bluuebunny/crossref_metadata_2025 huggingface dataset:
Manipulation of electromagnetically-induced transparency in planar metamaterials based on phase coupling
Authors: Jin Xing-Ri , Lu Yuehui , Park Jinwoo , Zheng Haiyu , Gao Feng , Lee YoungPak , Yull Rhee Joo , Won Kim Ki , Cheong H. , Jang Won Ho
Published: April 2012

We experimentally demonstrated a controllable electromagnetically induced transparency (EIT)-like spectral response at microwave frequencies in a planar metamaterial consisting of two identical split-ring resonators (SRRs) with side-by-side symmetry. In our scheme, phase coupling between the two SRRs (serving as the bright mode), which were excited strongly by the incident wave, was employed, and it was found that the EIT-like spectral response could be controlled by simply adjusting the incident angle. Thus, our scheme may be used for electromagnetic-wave switching. A high group index for slow-light application and a high quality factor could be obtained by simply controlling the incident angle.
X-ray magnetic dichroism in the (Zn, Co)O diluted magnetic semiconductors from first principle calculations
Authors: Antonov V. N. , Bekenov L. V. , Jepsen O. , Mazur D. V. , Germash L. P.
Published: April 2012

The electronic structure of the (Zn, Co)O diluted magnetic semiconductors (DMSs) were investigated theoretically from first principles, using the fully relativistic Dirac linear muffin-tin orbital band structure method. The electronic structure was obtained with the local spin-density approximation. The x-ray absorption spectra (XAS), x-ray magnetic circular dichroism (XMCD), and x-ray linear dichroism (XLD) spectra at the Co, Zn, and O K and Zn, Co L2,3 edges were investigated theoretically from first principles. The origin of the XMCD and XLD spectra in these compounds was examined. The orientation dependence of the XAS at the Co and Zn K edges were investigated by calculating the XAS spectra for the 〈001〉 and 〈110〉 magnetization axis. The calculated results are compared with available experimental data.
Formation of embryoid bodies using dielectrophoresis
Authors: Agarwal Sneha , Sebastian Anil , Forrester Lesley M. , Markx Gerard H.
Published: April 2012

Embryoid body (EB) formation forms an important step in embryonic stem cell differentiation invivo. In murine embryonic stem cell (mESC) cultures EB formation is inhibited by the inclusion of leukaemic inhibitory factor (LIF) in the medium. Assembly of mESCs into aggregates by positive dielectrophoresis (DEP) in high field regions between interdigitated oppositely castellated electrodes was found to initiate EB formation. Embryoid body formation in aggregates formed with DEP occurred at a more rapid rate—in fact faster compared to conventional methods—in medium without LIF. However, EB formation also occurred in medium in which LIF was present when the cells were aggregated with DEP. The optimum characteristic size for the electrodes for EB formation with DEP was found to be 75–100 microns; aggregates smaller than this tended to merge, whilst aggregates larger than this tended to split to form multiple EBs. Experiments with ESCs in which green fluorescent protein (GFP) production was targeted to the mesodermal gene brachyury indicated that differentiation within embryoid bodies of this size may preferentially occur along the mesoderm lineage. As hematopoietic lineages during normal development derive from mesoderm, the finding points to a possible application of DEP formed EBs in the production of blood-based products from ESCs.
Microfluidics based on ZnO/nanocrystalline diamond surface acoustic wave devices
Authors: Fu Y. Q. , Garcia-Gancedo L. , Pang H. F. , Porro S. , Gu Y. W. , Luo J. K. , Zu X. T. , Placido F. , Wilson J. I. B. , Flewitt A. J. , Milne W. I.
Published: April 2012

Surface acoustic wave (SAW) devices with 64 μm wavelength were fabricated on a zinc oxide (ZnO) film deposited on top of an ultra-smooth nanocrystalline diamond (UNCD) layer. The smooth surface of the UNCD film allowed the growth of the ZnO film with excellent c-axis orientation and low surface roughness, suitable for SAW fabrication, and could restrain the wave from significantly dissipating into the substrate. The frequency response of the fabricated devices was characterized and a Rayleigh mode was observed at ∼65.4 MHz. This mode was utilised to demonstrate that the ZnO/UNCD SAW device can be successfully used for microfluidic applications. Streaming, pumping, and jetting using microdroplets of 0.5 and 20 μl were achieved and characterized under different powers applied to the SAW device, focusing more on the jetting behaviors induced by the ZnO SAW.
Metallic and molecular orbital concepts in XMg8 clusters, X = Be-F
Authors: Medel Victor M. , Reber Arthur C. , Ulises Reveles J. , Khanna Shiv N.
Published: April 2012

The electronic structure and stability of the XMg8 clusters (X = Be, B, C, N, O, and F) are studied using first principles theoretical calculations to understand the variation in bonding in heteroatomic clusters which mix simple divalent metals with main group dopants. We examine these progressions with two competing models, the first is a distorted nearly free electron gas model and the second is a molecular orbital picture examining the orbital overlap between the dopant and the cluster. OMg8 is found to be the most energetically stable cluster due to strong bonding of O with the Mg8 cluster. BeMg8 has the largest HOMO-LUMO gap due to strong hybridization between the Mg8 and the Be dopant states that form a delocalized pool of 18 valence electrons with a closed electronic shell due to crystal field effects. Be, B, and C are best described by the nearly free electron gas model, while N, O, and F are best described through molecular orbital concepts.
Resistive switching characteristics of solution-deposited Gd, Dy, and Ce-doped ZrO2 films
Authors: Soo Lee Myung , Choi Sungho , An Chee-Hong , Kim Hyoungsub
Published: April 2012

