC layer adsorbing to a surface of an alignment layer under application of DC offset voltage. We clarified the adsorption and desorption of the ions to and from the surface of the alignment layer with a kinetic model proposed by us. The analysis with using the kinetic model made clear that the processes of the adsorption and desorption occur due to the thermal fluctuation followed by the Boltzmann distribution. The ions adsorb to the surface of the alignment layer by a weak binding, such as the van der Waals interaction.
Ionization and Coulomb explosion of small group 10 transition metal oxide clusters in strong light fields
Authors: Ross Matt W. , Castleman A. W.
Published: August 2012

The ionization properties of small group 10 metal oxide clusters are explored using ultrafast pulses centered at 624 nm. Maximum atomic charge states resulting from Coulomb explosion were observed to be Ni3+, Pd3+, Pt5+, and O2+ species with similar ionization potentials ∼30–35 eV. Ion signal as a function of laser intensity of each charge state of Ni, Pd, Pt, and O resulting from Coulomb explosion was mapped and compared to that predicted from semi-classical tunneling theory using sequential ionization potentials to quantify observed enhancements in ionization. The saturation intensity (Isat) of each charge state is measured and compared to previous studies on group 5 transition metal oxides. The atomic charge states of nickel showed a large enhancement in ionization compared to palladium and platinum, reflective of the differing bonding properties of each metal with oxygen. Results indicate that nickel oxide clusters undergo a greater extent of ionization enhancement as a result of multiple ionization mechanisms. The ionization enhancement behavior of each metal oxide species is explored herein.
The combined effect of surface roughness and internal stresses on nanoindentation tests of polysilicon thin films
Authors: Wang Quan , Hu Ran , Shao Ying
Published: August 2012

Flat, low-stress, boron-doped polysilicon thin films were prepared on crystalline silicon substrates by low pressure chemical vapor deposition. The films’ surface morphologies and internal stresses were investigated using scanning probe microscope and AFM-Raman, respectively. The elastic modulus (E) was measured along with the hardness (H) using the nanoindentation technique. It was found that films deposited at the highest temperature had the largest grain size and surface roughness. The internal stresses in the films are tensile stresses, which are not uniform over the surfaces and present the gradient distribution along the thickness. Both the surface roughness and the internal stresses affect the nanoindentation tests. The tensile stresses in the films give extra forces to the diamond indenter, so the depths of penetration should be larger than those obtained from the films with stress free for a given load, which leads to an underestimation of E as well as H. But under the applied conditions, the increasing surface roughness can not only lead to the reductions of depths of penetration but also cause the measurement values of E and H to be more dispersive and uncertain. So for a given load, if the maximum depth of penetration in the rough surface is smaller than that in the smooth surface, the surface roughness is the main factor affecting the nanoindentation tests. On the contrary, the tensile stress is the main factor.
Hydrogen diffusion in lead zirconate titanate and barium titanate
Authors: Alvine K. J. , Vijayakumar M. , Bowden M. E. , Schemer-Kohrn A. L. , Pitman S. G.
Published: August 2012

Hydrogen is a potential clean-burning, next-generation fuel for vehicle and stationary power. Unfortunately, hydrogen is also well known to have serious materials compatibility issues in metals, polymers, and ceramics. Piezoelectric actuator materials proposed for low-cost, high efficiency high-pressure hydrogen internal combustion engines (HICE) are known to degrade rapidly in hydrogen. This limits their potential use and poses challenges for HICE. Hydrogen-induced degradation of piezoelectrics is also an issue for low-pressure hydrogen passivation in ferroelectric random access memory. Currently, there is a lack of data in the literature on hydrogen species diffusion in piezoelectrics in the temperature range appropriate for the HICE as charged via a gaseous route. We present 1HNMR quantification of the local hydrogen species diffusion within lead zirconate titanate and barium titanate on samples charged by exposure to high-pressure gaseous hydrogen ∼32 MPa. Results are discussed in context of theoretically predicted interstitial hydrogen lattice sites and aqueous charging experiments from existing literature.
Effect of Pt bottom electrode texture selection on the tetragonality and physical properties of Ba0.8Sr0.2TiO3 thin films produced by pulsed laser deposition
Authors: Silva J. P. B. , Sekhar K. C. , Almeida A. , Moreira J. Agostinho , Martín-Sánchez J. , Pereira M. , Khodorov A. , Gomes M. J. M.
Published: August 2012

The effect of platinum (Pt) bottom electrode texture on the tetragonality, dielectric, ferroelectric, and polarization switching response of pulsed laser deposited Ba0.8Sr0.2TiO3 (BST) thin films has been studied. The x-ray diffraction and Raman analysis revealed the higher tetragonality of BST films when they were grown on higher (111) textured Pt layer. The properties like dielectric permittivity, polarization, switching time, and leakage currents were found to be correlated to tetragonality and orientation of the BST films. The polarization current was observed to be higher in BST films on Pt epitaxial layer and it exhibits exponential dependence on the electric field. The voltage-current measurements displayed Ohmic behavior of leakage current irrespective of Pt texture for low voltages (up to 1 V), whereas at higher voltages the conduction mechanism was found to be dependent on texture selection of bottom Pt electrode.
Dust-acoustic waves and stability in the permeating dusty plasma. II. Power-law distributions
Authors: Gong Jingyu , Liu Zhipeng , Du Jiulin
Published: August 2012

