bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconfigurable fabrication of scattering-free polymer network liquid crystal prism/grating/lens
Authors: Sun Jie , Xu Su , Ren Hongwen , Wu Shin-Tson
Published: April 2013

We report a simple reconfigurable printing method for fabricating submillisecond-response and scattering-free polymer network liquid crystal photonic devices, such as prism, grating, and lens. To suppress light scattering in the visible region, we reduce the domain sizes by controlling polymer concentration, selecting a high viscosity liquid crystal (LC) host, and performing UV curing at a low temperature. To demonstrate the configurability, we printed a LC micro-prism array with ∼300-μm feature size and a circular lens with 1.3-mm radius without any pre-patterned templates. This reconfigurable printing technique enables fast design iterations and should have widespread applications for fabricating display and photonic devices.
Formation of charge-transfer-complex in organic:metal oxides systems
Authors: Wu S. P. , Kang Y. , Liu T. L. , Jin Z. H. , Jiang N. , Lu Z. H.
Published: April 2013

It is found that composite systems consisting of 4,4′-bis(carbazol-9-yl)biphenyl (CBP) and molybdenum trioxide (MoO3) form an IR absorption band around 847 nm. It is also found that the vibrational modes of the CBP, as measured by Fourier Transform Infrared Spectroscopy, are quenched upon the formation of charge-transfer-complex (CTC) between CBP and MoO3. By examining several sets of organic:metal oxides systems, we discovered that the IR absorption band of the CTCs follow two distinct mechanisms depending on the nature and location of the HOMOs in the organic molecules.
Protein sensing by nanofluidic crystal and its signal enhancement
Authors: Sang Jianming , Du Hongtan , Wang Wei , Chu Ming , Wang Yuedan , Li Haichao , Alice Zhang Haixia , Wu Wengang , Li Zhihong
Published: April 2013

Nanofluidics has a unique property that ionic conductance across a nanometer-sized confined space is strongly affected by the space surface charge density, which can be utilized to construct electrical read-out biosensor. Based on this principle, this work demonstrated a novel protein sensor along with a sandwich signal enhancement approach. Nanoparticles with designed aptamer onside are assembled in a suspended micropore to form a 3-dimensional network of nanometer-sized interstices, named as nanofluidic crystal hereafter, as the basic sensing unit. Proteins captured by aptamers will change the surface charge density of nanoparticles and thereby can be detected by monitoring the ionic conductance across this nanofluidic crystal. Another aptamer can further enlarge the variations of the surface charge density by forming a sandwich structure (capturing aptamer/protein/signal enhancement aptamer) and the read-out conductance as well. The preliminary experimental results indicated that human α-thrombin was successfully detected by the corresponding aptamer modified nanofluidic crystal with the limit of detection of 5 nM (0.18 μg/ml) and the read-out signal was enhanced up to 3 folds by using another thrombin aptamer. Being easy to graft probe, facile and low-cost to prepare the nano-device, and having an electrical read-out, the present nanofluidic crystal scheme is a promising and universal strategy for protein sensing.
Interfacial perpendicular magnetic anisotropy and damping parameter in ultra thin Co2FeAl films
Authors: Cui Yishen , Khodadadi Behrouz , Schäfer Sebastian , Mewes Tim , Lu Jiwei , Wolf Stuart A.
Published: April 2013

B2-ordered Co2FeAl films were synthesized using an ion beam deposition tool. A high degree of chemical ordering ∼81.2% with a low damping parameter (α) less than 0.004 was obtained in a 50 nm thick film via rapid thermal annealing at 600 °C. The perpendicular magnetic anisotropy (PMA) was optimized in ultra thin Co2FeAl films annealed at 350 °C without an external magnetic field. The reduced thickness and annealing temperature to achieve PMA introduced extrinsic factors thus increasing α significantly. However, the observed damping of Co2FeAl films was still lower than that of Co60Fe20B20 films prepared at the same thickness and annealing temperature.
Room temperature and high responsivity short wavelength II-VI quantum well infrared photodetector
Authors: Ravikumar Arvind P. , Chen Guopeng , Zhao Kuaile , Tian Yue , Prucnal Paul , Tamargo Maria C. , Gmachl Claire F. , Shen Aidong
Published: April 2013

We report the experimental demonstration of a room temperature, high responsivity, short wavelength II-VI Zn0.51Cd0.49Se/Zn0.29Cd0.26Mg0.45Se based quantum well infrared photodetector operating between 3 and 5 μm. Spectral response was observed up to room temperature with a cut off wavelength of 5 μm at 280 K. Measurements with a calibrated blackbody source yielded a peak responsivity of over 30 A/W at 280 K and an applied bias of −3 V. The dark current limited peak detectivity at 80 K and 280 K were measured to be 2 × 109 cm √Hz/W and 4 × 107 cm √Hz/W, respectively. These results are consistent with theoretical calculations that predict a maximum detectivity of the order of 107 cm √Hz/W at room temperature for typical carrier lifetimes and optimized doping levels.
Realization of tellurium-based all dielectric optical metamaterials using a multi-cycle deposition-etch process
Authors: Liu Sheng , Ihlefeld Jon F. , Dominguez Jason , Gonzales Edward F. , Eric Bower John , Bruce Burckel D. , Sinclair Michael B. , Brener Igal
Published: April 2013