Several rare earth elements (Gd, Dy, and Ce) having different valence numbers were doped into a solution-synthesized ZrO2 film, and the corresponding resistive memory characteristics were discussed in relation to the oxygen vacancies and film microstructure. Pure and trivalent ion-doped ZrO2 films showed forming-free behavior, probably because of the large amount of inherent and additional dopant-incurred oxygen vacancies, respectively. In contrast, tetravalent Ce ion doping caused the forming process to be required and afforded stable long-term switching characteristics with a relatively large memory window, which is attributed to the dopant-enhanced crystallization/densification effect without excessive oxygen vacancy generation.
Free carrier accumulation at cubic AlGaN/GaN heterojunctions
Authors: Wei Q. Y. , Li T. , Huang J. Y. , Ponce F. A. , Tschumak E. , Zado A. , As D. J.
Published: April 2012

Cubic Al0.3Ga0.7N/GaN heterostructures were grown by plasma-assisted molecular beam epitaxy on 3C-SiC (001) substrates. A profile of the electrostatic potential across the cubic-AlGaN/GaN heterojunction was obtained using electron holography in the transmission electron microscope. The experimental potential profile indicates that the unintentionally doped layers show n-type behavior and accumulation of free electrons at the interface with a density of 5.1 × 1011/cm2, about one order of magnitude less than in wurtzite AlGaN/GaN junctions. A combination of electron holography and cathodoluminescence measurements yields a conduction-to-valence band offset ratio of 5:1 for the cubic AlGaN/GaN interface, which also promotes the electron accumulation. Band diagram simulations show that the donor states in the AlGaN layer provide the positive charges that to a great extent balance the two-dimensional electron gas.
Temperature dependence of dynamic nuclear polarization and its effect on electron spin relaxation and dephasing in InAs/GaAs quantum dots
Authors: Beyer J. , Puttisong Y. , Buyanova I. A. , Suraprapapich S. , Tu C. W. , Chen W. M.
Published: April 2012

Electron spin dephasing and relaxation due to hyperfine interaction with nuclear spins is studied in an InAs/GaAs quantum dot ensemble as a function of temperature up to 85 K, in an applied longitudinal magnetic field. The extent of hyperfine-induced dephasing is found to decrease, whereas dynamic nuclear polarization increases with increasing temperature. We attribute both effects to an accelerating electron spin relaxation through phonon-assisted electron-nuclear spin flip-flops driven by hyperfine interactions, which could become the dominating contribution to electron spin depolarization at high temperatures.
The prevalence of lice (Bovicola ovis) in sheep flocks on the central and southern Tablelands of New South Wales
Authors: Popp S. , Eppleston J. , Watt B. R. , Mansfield S. , Bush R. D.
Published: April 2012

In response to suggestions that the incidence of louse infestations in New South Wales has increased markedly, a survey of 173 producers was conducted in the Tablelands Livestock Health and Pest Authority region using visual detection and a questionnaire to document retrospective lice history. An estimated apparent prevalence of 16.5% is a moderate increase from the 10% reported in 2004. On a subset of the surveyed sheep flocks sheep, lice-specific immunoassay conducted by the New South Wales Department of Primary Industries were used to detect low levels of infestation that were not identified by visual detection. This provided a true prevalence estimate of 30%. These results will be used to promote improved control and preventative strategies.
Diurnal grazing pattern: its physiological basis and strategic management
Authors: Gregorini P.
Published: April 2012

Within a day, grazing decisions such as ‘when’ to begin, ‘which’ frequency and ‘how’ to distribute grazing events determine ruminants’ diurnal grazing pattern. Ruminants can have between three and five daily grazing events. The major grazing events occur in the early morning and late afternoon/early evening; the later grazing event is the longest and most significant in terms of herbage intake. This review first attempts to answer ‘why does this happen?’ and then to examine evidence for managing this pattern to improve animal production. Due to photosynthesis and transpiration during the day, herbage accumulates DM, sugars and essential fatty acids, which dilute fibre and protein contents and facilitate herbage particle breakdown during ingestion. Diurnal fluctuations in light intensity stimulate circadian release of neuropetides and hormones, providing the cue to start grazing and modulating ingestive-digestive behaviours that interact with the diurnal fluctuation in herbage feeding value. Grazing decisions depend on grazing environments, the current state of the animal, and on past and anticipated states of the animal. The dusk grazing event seems to be an adaptative feeding strategy to maximise daily energy acquisition, providing a steady release of nutrients over night. Hunger deceives ruminants and makes them graze at dawn, when herbage presents the lowest feeding value. Hunger, however, can be used to concentrate and intensify grazing events. Strategic management of these interactions emerges as the tool to alter the frequency, intensity and temporal distribution of diurnal grazing events, and thereby to increase and modulate nutrient supply to and productivity of grazing ruminants.
Use of health services for sexually transmitted and blood-borne viral infections by young Aboriginal people in New South Wales
Authors: Ward James , Bryant Joanne , Worth Heather , Hull Peter , Solar Sarina , Bailey Sandra
Published: April 2012

