bluuebunny/crossref_metadata_2025 huggingface dataset:
Phase and texture evolution in solution deposited lead zirconate titanate thin films: Formation and role of the Pt3Pb intermetallic phase
Authors: Nittala Krishna , Mhin Sungwook , Dunnigan Katherine M. , Robinson Douglas S. , Ihlefeld Jon F. , Kotula Paul G. , Brennecka Geoff L. , Jones Jacob L.
Published: June 2013

Solution deposition is widely used for the fabrication of lead zirconate titanate (PZT) thin films on platinized silicon substrates. However, phase and texture evolution during the crystallization process is not well understood, particularly due to the difficulty in tracking changes in the thin films in situ during heating. In this work, we characterized phase and texture evolution in situ during heating and crystallization of PZT thin films using high-energy X-ray diffraction. Films were pyrolyzed at either 300 °C or 400 °C and heated at various rates between 0.5 °C/s and ∼150 °C/s. For films that were pyrolyzed at 300 °C, the most rapid heating rates first induced strong intensities from a transient Pt3Pb phase. The Pt3Pb phase inherited the texture of the pre-existing platinum layer. Combined with other observations, the results suggest the conversion of the platinum to the intermetallic phase near the interface due to the interdiffusion of lead. In all experimental variations, the pyrochlore phase was observed to form concurrently with the disappearance of the Pt3Pb phase after which the perovskite phase ultimately crystallized. For films that were pyrolyzed at 400 °C, the Pt3Pb phase was not observed at any of the heating rates; instead, the pyrochlore phase was first observed, followed by the perovskite phase. Independent of the pyrolysis temperature or observation of Pt3Pb, a 111-dominant crystallographic texture formed in the perovskite phase when crystallized using fast heating rates. These results demonstrate that 111 textures in solution-derived PZT thin films are not correlated with the observation of Pt3Pb or other intermetallic or transient phases.
Electrical control of the spin polarization of a current in “pure-carbon” systems based on partially hydrogenated graphene nanoribbon
Authors: Guo Yan-Dong , Yan Xiao-Hong , Xiao Yang
Published: June 2013

Controlling a spin current by electrical means and eliminating the use of ferromagnetic contacts becomes a focus of research in spintronics, as compared with conventional magnetic control methods, electrical one could reduce the dimensions and energy consumption of integrated devices. Inspired by recent progress of controlling the hydrogenation on graphene [Xie et al., Appl. Phys. Lett. 98, 193113 (2011)], we investigate the electronic structure and spin-current transport of partially hydrogenated zigzag graphene nanoribbon (ZGNR) with various hydrogenation geometries, through first-principles calculations. It is found that for ZGNR in ferromagnetic edge-coupling state, near-edge hydrogenation would suppress the magnetization on the edge of ZGNR, and lower down the transmission around EF to zero except two peaks, which reside discretely on both sides of EF with opposite spins. Based on this feature, we propose and demonstrate a three-terminal device, where the spin polarization of the current can be modulated by gate voltage (Vg) to vary from (almost) 100% to −100%, which could serve as a perfect electrically-controlled “pure-carbon” dual-spin filter. Especially, the spin polarization varies gradually with Vg, so a current with any ratio of spin-up to spin-down electron numbers can be achieved. Moreover, the influences of ZGNR width and hydrogenation-region length on the system's performance are also discussed and a large range of ZGNR configurations are found to be suitable for the application of such a device.
Adhesion of graphene sheet on nano-patterned substrates with nano-pillar array
Authors: Li Guangxu , Yilmaz Cihan , An Xiaohong , Somu Sivasubramanian , Kar Swastik , Joon Jung Yung , Busnaina Ahmed , Wan Kai-Tak
Published: June 2013

An array of gold nano-pillars is fabricated on silicon, before chemical vapor deposited graphene is transferred to the substrate. Intrinsic intersurface attraction pulls the monolayer into intimate contact conforming to the substrate geometry, but the pillars support an array of circular blisters. A simple delamination mechanics model is constructed to extract the materials and interface properties. The graphene-gold interfacial adhesion energy is found to be γ = 450 ± 100 mJ m−2 by measuring the blister dimension. Should the ratio of pillar height to inter-pillar separation falls short of (γ/Eh)1/4 with graphene elastic modulus, E and thickness, h, the blisters stay isolated; otherwise, adjacent blisters coalesce. Critical design guidelines are set for graphene devices.
Communication: Singularity-free hybrid functional with a Gaussian-attenuating exact exchange in a plane-wave basis
Authors: Song Jong-Won , Giorgi Giacomo , Yamashita Koichi , Hirao Kimihiko
Published: June 2013

Integrable singularity in the exact exchange calculations in hybrid functionals is an old and well-known problem in plane-wave basis. Recently, we developed a hybrid functional named Gaussian-attenuating Perdew-Burke-Ernzerhof (Gau-PBE), which uses a Gaussian function as a modified Coulomb potential for the exact exchange. We found that the modified Coulomb potential of Gaussian function enables the exact exchange calculation in plane-wave basis to be singularity-free and, as a result, the Gau-PBE functional shows faster energy convergence on k and q grids for the exact exchange calculations. Also, a tight comparison (same k and q meshes) between Gau-PBE and two other hybrid functionals, i.e., PBE0 and HSE06, indicates Gau-PBE functional as the least computational time consuming. The Gau-PBE functional employed in conjunction with a plane wave basis provides bandgaps with higher accuracy than the PBE0 and HSE06 in agreement with bandgaps previously calculated using Gaussian-type-orbitals.
Fano resonance in a metamaterial consisting of two identical arrays of square metallic patch elements separated by a dielectric spacer
Authors: Kanjanasit Komsan , Wang C. H.
Published: June 2013