Tellurium (Te) dielectric resonator metamaterials for thermal infrared applications were fabricated using a multi-cycle deposition-etch process that circumvents pinch-off issues during deposition. Deposition and etching of Te were studied in detail. Metamaterial samples with varying resonator dimensions were fabricated using this technique. All the samples showed two transmission minima corresponding to magnetic and electric dipole resonances. Longer resonant wavelengths were observed as the resonator dimension was increased. Observation of spectral overlap between magnetic and electric resonances gives us the potential opportunity to realize a negative refractive index material.
Fast photochromism in polymer matrix with plasticizer and real-time dynamic holographic properties
Authors: Ishii Norihito , Abe Jiro
Published: April 2013

We have developed a photochromic polymer film for the use of real-time dynamic hologram, fabricated by the plasticized polymer doped with the fast photochromic molecule. The addition of a plasticizer into the conventional polymer is proved to be effective to improve the photochromic performances for the polymer film doped with the fast photochromic molecule that shows instantaneous coloration upon exposure to UV light and rapid fading in the dark. The plasticized photochromic polymers enable the real-time control of the writing and erasing of a holographic grating and show a higher recording sensitivity compared with other organic holographic materials.
Surface plasmon coupling with a radiating dipole near a Ag nanoparticle embedded in GaN
Authors: Kuo Yang , Chang Wen-Yen , Chen Horng-Shyang , Kiang Yean-Woei , Yang C. C.
Published: April 2013

The localized surface plasmon (LSP) coupling behaviors of a radiating dipole with a Ag nanosphere (NS) embedded in GaN are evaluated based on a numerical algorithm, which takes account of the induction of the LSP resonance on the Ag NS by the radiating dipole and the feedback of the LSP resonance to the radiating behavior of the dipole. In particular, we compute the enhancements of dipole strength and radiated power through such a coupling process for the radiating dipoles oriented along the radial and orbital directions with respect to the Ag NS. The enhancements of radiated power of a radial and an orbital dipole are induced through the coupling with the LSP dipole and higher-order resonance, respectively. These results are interpreted with the interference behaviors between the radiations of the source dipole and the LSP mode of the Ag NS.
C-Alkynylation of Chromones by Sonogashira Reaction
Authors: Patonay Tamás , Pazurik István , Ábrahám Anita
Published: April 2013

Sonogashira reaction of bromochromones and -flavones with a bromine atom on their benzene or heterocyclic ring with various terminal alkynes gave the desired products with nearly the same efficiency as the previously used iodine derivatives. The coupling reactions were performed in the presence of [tetrakis(triphenylphosphine)palladium(0)], copper(i) co-catalyst, and triethylamine, resulting in the formation of numerous hitherto unknown alkynylated oxygen heterocycles, and provide further proof for the applicability of this reaction for these O-heterocycles. Chromones with ethynyl functionality were prepared by removal of the trimethylsilyl protecting group and used as terminal alkynes in a second cross-coupling reaction.
Estimating wildfire risk on a Mojave Desert landscape using remote sensing and field sampling
Authors: Van Linn Peter F. , Nussear Kenneth E. , Esque Todd C. , DeFalco Lesley A. , Inman Richard D. , Abella Scott R.
Published: April 2013

Predicting wildfires that affect broad landscapes is important for allocating suppression resources and guiding land management. Wildfire prediction in the south-western United States is of specific concern because of the increasing prevalence and severe effects of fire on desert shrublands and the current lack of accurate fire prediction tools. We developed a fire risk model to predict fire occurrence in a north-eastern Mojave Desert landscape. First we developed a spatial model using remote sensing data to predict fuel loads based on field estimates of fuels. We then modelled fire risk (interactions of fuel characteristics and environmental conditions conducive to wildfire) using satellite imagery, our model of fuel loads, and spatial data on ignition potential (lightning strikes and distance to roads), topography (elevation and aspect) and climate (maximum and minimum temperatures). The risk model was developed during a fire year at our study landscape and validated at a nearby landscape; model performance was accurate and similar at both sites. This study demonstrates that remote sensing techniques used in combination with field surveys can accurately predict wildfire risk in the Mojave Desert and may be applicable to other arid and semiarid lands where wildfires are prevalent.
Origin of seasonal predictability for summer climate over the Northwestern Pacific
Authors: Kosaka Yu , Xie Shang-Ping , Lau Ngar-Cheung , Vecchi Gabriel A.
Published: April 2013

Summer climate in the Northwestern Pacific (NWP) displays large year-to-year variability, affecting densely populated Southeast and East Asia by impacting precipitation, temperature, and tropical cyclones. The Pacific–Japan (PJ) teleconnection pattern provides a crucial link of high predictability from the tropics to East Asia. Using coupled climate model experiments, we show that the PJ pattern is the atmospheric manifestation of an air–sea coupled mode spanning the Indo-NWP warm pool. The PJ pattern forces the Indian Ocean (IO) via a westward propagating atmospheric Rossby wave. In response, IO sea surface temperature feeds back and reinforces the PJ pattern via a tropospheric Kelvin wave. Ocean coupling increases both the amplitude and temporal persistence of the PJ pattern. Cross-correlation of ocean–atmospheric anomalies confirms the coupled nature of this PJIO mode. The ocean–atmosphere feedback explains why the last echoes of El Niño–Southern Oscillation are found in the IO-NWP in the form of the PJIO mode. We demonstrate that the PJIO mode is indeed highly predictable; a characteristic that can enable benefits to society.
Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in
Escherichia coli
Authors: Howard Thomas P. , Middelhaufe Sabine , Moore Karen , Edner Christoph , Kolak Dagmara M. , Taylor George N. , Parker David A. , Lee Rob , Smirnoff Nicholas , Aves Stephen J. , Love John
Published: April 2013