The objective of the present study was to describe use of health services for sexually transmitted infections (STI), blood borne viral infections (BBV) and drug and alcohol issues by young Aboriginal people in New South Wales (NSW). A cross-sectional survey was conducted at two Aboriginal sports and cultural events in NSW, in 2007 and 2008, among Aboriginal people aged 16–30 years to ascertain their knowledge of STI, BBV, associated risk behaviours and health service access in NSW. A total of 293 young Aboriginal people completed the survey; 58% were female, the mean age was 20 years, and almost 70% were single. Just over one-third (34%) of participants had been tested for an STI in the past 12 months, and over half (58%) reported that they had ever had an STI test (including HIV). Of respondents who had had an STI test in the past 12 months, 54.0% had done so at an Aboriginal Community Controlled Health Service (ACCHS) and 29% by a GP. Just over one-third (36%) of participants had ever had a test for hepatitis C, 45% of whom had received their test at an ACCHS. Participants were also asked about the types of services they had used for advice about STI and BBV. Of the 69% who had sought STI advice, ACCHS was the most common clinical location for doing so (36% for STI and 26% for hepatitis C). This study highlights the important role that ACCHS play in the provision of STI and BBV testing care and management for a cohort of young Aboriginal people in NSW.
Step-by-step self-assembled hybrids that feature control over energy and charge transfer
Authors: Grimm Bruno , Schornbaum Julia , Jasch Hannelore , Trukhina Olga , Wessendorf Florian , Hirsch Andreas , Torres Tomas , Guldi Dirk M.
Published: April 2012

In the current work, we have documented the use of two complementary supramolecular motifs, namely multipoint hydrogen bonding and metal complexation, as a means to control the step-by-step assembly of a panchromatically absorbing and highly versatile solar energy conversion system. On one hand, two different perylenediimides (
1a/1b
) have been integrated together with a metalloporphyrin (
2
) by means of the Hamilton receptor/cyanuric acid hydrogen bonding motif into energy transduction systems
1a•2
or
1b•2
. Steady-state and time-resolved measurements corroborated that upon selective photoexcitation of the perylenediimides (
1a/1b
), an energy transfer evolved from the singlet excited state of the perylenediimides (
1a/1b
) to that of the metalloporphyrin (
2
). On the other hand, fullerene (
3
) and metalloporphyrin (
2
) form the electron donor–acceptor system
2•3
via axial complexation. Photophysical measurements confirm that an electron transfer prevails from the singlet excited state of
2
to the electron-accepting
3
. The correspondingly formed radical ion pair state decays with a lifetime of 1.0 ± 0.1 ns. As a complement to the aforementioned, the energy transduction features of
1a•2
were combined with the electron donor–acceptor characteristics of
2•3
to afford
1a•2•3
. To this end, time-resolved measurements reveal that the initially occurring energy-transfer interaction (53 ± 3 ps) between
1a/1b
and
2
is followed by an electron transfer (12 ± 1 ps) from
2
to
3
. From multiwavelength analyses, the lifetime of the radical ion pair state in
1a•2•3
—as a product of a cascade of light-induced energy and electron transfer—was derived as 3.8 ± 0.2 ns.
Natural disasters and population mobility in Bangladesh
Authors: Gray Clark L. , Mueller Valerie
Published: April 2012

The consequences of environmental change for human migration have gained increasing attention in the context of climate change and recent large-scale natural disasters, but as yet relatively few large-scale and quantitative studies have addressed this issue. We investigate the consequences of climate-related natural disasters for long-term population mobility in rural Bangladesh, a region particularly vulnerable to environmental change, using longitudinal survey data from 1,700 households spanning a 15-y period. Multivariate event history models are used to estimate the effects of flooding and crop failures on local population mobility and long-distance migration while controlling for a large set of potential confounders at various scales. The results indicate that flooding has modest effects on mobility that are most visible at moderate intensities and for women and the poor. However, crop failures unrelated to flooding have strong effects on mobility in which households that are not directly affected but live in severely affected areas are the most likely to move. These results point toward an alternate paradigm of disaster-induced mobility that recognizes the significant barriers to migration for vulnerable households as well their substantial local adaptive capacity.
Microstratigraphic evidence of in situ fire in the Acheulean strata of Wonderwerk Cave, Northern Cape province, South Africa
Authors: Berna Francesco , Goldberg Paul , Horwitz Liora Kolska , Brink James , Holt Sharon , Bamford Marion , Chazan Michael
Published: April 2012

The ability to control fire was a crucial turning point in human evolution, but the question when hominins first developed this ability still remains. Here we show that micromorphological and Fourier transform infrared microspectroscopy (mFTIR) analyses of intact sediments at the site of Wonderwerk Cave, Northern Cape province, South Africa, provide unambiguous evidence—in the form of burned bone and ashed plant remains—that burning took place in the cave during the early Acheulean occupation, approximately 1.0 Ma. To the best of our knowledge, this is the earliest secure evidence for burning in an archaeological context.
9,400 years of cosmic radiation and solar activity from ice cores and tree rings
Authors: Steinhilber Friedhelm , Abreu Jose A. , Beer Jürg , Brunner Irene , Christl Marcus , Fischer Hubertus , Heikkilä Ulla , Kubik Peter W. , Mann Mathias , McCracken Ken G. , Miller Heinrich , Miyahara Hiroko , Oerter Hans , Wilhelms Frank
Published: April 2012

