bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Task Selection in Learning Arithmetic: The Role of Learner Control and Adaptation Based on a Hierarchy of Skills 1Dieser Beitrag wurde unter der geschäftsführenden Herausgeberschaft von Jens Möller angenommen
Authors: Schoppek Wolfgang
Published: January 2012

Abstract.The effects of locus of instructional control in computer-assisted practice of arithmetic skills and word problem solving were investigated in a field experiment with 13 third grade classes. In a program-controlled condition (n = 95), the selection of practice problems was based on a hypothetical hierarchy of skills. This was expected to regulate cognitive load to a moderate level. In a condition with shared control (n = 89), subjects could select problems from a subset provided by the program. Results show that program-controlled selection of problems based on the hierarchy of skills was more successful in supporting skill development than the students’ selection. In the shared control condition, students tended to select too easy problems, regardless of their level of expertise. Both conditions with computer assisted instruction caused more progress than traditional instruction (n = 94). Ways of improving the regulation of cognitive load within a shared control approach are discussed.
Educational Psychology in China 1Dieser Beitrag wurde unter der Herausgeberschaft von Detlef H. Rost angenommen.
Authors: Zhang Dajun , Wang Jinliang , Li Xiaohui , Feng Xiaoli
Published: January 2012

Abstract: Educational psychology in China has experienced a history of around 100 years. It has gone through many stages, including introduction and imitation of research in Western countries, learning from others’ experience and reform, and getting independent from western psychology. Especially, profound development has been achieved in the recent 30 years. The educational psychology system in China has begun to show its own characteristics. The field of research has been extended continuously. The educational psychology has been developed by Chinese educational psychologists from the research into learning psychology to the studies of many subjects, including learning psychology, teaching psychology, teachers’ psychology, moral psychology, and research on individual differences in educational contexts. Many studies based on reality in China have been initiated, which help to improve the educational psychology system. The development of educational psychology in China is characterized by localized orientation research, high ecological validity of research condition, comprehensiveness of research goals, and diversification of research methods.
Continental scale, high order, high spatial resolution, ice sheet modeling using the Ice Sheet System Model (ISSM)
Authors: Larour E. , Seroussi H. , Morlighem M. , Rignot E.
Published: January 2012

Ice flow models used to project the mass balance of ice sheets in Greenland and Antarctica usually rely on the Shallow Ice Approximation (SIA) and the Shallow‐Shelf Approximation (SSA), sometimes combined into so‐called “hybrid” models. Such models, while computationally efficient, are based on a simplified set of physical assumptions about the mechanical regime of the ice flow, which does not uniformly apply everywhere on the ice sheet/ice shelf system, especially near grounding lines, where rapid changes are taking place at present. Here, we present a new thermomechanical finite element model of ice flow named ISSM (Ice Sheet System Model) that includes higher‐order stresses, high spatial resolution capability and data assimilation techniques to better capture ice dynamics and produce realistic simulations of ice sheet flow at the continental scale. ISSM includes several approximations of the momentum balance equations, ranging from the two‐dimensional SSA to the three‐dimensional full‐Stokes formulation. It also relies on a massively parallelized architecture and state‐of‐the‐art scalable tools. ISSM employs data assimilation techniques, at all levels of approximation of the momentum balance equations, to infer basal drag at the ice‐bed interface from satellite radar interferometry‐derived observations of ice motion. Following a validation of ISSM with standard benchmarks, we present a demonstration of its capability in the case of the Greenland Ice Sheet. We show ISSM is able to simulate the ice flow of an entire ice sheet realistically at a high spatial resolution, with higher‐order physics, thereby providing a pathway for improving projections of ice sheet evolution in a warming climate.
Incorporating spatial heterogeneity created by permafrost thaw into a landscape carbon estimate
Authors: Belshe E. F. , Schuur E. A. G. , Bolker B. M. , Bracho R.
Published: January 2012