We report studies of Fano resonance in a double layer metamaterial consisting of two identical metallic square patch arrays separated by a dielectric spacer. The metallic patch arrays are arranged in mirror symmetry with respect to the dielectric spacer. It is shown that such a metamaterial can exhibit sharp Fano resonances. A good agreement is obtained between the experimental and simulation results for such a metamaterial fabricated on an FR4 substrate. The square patch based design is less sensitive to polarization due to its higher degree of symmetry than the metallic elements based on split rings in the previous work.
Coherent and incoherent spin torque oscillations in a nanopillar magnetic spin-valve
Authors: Braganca P. M. , Lee O. J. , Ozatay O. , Liu L. , Finocchio G. , Ralph D. C. , Buhrman R. A.
Published: June 2013

We report enhanced spin-torque oscillator results obtained in spin-valve nanopillars. When biased within the optimal range of a moderate, ≤600 Oe, hard axis field, the spin-torque-driven oscillations exhibit a sharp increase in power and a sharply narrowed linewidth, ≤10 MHz, which, based on micromagnetic simulations, we ascribe to a transition from incoherent to coherent dynamics. The simulations indicate that the coherent dynamics are enabled by the combination of strong coupling between the two oscillator end modes of the magnetic free layer and strong non-linear damping arising from a non-uniform magnetization that leads to a spatially varying anti-damping spin torque.
Level set based topology optimization for optical cloaks
Authors: Fujii Garuda , Watanabe Hayato , Yamada Takayuki , Ueta Tsuyoshi , Mizuno Mamoru
Published: June 2013

This letter presents a level set-based topology optimization method that provides discrete cloaking configurations with superior performance. In some cases, the amount of light scattered around the two-dimensional cloaking structures is less than one-tenth that obtained in previous studies. Optimal configurations that express different geometrical characteristics can be obtained by adjusting a regularization parameter. The obtained configurations are free from grayscales, areas of intermediate density between that of dielectric materials or air, and the use of a level set method provides clear structural boundaries. The level set functions are given on grid points and the dielectric boundaries are interpreted as lines on the iso-surface of the level set functions. The finite element method is used for light scattering analyses, computations of the adjoint variable field, and when updating the level set functions.
Thermo-magnetic stability of superconducting films controlled by nano-morphology
Authors: Yurchenko V. V. , Ilin K. , Meckbach J. M. , Siegel M. , Qviller A. J. , Galperin Y. M. , Johansen T. H.
Published: June 2013

Appearance of dendritic magnetic flux avalanches in superconducting films, which are associated with thermo-magnetic instability (TMI), very often indicates serious limitations for the ultimate performance of superconducting devices made of type-II superconducting thin films. We demonstrate that the stability can be controlled by a thorough adjustment of samples morphology at nano-scale, which affects internal material parameters. By this, the metal coating, commonly used as for stabilization, becomes redundant. Most importantly, we directly show by the mean of magneto-optical imaging that introduction of nano-scaled disorder dramatically changes the mode of magnetic flux propagation in the superconductors, from uniform motion of individual vortices to correlated jumps of relatively large vortex bundles, revealing the triggering mechanism of TMI.
Phase field approach to interaction of phase transformation and dislocation evolution
Authors: Levitas Valery I. , Javanbakht Mahdi
Published: June 2013

Phase field approach to coupled evolution of martensitic phase transformations (PTs) and dislocation is developed. A fully geometrically nonlinear formulation is utilized. The finite element method procedure is developed and applied to study the hysteretic behavior and propagation of an austenite (A)–martensite (M) interface with incoherency dislocations, the growth and arrest of martensitic plate for temperature-induced PT, and the evolution of phase and dislocation structures for stress-induced PT. A similar approach can be developed for the interaction of dislocations with twins and diffusive PTs described by Cahn-Hilliard theory.
Structural and functional insights into caseinolytic proteases reveal an unprecedented regulation principle of their catalytic triad
Authors: Zeiler Evelyn , List Anja , Alte Ferdinand , Gersch Malte , Wachtel Rudolf , Poreba Marcin , Drag Marcin , Groll Michael , Sieber Stephan A.
Published: June 2013

Caseinolytic proteases (ClpPs) are large oligomeric protein complexes that contribute to cell homeostasis as well as virulence regulation in bacteria. Although most organisms possess a single ClpP protein, some organisms encode two or more ClpP isoforms. Here, we elucidated the crystal structures of ClpP1 and ClpP2 from pathogenic
Listeria monocytogenes
and observe an unprecedented regulation principle by the catalytic triad. Whereas
L. monocytogenes
(Lm)ClpP2 is both structurally and functionally similar to previously studied tetradecameric ClpP proteins from
Escherichia coli
and
Staphylococcus aureus
, heptameric LmClpP1 features an asparagine in its catalytic triad. Mutation of this asparagine to aspartate increased the reactivity of the active site and led to the assembly of a tetradecameric complex. We analyzed the heterooligomeric complex of LmClpP1 and LmClpP2 via coexpression and subsequent labeling studies with natural product-derived probes. Notably, the LmClpP1 peptidase activity is stimulated 75-fold in the complex providing insights into heterooligomerization as a regulatory mechanism. Collectively, our data point toward different preferences for substrates and inhibitors of the two ClpP enzymes and highlight their structural and functional characteristics.
Negative regulation of Toll-like receptor 4 signaling by IL-10–dependent microRNA-146b
Authors: Curtale Graziella , Mirolo Massimiliano , Renzi Tiziana Ada , Rossato Marzia , Bazzoni Flavia , Locati Massimo
Published: June 2013