Understanding the temporal variation of cosmic radiation and solar activity during the Holocene is essential for studies of the solar-terrestrial relationship. Cosmic-ray produced radionuclides, such as10Be and14C which are stored in polar ice cores and tree rings, offer the unique opportunity to reconstruct the history of cosmic radiation and solar activity over many millennia. Although records from different archives basically agree, they also show some deviations during certain periods. So far most reconstructions were based on only one single radionuclide record, which makes detection and correction of these deviations impossible. Here we combine different10Be ice core records from Greenland and Antarctica with the global14C tree ring record using principal component analysis. This approach is only possible due to a new high-resolution10Be record from Dronning Maud Land obtained within the European Project for Ice Coring in Antarctica in Antarctica. The new cosmic radiation record enables us to derive total solar irradiance, which is then used as a proxy of solar activity to identify the solar imprint in an Asian climate record. Though generally the agreement between solar forcing and Asian climate is good, there are also periods without any coherence, pointing to other forcings like volcanoes and greenhouse gases and their corresponding feedbacks. The newly derived records have the potential to improve our understanding of the solar dynamics and to quantify the solar influence on climate.
Structures of KIX domain of CBP in complex with two FOXO3a transactivation domains reveal promiscuity and plasticity in coactivator recruitment
Authors: Wang Feng , Marshall Christopher B. , Yamamoto Kazuo , Li Guang-Yao , Gasmi-Seabrook Geneviève M. C. , Okada Hitoshi , Mak Tak W. , Ikura Mitsuhiko
Published: April 2012

Forkhead box class O 3a (FOXO3a) is a transcription factor and tumor suppressor linked to longevity that determines cell fate through activating transcription of cell differentiation, survival, and apoptotic genes. Recruitment of the coactivator CBP/p300 is a crucial step in transcription, and we revealed that in addition to conserved region 3 (CR3) of FOXO3a, the C-terminal segment of CR2 (CR2C) binds CBP/p300 and contributes to transcriptional activity. CR2C and CR3 of FOXO3a interact with the KIX domain of CBP/p300 at both “MLL” and “c-Myb” binding sites simultaneously. A FOXO3a CR2C-CR3 peptide in complex with KIX exists in equilibrium between two equally populated conformational states, one of which has CR2C bound to the MLL site and CR3 bound to the c-Myb site, whereas in the other, CR2C and CR3 bind the c-Myb and MLL sites, respectively. This promiscuous interaction between FOXO3a and CBP/p300 is further supported by additional binding sites on CBP/p300, namely, the TAZ1 and TAZ2 domains. In functional studies, our structure-guided mutagenesis showed that both CR2C and CR3 are involved in the activation of certain endogenous FOXO3a target genes. Further, phosphorylation of S626, a known AMP-dependent protein kinase target in CR3, increased affinity for CBP/p300 and the phosphomimetic mutation enhanced transactivation of luciferase. These findings underscore the significance of promiscuous multivalent interactions and posttranslational modification in the recruitment of transcriptional coactivators, which may allow transcription factors to adapt to various gene-specific genomic and chromatin structures and respond to cell signals.
Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of early primate evolution
Authors: Steiper Michael E. , Seiffert Erik R.
Published: April 2012

A long-standing problem in primate evolution is the discord between paleontological and molecular clock estimates for the time of crown primate origins: the earliest crown primate fossils are ∼56 million y (Ma) old, whereas molecular estimates for the haplorhine-strepsirrhine split are often deep in the Late Cretaceous. One explanation for this phenomenon is that crown primates existed in the Cretaceous but that their fossil remains have not yet been found. Here we provide strong evidence that this discordance is better-explained by a convergent molecular rate slowdown in early primate evolution. We show that molecular rates in primates are strongly and inversely related to three life-history correlates: body size (BS), absolute endocranial volume (EV), and relative endocranial volume (REV). Critically, these traits can be reconstructed from fossils, allowing molecular rates to be predicted for extinct primates. To this end, we modeled the evolutionary history of BS, EV, and REV using data from both extinct and extant primates. We show that the primate last common ancestor had a very small BS, EV, and REV. There has been a subsequent convergent increase in BS, EV, and REV, indicating that there has also been a convergent molecular rate slowdown over primate evolution. We generated a unique timescale for primates by predicting molecular rates from the reconstructed phenotypic values for a large phylogeny of living and extinct primates. This analysis suggests that crown primates originated close to the K–Pg boundary and possibly in the Paleocene, largely reconciling the molecular and fossil timescales of primate evolution.
RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities
Authors: Barczak Amy K. , Gomez James E. , Kaufmann Benjamin B. , Hinson Ella R. , Cosimi Lisa , Borowsky Mark L. , Onderdonk Andrew B. , Stanley Sarah A. , Kaur Devinder , Bryant Kevin F. , Knipe David M. , Sloutsky Alexander , Hung Deborah T.
Published: April 2012

With rising rates of drug-resistant infections, there is a need for diagnostic methods that rapidly can detect the presence of pathogens and reveal their susceptibility to antibiotics. Here we propose an approach to diagnosing the presence and drug-susceptibility of infectious diseases based on direct detection of RNA from clinical samples. We demonstrate that species-specific RNA signatures can be used to identify a broad spectrum of infectious agents, including bacteria, viruses, yeast, and parasites. Moreover, we show that the behavior of a small set of bacterial transcripts after a brief antibiotic pulse can rapidly differentiate drug-susceptible and -resistant organisms and that these measurements can be made directly from clinical materials. Thus, transcriptional signatures could form the basis of a uniform diagnostic platform applicable across a broad range of infectious agents.
Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes
Authors: Kopek Benjamin G. , Shtengel Gleb , Xu C. Shan , Clayton David A. , Hess Harald F.
Published: April 2012