The future carbon balance of high‐latitude ecosystems is dependent on the sensitivity of biological processes (photosynthesis and respiration) to the physical changes occurring with permafrost thaw. Predicting C exchange in these ecosystems is difficult because the thawing of permafrost is a heterogeneous process that creates a complex landscape. We measured net ecosystem exchange of C using eddy covariance (EC) in a tundra landscape visibly undergoing thaw during two 6 month campaigns in 2008 and 2009. We developed a spatially explicit quantitative metric of permafrost thaw based on variation in microtopography and incorporated it into an EC carbon flux estimate using a generalized additive model (GAM). This model allowed us to make predictions about C exchange for the landscape as a whole and for specific landscape patches throughout the continuum of permafrost thaw and ground subsidence. During June through November 2008, the GAM predicted that the landscape on average took up 337.1 g C m−2 via photosynthesis and released 289.5 g C m−2 via respiration, resulting in a net C gain of 47.5 g C m−2 by the tundra ecosystem. During April through October 2009, the landscape on average took up 498.7 g C m−2 and released 410.3 g C m−2, resulting in a net C gain of 87.8 g C m−2. On average, between the years, areas with the highest permafrost thaw and ground subsidence photosynthesized 17.7% more and respired 3.3% more C than the average landscape. Areas with the least thaw and subsidence photosynthesized 15% less and respired 5.1% less than the landscape on average. By incorporating spatial variation into the EC C estimate, we were able to estimate the C balance of a heterogeneous landscape and determine the collective effect of permafrost thaw on the plant and soil processes that drive ecosystem C flux. In these study years, permafrost thaw appeared to increase the amplitude of the C cycle by stimulating both C release and sequestration, while the ecosystem remained a C sink at the landscape scale.
Low‐temperature evolution of the Morondava rift basin shoulder in western Madagascar: An apatite fission track study
Authors: Giese Jörg , Seward Diane , Schreurs Guido
Published: January 2012

The evolution of the rift shoulder and the sedimentary sequence of the Morondava basin in western Madagascar was mainly influenced by a Permo‐Triassic continental failed rift (Karroo rift), and the early Jurassic separation of Madagascar from Africa. Karroo deposits are restricted to a narrow corridor along the basement‐basin contact and parts of this contact feature a steep escarpment. Here, apatite fission track (AFT) analysis of a series of both basement and sediment samples across the escarpment reveals the low‐temperature evolution of the exhuming Precambrian basement in the rift basin shoulder and the associated thermal evolution of the sedimentary succession. Seven basement and four Karroo sediment samples yield apparent AFT ages between ∼330 and ∼215 Ma and ∼260 and ∼95 Ma, respectively. Partially annealed fission tracks and thermal modeling indicate post‐depositional thermal overprinting of both basement and Karroo sediment. Rocks presently exposed in the rift shoulder indicate temperatures of >60°C associated with this reheating whereby the westernmost sample in the sedimentary plain experienced almost complete resetting of the detrital apatite grains at temperatures of about ∼90–100°C. The younging of AFT ages westward indicates activity of faults, re‐activating inherited Precambrian structures during Karroo sedimentation. Furthermore, our data suggest onset of final cooling/exhumation linked to (1) the end of Madagascar's drift southward relative to Africa during the Early Cretaceous, (2) activity of the Marion hot spot and associated Late Cretaceous break‐up between Madagascar and India, and (3) the collision of India with Eurasia and subsequent re‐organization of spreading systems in the Indian Ocean.
Toxics Release Inventory indicates big increases in releases
Authors: Showstack Randy
Published: January 2012

Nearly 4 billion pounds of tracked toxic chemicals were released into the environment throughout the United States during 2010, according to an analysis by the U.S. Environmental Protection Agency (EPA) of the Toxics Release Inventory (TRI), the agency announced on 5 January. This is a 16% increase above 2009. The agency said the increase is mainly due to changes in the metal‐mining sector, where differences in the chemical composition of ore being mined can result in significant changes in the amount of toxic chemicals. The chemical and primary metals industries were other sectors with increases in toxic releases in 2010, the latest year for which data collection is complete. EPA also noted that although releases in 2010 were higher than during the previous 2 years, they were lower than in 2007 and in prior years.
Project Gemini online digital archive
Authors: Showstack Randy
Published: January 2012

An archive containing the first high‐resolution digital scans of the original flight films from Project Gemini, the second U.S. human spaceflight program, was unveiled by the NASA Johnson Space Center and Arizona State University's (ASU) School of Earth and Space Exploration on 6 January. The archive includes images from 10 flights. Project Gemini, which ran from 1964 to 1966, followed Project Mercury and preceded the Apollo spacecraft. Mercury and Apollo imagery are also available through ASU. For more information, see http://tothemoon.ser.asu.edu/gallery/gemini and http://apollo.sese.asu.edu/index.html.
Connor receives David Perlman Award for Excellence in Science Journalism–News: Citation
Authors: Duff Oliver
Published: January 2012