Toll-like receptors (TLRs) play key roles in detecting pathogens and initiating inflammatory responses that, subsequently, prime specific adaptive responses. Several mechanisms control TLR activity to avoid excessive inflammation and consequent immunopathology, including the anti-inflammatory cytokine IL-10. Recently, several TLR-responsive microRNAs (miRs) have also been proposed as potential regulators of this signaling pathway, but their functional role during the inflammatory response still is incompletely understood. In this study, we report that, after LPS engagement, monocytes up-regulate miR-146b via an IL-10–mediated STAT3-dependent loop. We show evidence that miR-146b modulates the TLR4 signaling pathway by direct targeting of multiple elements, including the LPS receptor TLR4 and the key adaptor/signaling proteins myeloid differentiation primary response (MyD88), interleukin-1 receptor-associated kinase 1 (IRAK-1), and TNF receptor-associated factor 6 (TRAF6). Furthermore, we demonstrate that the enforced expression of miR-146b in human monocytes led to a significant reduction in the LPS-dependent production of several proinflammatory cytokines and chemokines, including IL-6, TNF-α, IL-8, CCL3, CCL2, CCL7, and CXCL10. Our results thus identify miR-146b as an IL-10–responsive miR with an anti-inflammatory activity based on multiple targeting of components of the TLR4 pathway in monocytes and candidate miR-146b as a molecular effector of the IL-10 anti-inflammatory activity.
Cognitive relevance of the community structure of the human brain functional coactivation network
Authors: Crossley Nicolas A. , Mechelli Andrea , Vértes Petra E. , Winton-Brown Toby T. , Patel Ameera X. , Ginestet Cedric E. , McGuire Philip , Bullmore Edward T.
Published: June 2013

There is growing interest in the complex topology of human brain functional networks, often measured using resting-state functional MRI (fMRI). Here, we used a meta-analysis of the large primary literature that used fMRI or PET to measure task-related activation (>1,600 studies; 1985–2010). We estimated the similarity (Jaccard index) of the activation patterns across experimental tasks between each pair of 638 brain regions. This continuous coactivation matrix was used to build a weighted graph to characterize network topology. The coactivation network was modular, with occipital, central, and default-mode modules predominantly coactivated by specific cognitive domains (perception, action, and emotion, respectively). It also included a rich club of hub nodes, located in parietal and prefrontal cortex and often connected over long distances, which were coactivated by a diverse range of experimental tasks. Investigating the topological role of edges between a deactivated and an activated node, we found that such competitive interactions were most frequent between nodes in different modules or between an activated rich-club node and a deactivated peripheral node. Many aspects of the coactivation network were convergent with a connectivity network derived from resting state fMRI data (
n
= 27, healthy volunteers); although the connectivity network was more parsimoniously connected and differed in the anatomical locations of some hubs. We conclude that the community structure of human brain networks is relevant to cognitive function. Deactivations may play a role in flexible reconfiguration of the network according to cognitive demand, varying the integration between modules, and between the periphery and a central rich club.
Increased stray gas abundance in a subset of drinking water wells near Marcellus shale gas extraction
Authors: Jackson Robert B. , Vengosh Avner , Darrah Thomas H. , Warner Nathaniel R. , Down Adrian , Poreda Robert J. , Osborn Stephen G. , Zhao Kaiguang , Karr Jonathan D.
Published: June 2013

Horizontal drilling and hydraulic fracturing are transforming energy production, but their potential environmental effects remain controversial. We analyzed 141 drinking water wells across the Appalachian Plateaus physiographic province of northeastern Pennsylvania, examining natural gas concentrations and isotopic signatures with proximity to shale gas wells. Methane was detected in 82% of drinking water samples, with average concentrations six times higher for homes <1 km from natural gas wells (
P
= 0.0006). Ethane was 23 times higher in homes <1 km from gas wells (
P
= 0.0013); propane was detected in 10 water wells, all within approximately 1 km distance (
P
= 0.01). Of three factors previously proposed to influence gas concentrations in shallow groundwater (distances to gas wells, valley bottoms, and the Appalachian Structural Front, a proxy for tectonic deformation), distance to gas wells was highly significant for methane concentrations (
P
= 0.007; multiple regression), whereas distances to valley bottoms and the Appalachian Structural Front were not significant (
P
= 0.27 and
P
= 0.11, respectively). Distance to gas wells was also the most significant factor for Pearson and Spearman correlation analyses (
P
< 0.01). For ethane concentrations, distance to gas wells was the only statistically significant factor (
P
< 0.005). Isotopic signatures (δ
13
C-CH
4
, δ
13
C-C
2
H
6
, and δ
2
H-CH
4
), hydrocarbon ratios (methane to ethane and propane), and the ratio of the noble gas
4
He to CH
4
in groundwater were characteristic of a thermally postmature Marcellus-like source in some cases. Overall, our data suggest that some homeowners living <1 km from gas wells have drinking water contaminated with stray gases.
Rational modification of protein stability by targeting surface sites leads to complicated results
Authors: Xiao Shifeng , Patsalo Vadim , Shan Bing , Bi Yuan , Green David F. , Raleigh Daniel P.
Published: June 2013