Microscopic images of specific proteins in their cellular context yield important insights into biological processes and cellular architecture. The advent of superresolution optical microscopy techniques provides the possibility to augment EM with nanometer-resolution fluorescence microscopy to access the precise location of proteins in the context of cellular ultrastructure. Unfortunately, efforts to combine superresolution fluorescence and EM have been stymied by the divergent and incompatible sample preparation protocols of the two methods. Here, we describe a protocol that preserves both the delicate photoactivatable fluorescent protein labels essential for superresolution microscopy and the fine ultrastructural context of EM. This preparation enables direct 3D imaging in 500- to 750-nm sections with interferometric photoactivatable localization microscopy followed by scanning EM images generated by focused ion beam ablation. We use this process to “colorize” detailed EM images of the mitochondrion with the position of labeled proteins. The approach presented here has provided a new level of definition of the in vivo nature of organization of mitochondrial nucleoids, and we expect this straightforward method to be applicable to many other biological questions that can be answered by direct imaging.
ATP drives direct photosynthetic production of 1-butanol in cyanobacteria
Authors: Lan Ethan I. , Liao James C.
Published: April 2012

While conservation of ATP is often a desirable trait for microbial production of chemicals, we demonstrate that additional consumption of ATP may be beneficial to drive product formation in a nonnatural pathway. Although production of 1-butanol by the fermentative coenzyme A (CoA)-dependent pathway using the reversal of β-oxidation exists in nature and has been demonstrated in various organisms, the first step of the pathway, condensation of two molecules of acetyl-CoA to acetoacetyl-CoA, is thermodynamically unfavorable. Here, we show that artificially engineered ATP consumption through a pathway modification can drive this reaction forward and enables for the first time the direct photosynthetic production of 1-butanol from cyanobacteria
Synechococcus elongatus
PCC 7942. We further demonstrated that substitution of bifunctional aldehyde/alcohol dehydrogenase (AdhE2) with separate butyraldehyde dehydrogenase (Bldh) and NADPH-dependent alcohol dehydrogenase (YqhD) increased 1-butanol production by 4-fold. These results demonstrated the importance of ATP and cofactor driving forces as a design principle to alter metabolic flux.
A hydrogen-bonding network plays a catalytic role in photosynthetic oxygen evolution
Authors: Polander Brandon C. , Barry Bridgette A.
Published: April 2012

In photosystem II, oxygen evolution occurs by the accumulation of photo-induced oxidizing equivalents at the oxygen-evolving complex (OEC). The sequentially oxidized states are called the S0-S4states, and the dark stable state is S1. Hydrogen bonds to water form a network around the OEC; this network is predicted to involve multiple peptide carbonyl groups. In this work, we tested the idea that a network of hydrogen bonded water molecules plays a catalytic role in water oxidation. As probes, we used OEC peptide carbonyl frequencies, the substrate-based inhibitor, ammonia, and the sugar, trehalose. Reaction-induced FT-IR spectroscopy was used to describe the protein dynamics associated with the S1to S2transition. A shift in an amide CO vibrational frequency (1664 (S1) to 1653 (S2) cm-1) was observed, consistent with an increase in hydrogen bond strength when the OEC is oxidized. Treatment with ammonia/ammonium altered these CO vibrational frequencies. The ammonia-induced spectral changes are attributed to alterations in hydrogen bonding, when ammonia/ammonium is incorporated into the OEC hydrogen bond network. The ammonia-induced changes in CO frequency were reversed or blocked when trehalose was substituted for sucrose. This trehalose effect is attributed to a displacement of ammonia molecules from the hydrogen bond network. These results imply that ammonia, and by extension water, participate in a catalytically essential hydrogen bond network, which involves OEC peptide CO groups. Comparison to the ammonia transporter, AmtB, reveals structural similarities with the bound water network in the OEC.
Relative luminance and binocular disparity preferences are correlated in macaque primary visual cortex, matching natural scene statistics
Authors: Samonds Jason M. , Potetz Brian R. , Lee Tai Sing
Published: April 2012

Humans excel at inferring information about 3D scenes from their 2D images projected on the retinas, using a wide range of depth cues. One example of such inference is the tendency for observers to perceive lighter image regions as closer. This psychophysical behavior could have an ecological basis because nearer regions tend to be lighter in natural 3D scenes. Here, we show that an analogous association exists between the relative luminance and binocular disparity preferences of neurons in macaque primary visual cortex. The joint coding of relative luminance and binocular disparity at the neuronal population level may be an integral part of the neural mechanisms for perceptual inference of depth from images.
NSP4, an elastase-related protease in human neutrophils with arginine specificity
Authors: Perera Natascha C. , Schilling Oliver , Kittel Heike , Back Walter , Kremmer Elisabeth , Jenne Dieter E.
Published: April 2012