Steve Connor, science editor of the Independent newspaper of London, received the David Perlman Award for Excellence in Science Journalism–News at the AGU Fall Meeting Honors Ceremony, held on 7 December 2011 in San Francisco, Calif. Connor was honored for his article “Expect more extreme winters thanks to global warming, say scientists,” published 24 December 2010 in theIndependent. The article covers a computer modeling study that found that losses in sea ice north of Scandinavia and Russia caused by global warming could paradoxically cause harsh, cold winters in the United Kingdom and elsewhere. The Perlman award is for work published with a deadline pressure of 1 week or less.
Rhythmic seismic events triggered by ocean noise
Authors: Balcerak Ernie
Published: January 2012

Seismic events are often detected near volcanoes, but their timing is usually irregular.Stich et al. detected swarms of regularly repeating long‐period events at the Deception Island volcano in Antarctica during Seismic events are often detected near volcanoes, but their timing is usually irregular. Stich et al. detected swarms of regularly repeating long‐period events at the Deception Island volcano in Antarctica during
Variation in local carrying capacity and the individual fate of bacterial colonizers in the phyllosphere
Authors: Remus-Emsermann Mitja N P , Tecon Robin , Kowalchuk George A , Leveau Johan H J
Published: January 2012

Using a phyllosphere model system, we demonstrated that the term ‘carrying capacity’, as it is commonly used in microbial ecology, needs to be understood as the sum of many ‘local carrying capacities’ in order to better explain and predict the course and outcome of bacterial colonization of an environment. Using a green fluorescent protein-based bioreporter system for the quantification of reproductive success (RS) in individual Erwinia herbicola cells, we were able to reconstruct the contribution of individual immigrants to bacterial population sizes on leaves. Our analysis revealed that plant foliage represents to bacteria an environment where individual fate is determined by the local carrying capacity of the site where an immigrant cell lands. With increasing inoculation densities, the RS of most immigrants declined, suggesting that local carrying capacity under the tested conditions was linked to local nutrient availability. Fitting the observed experimental data to an adapted model of phyllosphere colonization indicated that there might exist three types of sites on leaves, which differ in their frequency of occurrence and local carrying capacity. Specifically, our data were consistent with a leaf environment that is characterized by few sites where individual immigrants can produce high numbers of offspring, whereas the remainder of the leaf offered an equal number of sites with low and medium RS. Our findings contribute to a bottom–up understanding of bacterial colonization of leaf surfaces, which includes a quantifiable role of chance in the experience at the individual level and in the outcome at the population level.
Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions
Authors: Gierga Gregor , Voss Björn , Hess Wolfgang R
Published: January 2012

Regulatory small RNAs (sRNAs) have crucial roles in the adaptive responses of bacteria to changes in the environment. Thus far, potential regulatory RNAs have been studied mainly in marine picocyanobacteria in genetically intractable Prochlorococcus, rendering their molecular analysis difficult. Synechococcus sp. WH7803 is a model cyanobacterium, representative of the picocyanobacteria from the mesotrophic areas of the ocean. Similar to the closely related Prochlorococcus it possesses a relatively streamlined genome and a small number of genes, but is genetically tractable. Here, a comparative genome analysis was performed for this and four additional marine Synechococcus to identify the suite of possible sRNAs and other RNA elements. Based on the prediction and on complementary microarray profiling, we have identified several known as well as 32 novel sRNAs. Some sRNAs overlap adjacent coding regions, for instance for the central photosynthetic gene psbA. Several of these novel sRNAs responded specifically to environmentally relevant stress conditions. Among them are six sRNAs changing their accumulation level under cold stress, six responding to high light and two to iron limitation. Target predictions suggested genes encoding components of the light-harvesting apparatus as targets of sRNAs originating from genomic islands and that one of the iron-regulated sRNAs might be a functional homolog of RyhB. These data suggest that marine Synechococcus mount adaptive responses to these different stresses involving regulatory sRNAs.
The small Rho GTPase Rif and actin cytoskeletal remodelling
Authors: Fan Lifei , Mellor Harry
Published: January 2012

The Rif GTPase is a recent addition to small Rho GTPase family; it shares low homology with other members in the family and evolutionarily parallels with the development of vertebrates. Rif has the conserved Rho GTPase domain structures and cycles between a GDP-bound inactive form and a GTP-bound active form. In its active form, Rif signals through multiple downstream effectors. In the present review, our aim is to summarize the current information about the Rif effectors and how Rif remodels actin cytoskeleton in many aspects.
Role of Epac in brain and heart
Authors: Laurent Anne-Coline , Breckler Magali , Berthouze Magali , Lezoualc'h Frank
Published: January 2012