The rational modification of protein stability is an important goal of protein design. Protein surface electrostatic interactions are not evolutionarily optimized for stability and are an attractive target for the rational redesign of proteins. We show that surface charge mutants can exert stabilizing effects in distinct and unanticipated ways, including ones that are not predicted by existing methods, even when only solvent-exposed sites are targeted. Individual mutation of three solvent-exposed lysines in the villin headpiece subdomain significantly stabilizes the protein, but the mechanism of stabilization is very different in each case. One mutation destabilizes native-state electrostatic interactions but has a larger destabilizing effect on the denatured state, a second removes the desolvation penalty paid by the charged residue, whereas the third introduces unanticipated native-state interactions but does not alter electrostatics. Our results show that even seemingly intuitive mutations can exert their effects through unforeseen and complex interactions.
Calcium-dependent N-cadherin up-regulation mediates reactive astrogliosis and neuroprotection after brain injury
Authors: Kanemaru Kazunori , Kubota Jun , Sekiya Hiroshi , Hirose Kenzo , Okubo Yohei , Iino Masamitsu
Published: June 2013

Brain injury induces phenotypic changes in astrocytes, known as reactive astrogliosis, which may influence neuronal survival. Here we show that brain injury induces inositol 1,4,5-trisphosphate (IP
3
)-dependent Ca
2+
signaling in astrocytes, and that the Ca
2+
signaling is required for astrogliosis. We found that type 2 IP
3
receptor knockout (IP
3
R2KO) mice deficient in astrocytic Ca
2+
signaling have impaired reactive astrogliosis and increased injury-associated neuronal death. We identified N-cadherin and pumilio 2 (Pum2) as downstream signaling molecules, and found that brain injury induces up-regulation of N-cadherin around the injured site. This effect is mediated by Ca
2+
-dependent down-regulation of Pum2, which in turn attenuates Pum2-dependent translational repression of N-cadherin. Furthermore, we show that astrocyte-specific knockout of N-cadherin results in impairment of astrogliosis and neuroprotection. Thus, astrocytic Ca
2+
signaling and the downstream function of N-cadherin play indispensable roles in the cellular responses to brain injury. These findings define a previously unreported signaling axis required for reactive astrogliosis and neuroprotection following brain injury.
Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT
Authors: Doki Shintaro , Kato Hideaki E. , Solcan Nicolae , Iwaki Masayo , Koyama Michio , Hattori Motoyuki , Iwase Norihiko , Tsukazaki Tomoya , Sugita Yuji , Kandori Hideki , Newstead Simon , Ishitani Ryuichiro , Nureki Osamu
Published: June 2013

Proton-dependent oligopeptide transporters (POTs) are major facilitator superfamily (MFS) proteins that mediate the uptake of peptides and peptide-like molecules, using the inwardly directed H
+
gradient across the membrane. The human POT family transporter peptide transporter 1 is present in the brush border membrane of the small intestine and is involved in the uptake of nutrient peptides and drug molecules such as β-lactam antibiotics. Although previous studies have provided insight into the overall structure of the POT family transporters, the question of how transport is coupled to both peptide and H
+
binding remains unanswered. Here we report the high-resolution crystal structures of a bacterial POT family transporter, including its complex with a dipeptide analog, alafosfalin. These structures revealed the key mechanistic and functional roles for a conserved glutamate residue (Glu310) in the peptide binding site. Integrated structural, biochemical, and computational analyses suggested a mechanism for H
+
-coupled peptide symport in which protonated Glu310 first binds the carboxyl group of the peptide substrate. The deprotonation of Glu310 in the inward open state triggers the release of the bound peptide toward the intracellular space and salt bridge formation between Glu310 and Arg43 to induce the state transition to the occluded conformation.
Anxiety-associated alternative polyadenylation of the serotonin transporter mRNA confers translational regulation by hnRNPK
Authors: Yoon YoneJung , McKenna Morgan C. , Rollins David A. , Song Minseok , Nuriel Tal , Gross Steven S. , Xu Guoqiang , Glatt Charles E.
Published: June 2013

The serotonin transporter (SERT) is a major regulator of serotonergic neurotransmission and anxiety-related behaviors. SERT is expressed in two alternative polyadenylation forms that differ by an evolutionarily conserved element in the 3′ untranslated region of its mRNA. Expression of SERT mRNA containing the distal polyadenylation element is associated with decreased anxiety-related behaviors in mice and humans, suggesting that this element has behaviorally relevant modulatory effects on SERT expression. We have identified heterogeneous nuclear ribonucleoprotein K (hnRNPK), a protein known to integrate multiple signal transduction pathways with gene expression, as a SERT distal polyadenylation element binding protein. This interaction is functionally meaningful because genetic manipulation of hnRNPK alters expression of the SERT protein. Furthermore, the trophic factor S100β induces Src-family kinase-mediated tyrosine phosphorylation of hnRNPK and increased SERT expression. These results identify a previously unknown mechanism of regulated SERT expression and provide a putative mechanism by which the SERT distal polyadenylation element modulates anxiety-related behaviors.
Crystal structure of Ca
2+
/H
+
antiporter protein YfkE reveals the mechanisms of Ca
2+
efflux and its pH regulation
Authors: Wu Mousheng , Tong Shuilong , Waltersperger Sandro , Diederichs Kay , Wang Meitian , Zheng Lei
Published: June 2013