Neutrophil serine proteases (NSPs) in cytoplasmic granules of neutrophils are regarded as important antimicrobial defense weapons after engulfment and exposure of pathogens to the content of primary granules. Despite intensive studies on neutrophils during the last three decades, only three active serine proteases, neutrophil elastase (NE), cathepsin G (CG), and proteinase 3 (PR3) have been identified in these short-lived cells. Here, we report on the identification of a fourth serine protease (NSP4) with 39% identity to NE and PR3, but arginine specificity, yet sharing features like propeptide processing by dipeptidyl peptidase I, storage, and release as an active enzyme with the three active proteases. We established monoclonal antibodies against NSP4, excluded cross-reactivity to human granzymes, NE, CG, PR3, and azurocidin, and screened for NSP4 protein expression in various human tissues and blood leukocyte populations. Only granulocyte precursors and neutrophil populations from peripheral blood were positive. The content of NSP4 in neutrophil lysates, however, was about 20-fold lower compared with CG. Upon neutrophil activation, NSP4 was released into the supernatant. Profiling its specificity with peptide libraries fromEscherichia colirevealed a preference for arginine in P1; it cleaved Tyr-Arg-Phe-Arg-AMC and Ala-Pro-Nva-thiobenzyl esters. NSP4 was inhibited by α1-proteinase inhibitor (α1–antitrypsin), C1 inhibitor, and most efficiently by antithrombin-heparin, but not by elafin, secretory leukocyte protease inhibitor, α1–antichymotrypsin, and monocyte-neutrophil elastase inhibitor. Functional specialization and preferred natural substrates of NSP4 remain to be determined to understand the biological interplay of all four NSPs during neutrophil responses.
Evolution of the global virtual water trade network
Authors: Dalin Carole , Konar Megan , Hanasaki Naota , Rinaldo Andrea , Rodriguez-Iturbe Ignacio
Published: April 2012

Global freshwater resources are under increasing pressure from economic development, population growth, and climate change. The international trade of water-intensive products (e.g., agricultural commodities) or virtual water trade has been suggested as a way to save water globally. We focus on the virtual water trade network associated with international food trade built with annual trade data and annual modeled virtual water content. The evolution of this network from 1986 to 2007 is analyzed and linked to trade policies, socioeconomic circumstances, and agricultural efficiency. We find that the number of trade connections and the volume of water associated with global food trade more than doubled in 22 years. Despite this growth, constant organizational features were observed in the network. However, both regional and national virtual water trade patterns significantly changed. Indeed, Asia increased its virtual water imports by more than 170%, switching from North America to South America as its main partner, whereas North America oriented to a growing intraregional trade. A dramatic rise in China's virtual water imports is associated with its increased soy imports after a domestic policy shift in 2000. Significantly, this shift has led the global soy market to save water on a global scale, but it also relies on expanding soy production in Brazil, which contributes to deforestation in the Amazon. We find that the international food trade has led to enhanced savings in global water resources over time, indicating its growing efficiency in terms of global water use.
Gene selective mRNA cleavage inhibits the development of
Plasmodium falciparum
Authors: Augagneur Yoann , Wesolowski Donna , Tae Hyun Seop , Altman Sidney , Ben Mamoun Choukri
Published: April 2012

Unique peptide-morpholino oligomer (PMO) conjugates have been designed to bind and promote the cleavage of specific mRNA as a tool to inhibit gene function and parasite growth. The new conjugates were validated using the
P. falciparum
gyrase mRNA as a target (PfGyrA). Assays in vitro demonstrated a selective degradation of the
PfGyrA
mRNA directed by the external guide sequences, which are morpholino oligomers in the conjugates. Fluorescence microscopy revealed that labeled conjugates are delivered into
Plasmodium
-infected erythrocytes during all intraerythrocytic stages of parasite development. Consistent with the expression of
PfGyrA
in all stages of parasite development, proliferation assays showed that these conjugates have potent antimalarial activity, blocking early development, maturation, and replication of the parasite. The conjugates were equally effective against drug sensitive and resistant
P. falciparum
strains. The potency, selectivity, and predicted safety of PMO conjugates make this approach attractive for the development of a unique class of target-specific antimalarials and for large-scale functional analysis of the malarial genome.
Clusters of secretagogin-expressing neurons in the aged human olfactory tract lack terminal differentiation
Authors: Attems Johannes , Alpar Alan , Spence Lauren , McParland Shane , Heikenwalder Mathias , Uhlén Mathias , Tanila Heikki , Hökfelt Tomas G. M. , Harkany Tibor
Published: April 2012

Expanding the repertoire of molecularly diverse neurons in the human nervous system is paramount to characterizing the neuronal networks that underpin sensory processing. Defining neuronal identities is particularly timely in the human olfactory system, whose structural differences from nonprimate macrosmatic species have recently gained momentum. Here, we identify clusters of bipolar neurons in a previously unknown outer “shell” domain of the human olfactory tract, which express secretagogin, a cytosolic Ca
2+
binding protein. These “shell” neurons are wired into the olfactory circuitry because they can receive mixed synaptic inputs. Unexpectedly, secretagogin is often coexpressed with polysialylated–neural cell adhesion molecule, β-III-tubulin, and calretinin, suggesting that these neurons represent a cell pool that might have escaped terminal differentiation into the olfactory circuitry. We hypothesized that secretagogin-containing “shell” cells may be eliminated from the olfactory axis under neurodegenerative conditions. Indeed, the density, but not the morphological or neurochemical integrity, of secretagogin-positive neurons selectively decreases in the olfactory tract in Alzheimer's disease. In conclusion, secretagogin identifies a previously undescribed cell pool whose cytoarchitectonic arrangements and synaptic connectivity are poised to modulate olfactory processing in humans.
Phosphorylation regulates human OCT4
Authors: Brumbaugh Justin , Hou Zhonggang , Russell Jason D. , Howden Sara E. , Yu Pengzhi , Ledvina Aaron R. , Coon Joshua J. , Thomson James A.
Published: April 2012