Biofuels are the most immediate, practical solution for mitigating dependence on fossil hydrocarbons, but current biofuels (alcohols and biodiesels) require significant downstream processing and are not fully compatible with modern, mass-market internal combustion engines. Rather, the ideal biofuels are structurally and chemically identical to the fossil fuels they seek to replace (i.e., aliphatic
n
- and
iso
-alkanes and -alkenes of various chain lengths). Here we report on production of such petroleum-replica hydrocarbons in
Escherichia coli
. The activity of the fatty acid (FA) reductase complex from
Photorhabdus luminescens
was coupled with aldehyde decarbonylase from
Nostoc punctiforme
to use free FAs as substrates for alkane biosynthesis. This combination of genes enabled rational alterations to hydrocarbon chain length (C

n

) and the production of branched alkanes through upstream genetic and exogenous manipulations of the FA pool. Genetic components for targeted manipulation of the FA pool included expression of a thioesterase from
Cinnamomum camphora
(camphor) to alter alkane C

n

and expression of the branched-chain α-keto acid dehydrogenase complex and β-keto acyl-acyl carrier protein synthase III from
Bacillus subtilis
to synthesize branched (
iso
-) alkanes. Rather than simply reconstituting existing metabolic routes to alkane production found in nature, these results demonstrate the ability to design and implement artificial molecular pathways for the production of renewable, industrially relevant fuel molecules.
Mapping remodeling of thalamocortical projections in the living
reeler
mouse brain by diffusion tractography
Authors: Harsan Laura-Adela , Dávid Csaba , Reisert Marco , Schnell Susanne , Hennig Jürgen , von Elverfeldt Dominik , Staiger Jochen F.
Published: April 2013

Significance

Alterations of brain connectional circuits are often associated with developing brain disorders. Pathology, however, can also trigger adaptive brain plasticity and compensatory connectivity changes. This paper provides a verified noninvasive framework for high-resolution mapping of living mouse brain connectional anatomy. We show that pathological changes in the formation of the cortical sheet, such as gross laminar distortions induced by
reelin
gene mutation in mice, lead to spectacular compensatory remodeling of thalamocortical projections. Our findings reveal extensive brain plasticity in the
reeler
mutant mouse, a frequently used model of brain developmental pathology, with great translational value for human brain disorders.
Transient formation of water-conducting states in membrane transporters
Authors: Li Jing , Shaikh Saher A. , Enkavi Giray , Wen Po-Chao , Huang Zhijian , Tajkhorshid Emad
Published: April 2013

Membrane transporters rely on highly coordinated structural transitions between major conformational states for their function, to prevent simultaneous access of the substrate binding site to both sides of the membrane—a mode of operation known as the alternating access model. Although this mechanism successfully accounts for the efficient exchange of the primary substrate across the membrane, accruing evidence on significant water transport and even uncoupled ion transport mediated by transporters has challenged the concept of perfect mechanical coupling and coordination of the gating mechanism in transporters, which might be expected from the alternating access model. Here, we present a large set of extended equilibrium molecular dynamics simulations performed on several classes of membrane transporters in different conformational states, to test the presence of the phenomenon in diverse transporter classes and to investigate the underlying molecular mechanism of water transport through membrane transporters. The simulations reveal spontaneous formation of transient water-conducting (channel-like) states allowing passive water diffusion through the lumen of the transporters. These channel-like states are permeable to water but occluded to substrate, thereby not hindering the uphill transport of the primary substrate, i.e., the alternating access model remains applicable to the substrate. The rise of such water-conducting states during the large-scale structural transitions of the transporter protein is indicative of imperfections in the coordinated closing and opening motions of the cytoplasmic and extracellular gates. We propose that the observed water-conducting states likely represent a universal phenomenon in membrane transporters, which is consistent with their reliance on large-scale motion for function.
Genomic rearrangements and the evolution of clusters of locally adaptive loci
Authors: Yeaman Sam
Published: April 2013

Significance

Genome scans often find that the loci involved in local adaptation tend to cluster together on chromosomes. A leading explanation suggests that clusters evolve because the probability of a new mutation establishing is higher when occurring near another locally adapted mutation, because such architectures are seldom disrupted by recombination. I show that this theory is unlikely to explain empirically observed clusters. Instead, simulations show that clusters are more likely to form through genomic rearrangements that bring coadapted loci close together. This suggests that ecological selection may play an important role in shaping genome architecture, in contrast to many nonadaptive explanations.
Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts
Authors: Damkiær Søren , Yang Lei , Molin Søren , Jelsbak Lars
Published: April 2013