The dust-acoustic waves and the stability theory for the permeating dusty plasma with power-law distributions are studied by using nonextensive q-statistics. In two limiting physical cases, when the thermal velocity of the flowing dusty plasma is much larger than, and much smaller than the phase velocity of the waves, we derived the dust-acoustic wave frequency, the instability growth rate, and the instability critical flowing velocity. As compared with the formulae obtained in part I [Gong et al., Phys. Plasmas 19, 043704 (2012)], all formulae of the present cases and the resulting plasma characteristics are q-dependent, and the power-law distribution of each plasma component of the permeating dusty plasma has a different q-parameter and thus has a different nonextensive effect. Further, we make numerical analyses of an example that a cometary plasma tail is passing through the interplanetary space dusty plasma and we show that these power-law distributions have significant effects on the plasma characteristics of this kind of plasma environment.
Energy spread inhibition of compact electron bunch driven by circularly polarized laser pulse
Authors: Wen Meng , Wu Haicheng , Jin Luling , Lu Yuanrong , Chen Jiaer , Yan Xueqing
Published: August 2012

The problem of energy dispersion of a direct laser accelerated electron bunch emerging from a nano-meshed graphene target is investigated. To study the effects of the laser polarization state on the energy spread, numerical calculations and particle-in-cell simulations of evolving one-dimensional confined electron bunch dynamics are performed. It is proved that a circularly polarized laser pulse can inhibit energy dispersion more efficiently than a linearly polarized laser pulse with the same laser and target parameters. That is because the Coulomb expansion of the electron bunch gets more attenuated for a circularly polarized laser pulse compared with a linearly polarized pulse due to the slowly varying temporal laser intensity.
Attentional Capture without Awareness in Complex Visual Tasks
Authors: Seya Yasuhiro , Tsutsui Ken-Ichiro , Watanabe Katsumi , Kimura Kenji
Published: August 2012

Abrupt onsets of visual cues capture an observer's attention, even when the cues do not reach the observer's visual awareness. In the present study, we investigated the effects of subthreshold cues on the performance of a useful field of view task. Participants localized a target stimulus presented in the peripheral visual field while identifying a character presented at the fovea. Before the presentation of central and peripheral targets, a suprathreshold or subthreshold cue indicating a likely location of the peripheral target was presented. We found that the suprathreshold cue led to both a benefit in the valid trials and cost in the invalid trials, while the subthreshold cue produced only a benefit in the valid trials without a cost in the invalid trials. Similar patterns of results were also observed when the cue preceded the targets by 10–200 ms, although a small cost was observed for the 12 deg eccentricity at the stimulus onset asynchronies of 50 ms and 100 ms in the subthreshold condition. These results indicate that attentional capture occurs without awareness of the cue and suggest that the effect of the cue on the spatial shift of attention would be different between the suprathreshold and subthreshold conditions.
The Identification of Unfolding Facial Expressions
Authors: Fiorentini Chiara , Schmidt Susanna , Viviani Paolo
Published: August 2012

We asked whether the identification of emotional facial expressions (FEs) involves the simultaneous perception of the facial configuration or the detection of emotion-specific diagnostic cues. We recorded at high speed (500 frames s−1) the unfolding of the FE in five actors, each expressing six emotions (anger, surprise, happiness, disgust, fear, sadness). Recordings were coded every 10 frames (20 ms of real time) with the Facial Action Coding System (FACS, Ekman et al 2002, Salt Lake City, UT: Research Nexus eBook) to identify the facial actions contributing to each expression, and their intensity changes over time. Recordings were shown in slow motion (1/20 of recording speed) to one hundred observers in a forced-choice identification task. Participants were asked to identify the emotion during the presentation as soon as they felt confident to do so. Responses were recorded along with the associated response times (RTs). The RT probability density functions for both correct and incorrect responses were correlated with the facial activity during the presentation. There were systematic correlations between facial activities, response probabilities, and RT peaks, and significant differences in RT distributions for correct and incorrect answers. The results show that a reliable response is possible long before the full FE configuration is reached. This suggests that identification is reached by integrating in time individual diagnostic facial actions, and does not require perceiving the full apex configuration.
Payoff Changes Sensitivity by Modulating the Processing Style
Authors: Krol Magdalena , El-Deredy Wael
Published: August 2012

In a perceptual decision-making task, we compared a neutral payoff and two asymmetric payoffs: a liberal one, favouring positive responses, and a conservative one, favouring negative responses. Participants were presented with ambiguous images composed of superimposed target and non-target photographs, and asked to decide whether the target dominated in the picture. Signal-detection analysis demonstrated that the liberal payoff yielded significantly higher sensitivity than other payoffs. We argue that the liberal payoff encourages confirming the target's domination, hence making it easier to ignore non-target elements of the picture. We conclude that payoff can influence perceptual decisions by changing the approach to the perceptual task, and how attention is allocated between different elements of the sensory input.
Forward Masking of Dynamic Acoustic Intensity: Effects of Intensity Region and End-Level
Authors: Olsen Kirk N , Stevens Catherine J
Published: August 2012