Ca
2+
efflux by Ca
2+
cation antiporter (CaCA) proteins is important for maintenance of Ca
2+
homeostasis across the cell membrane. Recently, the monomeric structure of the prokaryotic Na
+
/Ca
2+
exchanger (NCX) antiporter NCX_Mj protein from
Methanococcus jannaschii
shows an outward-facing conformation suggesting a hypothesis of alternating substrate access for Ca
2+
efflux. To demonstrate conformational changes essential for the CaCA mechanism, we present the crystal structure of the Ca
2+
/H
+
antiporter protein YfkE from
Bacillus subtilis
at 3.1-Å resolution. YfkE forms a homotrimer, confirmed by disulfide crosslinking. The protonated state of YfkE exhibits an inward-facing conformation with a large hydrophilic cavity opening to the cytoplasm in each protomer and ending in the middle of the membrane at the Ca
2+
-binding site. A hydrophobic “seal” closes its periplasmic exit. Four conserved α-repeat helices assemble in an X-like conformation to form a Ca
2+
/H
+
exchange pathway. In the Ca
2+
-binding site, two essential glutamate residues exhibit different conformations compared with their counterparts in NCX_Mj, whereas several amino acid substitutions occlude the Na
+
-binding sites. The structural differences between the inward-facing YfkE and the outward-facing NCX_Mj suggest that the conformational transition is triggered by the rotation of the kink angles of transmembrane helices 2 and 7 and is mediated by large conformational changes in their adjacent transmembrane helices 1 and 6. Our structural and mutational analyses not only establish structural bases for mechanisms of Ca
2+
/H
+
exchange and its pH regulation but also shed light on the evolutionary adaptation to different energy modes in the CaCA protein family.
Oxytocin blunts social vigilance in the rhesus macaque
Authors: Ebitz R. Becket , Watson Karli K. , Platt Michael L.
Published: June 2013

Exogenous application of the neuromodulatory hormone oxytocin (OT) promotes prosocial behavior and can improve social function. It is unclear, however, whether OT promotes prosocial behavior per se, or whether it facilitates social interaction by reducing a state of vigilance toward potential social threats. To disambiguate these two possibilities, we exogenously delivered OT to male rhesus macaques, which have a characteristic pattern of species-typical social vigilance, and examined their performance in three social attention tasks. We first determined that, in the absence of competing task demands or goals, OT increased attention to faces and eyes, as in humans. By contrast, OT reduced species typical social vigilance for unfamiliar, dominant, and emotional faces in two additional tasks. OT eliminated the emergence of a typical state of vigilance when dominant face images were available during a social image choice task. Moreover, OT improved performance on a reward-guided saccade task, despite salient social distractors: OT reduced the interference of unfamiliar faces, particularly emotional ones, when these faces were task irrelevant. Together, these results demonstrate that OT suppresses vigilance toward potential social threats in the rhesus macaque. We hypothesize that a basic role for OT in regulating social vigilance may have facilitated the evolution of prosocial behaviors in humans.
Manganese-oxidizing photosynthesis before the rise of cyanobacteria
Authors: Johnson Jena E. , Webb Samuel M. , Thomas Katherine , Ono Shuhei , Kirschvink Joseph L. , Fischer Woodward W.
Published: June 2013

The emergence of oxygen-producing (oxygenic) photosynthesis fundamentally transformed our planet; however, the processes that led to the evolution of biological water splitting have remained largely unknown. To illuminate this history, we examined the behavior of the ancient Mn cycle using newly obtained scientific drill cores through an early Paleoproterozoic succession (2.415 Ga) preserved in South Africa. These strata contain substantial Mn enrichments (up to ∼17 wt %) well before those associated with the rise of oxygen such as the ∼2.2 Ga Kalahari Mn deposit. Using microscale X-ray spectroscopic techniques coupled to optical and electron microscopy and carbon isotope ratios, we demonstrate that the Mn is hosted exclusively in carbonate mineral phases derived from reduction of Mn oxides during diagenesis of primary sediments. Additional observations of independent proxies for O
2
—multiple S isotopes (measured by isotope-ratio mass spectrometry and secondary ion mass spectrometry) and redox-sensitive detrital grains—reveal that the original Mn-oxide phases were not produced by reactions with O
2
, which points to a different high-potential oxidant. These results show that the oxidative branch of the Mn cycle predates the rise of oxygen, and provide strong support for the hypothesis that the water-oxidizing complex of photosystem II evolved from a former transitional photosystem capable of single-electron oxidation reactions of Mn.
Mechanics of the
Toxoplasma gondii
oocyst wall
Authors: Dumètre Aurélien , Dubey Jitender P. , Ferguson David J. P. , Bongrand Pierre , Azas Nadine , Puech Pierre-Henri
Published: June 2013

The ability of microorganisms to survive under extreme conditions is closely related to the physicochemical properties of their wall. In the ubiquitous protozoan parasite
Toxoplasma gondii
, the oocyst stage possesses a bilayered wall that protects the dormant but potentially infective parasites from harsh environmental conditions until their ingestion by the host. None of the common disinfectants are effective in killing the parasite because the oocyst wall acts as a primary barrier to physical and chemical attacks. Here, we address the structure and chemistry of the wall of the
T. gondii
oocyst by combining wall surface treatments, fluorescence imaging, EM, and measurements of its mechanical characteristics by using atomic force microscopy. Elasticity and indentation measurements indicated that the oocyst wall resembles common plastic materials, based on the Young moduli,
E
, evaluated by atomic force microscopy. Our study demonstrates that the inner layer is as robust as the bilayered wall itself. Besides wall mechanics, our results suggest important differences regarding the nonspecific adhesive properties of each layer. All together, these findings suggest a key biological role for the oocyst wall mechanics in maintaining the integrity of the
T. gondii
oocysts in the environment or after exposure to disinfectants, and therefore their potential infectivity to humans and animals.
Quality of early parent input predicts child vocabulary 3 years later
Authors: Cartmill Erica A. , Armstrong Benjamin F. , Gleitman Lila R. , Goldin-Meadow Susan , Medina Tamara N. , Trueswell John C.
Published: June 2013