The genetic basis of bacterial adaptation to a natural environment has been investigated in a highly successfulPseudomonas aeruginosalineage (DK2) that evolved within the airways of patients with cystic fibrosis (CF) for more than 35 y. During evolution in the CF airways, the DK2 lineage underwent substantial phenotypic changes, which correlated with temporal fixation of specific mutations in the genesmucA(frame-shift),algT(substitution),rpoN(substitution),lasR(deletion), andrpoD(in-frame deletion), all encoding regulators of large gene networks. To clarify the consequences of these genetic changes, we moved the specific mutations, alone and in combination, to the genome of the reference strain PAO1. The phenotypes of the engineered PAO1 derivatives showed striking similarities with phenotypes observed among the DK2 isolates. The phenotypes observed in the DK2 isolates and PAO1 mutants were the results of individual, additive and epistatic effects of the regulatory mutations. The mutations fixed in the σ factor encoding genesalgT,rpoN,and rpoDcaused minor changes in σ factor activity, resulting in remodeling of the regulatory networks to facilitate generation of unexpected phenotypes. Our results suggest that adaptation to a highly selective environment, such as the CF airways, is a highly dynamic and complex process, which involves continuous optimization of existing regulatory networks to match the fluctuations in the environment.
Renal intercalated cells are rather energized by a proton than a sodium pump
Authors: Chambrey Régine , Kurth Ingo , Peti-Peterdi Janos , Houillier Pascal , Purkerson Jeffrey M. , Leviel Françoise , Hentschke Moritz , Zdebik Anselm A. , Schwartz George J. , Hübner Christian A. , Eladari Dominique
Published: April 2013

The Na
+
concentration of the intracellular milieu is very low compared with the extracellular medium. Transport of Na
+
along this gradient is used to fuel secondary transport of many solutes, and thus plays a major role for most cell functions including the control of cell volume and resting membrane potential. Because of a continuous leak, Na
+
has to be permanently removed from the intracellular milieu, a process that is thought to be exclusively mediated by the Na
+
/K
+
-ATPase in animal cells. Here, we show that intercalated cells of the mouse kidney are an exception to this general rule. By an approach combining two-photon imaging of isolated renal tubules, physiological studies, and genetically engineered animals, we demonstrate that inhibition of the H
+
vacuolar-type ATPase (V-ATPase) caused drastic cell swelling and depolarization, and also inhibited the NaCl absorption pathway that we recently discovered in intercalated cells. In contrast, pharmacological blockade of the Na
+
/K
+
-ATPase had no effects. Basolateral NaCl exit from β-intercalated cells was independent of the Na
+
/K
+
-ATPase but critically relied on the presence of the basolateral ion transporter anion exchanger 4. We conclude that not all animal cells critically rely on the sodium pump as the unique bioenergizer, but can be replaced by the H
+
V-ATPase in renal intercalated cells. This concept is likely to apply to other animal cell types characterized by plasma membrane expression of the H
+
V-ATPase.
Bacillus subtilis
RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates
Authors: Piton Jérémie , Larue Valéry , Thillier Yann , Dorléans Audrey , Pellegrini Olivier , Li de la Sierra-Gallay Inés , Vasseur Jean-Jacques , Debart Françoise , Tisné Carine , Condon Ciarán
Published: April 2013

The initiation of mRNA degradation often requires deprotection of its 5′ end. In eukaryotes, the 5′-methylguanosine (cap) structure is principally removed by the Nudix family decapping enzyme Dcp2, yielding a 5′-monophosphorylated RNA that is a substrate for 5′ exoribonucleases. In bacteria, the 5′-triphosphate group of primary transcripts is also converted to a 5′ monophosphate by a Nudix protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5′ exoribonucleases. Here we present the crystal structures of
Bacillus subtilis
RppH (BsRppH) bound to GTP and to a triphosphorylated dinucleotide RNA. In contrast to
Bdellovibrio bacteriovorus
RppH, which recognizes the first nucleotide of its RNA targets, the
B. subtilis
enzyme has a binding pocket that prefers guanosine residues in the second position of its substrates. The identification of sequence specificity for RppH in an internal position was a highly unexpected result. NMR chemical shift mapping in solution shows that at least three nucleotides are required for unambiguous binding of RNA. Biochemical assays of BsRppH on RNA substrates with single-base–mutation changes in the first four nucleotides confirm the importance of guanosine in position two for optimal enzyme activity. Our experiments highlight important structural and functional differences between BsRppH and the RNA deprotection enzymes of distantly related bacteria.
Coupling social attention to the self forms a network for personal significance
Authors: Sui Jie , Rotshtein Pia , Humphreys Glyn W.
Published: April 2013

Prior social psychological studies show that newly assigned personal significance can modulate high-level cognitive processes, e.g., memory and social evaluation, with self- and other-related information processed in dissociated prefrontal structure: ventral vs. dorsal, respectively. Here, we demonstrate the impact of personal significance on perception and show the neural network that supports this effect. We used an associative learning procedure in which we “tag” a neutral shape with a self-relevant label. Participants were instructed to associate three neutral shapes with labels for themselves, their best friend, or an unfamiliar other. Functional magnetic resonance imaging data were acquired while participants judged whether the shape-label pairs were maintained or swapped. Behaviorally, participants rapidly tagged a neutral stimulus with self-relevance, showing a robust advantage for self-tagged stimuli. Self-tagging responses were associated with enhanced activity in brain regions linked to self-representation [the ventral medial prefrontal cortex (vmPFC)] and to sensory-driven regions associated with social attention [the left posterior superior temporal sulcus (LpSTS)]. In contrast, associations formed with other people recruited a dorsal frontoparietal control network, with the two networks being inversely correlated. Responses in the vmPFC and LpSTS predicted behavioral self-bias effects. Effective connectivity analyses showed that the vmPFC and the LpSTS were functionally coupled, with the strength of coupling associated with behavioral self-biases. The data show that assignment of personal social significance affects perceptual matching by coupling internal self-representations to brain regions modulating attentional responses to external stimuli.
Different 3D domain-swapped oligomeric cyanovirin-N structures suggest trapped folding intermediates
Authors: Koharudin Leonardus M. I. , Liu Lin , Gronenborn Angela M.
Published: April 2013