The transcription factor OCT4 is fundamental to maintaining pluripotency and self-renewal. To better understand protein-level regulation of OCT4, we applied liquid chromatography–MS to identify 14 localized sites of phosphorylation, 11 of which were previously unknown. Functional analysis of two sites, T234 and S235, suggested that phosphorylation within the homeobox region of OCT4 negatively regulates its activity by interrupting sequence-specific DNA binding. Mutating T234 and S235 to mimic constitutive phosphorylation at these sites reduces transcriptional activation from an OCT4-responsive reporter and decreases reprogramming efficiency. We also cataloged 144 unique phosphopeptides on known OCT4 interacting partners, including SOX2 and SALL4, that copurified during immunoprecipitation. These proteins were enriched for phosphorylation at motifs associated with ERK signaling. Likewise, OCT4 harbored several putative ERK phosphorylation sites. Kinase assays confirmed that ERK2 phosphorylated these sites in vitro, providing a direct link between ERK signaling and the transcriptional machinery that governs pluripotency.
Age Differences in Contingency Judgement Linked to Perceptual Segregation
Authors: Hannah Samuel D. , Allan Lorraine G. , Young Meredith E.
Published: April 2012

We demonstrate large differences in judging positive and null contingencies between younger and older adults with a task commonly used to explore cue competition in both contingency and causality judgements. The one-phase blocking task uses two cues, with separate contingencies with the same outcome. The age differences persisted even when participants knew in advance which of the two contingencies to judge. The age differences disappeared, however, when the stimulus display contained markers aiding perceptual segregation. We suggest that the age differences elicited in the one-phase blocking task are linked to decrements in perceptual segregation.
Cockayne syndrome group B protein prevents the accumulation of damaged mitochondria by promoting mitochondrial autophagy
Authors: Scheibye-Knudsen Morten , Ramamoorthy Mahesh , Sykora Peter , Maynard Scott , Lin Ping-Chang , Minor Robin K. , Wilson David M. , Cooper Marcus , Spencer Richard , de Cabo Rafael , Croteau Deborah L. , Bohr Vilhelm A.
Published: April 2012

Cockayne syndrome (CS) is a devastating autosomal recessive disease characterized by neurodegeneration, cachexia, and accelerated aging. 80% of the cases are caused by mutations in the CS complementation group B (CSB) gene known to be involved in DNA repair and transcription. Recent evidence indicates that CSB is present in mitochondria, where it associates with mitochondrial DNA (mtDNA). We report an increase in metabolism in the CSBm/m mouse model and CSB-deficient cells. Mitochondrial content is increased in CSB-deficient cells, whereas autophagy is down-regulated, presumably as a result of defects in the recruitment of P62 and mitochondrial ubiquitination. CSB-deficient cells show increased free radical production and an accumulation of damaged mitochondria. Accordingly, treatment with the autophagic stimulators lithium chloride or rapamycin reverses the bioenergetic phenotype of CSB-deficient cells. Our data imply that CSB acts as an mtDNA damage sensor, inducing mitochondrial autophagy in response to stress, and that pharmacological modulators of autophagy are potential treatment options for this accelerated aging phenotype.
The hypoxia imaging agent CuII(atsm) is neuroprotective and improves motor and cognitive functions in multiple animal models of Parkinson’s disease
Authors: Hung Lin W. , Villemagne Victor L. , Cheng Lesley , Sherratt Nicki A. , Ayton Scott , White Anthony R. , Crouch Peter J. , Lim SinChun , Leong Su Ling , Wilkins Simon , George Jessica , Roberts Blaine R. , Pham Chi L.L. , Liu Xiang , Chiu Francis C.K. , Shackleford David M. , Powell Andrew K. , Masters Colin L. , Bush Ashley I. , O’Keefe Graeme , Culvenor Janetta G. , Cappai Roberto , Cherny Robert A. , Donnelly Paul S. , Hill Andrew F. , Finkelstein David I. , Barnham Kevin J.
Published: April 2012

Parkinson’s disease (PD) is a progressive, chronic disease characterized by dyskinesia, rigidity, instability, and tremors. The disease is defined by the presence of Lewy bodies, which primarily consist of aggregated α-synuclein protein, and is accompanied by the loss of monoaminergic neurons. Current therapeutic strategies only give symptomatic relief of motor impairment and do not address the underlying neurodegeneration. Hence, we have identified CuII(atsm) as a potential therapeutic for PD. Drug administration to four different animal models of PD resulted in improved motor and cognition function, rescued nigral cell loss, and improved dopamine metabolism. In vitro, this compound is able to inhibit the effects of peroxynitrite-driven toxicity, including the formation of nitrated α-synuclein oligomers. Our results show that CuII(atsm) is effective in reversing parkinsonian defects in animal models and has the potential to be a successful treatment of PD.
Essential role of EBF1 in the generation and function of distinct mature B cell types
Authors: Vilagos Bojan , Hoffmann Mareike , Souabni Abdallah , Sun Qiong , Werner Barbara , Medvedovic Jasna , Bilic Ivan , Minnich Martina , Axelsson Elin , Jaritz Markus , Busslinger Meinrad
Published: April 2012