Children vary greatly in the number of words they know when they enter school, a major factor influencing subsequent school and workplace success. This variability is partially explained by the differential quantity of parental speech to preschoolers. However, the contexts in which young learners hear new words are also likely to vary in referential transparency; that is, in how clearly word meaning can be inferred from the immediate extralinguistic context, an aspect of input quality. To examine this aspect, we asked 218 adult participants to guess 50 parents’ words from (muted) videos of their interactions with their 14- to 18-mo-old children. We found systematic differences in how easily individual parents’ words could be identified purely from this socio-visual context. Differences in this kind of input quality correlated with the size of the children’s vocabulary 3 y later, even after controlling for differences in input quantity. Although input quantity differed as a function of socioeconomic status, input quality (as here measured) did not, suggesting that the quality of nonverbal cues to word meaning that parents offer to their children is an individual matter, widely distributed across the population of parents.
On revenue maximization for selling multiple independently distributed items
Authors: Li Xinye , Yao Andrew Chi-Chih
Published: June 2013

Consider the revenue-maximizing problem in which a single seller wants to sell
k
different items to a single buyer, who has independently distributed values for the items with additive valuation. The

case was completely resolved by Myerson’s classical work in 1981, whereas for larger
k
the problem has been the subject of much research efforts ever since. Recently, Hart and Nisan analyzed two simple mechanisms: selling the items separately, or selling them as a single bundle. They showed that selling separately guarantees at least a

fraction of the optimal revenue; and for identically distributed items, bundling yields at least a

fraction of the optimal revenue. In this paper, we prove that selling separately guarantees at least

fraction of the optimal revenue, whereas for identically distributed items, bundling yields at least a constant fraction of the optimal revenue. These bounds are tight (up to a constant factor), settling the open questions raised by Hart and Nisan. The results are valid for arbitrary probability distributions without restrictions. Our results also have implications on other interesting issues, such as monotonicity and randomization of selling mechanisms.
Correlations in ion channel expression emerge from homeostatic tuning rules
Authors: O'Leary Timothy , Williams Alex H. , Caplan Jonathan S. , Marder Eve
Published: June 2013

Significance

A deep puzzle in neuroscience is how neurons maintain their electrical properties despite continuous ion channel turnover and activity perturbations. Previous work proposed that activity-dependent homeostatic rules ensure robust development of excitability by regulating channel density, although it is not understood how these rules shape the distribution of ion channel types nor how finely tuned these rules must be. We show that generic homeostatic regulation rules impose correlations in the steady-state distribution of ion channels, as has been recently observed experimentally. Specific correlations depend on relative expression rates, and the regulation rules themselves are far more robust than previously thought.
Religious bias and stigma: attitudes toward working with a Muslim co-worker
Authors: King James E. , McKay Patrick F. , Stewart Marcus M.
Published: June 2013

Using social identity and stigma frameworks, this study investigated the extent to which Christians exhibited biased reactions toward a Muslim co-worker. The authors hypothesized that Christians would view a potential Muslim co-worker as lower on competence and less desirable in terms
of a working relationship and would be less attracted to an organization when a potential co-worker was Muslim, and that these in-group preferences would be moderated by participant religiosity. Though no main effect for religious group affiliation was found, moderator analyses revealed that
highly religious individuals had a lower desire to establish working relationships with or work for a firm employing a prospective Muslim co-worker, while lower religiosity individuals exhibited no such preferences. Research and practical implications are discussed.
T cell–derived inducible nitric oxide synthase switches off TH17 cell differentiation
Authors: Yang Jianjun , Zhang Ruihua , Lu Geming , Shen Yu , Peng Liang , Zhu Chen , Cui Miao , Wang Weidong , Arnaboldi Paul , Tang Meng , Gupta Monica , Qi Chen-Feng , Jayaraman Padmini , Zhu Hongfa , Jiang Bo , Chen Shu-hsia , He John Cijiang , Ting Adrian T. , Zhou Ming-Ming , Kuchroo Vijay K. , Morse Herbert C. , Ozato Keiko , Sikora Andrew G. , Xiong Huabao
Published: June 2013

RORγt is necessary for the generation of TH17 cells but the molecular mechanisms for the regulation of TH17 cells are still not fully understood. We show that activation of CD4+ T cells results in the expression of inducible nitric oxide synthase (iNOS). iNOS-deficient mice displayed enhanced TH17 cell differentiation but without major effects on either TH1 or TH2 cell lineages, whereas endothelial NOS (eNOS) or neuronal NOS (nNOS) mutant mice showed comparable TH17 cell differentiation compared with wild-type control mice. The addition of N6-(1-iminoethyl)-l-lysine dihydrochloride (L-NIL), the iNOS inhibitor, significantly enhanced TH17 cell differentiation, and S-nitroso-N-acetylpenicillamine (SNAP), the NO donor, dose-dependently reduced the percentage of IL-17–producing CD4+ T cells. NO mediates nitration of tyrosine residues in RORγt, leading to the suppression of RORγt-induced IL-17 promoter activation, indicating that NO regulates IL-17 expression at the transcriptional level. Finally, studies of an experimental model of colitis showed that iNOS deficiency results in more severe inflammation with an enhanced TH17 phenotype. These results suggest that NO derived from iNOS in activated T cells plays a negative role in the regulation of TH17 cell differentiation and highlight the importance of intrinsic programs for the control of TH17 immune responses.
Impact of the 2009 Influenza A (H1N1) Pandemic on Healthcare Workers at a Tertiary Care Center in New York City
Authors: Bhadelia Nahid , Sonti Rajiv , McCarthy Jennifer Wright , Vorenkamp Jaclyn , Jia Haomiao , Saiman Lisa , Furuya E. Yoko
Published: June 2013

Background and Objective.