Overestimation of loudness change typically occurs in response to up-ramp auditory stimuli (increasing intensity) relative to down-ramps (decreasing intensity) matched on frequency, duration, and end-level. In the experiment reported, forward masking is used to investigate a sensory component of up-ramp overestimation: persistence of excitation after stimulus presentation. White-noise and synthetic vowel 3.6 s up-ramp and down-ramp maskers were presented over two regions of intensity change (40–60 dB SPL, 60–80 dB SPL). Three participants detected 10 ms 1.5 kHz pure tone signals presented at masker-offset to signal-offset delays of 10, 20, 30, 50, 90, 170 ms. Masking magnitude was significantly greater in response to up-ramps compared with down-ramps for masker-signal delays up to and including 50 ms. When controlling for an end-level recency bias (40–60 dB SPL up-ramp vs 80–60 dB SPL down-ramp), the difference in masking magnitude between up-ramps and down-ramps was not significant at each masker–signal delay. Greater sensory persistence in response to up-ramps is argued to have minimal effect on perceptual overestimation of loudness change when response biases are controlled. An explanation based on sensory adaptation is discussed.
Perceptually Plausible Sounds Facilitate Visually Induced Self-Motion Perception (Vection)
Authors: Seno Takeharu , Hasuo Emi , Ito Hiroyuki , Nakajima Yoshitaka
Published: August 2012

We examined whether and how sounds influence visually induced illusory self-motion (vection). Visual stimuli were presented for 40 s. They were made radially, expanding or contracting visual motion field and luminance-defined gratings drifting in a vertical or horizontal direction. Auditory stimuli were presented with the visual stimuli in most conditions; we employed sounds that increased or decreased in intensity, or ascended or descended in frequency. As a result, the sound which increased in intensity facilitated forward vection, and the sound which ascended/descended in frequency facilitated upward/downward vection. The perceptual plausibility of the sound for the corresponding self-motion seemed an important factor of enhancing vection.
Matching Reality in the Arts: Self-Referential Neural Processing of Naturalistic Compared to Surrealistic Images
Authors: Silveira Sarita , Graupmann Verena , Frey Dieter , Blautzik Janusch , Meindl Thomas , Reiser Maximilian , Chen Cheng , Wang Yizhou , Bao Yan , Pöppel Ernst , Gutyrchik Evgeny
Published: August 2012

How are works of art that present scenes that match potential expectations processed in the brain, in contrast to such scenes that can never occur in real life because they would violate physical laws? Using functional magnetic resonance imaging, we investigated the processing of surrealistic and naturalistic images in visual artworks. Looking at naturalistic paintings leads to a significantly higher activation in the visual cortex and in the precuneus. Humans apparently own a sensitive mechanism even for artistic representations of the visual world to separate the impossible from what potentially matches physical reality. The observation reported here also suggests that sensory input corresponding to a realistic representation of the visual world elicits higher self-referential processing.
Cross-Sensory Correspondences and Naive Conceptions of Natural Phenomena
Authors: Walker Peter
Published: August 2012

Cross-sensory correspondences automatically intrude on performance in elaborate laboratory tasks (see Spence 2011 Attention, Perception, & Psychophysics73 971–995, for a review). Outside such tasks, might they be responsible for some popular misconceptions about natural phenomena? Four simple demonstrations reveal how the correspondences between surface-lightness and weight, and between surface-lightness and auditory pitch, generate misconceptions about the weight and movement of objects and the vocalisations of animals. Specifically, people expect darker objects to be heavier than lighter-coloured objects, to free-fall more quickly, to roll across a table more slowly, and to make lower-pitched vocalisations when they come to life.
The Nature and Origin of Cross-Modal Associations to Odours
Authors: Stevenson Richard J , Rich Anina , Russell Alex
Published: August 2012

Several studies have demonstrated reliable cross-modal associations between odours and various visual, auditory, taste, and somatosensory attributes. How these associations arise is not well understood. We examined whether cross-modal associations to odours themselves form distinct groups, and whether these groupings relate to semantic (nameability, familiarity) and perceptual (intensity, irritancy, and hedonics) olfactory attributes. Participants evaluated 20 odours, varying in all of the latter attributes, and reported their visual, auditory, gustatory, and somatosensory associations for each. Significant inter-rater agreement was observed for all modalities except audition, and responses in all modalities were consistent with those obtained on a repeat test session 2 weeks later. Two groups of cross-modal odour associates emerged: one of which was related to the semantic attributes of odours and another which related to their perceptual attributes. The exception was taste, which was significantly associated with both. While these results suggest that both semantic and perceptual mechanisms underpin odour cross-modal matches, the data also point to the importance of hedonics as a further contributing mechanism.
Demystifying cultural sensitivity and equity of care
Authors: Isaacs Anton N.
Published: August 2012