Although it has long been established that the amino acid sequence encodes the fold of a protein, how individual proteins arrive at their final conformation is still difficult to predict, especially for oligomeric structures. Here, we present a comprehensive characterization of oligomeric species of cyanovirin-N that all are formed by a polypeptide chain with the identical amino acid sequence. Structures of the oligomers were determined by X-ray crystallography, and each one exhibits 3D domain swapping. One unique 3D domain-swapped structure is observed for the trimer, while for both dimer and tetramer, two different 3D domain-swapped structures were obtained. In addition to the previously identified hinge-loop region of the 3D domain-swapped dimer, which resides between strands β5 and β6 in the middle of the polypeptide sequence, another hinge-loop region is observed between strands β7 and β8 in the structures. Plasticity in these two regions allows for variability in dihedral angles and concomitant differences in chain conformation that results in the differently 3D domain-swapped multimers. Based on all of the different structures, we propose possible folding pathways for this protein. Altogether, our results illuminate the amazing ability of cyanovirin-N to proceed down different folding paths and provide general insights into oligomer formation via 3D domain swapping.
Castor is required for Hedgehog-dependent cell-fate specification and follicle stem cell maintenance in
Drosophila
oogenesis
Authors: Chang Yu-Chiuan , Jang Anna C.-C. , Lin Cheng-Han , Montell Denise J.
Published: April 2013

Significance

Understanding the molecules that govern production of specific cell types from adult tissue stem cells is a major challenge, and
Drosophila
follicle stem cells (FSCs) are an outstanding model. We report identification of a gene,
castor
, which is required for FSC maintenance. Castor also functions in a genetic circuit with two other genes,
hedgehog
and
eyes absent
, to determine specific progeny cell fates. Our studies provide a marker for the earliest cell-fate decisions in this model and insight into the molecular and cellular mechanisms by which stem cells produce specific and diverse types of progeny.
Phase transition in the economically modeled growth of a cellular nervous system
Authors: Nicosia Vincenzo , Vértes Petra E. , Schafer William R. , Latora Vito , Bullmore Edward T.
Published: April 2013

Spatially embedded complex networks, such as nervous systems, the Internet, and transportation networks, generally have nontrivial topological patterns of connections combined with nearly minimal wiring costs. However, the growth rules shaping these economical tradeoffs between cost and topology are not well understood. Here, we study the cellular nervous system of the nematode worm
Caenorhabditis elegans
, together with information on the birth times of neurons and on their spatial locations. We find that the growth of this network undergoes a transition from an accelerated to a constant increase in the number of links (synaptic connections) as a function of the number of nodes (neurons). The time of this phase transition coincides closely with the observed moment of hatching, when development switches metamorphically from oval to larval stages. We use graph analysis and generative modeling to show that the transition between different growth regimes, as well as its coincidence with the moment of hatching, may be explained by a dynamic economical model that incorporates a tradeoff between topology and cost that is continuously negotiated and renegotiated over developmental time. As the body of the animal progressively elongates, the cost of longer-distance connections is increasingly penalized. This growth process regenerates many aspects of the adult nervous system’s organization, including the neuronal membership of anatomically predefined ganglia. We expect that similar economical principles may be found in the development of other biological or manmade spatially embedded complex systems.
Interdomain lateral gene transfer of an essential ferrochelatase gene in human parasitic nematodes
Authors: Wu Bo , Novelli Jacopo , Jiang Daojun , Dailey Harry A. , Landmann Frédéric , Ford Louise , Taylor Mark J. , Carlow Clotilde K. S. , Kumar Sanjay , Foster Jeremy M. , Slatko Barton E.
Published: April 2013

Lateral gene transfer events between bacteria and animals highlight an avenue for evolutionary genomic loss/gain of function. Herein, we report functional lateral gene transfer in animal parasitic nematodes. Members of the Nematoda are heme auxotrophs, lacking the ability to synthesize heme; however, the human filarial parasite
Brugia malayi
has acquired a bacterial gene encoding ferrochelatase (BmFeCH), the terminal step in heme biosynthesis. BmFeCH, encoded by a 9-exon gene, is a mitochondrial-targeted, functional ferrochelatase based on enzyme assays, complementation, and inhibitor studies. Homologs have been identified in several filariae and a nonfilarial nematode. RNAi and ex vivo inhibitor experiments indicate that BmFeCH is essential for viability, validating it as a potential target for filariasis control.
Diversification of the eutherian placenta is associated with changes in the pace of life
Authors: Garratt Michael , Gaillard Jean-Michel , Brooks Robert C. , Lemaître Jean-François
Published: April 2013