Assessing the impact of 2009 influenza A (H1N1) on healthcare workers (HCWs) is important for pandemic planning.

Methods.

We retrospectively analyzed employee health records of HCWs at a tertiary care center in New York City with influenza-like illnesses (ILI) and confirmed influenza from March 31, 2009, to February 28, 2010. We evaluated HCWs' clinical presentations during the first and second wave of the pandemic, staff absenteeism, exposures among HCWs, and association between high-risk occupational exposures to respiratory secretions and infection.

Results.

During the pandemic, 40% (141/352) of HCWs with ILI tested positive for influenza, representing a 1% attack rate among our 13,066 employees. HCWs with influenza were more likely to have fever, cough, and tachycardia. When compared with the second wave, cases in the first wave were sicker and at higher risk of exposure to patients' respiratory secretions (P = .049). HCWs with ILI- with and without confirmed influenza-missed on average 4.7 and 2.7 work days, respectively (P = .001). Among HCWs asked about working while ill, 65% (153/235) reported they did so (mean, 2 days).

Conclusions.

HCWs in the first wave had more severe ILI than those in the second wave and were more likely to be exposed to patients' respiratory secretions. HCWs with ILI often worked while ill. Timely strategies to educate and support HCWs were critical to managing this population during the pandemic.
Public Reporting of Hospital-Acquired Infections Is Not Associated with Improved Processes or Outcomes
Authors: Linkin Darren R. , Fishman Neil O. , Shea Judy A. , Yang Wei , Cary Mark S. , Lautenbach Ebbing
Published: June 2013

Most US states have enacted or are considering legislation mandating hospitals to publicly report hospital-acquired infection (HAI) rates. We conducted a survey of infection control professionals and found that state-legislated public reporting of HAIs is not associated with perceived improvements in infection prevention program process measures or HAI rates.
On the diagonalization of the Ricci flow on Lie groups
Authors: Lauret Jorge , Will Cynthia
Published: June 2013

The main purpose of this note is to prove that any basis of a nilpotent Lie algebra for which all diagonal left-invariant metrics have diagonal Ricci tensor necessarily produce quite a simple set of structural constants; namely, the bracket of any pair of elements of the basis must be a multiple of one of them, and only the bracket of disjoint pairs can be a nonzero multiple of the same element. Some applications to the Ricci flow of left-invariant metrics on Lie groups concerning diagonalization are also given.
Lofoten–Vesterålen: for cod and cod fisheries, but not for oil?
Authors: Misund Ole Arve , Olsen Erik
Published: June 2013

Misund, O. A., and Olsen, E. 2013. .Lofoten–Vesterålen: for cod and cod fisheries, but not for oil? – ICES Journal of Marine Science, 70: 722–725. Over the last decade, the most controversial issue regarding the management of Norwegian marine waters has been about opening the Lofoten–Vesterålen areas for offshore oil and gas exploration. This paper outlines the political and management processes and reviews the arguments for and against. Our conclusion is that these valuable areas should not be opened for such activity because of their high biological significance as the main spawning grounds for northeast Arctic cod (Gadus morhua) and other important fish stocks in the northeast Arctic waters.
α1,6‐Fucosylation regulates neurite formation via the activin/phospho‐Smad2 pathway in PC12 cells: the implicated dual effects of Fut8 for TGF‐β/activin‐mediated signaling
Authors: Gu Wei , Fukuda Tomohiko , Isaji Tomoya , Hashimoto Hirokazu , Wang Yuqin , Gu Jianguo
Published: June 2013

It is well known that α1,6‐fucosyltransferase (Fut8) and its products, α1,6‐fucosylated N‐glycans, are highly expressed in brain tissue. Recently, we reported that Fut8‐knockout mice exhibited multiple behavioral abnormalities with a schizophrenia‐like phenotype, suggesting that α1,6‐fucosylation plays important roles in the brain and neuron system. In the present study, we screened several neural cell lines and found that PC12 cells express the highest levels of α1,6‐fucosylation. The knockdown (KD) of Fut8 promoted a significant enhancement of neurite formation and induction of neurofilament expression. Surprisingly, the levels of phospho‐Smad2 were greatly increased in the KD cells. Finally, we found that the activin‐mediated signal pathway was essential for these changes in KD cells. Exogenous activin, not TGF‐β1, induced neurite outgrowth and phospho‐Smad2. In addition, the α1,6‐fucosylation level on the activin receptors was greatly decreased in KD cells, while the total expression level was unchanged, suggesting that α1,6‐fucosylation negatively regulated activin‐mediated signaling. Furthermore, inhibition of activin receptor‐mediated signaling or restoration of Fut8 expression rescued cell morphology and phospho‐Smad2 levels, which were enhanced in KD cells. Considering the fact that α1,6‐fucosylation is important for TGF‐β‐mediated signaling, the results of this study strongly suggest that Fut8 plays a dual role in TGF‐β/activin‐mediated signaling.—Gu, W., Fukuda, T., Isaji, T., Hashimoto, H., Wang, Y., Gu, J., α1,6‐Fucosylation regulates neurite formation via the activin/phospho‐Smad2 pathway in PC12 cells: the implicated dual effects of Fut8 for TGF‐β/activin‐mediated signaling. FASEB J. 27, 3947–3958 (2013). www.fasebj.org
Measurement of Hepatic Venous Pressure Gradient Is Feasible and Safe in Children
Authors: Woolfson Jessica , John Philip , Kamath Binita , Ng Vicky L. , Ling Simon C.
Published: June 2013