Epacs (exchange proteins directly activated by cAMP) are guanine-nucleotide-exchange factors for the Ras-like small GTPases Rap1 and Rap2. Epacs were discovered in 1998 as new sensors for the second messenger cAMP acting in parallel to PKA (protein kinase A). As cAMP regulates many important physiological functions in brain and heart, the existence of Epacs raises many questions regarding their role in these tissues. The present review focuses on the biological roles and signalling pathways of Epacs in neurons and cardiac myocytes. We discuss the potential involvement of Epacs in the manifestation of cardiac and central diseases such as cardiac hypertrophy and memory disorders.
Roles of p38 MAPKs in invasion and metastasis
Authors: del Barco Barrantes Ivan , Nebreda Angel R.
Published: January 2012

Cells from primary tumours need to go through several steps to become fully metastatic. During this process, cancer cells acquire the ability to invade, migrate across the surrounding tissue, enter into the circulation and colonize distant organs. In the present paper, we review recent progress in understanding how the p38 MAPK (mitogen-activated protein kinase) signalling pathway participates in the different steps of metastasis. Experimental evidence suggests that tumour cells need to modulate p38 MAPK activity levels to successfully metastasize.
Phosphorylation of basic helix–loop–helix transcription factor Twist in development and disease
Authors: Xue Gongda , Hemmings Brian A.
Published: January 2012

The transcription factor Twist plays vital roles during embryonic development through regulating/controlling cell migration. However, postnatally, in normal physiological settings, Twist is either not expressed or inactivated. Increasing evidence shows a strong correlation between Twist reactivation and both cancer progression and malignancy, where the transcriptional activities of Twist support cancer cells to disseminate from primary tumours and subsequently establish a secondary tumour growth in distant organs. However, it is largely unclear how this signalling programme is reactivated or what signalling pathways regulate its activity. The present review discusses recent advances in Twist regulation and activity, with a focus on phosphorylation-dependent Twist activity, potential upstream kinases and the contribution of these factors in transducing biological signals from upstream signalling complexes. The recent advances in these areas have shed new light on how phosphorylation-dependent regulation of the Twist proteins promotes or suppresses Twist activity, leading to differential regulation of Twist transcriptional targets and thereby influencing cell fate.
Roles of the mammalian target of rapamycin, mTOR, in controlling ribosome biogenesis and protein synthesis
Authors: Iadevaia Valentina , Huo Yilin , Zhang Ze , Foster Leonard J. , Proud Christopher G.
Published: January 2012

mTORC1 (mammalian target of rapamycin complex 1) is controlled by diverse signals (e.g. hormones, growth factors, nutrients and cellular energy status) and regulates a range of processes including anabolic metabolism, cell growth and cell division. We have studied the impact of inhibiting mTOR on protein synthesis in human cells. Partial inhibition of mTORC1 by rapamycin has only a limited impact on protein synthesis, but inhibiting mTOR kinase activity causes much greater inhibition of protein synthesis. Using a pulsed stable-isotope-labelling technique, we show that the rapamycin and mTOR (mammalian target of rapamycin) kinase inhibitors have differential effects on the synthesis of specific proteins. In particular, the synthesis of proteins encoded by mRNAs that have a 5′-terminal pyrimidine tract is strongly inhibited by mTOR kinase inhibitors. Many of these mRNAs encode ribosomal proteins. mTORC1 also promotes the synthesis of rRNA, although the mechanisms involved remain to be clarified. We found that mTORC1 also regulates the processing of the precursors of rRNA. mTORC1 thus co-ordinates several steps in ribosome biogenesis.
Structural phase transitions of FeCo and FeNi nanoparticles: A molecular dynamics study
Authors: Meng L. J. , Peng X. Y. , Zhang K. W. , Tang C. , Zhong J. X.
Published: January 2012

We have investigated the structural phase transition of FeCo and FeNi nanoparticles by molecular dynamics (MD) simulation using the generalized embedded atom potential (GEAM). It is found that the phase varies with the atomic compositions and annealing processes. By using the Honeycutt and Andersen index (HA index), bond order parameters (BOP) and pair correlation function (PCF), we found that a BCC to defective icosahedra phase transition occurs in the FeCo nanoparticle when Co composition is increased to about 60 at %. In the FeNi nanoparticle, three phases have been identified, namely, the BCC phase, the mixed BCC/FCC phase, and the multilayer defective icosahedral phase, which correspond to the Ni compositions of 0–20 at %, 20–70 at %, and 70–100 at %, respectively. Our simulations have well reproduced the phase transition points and most of the phases observed in recent experiments.
Fractal variability: An emergent property of complex dissipative systems
Authors: Seely Andrew J. E. , Macklem Peter
Published: January 2012