While most health professionals would like to believe that the care they provide is culturally sensitive, a poor understanding of the concepts of cultural sensitivity and equity of care often results in the contrary. In order to ensure equity of care for all its clients, it becomes necessary for health services to provide care that is culturally sensitive. This letter attempts to explain these concepts with the help of two everyday examples.
Development and evaluation of electroejaculation techniques in the Tasmanian devil (Sarcophilus harrisii)
Authors: Keeley T. , Harris M. , McGreevy P. D. , Hudson D. , O'Brien J. K.
Published: August 2012

Electroejaculation (EEJ) has been used successfully to collect samples suitable for genome resource banking from a variety of endangered wildlife species. Ejaculates can also be used to evaluate the reproductive potential of individuals and provide information on seminal characteristics to aid in the development of sperm cryopreservation techniques. Electroejaculation techniques used for marsupial and eutherian species were tested on Tasmanian devils (n = 35). Spermic ejaculates were collected in 54% (19/35) of EEJ attempts. Spermic ejaculates were low in volume (3.9 ± 6.5 × 102 µL, range 10–3000 µL) and contained low numbers of spermatozoa (3.3 ± 7.8 × 103 spermatozoa per ejaculate, range 6–33 000). The osmolality and pH of presumptive urine-free ejaculates were 389 ± 130 mOsm kg–1 (range 102–566) and 7.0 ± 0.9 (range 6.0–8.0), respectively. Prostatic bodies were observed in 79% (26/33) of ejaculates. Episodic fluctuations in serum testosterone concentrations were not detected during the EEJ procedure (P > 0.05). Increases observed in serum cortisol concentrations during EEJ were less (P < 0.05) than those observed after an adrenalcorticotropic hormone challenge and diurnal variation suggested that cortisol concentrations are greater during the day than at night (P < 0.05). This information can be used to provide range values for the future examination of basic endocrine responses and the adrenal–pituitary axis of this species. This study also demonstrated that spermatozoa-rich devil electroejaculates are more difficult to obtain and poorer in quality than those of other marsupials.
Manipulating superconducting fluctuations by the Little–Parks–de Gennes effect in ultrasmall Al loops
Authors: Staley Neal E. , Liu Ying
Published: August 2012

The destruction of superconducting phase coherence by quantum fluctuations and the control of these fluctuations are a problem of long-standing interest, with recent impetus provided by the relevance of these issues to the pursuit of high temperature superconductivity. Building on the work of Little and Parks, de Gennes predicted more than three decades ago that superconductivity could be destroyed near half-integer-flux quanta in ultrasmall loops, resulting in a destructive regime, and restored by adding a superconducting side branch, which does not affect the flux quantization condition. We report the experimental observation of this Little–Parks–de Gennes effect in Al loops prepared by advanced e-beam lithography. We show that the effect can be used to restore the lost phase coherence by employing side branches.
Regulation of planar growth by the
Arabidopsis
AGC protein kinase UNICORN
Authors: Enugutti Balaji , Kirchhelle Charlotte , Oelschner Maxi , Torres Ruiz Ramón Angel , Schliebner Ivo , Leister Dario , Schneitz Kay
Published: August 2012

The spatial coordination of growth is of central importance for the regulation of plant tissue architecture. Individual layers, such as the epidermis, are clonally propagated and structurally maintained by symmetric cell divisions that are oriented along the plane of the layer. The developmental control of this process is poorly understood. The simple cellular basis and sheet-like structure of
Arabidopsis
integuments make them an attractive model system to address planar growth. Here we report on the characterization of the
Arabidopsis UNICORN
(
UCN
) gene. Analysis of
ucn
integuments reveals localized distortion of planar growth, eventually resulting in an ectopic multicellular protrusion. In addition,
ucn
mutants exhibit ectopic growth in filaments and petals, as well as aberrant embryogenesis. We further show that
UCN
encodes an active AGC VIII kinase. Genetic, biochemical, and cell biological data suggest that UCN suppresses ectopic growth in integuments by directly repressing the KANADI transcription factor ABERRANT TESTA SHAPE. Our findings indicate that
UCN
represents a unique plant growth regulator that maintains planar growth of integuments by repressing a developmental regulator involved in the control of early integument growth and polarity.
Foldon unfolding mediates the interconversion between Mpro-C monomer and 3D domain-swapped dimer
Authors: Kang Xue , Zhong Nan , Zou Peng , Zhang Shengnan , Jin Changwen , Xia Bin
Published: August 2012