Few mammalian organs vary as dramatically among species as the placenta. This variation is remarkable considering that the placenta’s primary function—transfer of nutrients and waste between mother and offspring—does not differ among species. Evolutionary changes in placental morphology remain poorly understood, with suggestions that parent–offspring conflict or evolutionary changes in life history might drive placental evolution. Here we demonstrate that life history differences among eutherian mammals are associated with major transitions in maternofetal interdigitation and placental invasiveness. We show that the repeated evolution of villous interdigitation is associated with reduced offspring production early in life and an increased lifespan. Further changes in placental morphology that reestablish a larger surface area are also associated with a change back to greater offspring production. After controlling for these differences in interdigitation, we also show that the least invasive placental type is associated with a fast pace of life. We predict that selection for a faster pace of life intensifies parent–offspring conflict, and that the repeated evolution of less-invasive placental structures might have allowed mothers to wrest back control of gestation from the fetus and alter their relative allocation to offspring production across life.
Early (300−100 B.C.) temple precinct in the Valley of Oaxaca, Mexico
Authors: Redmond Elsa M. , Spencer Charles S.
Published: April 2013

Significance

Recent excavations at the site of El Palenque have recovered the earliest-known temple precinct in the Valley of Oaxaca, Mexico, dating to the Late Monte Albán I phase (300–100 B.C.). This precinct exhibits characteristics similar to the temple precincts of 16
th
century Mesoamerican states. A walled enclosure contains differentiated temples, priests’ residences, and ritual features. We propose that the precinct’s components represent a hierarchy of temples staffed by a specialized full-time priesthood. A series of radiocarbon dates indicate that the El Palenque temple precinct was in use during the 300–100 B.C. period of archaic state emergence in Oaxaca.
A monocular contribution to stimulus rivalry
Authors: Brascamp Jan , Sohn Hansem , Lee Sang-Hun , Blake Randolph
Published: April 2013

When corresponding areas of the two eyes view dissimilar images, stable perception gives way to visual competition wherein perceptual awareness alternates between those images. Moreover, a given image can remain visually dominant for several seconds at a time even when the competing images are swapped between the eyes multiple times each second. This perceptual stability across eye swaps has led to the widespread belief that this unique form of visual competition, dubbed stimulus rivalry, is governed by eye-independent neural processes at a purely binocular stage of cortical processing. We tested this idea by investigating the influence of stimulus rivalry on the buildup of the threshold elevation aftereffect, a form of contrast adaptation thought to transpire at early cortical stages that include eye-specific neural activity. Weaker threshold elevation aftereffects were observed when the adapting image was engaged in stimulus rivalry than when it was not, indicating diminished buildup of adaptation during stimulus-rivalry suppression. We then confirmed that this reduction occurred, in part, at eye-specific neural stages by showing that suppression of an image at a given moment specifically diminished adaptation associated with the eye viewing the image at that moment. Considered together, these results imply that eye-specific neural events at early cortical processing stages contribute to stimulus rivalry. We have developed a computational model of stimulus rivalry that successfully implements this idea.
Long tethers provide high-force coupling of the Dam1 ring to shortening microtubules
Authors: Volkov Vladimir A. , Zaytsev Anatoly V. , Gudimchuk Nikita , Grissom Paula M. , Gintsburg Alexander L. , Ataullakhanov Fazly I. , McIntosh J. Richard , Grishchuk Ekaterina L.
Published: April 2013

Microtubule kinetochore attachments are essential for accurate mitosis, but how these force-generating connections move chromosomes remains poorly understood. Processive motion at shortening microtubule ends can be reconstituted in vitro using microbeads conjugated to the budding yeast kinetochore protein Dam1, which forms microtubule-encircling rings. Here, we report that, when Dam1 is linked to a bead cargo by elongated protein tethers, the maximum force transmitted from a disassembling microtubule increases sixfold compared with a short tether. We interpret this significant improvement with a theory that considers the geometry and mechanics of the microtubule–ring–bead system. Our results show the importance of fibrillar links in tethering microtubule ends to cargo: fibrils enable the cargo to align coaxially with the microtubule, thereby increasing the stability of attachment and the mechanical work that it can do. The force-transducing characteristics of fibril-tethered Dam1 are similar to the analogous properties of purified yeast kinetochores, suggesting that a tethered Dam1 ring comprises the main force-bearing unit of the native attachment.
All-optical control of a solid-state spin using coherent dark states
Authors: Yale Christopher G. , Buckley Bob B. , Christle David J. , Burkard Guido , Heremans F. Joseph , Bassett Lee C. , Awschalom David D.
Published: April 2013

The study of individual quantum systems in solids, for use as quantum bits (qubits) and probes of decoherence, requires protocols for their initialization, unitary manipulation, and readout. In many solid-state quantum systems, these operations rely on disparate techniques that can vary widely depending on the particular qubit structure. One such qubit, the nitrogen-vacancy (NV) center spin in diamond, can be initialized and read out through its special spin-selective intersystem crossing, while microwave electron spin resonance techniques provide unitary spin rotations. Instead, we demonstrate an alternative, fully optical approach to these control protocols in an NV center that does not rely on its intersystem crossing. By tuning an NV center to an excited-state spin anticrossing at cryogenic temperatures, we use coherent population trapping and stimulated Raman techniques to realize initialization, readout, and unitary manipulation of a single spin. Each of these techniques can be performed directly along any arbitrarily chosen quantum basis, removing the need for extra control steps to map the spin to and from a preferred basis. Combining these protocols, we perform measurements of the NV center’s spin coherence, a demonstration of this full optical control. Consisting solely of optical pulses, these techniques enable control within a smaller footprint and within photonic networks. Likewise, this unified approach obviates the need for both electron spin resonance manipulation and spin addressability through the intersystem crossing. This method could therefore be applied to a wide range of potential solid-state qubits, including those which currently lack a means to be addressed.
RETRACTED: Mutual antagonism between hypoxia-inducible factors 1α and 2α regulates oxygen sensing and cardio-respiratory homeostasis
Authors: Yuan Guoxiang , Peng Ying-Jie , Reddy Vaddi Damodara , Makarenko Vladislav V. , Nanduri Jayasri , Khan Shakil A. , Garcia Joseph A. , Kumar Ganesh K. , Semenza Gregg L. , Prabhakar Nanduri R.
Published: April 2013