The patterns of variation of physiologic parameters, such as heart and respiratory rate, and their alteration with age and illness have long been under investigation; however, the origin and significance of scale-invariant fractal temporal structures that characterize healthy biologic variability remain unknown. Quite independently, atmospheric and planetary scientists have led breakthroughs in the science of non-equilibrium thermodynamics. In this paper, we aim to provide two novel hypotheses regarding the origin and etiology of both the degree of variability and its fractal properties. In a complex dissipative system, we hypothesize that the degree of variability reflects the adaptability of the system and is proportional to maximum work output possible divided by resting work output. Reductions in maximal work output (and oxygen consumption) or elevation in resting work output (or oxygen consumption) will thus reduce overall degree of variability. Second, we hypothesize that the fractal nature of variability is a self-organizing emergent property of complex dissipative systems, precisely because it enables the system’s ability to optimally dissipate energy gradients and maximize entropy production. In physiologic terms, fractal patterns in space (e.g., fractal vasculature) or time (e.g., cardiopulmonary variability) optimize the ability to deliver oxygen and clear carbon dioxide and waste. Examples of falsifiability are discussed, along with the need to further define necessary boundary conditions. Last, as our focus is bedside utility, potential clinical applications of this understanding are briefly discussed. The hypotheses are clinically relevant and have potential widespread scientific relevance.
X-ray emission spectroscopy and density functional study of CO/Fe(100)
Authors: Gladh J. , Öberg H. , Li Jibiao , Ljungberg M. P. , Matsuda A. , Ogasawara H. , Nilsson A. , Pettersson L. G. M. , Öström H.
Published: January 2012

We report x-ray emission and absorption spectroscopy studies of the electronic structure of the predissociative α3 phase of CO bound at hollow sites of Fe(100) as well as of the on-top bound species in the high-coverage α1 phase. The analysis is supported by density functional calculations of structures and spectra. The bonding of “lying down” CO in the hollow site is well described in terms of π to π* charge transfer made possible through bonding interaction also at the oxygen in the minority spin-channel. The on-top CO in the mixed, high-coverage α1 phase is found to be tilted due to adsorbate-adsorbate interaction, but still with bonding mainly characteristic of “vertical” on-top adsorbed CO similar to other transition-metal surfaces.
Bath-induced correlations and relaxation of vibronic dimers
Authors: Gelin Maxim F. , Sharp Leah Z. , Egorova Dassia , Domcke Wolfgang
Published: January 2012

We consider a vibronic dimer bilinearly coupled through its two vibrational monomer modes to two harmonic reservoirs and study, both analytically and numerically, how correlations of the reservoir-induced fluctuations affect dimer relaxation. For reservoirs with fully correlated fluctuations, we derive an exact quantum master equation for the density matrix of the symmetric vibronic dimer. We demonstrate that reservoirs with fully correlated or anticorrelated fluctuations do not allow for complete vibrational relaxation of the dimer due to the existence of decoherence-free subspaces. For reservoirs with partially correlated fluctuations, we establish the existence of three different mechanisms of vibrational relaxation. Weak inter-monomer couplings, as well as predominantly correlated or anticorrelated fluctuations, render two of these mechanisms relatively inefficient, leading to slow decays of the populations and coherences of the dimer density matrix. The analytical results are illustrated and substantiated by numerical studies of the relaxation behavior of photoexcited dimers.
Atomic volumes and polarizabilities in density-functional theory
Authors: Kannemann Felix O. , Becke Axel D.
Published: January 2012

Becke and Johnson introduced an ad hoc definition of atomic volume [J. Chem. Phys. 124, 014204 (2006)] in order to obtain atom-in-molecule polarizabilities from free-atom polarizabilities in their nonempirical exchange-hole dipole moment model of dispersion interactions. Here we explore the dependence of Becke-Johnson atomic volumes on basis sets and density-functional approximations and provide reference data for all atoms H–Lr. A persuasive theoretical foundation for the Becke-Johnson definition is also provided.
Induced magnetic anisotropy and spin polarization in pulsed laser–deposited Co2MnSb thin films
Authors: Paudel Moti R. , Wolfe Christopher S. , Pathak Arjun K. , Dubenko Igor , Ali Naushad , Osofsky M. S. , Prestigiacomo Joseph C. , Stadler Shane
Published: January 2012