The C-terminal domain (Mpro-C) of SARS-CoV main protease adopts two different fold topologies, a monomer and a 3D domain-swapped dimer. Here, we report that Mpro-C can reversibly interconvert between these two topological states under physiological conditions. Although the swapped α1-helix is fully buried inside the protein hydrophobic core, the interconversion of Mpro-C is carried out without the hydrophobic core being exposed to solvent. The 3D domain swapping of Mpro-C is activated by an order-to-disorder transition of its C-terminal α5-helix foldon. Unfolding of this foldon promotes self-association of Mpro-C monomers and functions to mediate the 3D domain swapping, without which Mpro-C can no longer form the domain-swapped dimer. Taken together, we propose that there exists a special dimeric intermediate enabling the protein core to unpack and the α1-helices to swap in a hydrophobic environment, which minimizes the energy cost of the 3D domain-swapping process.
Putative DNA/RNA helicase Schlafen-11 (SLFN11) sensitizes cancer cells to DNA-damaging agents
Authors: Zoppoli Gabriele , Regairaz Marie , Leo Elisabetta , Reinhold William C. , Varma Sudhir , Ballestrero Alberto , Doroshow James H. , Pommier Yves
Published: August 2012

DNA-damaging agents (DDAs) constitute the backbone of treatment for most human tumors. Here we used the National Cancer Institute Antitumor Cell Line Panel (the NCI-60) to identify predictors of cancer cell response to topoisomerase I (Top1) inhibitors, a widely used class of DDAs. We assessed the NCI-60 transcriptome using Affymetrix Human Exon 1.0 ST microarrays and correlated the in vitro activity of four Top1 inhibitors with gene expression in the 60 cell lines. A single gene, Schlafen-11 (SLFN11), showed an extremely significant positive correlation with the response not only to Top1 inhibitors, but also to Top2 inhibitors, alkylating agents, and DNA synthesis inhibitors. Using cells with endogenously high and low SLFN11 expression and siRNA-mediated silencing, we show that SLFN11 is causative in determining cell death and cell cycle arrest in response to DDAs in cancer cells from different tissues of origin. We next analyzed SLFN11 expression in ovarian and colorectal cancers and normal corresponding tissues from The Cancer Genome Atlas database and observed that SLFN11 has a wide expression range. We also observed that high SLFN11 expression independently predicts overall survival in a group of ovarian cancer patients treated with cisplatin-containing regimens. We conclude that SLFN11 expression is causally associated with the activity of DDAs in cancer cells, has a broad expression range in colon and ovarian adenocarcinomas, and may behave as a biomarker for prediction of response to DDAs in the clinical setting.
Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance
Authors: Sun Fei , Ding Yue , Ji Quanjiang , Liang Zhongjie , Deng Xin , Wong Catherine C. L. , Yi Chengqi , Zhang Liang , Xie Sherrie , Alvarez Sophie , Hicks Leslie M. , Luo Cheng , Jiang Hualiang , Lan Lefu , He Chuan
Published: August 2012

Protein posttranslational modifications (PTMs), particularly phosphorylation, dramatically expand the complexity of cellular regulatory networks. Although cysteine (Cys) in various proteins can be subject to multiple PTMs, its phosphorylation was previously considered a rare PTM with almost no regulatory role assigned. We report here that phosphorylation occurs to a reactive cysteine residue conserved in the staphylococcal accessary regulator A (SarA)/MarR family global transcriptional regulator A (MgrA) family of proteins, and is mediated by the eukaryotic-like kinase-phosphatase pair Stk1-Stp1 in
Staphylococcus aureus
. Cys-phosphorylation is crucial in regulating virulence determinant production and bacterial resistance to vancomycin. Cell wall-targeting antibiotics, such as vancomycin and ceftriaxone, inhibit the kinase activity of Stk1 and lead to decreased Cys-phosphorylation of SarA and MgrA. An in vivo mouse model of infection established that the absence of
stp1
, which results in elevated protein Cys-phosphorylation, significantly reduces staphylococcal virulence. Our data indicate that Cys-phosphorylation is a unique PTM that can play crucial roles in bacterial signaling and regulation.
Unifying the spatial epidemiology and molecular evolution of emerging epidemics
Authors: Pybus Oliver G. , Suchard Marc A. , Lemey Philippe , Bernardin Flavien J. , Rambaut Andrew , Crawford Forrest W. , Gray Rebecca R. , Arinaminpathy Nimalan , Stramer Susan L. , Busch Michael P. , Delwart Eric L.
Published: August 2012

We introduce a conceptual bridge between the previously unlinked fields of phylogenetics and mathematical spatial ecology, which enables the spatial parameters of an emerging epidemic to be directly estimated from sampled pathogen genome sequences. By using phylogenetic history to correct for spatial autocorrelation, we illustrate how a fundamental spatial variable, the diffusion coefficient, can be estimated using robust nonparametric statistics, and how heterogeneity in dispersal can be readily quantified. We apply this framework to the spread of the West Nile virus across North America, an important recent instance of spatial invasion by an emerging infectious disease. We demonstrate that the dispersal of West Nile virus is greater and far more variable than previously measured, such that its dissemination was critically determined by rare, long-range movements that are unlikely to be discerned during field observations. Our results indicate that, by ignoring this heterogeneity, previous models of the epidemic have substantially overestimated its basic reproductive number. More generally, our approach demonstrates that easily obtainable genetic data can be used to measure the spatial dynamics of natural populations that are otherwise difficult or costly to quantify.
Seasonal migration to high latitudes results in major reproductive benefits in an insect
Authors: Chapman Jason W. , Bell James R. , Burgin Laura E. , Reynolds Donald R. , Pettersson Lars B. , Hill Jane K. , Bonsall Michael B. , Thomas Jeremy A.
Published: August 2012