Breathing and blood pressure are under constant homeostatic regulation to maintain optimal oxygen delivery to the tissues. Chemosensory reflexes initiated by the carotid body and catecholamine secretion from the adrenal medulla are the principal mechanisms for maintaining respiratory and cardiovascular homeostasis; however, the underlying molecular mechanisms are not known. Here, we report that balanced activity of hypoxia-inducible factor-1 (HIF-1) and HIF-2 is critical for oxygen sensing by the carotid body and adrenal medulla, and for their control of cardio-respiratory function. In
Hif2α

+/−

mice, partial HIF-2α deficiency increased levels of HIF-1α and NADPH oxidase 2, leading to an oxidized intracellular redox state, exaggerated hypoxic sensitivity, and cardio-respiratory abnormalities, which were reversed by treatment with a HIF-1α inhibitor or a superoxide anion scavenger. Conversely, in
Hif1α

+/−

mice, partial HIF-1α deficiency increased levels of HIF-2α and superoxide dismutase 2, leading to a reduced intracellular redox state, blunted oxygen sensing, and impaired carotid body and ventilatory responses to chronic hypoxia, which were corrected by treatment with a HIF-2α inhibitor. None of the abnormalities observed in
Hif1α

+/−

mice or
Hif2α

+/−

mice were observed in
Hif1α

+/−

;
Hif2α

+/−

mice. These observations demonstrate that redox balance, which is determined by mutual antagonism between HIF-α isoforms, establishes the set point for hypoxic sensing by the carotid body and adrenal medulla, and is required for maintenance of cardio-respiratory homeostasis.
Role of host cell traversal by the malaria sporozoite during liver infection
Authors: Tavares Joana , Formaglio Pauline , Thiberge Sabine , Mordelet Elodie , Van Rooijen Nico , Medvinsky Alexander , Ménard Robert , Amino Rogerio
Published: April 2013

Malaria infection starts when the sporozoite stage of the Plasmodium parasite is injected into the skin by a mosquito. Sporozoites are known to traverse host cells before finally invading a hepatocyte and multiplying into erythrocyte-infecting forms, but how sporozoites reach hepatocytes in the liver and the role of host cell traversal (CT) remain unclear. We report the first quantitative imaging study of sporozoite liver infection in rodents. We show that sporozoites can cross the liver sinusoidal barrier by multiple mechanisms, targeting Kupffer cells (KC) or endothelial cells and associated or not with the parasite CT activity. We also show that the primary role of CT is to inhibit sporozoite clearance by KC during locomotion inside the sinusoid lumen, before crossing the barrier. By being involved in multiple steps of the sporozoite journey from the skin to the final hepatocyte, the parasite proteins mediating host CT emerge as ideal antibody targets for vaccination against the parasite.
Mendel: the Swiss army knife of genetic analysis programs
Authors: Lange Kenneth , Papp Jeanette C. , Sinsheimer Janet S. , Sripracha Ram , Zhou Hua , Sobel Eric M.
Published: April 2013

Summary: Mendel is one of the few statistical genetics packages that provide a full spectrum of gene mapping methods, ranging from parametric linkage in large pedigrees to genome-wide association with rare variants. Our latest additions to Mendel anticipate and respond to the needs of the genetics community. Compared with earlier versions, Mendel is faster and easier to use and has a wider range of applications. Supported platforms include Linux, MacOS and Windows.

Availability: Free from www.genetics.ucla.edu/software/mendel

Contact:  klange@ucla.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
La ‘Mort de l'auteur’ dans l'écriture autobiographique romantique: à propos du ‘jeune’ François-René de Chateaubriand (R
ené
) et d’Alfred de Musset
(La Confession d'un enfant du siècle)
Authors: Meier Franziska
Published: April 2013

Dans leurs réflexions sur la ‘mort de l'auteur’ et sur l'émergence contemporaine de l'écriture moderne, ni Roland Barthes ni Michel Foucault ne définissent précisément quand et comment ce changement a eu lieu. Leurs allusions fréquentes à Flaubert et Mallarmé laissent, pourtant, deviner que la deuxième moitié du dix-neuvième siècle pourrait en être considérée comme le point de départ. Cet article, en revanche, envisage de montrer que la ‘mort de l'auteur’ ainsi que l'émergence de l'écriture moderne remontent à la période post-révolutionnaire du romantisme. Certes, Chateaubriand aussi bien que Musset n'abandonnent pas encore les concepts traditionnels consistant à penser la figure de l'auteur et la littérature comme une fin en soi pour surmonter la mort, mais tous les deux sont amenés peu à peu à reconnaître que la représentation du ‘je’ dépend de son auto-distanciation traumatisante, voire qu'elle la requiert comme condition désormais inéluctable. Par le biais d'une micro-lecture de deux textes canoniques du romantisme français,
René
de Chateaubriand et
La Confession d'un enfant du siècle
d'Alfred de Musset, l'article met en évidence de quelle façon les deux romans écrits à la première personne, proches du genre autobiographique, sont forcés de mettre en scène le paradoxe d'une mort fictive du ‘je’ racontant afin de maintenir l'autorité de ce ‘je’ et de contenir les effets inattendus d'une écriture qui ne se réfère qu'à elle-même.
Perioperative Metoprolol and Risk of Stroke after Noncardiac Surgery
Authors: Mashour George A. , Sharifpour Milad , Freundlich Robert E. , Tremper Kevin K. , Shanks Amy , Nallamothu Brahmajee K. , Vlisides Phillip E. , Weightman Adam , Matlen Lisa , Merte Janna , Kheterpal Sachin
Published: April 2013