Co2MnSb thin films were grown on glass and GaAs (001) substrates using pulsed laser deposition. The films were grown in magnetic fields (HG = 500 Oe and 0 Oe) that were applied in the plane of the substrate during the deposition process. Angle-dependent magneto-optic Kerr effect measurements for films grown on glass revealed a uniaxial magnetic anisotropy in the direction of the applied growth field. Films grown on GaAs (001) exhibited more complicated magnetic anisotropy behavior, due to additional contributions from the substrate. Point contact Andreév reflection spectroscopy measurements indicated that the spin polarizations of the films were about P ∼ 50%, with negligible difference between films grown in zero and non-zero applied fields.
Notes on the Riccati operator equation in open quantum systems
Authors: Gardas Bartłomiej , Puchała Zbigniew
Published: January 2012

A recent problem [B. Gardas, J. Math. Phys. 52, 042104 (2011)] concerning an antilinear solution of the Riccati equation is solved. We also exemplify that a simplification of the Riccati equation, even under reasonable assumptions, can lead to a not equivalent equation.
Chemical ordering of FePt films using millisecond flash-lamp annealing
Authors: Brombacher C. , Schubert C. , Daniel M. , Liebig A. , Beddies G. , Schumann T. , Skorupa W. , Donges J. , Häberlein S. , Albrecht M.
Published: January 2012

The structural and magnetic properties of 20-nm-thick FexPt100-x films that were processed by 20 ms flash-lamp annealing were investigated. A maximum in coercivity of (10.4 ± 0.5) kOe was achieved for a composition of Fe53Pt47, which shows also a high degree of L10 chemical order. A variation of the chemical composition toward either higher or lower Fe content leads to a lowering of the coercivity, which can be attributed to a reduction in L10 ordered volume fraction. Thus, in the millisecond time regime, the fastest ordering transformation occurs for slightly Fe-rich FePt films.
Epitaxial graphene on SiC(0001¯): Stacking order and interfacial structure
Authors: Weng Xiaojun , Robinson Joshua A. , Trumbull Kathleen , Cavalero Randall , Fanton Mark A. , Snyder David
Published: January 2012

The fundamental structural properties of multilayer epitaxial graphene (MEG) on C-face SiC(0001¯) were revealed in a straightforward manner using cross-sectional transmission electron microscopy (TEM) and scanning TEM (STEM). The AB-stacking and the azimuthal rotational disorder of the graphene layers were directly identified by selected area electron diffraction and high-resolution TEM. The directly interpretable STEM revealed that the interlayer spacing between the first graphene layer and the top SiC bilayer is substantially larger than that of the bulk graphite. Such a large interlayer spacing combined with the regional partially decomposed top bilayers of the SiC substrate provides a plausible explanation to the weak bonding between the MEG film and the SiC(0001¯) substrate.
Microwire (Mg,Zn)O/ZnO and (Mg,Zn)O/(Cd,Zn)O non-polar quantum well heterostructures for cavity applications
Authors: Dietrich C. P. , Lange M. , Stölzel M. , Grundmann M.
Published: January 2012

Pulsed-laser deposited, non-polar MgxZn1−xO/ZnO and MgxZn1−xO/Zn1−yCdyO quantum well heterostructures were fabricated in radial direction on ZnO microwires with well-defined hexagonal cross section. Optical resonances modulate room-temperature luminescence spectra for all fabricated heterostructures demonstrating their applicability as microcavities. Quantum confinement was proven by time-integrated and time-resolved luminescence. The ZnO quantum well emission was tuned between 3.76 and 3.35 eV by adjusting the well thickness and barrier composition. In order to further reduce the QW emission energy, active Zn1−yCdyO quantum wells in MgxZn1−xO barriers were grown emitting between 3.07 and 2.70 eV for different well thicknesses but fixed barrier composition.
Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life
Authors: Pace Norman R. , Sapp Jan , Goldenfeld Nigel
Published: January 2012

In 1977, Carl Woese and George Fox published a brief paper in PNAS that established, for the first time, that the overall phylogenetic structure of the living world is tripartite. We describe the way in which this monumental discovery was made, its context within the historical development of evolutionary thought, and how it has impacted our understanding of the emergence of life and the characterization of the evolutionary process in its most general form.
Protein-binding dynamics imaged in a living cell
Authors: Phillip Yael , Kiss Vladimir , Schreiber Gideon
Published: January 2012