Little is known of the population dynamics of long-range insect migrants, and it has been suggested that the annual journeys of billions of nonhardy insects to exploit temperate zones during summer represent a sink from which future generations seldom return (the “Pied Piper” effect). We combine data from entomological radars and ground-based light traps to show that annual migrations are highly adaptive in the noctuid mothAutographa gamma(silver Y), a major agricultural pest. We estimate that 10–240 million immigrants reach the United Kingdom each spring, but that summer breeding results in a fourfold increase in the abundance of the subsequent generation of adults, all of which emigrate southward in the fall. Trajectory simulations show that 80% of emigrants will reach regions suitable for winter breeding in the Mediterranean Basin, for which our population dynamics model predicts a winter carrying capacity only 20% of that of northern Europe during the summer. We conclude not only that poleward insect migrations in spring result in major population increases, but also that the persistence of such species is dependent on summer breeding in high-latitude regions, which requires a fundamental change in our understanding of insect migration.
Human blood metabolite timetable indicates internal body time
Authors: Kasukawa Takeya , Sugimoto Masahiro , Hida Akiko , Minami Yoichi , Mori Masayo , Honma Sato , Honma Ken-ichi , Mishima Kazuo , Soga Tomoyoshi , Ueda Hiroki R.
Published: August 2012

A convenient way to estimate internal body time (BT) is essential for chronotherapy and time-restricted feeding, both of which use body-time information to maximize potency and minimize toxicity during drug administration and feeding, respectively. Previously, we proposed a molecular timetable based on circadian-oscillating substances in multiple mouse organs or blood to estimate internal body time from samples taken at only a few time points. Here we applied this molecular-timetable concept to estimate and evaluate internal body time in humans. We constructed a 1.5-d reference timetable of oscillating metabolites in human blood samples with 2-h sampling frequency while simultaneously controlling for the confounding effects of activity level, light, temperature, sleep, and food intake. By using this metabolite timetable as a reference, we accurately determined internal body time within 3 h from just two anti-phase blood samples. Our minimally invasive, molecular-timetable method with human blood enables highly optimized and personalized medicine.
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
Authors: Lee Sooncheol , Liu Botao , Lee Soohyun , Huang Sheng-Xiong , Shen Ben , Qian Shu-Bing
Published: August 2012

Understanding translational control in gene expression relies on precise and comprehensive determination of translation initiation sites (TIS) across the entire transcriptome. The recently developed ribosome-profiling technique enables global translation analysis, providing a wealth of information about both the position and the density of ribosomes on mRNAs. Here we present an approach, global translation initiation sequencing, applying in parallel the ribosome E-site translation inhibitors lactimidomycin and cycloheximide to achieve simultaneous detection of both initiation and elongation events on a genome-wide scale. This approach provides a view of alternative translation initiation in mammalian cells with single-nucleotide resolution. Systemic analysis of TIS positions supports the ribosome linear-scanning mechanism in TIS selection. The alternative TIS positions and the associated ORFs identified by global translation initiation sequencing are conserved between human and mouse cells, implying physiological significance of alternative translation. Our study establishes a practical platform for uncovering the hidden coding potential of the transcriptome and offers a greater understanding of the complexity of translation initiation.
Predictive computation of genomic logic processing functions in embryonic development
Authors: Peter Isabelle S. , Faure Emmanuel , Davidson Eric H.
Published: August 2012

Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model computes spatial and temporal gene expression according to the regulatory logic and gene interactions specified in a GRN model for embryonic development in the sea urchin. Additional information input into the model included the progressive embryonic geometry and gene expression kinetics. The resulting model predicted gene expression patterns for a large number of individual regulatory genes each hour up to gastrulation (30 h) in four different spatial domains of the embryo. Direct comparison with experimental observations showed that the model predictively computed these patterns with remarkable spatial and temporal accuracy. In addition, we used this model to carry out
in silico
perturbations of regulatory functions and of embryonic spatial organization. The model computationally reproduced the altered developmental functions observed experimentally. Two major conclusions are that the starting GRN model contains sufficiently complete regulatory information to permit explanation of a complex developmental process of gene expression solely in terms of genomic regulatory code, and that the Boolean model provides a tool with which to test
in silico
regulatory circuitry and developmental perturbations.
Arthropods in amber from the Triassic Period
Authors: Schmidt Alexander R. , Jancke Saskia , Lindquist Evert E. , Ragazzi Eugenio , Roghi Guido , Nascimbene Paul C. , Schmidt Kerstin , Wappler Torsten , Grimaldi David A.
Published: August 2012