The transcription factor EBF1 is essential for lineage specification in early B cell development. In this study, we demonstrate by conditional mutagenesis that EBF1 is required for B cell commitment, pro–B cell development, and subsequent transition to the pre–B cell stage. Later in B cell development, EBF1 was essential for the generation and maintenance of several mature B cell types. Marginal zone and B-1 B cells were lost, whereas follicular (FO) and germinal center (GC) B cells were reduced in the absence of EBF1. Activation of the B cell receptor resulted in impaired intracellular signaling, proliferation and survival of EBF1-deficient FO B cells. Immune responses were severely reduced upon Ebf1 inactivation, as GCs were formed but not maintained. ChIP- and RNA-sequencing of FO B cells identified EBF1-activated genes that encode receptors, signal transducers, and transcriptional regulators implicated in B cell signaling. Notably, ectopic expression of EBF1 efficiently induced the development of B-1 cells at the expense of conventional B cells. These gain- and loss-of-function analyses uncovered novel important functions of EBF1 in controlling B cell immunity.
Structure and morphology of platinum nanoparticles with critical new
issues of low- and high-index facets
Authors: Nguyen Viet-Long , Ohtaki Michitaka , Ngo Van Nong , Cao Minh-Thi , Nogami Masayuki
Published: April 2012

In this paper, Pt nanoparticles were successfully prepared by modified polyol method
using silver nitrate as an effective structure-modifying agent. The characterization
of Pt nanoparticles was investigated by using UV-Vis-NIR spectroscopy, transmission
electron microscopy (TEM) and high resolution (HR) TEM, and x-ray diffraction (XRD).
The method of selected area electron diffraction (SEAD) was used to study the
structure of Pt nanoparticles. The results showed that the as-prepared Pt
nanoparticles exhibiting the complexity of surface structure and morphology could be
used as efficient catalysts for polymer electrolyte membrane fuel cells (PEMFCs) and
direct methanol fuel cells (DMFCs).
Metalepsis and the
auteur supposé
in Raymond Queneau's
Œuvres complètes de Sally Mara
Authors: Ferguson Sam
Published: April 2012

Raymond Queneau's choice to publish the novel
On est toujours trop bon avec les femmes
(1947) under the pseudonym of Sally Mara, followed by her
Journal intime
(1950) and an edition of her
Œuvres complètes
(1962), has generally been a cause for the neglect of these works rather than an object of study in itself. This article treats the use of a pseudonym as part of a broader strategy that belongs to the tradition of the
auteur supposé
and contributes to an exploration of themes of authorship. It examines the texts using the narratological concept of metalepsis and with a focus on the manipulation of conventions of paratext. This analysis reveals that the prefaces, footnotes, and other paratextual apparatus constitute a narrative concerning the three author-figures whose signatures appear on the works — Raymond Queneau, Michel Presle, and Sally Mara — and which develops over the course of the publication history. An understanding of the complex and shifting diegetic framework is shown to be more helpful than the simplistic concept of a pseudonym, and challenges our assumptions concerning the boundaries between text, paratext, and author.
CO2‐dependent growth of Succinatimonas hippei YIT 12066T isolated from human feces
Authors: Morotomi Masami , Nagai Fumiko , Watanabe Yohei
Published: April 2012

Succinatimonas  hippei  is a new bacterial species isolated from human feces. Here we report that the growth of S. hippei YIT 12066T depends on CO2 or bicarbonate and the headspace gas produced by microbiota. Genetic defect for carbonic anhydrase in this bacterium suggested a reason for the syntrophic property of CO2 dependency and may suggest an adaptation to its habitat.
Estrogen receptor α and β in esophageal squamous cell carcinoma
Authors: Zuguchi Masashi , Miki Yasuhiro , Onodera Yoshiaki , Fujishima Fumiyoshi , Takeyama Daisuke , Okamoto Hiroshi , Miyata Go , Sato Akira , Satomi Susumu , Sasano Hironobu
Published: April 2012

A gender difference has been reported in the morbidity of esophageal squamous cell carcinoma (ESCC). Estrogens have been proposed to play a role in this difference but the details have not yet been clarified. Therefore, in the present study, we examined the status of estrogen receptor (ER)α and ERβ in 90 Japanese ESCC patients. ERα and ERβ immunoreactivity was detected in the nuclei of ESCC cells (41.1 and 97.8%, respectively). There was a significant positive association between the ERβ H score and histological differentiation (P = 0.0403), TNM‐pM (LYM) (P = 0.00164) and Ki67/MIB1 LI of carcinoma cells (P = 0.0497, r = 0.207). In addition, the ERβ status of carcinoma cells was significantly correlated with unfavorable clinical outcome of the patients. Multivariate analysis further revealed the ERβ status in carcinoma cells as an independent unfavorable prognostic factor of these patients. We further examined the effects of estrogen treatment on ESCC cell line (ECGI‐10) transfected with ERα or ERβ in vitro. The number of ECGI‐10 transfected with ERβ was increased by estradiol or ERβ specific agonist but estradiol did not exert any effect upon the cell number of ECGI‐10 transfected with ERα. In summary, the results of the present study clearly demonstrate that the status of ERβ in ESCC was closely associated with the unfavorable prognosis, possibly through altering cell proliferation of carcinoma cells. (Cancer Sci 2012; 103: 1348–1355)