Background and Objectives:

Hepatic venous pressure gradient (HVPG) is an indirect measure of portal venous pressure in cirrhosis, which is valid in cirrhotic adults for evaluating the severity of portal hypertension, predicting outcomes, and guiding therapeutic decisions. Published data on the measurement of HVPG in children are sparse. The aim of the present study was to determine the feasibility and safety of undertaking HVPG measurements in children.

Methods:

Children who underwent HVPG measurements between 2000 and 2011 were identified from our interventional radiology database. Medical charts were reviewed for clinical, procedural, and outcome data.

Results:

A total of 49 patients (25 boys, mean age 8.2 ± 5.6 years) underwent 52 HVPG measurements. Diagnoses included cirrhosis (n = 7), acute liver failure (n = 15), postliver transplant (n = 6), postbone marrow transplant (n = 9), vascular anomalies (n = 3), and others (n = 9). There were no complications related to HVPG measurement. HVPG values ranged between 0 and 28 mmHg, median 9.0 (range 0–28) mmHg, and were elevated >6 mmHg in 30 patients.

Conclusions:

HVPG measurement is feasible and safe in children with severe liver disease. The clinical use of HVPG measurements in managing children with portal hypertension or with acute liver diseases must now be determined.
Convergence in parameters and predictions using computational experimental design
Authors: Hagen David R. , White Jacob K. , Tidor Bruce
Published: June 2013

Typically, biological models fitted to experimental data suffer from significant parameter uncertainty, which can lead to inaccurate or uncertain predictions. One school of thought holds that accurate estimation of the true parameters of a biological system is inherently problematic. Recent work, however, suggests that optimal experimental design techniques can select sets of experiments whose members probe complementary aspects of a biochemical network that together can account for its full behaviour. Here, we implemented an experimental design approach for selecting sets of experiments that constrain parameter uncertainty. We demonstrated with a model of the epidermal growth factor–nerve growth factor pathway that, after synthetically performing a handful of optimal experiments, the uncertainty in all 48 parameters converged below 10 per cent. Furthermore, the fitted parameters converged to their true values with a small error consistent with the residual uncertainty. When untested experimental conditions were simulated with the fitted models, the predicted species concentrations converged to their true values with errors that were consistent with the residual uncertainty. This paper suggests that accurate parameter estimation is achievable with complementary experiments specifically designed for the task, and that the resulting parametrized models are capable of accurate predictions.
CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer
Authors: Ling Hui , Spizzo Riccardo , Atlasi Yaser , Nicoloso Milena , Shimizu Masayoshi , Redis Roxana S. , Nishida Naohiro , Gafà Roberta , Song Jian , Guo Zhiyi , Ivan Cristina , Barbarotto Elisa , De Vries Ingrid , Zhang Xinna , Ferracin Manuela , Churchman Mike , van Galen Janneke F. , Beverloo Berna H. , Shariati Maryam , Haderk Franziska , Estecio Marcos R. , Garcia-Manero Guillermo , Patijn Gijs A. , Gotley David C. , Bhardwaj Vikas , Shureiqi Imad , Sen Subrata , Multani Asha S. , Welsh James , Yamamoto Ken , Taniguchi Itsuki , Song Min-Ae , Gallinger Steven , Casey Graham , Thibodeau Stephen N. , Le Marchand Loïc , Tiirikainen Maarit , Mani Sendurai A. , Zhang Wei , Davuluri Ramana V. , Mimori Koshi , Mori Masaki , Sieuwerts Anieta M. , Martens John W.M. , Tomlinson Ian , Negrini Massimo , Berindan-Neagoe Ioana , Foekens John A. , Hamilton Stanley R. , Lanza Giovanni , Kopetz Scott , Fodde Riccardo , Calin George A.
Published: June 2013

The functional roles of SNPs within the 8q24 gene desert in the cancer phenotype are not yet well understood. Here, we report that CCAT2, a novel long noncoding RNA transcript (lncRNA) encompassing the rs6983267 SNP, is highly overexpressed in microsatellite-stable colorectal cancer and promotes tumor growth, metastasis, and chromosomal instability. We demonstrate that MYC, miR–17–5p, and miR–20a are up-regulated by CCAT2 through TCF7L2-mediated transcriptional regulation. We further identify the physical interaction between CCAT2 and TCF7L2 resulting in an enhancement of WNT signaling activity. We show that CCAT2 is itself a WNT downstream target, which suggests the existence of a feedback loop. Finally, we demonstrate that the SNP status affects CCAT2 expression and the risk allele G produces more CCAT2 transcript. Our results support a new mechanism of MYC and WNT regulation by the novel lncRNA CCAT2 in colorectal cancer pathogenesis, and provide an alternative explanation of the SNP-conferred cancer risk.