The occurrence of arthropods in amber exclusively from the Cretaceous and Cenozoic is widely regarded to be a result of the production and preservation of large amounts of tree resin beginningca.130 million years (Ma) ago. Abundant 230 million-year-old amber from the Late Triassic (Carnian) of northeastern Italy has previously yielded myriad microorganisms, but we report here that it also preserves arthropods some 100 Ma older than the earliest prior records in amber. The Triassic specimens are a nematoceran fly (Diptera) and two disparate species of mites,Triasacarus fedeleigen. et sp. nov., andAmpezzoa triassicagen. et sp. nov. These mites are the oldest definitive fossils of a group, the Eriophyoidea, which includes the gall mites and comprises at least 3,500 Recent species, 97% of which feed on angiosperms and represents one of the most specialized lineages of phytophagous arthropods. Antiquity of the gall mites in much their extant form was unexpected, particularly with the Triassic species already having many of their present-day features (such as only two pairs of legs); further, it establishes conifer feeding as an ancestral trait. Feeding by the fossil mites may have contributed to the formation of the amber droplets, but we find that the abundance of amber during the Carnian (ca.230 Ma) is globally anomalous for the pre-Cretaceous and may, alternatively, be related to paleoclimate. Further recovery of arthropods in Carnian-aged amber is promising and will have profound implications for understanding the evolution of terrestrial members of the most diverse phylum of organisms.
An injury-response mechanism conserved across kingdoms determines entry of the fungus
Trichoderma atroviride
into development
Authors: Hernández-Oñate Miguel A. , Esquivel-Naranjo Edgardo U. , Mendoza-Mendoza Artemio , Stewart Alison , Herrera-Estrella Alfredo H.
Published: August 2012

A conserved injury-defense mechanism is present in plants and animals, in which the production of reactive oxygen species (ROS) and lipid metabolism are essential to the response. Here, we describe that in the filamentous fungus
Trichoderma atroviride
, injury results in the formation of asexual reproduction structures restricted to regenerating cells. High-throughput RNA-seq analyses of the response to injury in
T. atroviride
suggested an oxidative response and activation of calcium-signaling pathways, as well as the participation of lipid metabolism, in this phenomenon. Gene-replacement experiments demonstrated that injury triggers NADPH oxidase (Nox)–dependent ROS production and that Nox1 and NoxR are essential for asexual development in response to damage. We further provide evidence of H
2
O
2
and oxylipin production that, as in plants and animals, may act as signal molecules in response to injury in fungi, suggesting that the three kingdoms share a conserved defense-response mechanism.
RETRACTED: Signing at the beginning makes ethics salient and decreases dishonest self-reports in comparison to signing at the end
Authors: Shu Lisa L. , Mazar Nina , Gino Francesca , Ariely Dan , Bazerman Max H.
Published: August 2012

Many written forms required by businesses and governments rely on honest
reporting. Proof of honest intent is typically provided through signature at the
end of, e.g., tax returns or insurance policy forms. Still, people sometimes
cheat to advance their financial self-interests—at great costs to society. We
test an easy-to-implement method to discourage dishonesty: signing at the
beginning rather than at the end of a self-report, thereby reversing the order
of the current practice. Using laboratory and field experiments, we find that
signing before—rather than after—the opportunity to cheat makes ethics salient
when they are needed most and significantly reduces dishonesty.
Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in
Escherichia coli
Authors: Chatterjee Abhishek , Xiao Han , Schultz Peter G.
Published: August 2012

The site-specific incorporation of unnatural amino acids (UAAs) into proteins in living cells relies on an engineered tRNA/aminoacyl-tRNA synthetase (tRNA/aaRS) pair, orthogonal to the host cell, to deliver the UAA of choice in response to a unique nonsense or frameshift codon. Here we report the generation of mutually orthogonal prolyl-tRNA/prolyl-tRNA synthase (ProRS) pairs derived from an archaebacterial ancestor for use in
Escherichia coli
. By reprogramming the anticodon-binding pocket of
Pyrococcus horikoshii
ProRS (PhProRS), we were able to identify synthetase variants that recognize engineered
Archaeoglobus fulgidus
prolyl-tRNAs (Af-tRNA
Pro
) with three different anticodons: CUA, AGGG, and CUAG. Several of these evolved PhProRSs show specificity toward a particular anticodon variant of Af-tRNA
Pro
, whereas others are promiscuous. Further evolution of the Af-tRNA
Pro
led to a variant exhibiting significantly improved amber suppression efficiency. Availability of a prolyl-tRNA/aaRS pair should enable site-specific incorporation of proline analogs and other N-modified UAAs into proteins in
E. coli
. The evolution of mutually orthogonal prolyl-tRNA/ProRS pairs demonstrates the plasticity of the tRNA–aaRS interface and should facilitate the incorporation of multiple, distinct UAAs into proteins.
Structure of Nectin-2 reveals determinants of homophilic and heterophilic interactions that control cell–cell adhesion
Authors: Samanta Dibyendu , Ramagopal Udupi A. , Rubinstein Rotem , Vigdorovich Vladimir , Nathenson Stanley G. , Almo Steven C.
Published: August 2012