Historically, rate constants were determined in vitro and it was unknown whether they were valid for in vivo biological processes. Here, we bridge this gap by measuring binding dynamics between a pair of proteins in living HeLa cells. Binding of a β-lactamase to its protein inhibitor was initiated by microinjection and monitored by Förster resonance energy transfer. Association rate constants for the wild-type and an electrostatically optimized mutant were only 25% and 50% lower than in vitro values, whereas no change in the rate constant was observed for a slower binding mutant. These changes are much smaller than might be anticipated considering the high macromolecular crowding within the cell. Single-cell analyses of association rate constants and fluorescence recovery after photobleaching reveals a naturally occurring variation in cell density, which is translated to an up to a twofold effect on binding rate constants. The data show that for this model protein interaction the intracellular environment had only a small effect on the association kinetics, justifying the extrapolation of in vitro data to processes in the cell.
Commodity durability, trader specialization, and market performance
Authors: Dickhaut John , Lin Shengle , Porter David , Smith Vernon
Published: January 2012

The original double auction studies of supply and demand markets established their strong efficiency and equilibrium convergence behavior using economically unsophisticated and untrained subjects. The results were unexpected because all individual costs and values were private and dependent entirely on the market trading process to aggregate the dispersed information into socially desirable outcomes. The exchange environment, however, corresponded to that of perishable, and not re-traded goods in which participants were specialized as buyers or sellers. We report experiments in repeated single-period markets where tradability, and buyer-seller role specialization, is varied by imposing or relaxing a restriction on re-trade within each period. In re-trade markets scope is given to speculative motives unavailable where goods perish on purchase. We observe greatly increased trade volume and decreased efficiency but subject experience increases efficiency. Observed speculation slows convergence by impeding the process whereby individuals learn from the market whether their private circumstances lead them to specialize as buyers or sellers.
Amphotericin primarily kills yeast by simply binding ergosterol
Authors: Gray Kaitlyn C. , Palacios Daniel S. , Dailey Ian , Endo Matthew M. , Uno Brice E. , Wilcock Brandon C. , Burke Martin D.
Published: January 2012

Amphotericin B (AmB) is a prototypical small molecule natural product that can form ion channels in living eukaryotic cells and has remained refractory to microbial resistance despite extensive clinical utilization in the treatment of life-threatening fungal infections for more than half a century. It is now widely accepted that AmB kills yeast primarily via channel-mediated membrane permeabilization. Enabled by the iterative cross-coupling-based synthesis of a functional group deficient derivative of this natural product, we have discovered that channel formation is not required for potent fungicidal activity. Alternatively, AmB primarily kills yeast by simply binding ergosterol, a lipid that is vital for many aspects of yeast cell physiology. Membrane permeabilization via channel formation represents a second complementary mechanism that further increases drug potency and the rate of yeast killing. Collectively, these findings (
i
) reveal that the binding of a physiologically important microbial lipid is a powerful and clinically validated antimicrobial strategy that may be inherently refractory to resistance, (
ii
) illuminate a more straightforward path to an improved therapeutic index for this clinically vital but also highly toxic antifungal agent, and (
iii
) suggest that the capacity for AmB to form protein-like ion channels might be separable from its cytocidal effects.
Syndecan-4 proteoliposomes enhance fibroblast growth factor-2 (FGF-2)–induced proliferation, migration, and neovascularization of ischemic muscle
Authors: Jang Eugene , Albadawi Hassan , Watkins Michael T. , Edelman Elazer R. , Baker Aaron B.
Published: January 2012

Ischemia of the myocardium and lower limbs is a common consequence of arterial disease and a major source of morbidity and mortality in modernized countries. Inducing neovascularization for the treatment of ischemia is an appealing therapeutic strategy for patients for whom traditional treatment modalities cannot be performed or are ineffective. In the past, the stimulation of blood vessel growth was pursued using direct delivery of growth factors, angiogenic gene therapy, or cellular therapy. Although therapeutic angiogenesis holds great promise for treating patients with ischemia, current methods have not found success in clinical trials. Fibroblast growth factor-2 (FGF-2) was one of the first growth factors to be tested for use in therapeutic angiogenesis. Here, we present a method for improving the biological activity of FGF-2 by codelivering the growth factor with a liposomally embedded coreceptor, syndecan-4. This technique was shown to increase FGF-2 cellular signaling, uptake, and nuclear localization in comparison with FGF-2 alone. Delivery of syndecan-4 proteoliposomes also increased endothelial proliferation, migration, and angiogenic tube formation in response to FGF-2. Using an animal model of limb ischemia, syndecan-4 proteoliposomes markedly improved the neovascularization following femoral artery ligation and recovery of perfusion of the ischemic limb. Taken together, these results support liposomal delivery of syndecan-4 as an effective means to improving the potential of using growth factors to achieve therapeutic neovascularization of ischemic tissue.
MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in
Medicago truncatula
Authors: Verdier Jerome , Zhao Jian , Torres-Jerez Ivone , Ge Shujun , Liu Chenggang , He Xianzhi , Mysore Kirankumar S. , Dixon Richard A. , Udvardi Michael K.
Published: January 2012