Background:

Numerous risk factors have been identified for perioperative stroke, but there are conflicting data regarding the role of β adrenergic receptor blockade in general and metoprolol in particular.

Methods:

The authors retrospectively screened 57,218 consecutive patients for radiologic evidence of stroke within 30 days after noncardiac procedures at a tertiary care university hospital. Incidence of perioperative stroke within 30 days of surgery and associated risk factors were assessed. Patients taking either metoprolol or atenolol were matched based on a number of risk factors for stroke. Parsimonious logistic regression was used to generate a preoperative risk model for perioperative stroke in the unmatched cohort.

Results:

The incidence of perioperative stroke was 55 of 57,218 (0.09%). Preoperative metoprolol was associated with an approximately 4.2-fold increase in perioperative stroke (P < 0.001; 95% CI, 2.2–8.1). Analysis of matched cohorts revealed a significantly higher incidence of stroke in patients taking preoperative metoprolol compared with atenolol (P = 0.016). However, preoperative metoprolol was not an independent predictor of stroke in the entire cohort, which included patients who were not taking β blockers. The use of intraoperative metoprolol was associated with a 3.3-fold increase in perioperative stroke (P = 0.003; 95% CI, 1.4–7.8); no association was found for intraoperative esmolol or labetalol.

Conclusions:

Routine use of preoperative metoprolol, but not atenolol, is associated with stroke after noncardiac surgery, even after adjusting for comorbidities. Intraoperative metoprolol but not esmolol or labetalol, is associated with increased risk of perioperative stroke. Drugs other than metoprolol should be considered during the perioperative period if β blockade is required.
Capsulated Metallic Debris Tumor Mass Mimicking Adjacent Segment Disease
Authors: Li Yi-Chen , Yang Shih-Chieh , Hsu Chao-Tien , Tu Yuan-Kun
Published: April 2013

Study design:

A case report.

Objective:

To inform the spine surgeons another cause of late complications after instrumented spinal fusion surgery.

Summary of Background Data:

Posterior lumbar instrumented fusion has been widely applied as an effective procedure for treating patients with degenerative lumbar spine disease. The development of pathology at the mobile segment adjacent to the lumbar spinal fusion has been termed as adjacent segment disease.

Methods:

Most patients with adjacent segment disease present with recurrent back pain, sciatica, intermittent claudication, or even muscle weakness. Herein, we report the case of a 58-year-old man with posterior lumbar instrumented fusion at L4–L5 who complained of recurrent neurological symptoms mimicking adjacent instability and stenosis. In addition to severe adjacent stenosis at L3–L4, preoperative magnetic resonance imaging showed an intraspinal extradural tumor-like mass with compression of the neurological elements.

Results:

The well-capsulated tumor mass was gently dissected and meticulously excised without injury to the adhesive dura or nerve roots. The tumor specimen was fixed in formalin, and then decalcified and tinted using several special stains, which conformed metallic wear debris, resulting in foreign body reaction.

Conclusions:

The metallic wear particulates may initiate a cascade of immune and inflammatory responses. Therefore, attention should be paid to patients who are found to have loosening of the implants at the metal-metal or metal-bone interface.
Silica-coated dimers of silver nanospheres as surface-enhanced Raman scattering tags for imaging cancer cells
Authors: Xia Xiaohu , Li Weiyang , Zhang Yu , Xia Younan
Published: April 2013

Surface-enhanced Raman scattering (SERS) tags have been actively explored as a multiplexing platform for sensitive detection of biomolecules. Here, we report a new type of SERS tags that was fabricated by sequentially functionalizing dimers made of 50 nm Ag nanospheres with 4-mercaptobenzoic acid as the Raman reporter molecule, silica coating as a protective shell and antibody as a targeting ligand. These dimer-based tags give highly enhanced and reproducible Raman signals owing to the presence of a well-defined SERS hot spot at the junction between two Ag nanospheres in the dimer. The SERS enhancement factor (EF) of an individual dimer tag supported on a glass slide can reach a level as high as 4.3 × 10
6
. In comparison, the EFs dropped to 2.8 × 10
5
and 8.7 × 10
5
, respectively, when Ag nanospheres and nanocubes with sizes similar to the spheres in the dimer were used to fabricate the tags using similar procedures. The SERS signals from aqueous suspensions of the dimer-based tags also showed high intensity and good stability. Potential use of the dimer-based tags was demonstrated by imaging cancer cells overexpressing HER2 receptors with good specificity and high sensitivity.