Nectins are members of the Ig superfamily that mediate cell–cell adhesion through homophilic and heterophilic interactions. We have determined the crystal structure of the nectin-2 homodimer at 1.3 Å resolution. Structural analysis and complementary mutagenesis studies reveal the basis for recognition and selectivity among the nectin family members. Notably, the close proximity of charged residues at the dimer interface is a major determinant of the binding affinities associated with homophilic and heterophilic interactions within the nectin family. Our structural and biochemical data provide a mechanistic basis to explain stronger heterophilic versus weaker homophilic interactions among these family members and also offer insights into nectin-mediated transinteractions between engaging cells.
Organelle positioning in muscles requires cooperation between two KASH proteins and microtubules
Authors: Elhanany-Tamir Hadas , Yu Yanxun V. , Shnayder Miri , Jain Ankit , Welte Michael , Volk Talila
Published: August 2012

Striated muscle fibers are characterized by their tightly organized cytoplasm. Here, we show that the Drosophila melanogaster KASH proteins Klarsicht (Klar) and MSP-300 cooperate in promoting even myonuclear spacing by mediating a tight link between a newly discovered MSP-300 nuclear ring and a polarized network of astral microtubules (aMTs). In either klar or msp-300ΔKASH, or in klar and msp-300 double heterozygous mutants, the MSP-300 nuclear ring and the aMTs retracted from the nuclear envelope, abrogating this even nuclear spacing. Anchoring of the myonuclei to the core acto-myosin fibrillar compartment was mediated exclusively by MSP-300. This protein was also essential for promoting even distribution of the mitochondria and ER within the muscle fiber. Larval locomotion is impaired in both msp-300 and klar mutants, and the klar mutants were rescued by muscle-specific expression of Klar. Thus, our results describe a novel mechanism of nuclear spacing in striated muscles controlled by the cooperative activity of MSP-300, Klar, and astral MTs, and demonstrate its physiological significance.
SUMOylated SoxE factors recruit Grg4 and function as transcriptional repressors in the neural crest
Authors: Lee Pei-Chih , Taylor-Jaffe Kimberly M. , Nordin Kara M. , Prasad Maneeshi S. , Lander Rachel M. , LaBonne Carole
Published: August 2012

A growing number of transcriptional regulatory proteins are known to be modified by the small ubiquitin-like protein, SUMO. Posttranslational modification by SUMO may be one means by which transcriptional regulatory factors that play context-dependent roles in multiple processes can be regulated such that they direct the appropriate cellular and developmental outcomes. In early vertebrate embryos, SUMOylation of SoxE transcription factors profoundly affects their function, inhibiting their neural crest–inducing activity and promoting ear formation. In this paper, we provide mechanistic insight into how SUMO modification modulates SoxE function. We show that SUMOylation dramatically altered recruitment of transcriptional coregulator factors by SoxE proteins, displacing coactivators CREB-binding protein/p300 while promoting the recruitment of a corepressor, Grg4. These data demonstrate that SoxE proteins can function as transcriptional repressors in a SUMO-dependent manner. They further suggest a novel multivalent mechanism for SUMO-mediated recruitment of transcriptional coregulatory factors.
Bacterial protein translocation requires only one copy of the SecY complex in vivo
Authors: Park Eunyong , Rapoport Tom A.
Published: August 2012

The transport of proteins across the plasma membrane in bacteria requires a channel formed from the SecY complex, which cooperates with either a translating ribosome in cotranslational translocation or the SecA ATPase in post-translational translocation. Whether translocation requires oligomers of the SecY complex is an important but controversial issue: it determines channel size, how the permeation of small molecules is prevented, and how the channel interacts with the ribosome and SecA. Here, we probe in vivo the oligomeric state of SecY by cross-linking, using defined co- and post-translational translocation intermediates in intact Escherichia coli cells. We show that nontranslocating SecY associated transiently through different interaction surfaces with other SecY molecules inside the membrane. These interactions were significantly reduced when a translocating polypeptide inserted into the SecY channel co- or post-translationally. Mutations that abolish the interaction between SecY molecules still supported viability of E. coli. These results show that a single SecY molecule is sufficient for protein translocation.
Chemokine-dependent T cell migration requires aquaporin-3–mediated hydrogen peroxide uptake
Authors: Hara-Chikuma Mariko , Chikuma Shunsuke , Sugiyama Yoshinori , Kabashima Kenji , Verkman Alan S. , Inoue Shintaro , Miyachi Yoshiki
Published: August 2012

Chemokine-dependent trafficking is indispensable for the effector function of antigen-experienced T cells during immune responses. In this study, we report that the water/glycerol channel aquaporin-3 (AQP3) is expressed on T cells and regulates their trafficking in cutaneous immune reactions. T cell migration toward chemokines is dependent on AQP3-mediated hydrogen peroxide (H2O2) uptake but not the canonical water/glycerol transport. AQP3-mediated H2O2 transport is essential for the activation of the Rho family GTPase Cdc42 and the subsequent actin dynamics. Coincidentally, AQP3-deficient mice are defective in the development of hapten-induced contact hypersensitivity, which is attributed to the impaired trafficking of antigen-primed T cells to the hapten-challenged skin. We therefore suggest that AQP3-mediated H2O2 uptake is required for chemokine-dependent T cell migration in sufficient immune response.