MtPAR (
Medicago truncatula
proanthocyanidin regulator) is an MYB family transcription factor that functions as a key regulator of proanthocyanidin (PA) biosynthesis in the model legume
Medicago truncatula
.
MtPAR
expression is confined to the seed coat, the site of PA accumulation. Loss-of-function
par
mutants contained substantially less PA in the seed coat than the wild type, whereas levels of anthocyanin and other specialized metabolites were normal in the mutants. In contrast, massive accumulation of PAs occurred when
MtPAR
was expressed ectopically in transformed hairy roots of
Medicago
. Transcriptome analysis of
par
mutants and
MtPAR
-expressing hairy roots, coupled with yeast one-hybrid analysis, revealed that MtPAR positively regulates genes encoding enzymes of the flavonoid–PA pathway via a probable activation of
WD40-1
. Expression of
MtPAR
in the forage legume alfalfa (
Medicago sativa
) resulted in detectable levels of PA in shoots, highlighting the potential of this gene for biotechnological strategies to increase PAs in forage legumes for reduction of pasture bloat in ruminant animals.
Reduction of dendritic spines and elevation of GABAergic signaling in the brains of mice treated with an estrogen receptor β ligand
Authors: Tan Xin-jie , Dai Yu-bing , Wu Wan-fu , Kim Hyun-Jin , Barros Rodrigo P. A. , Richardson Timothy I. , Yaden Benjamin C. , Warner Margaret , McKinzie David L. , Krishnan Venkatesh , Gustafsson Jan-Åke
Published: January 2012

An estrogen receptor (ER) β ligand (LY3201) with a preference for ERβ over ERα was administered in s.c. pellets releasing 0.04 mg/d. The brains of these mice were examined 3 d after treatment had begun. Although estradiol-17β is known to increase spine density and glutaminergic signaling, as measured by Golgi staining, a clear reduction in spines was evident on the dendritic branches in LY3201-treated mice but no morphological alteration and no difference in the number of dendritic spines on dendritic stems were observed. In the LY3201-treatment group, there was higher expression of glutamic acid decarboxylase (GAD) in layer V of cortex and in the CA1 of hippocampus, more GAD
+
terminals surrounding the pyramidal neurons and less glutamate receptor (NMDAR) on the neurons in layer V. There were no alterations in expression of Iba1 or in Olig2 or CNPase. However, GFAP
+
astrocytes were increased in the LY3201-treatment group. There were also more projections characteristic of activated astrocytes and increased expression of glutamine synthetase (GS). No expression of ERβ was detectable in the nuclei of astrocytes. Clearly, LY3201 caused a shift in the balance between excitatory and inhibitory neurotransmission in favor of inhibition. This shift was due in part to increased synthesis of GABA and increased removal of glutamate from the synaptic cleft by astrocytes. The data reveal that treatment with a selective ERβ agonist results in changes opposite to those reported in estradiol-17β–treated mice and suggests that ERα and ERβ play opposing roles in the brain.
A new construction of the asymptotic algebra associated to the 𝑞-Schur algebra
Authors: Brunat Olivier , Neunhöffer Max
Published: January 2012

We denote byAAthe ring of Laurent polynomials in the indeterminatevvand byKKits field of fractions. In this paper, we are interested in representation theory of the “generic”qq-Schur algebraSq(n,r)\mathcal {S}_q(n,r)overAA. We will associate to every symmetrising trace formτ\tauonKSq(n,r)K\mathcal {S}_q(n,r)a subalgebraJτ\mathcal {J}_{\tau }ofKSq(n,r)K\mathcal {S}_q(n,r)which is isomorphic to the “asymptotic” algebraJ(n,r)A\mathcal {J}(n,r)_Adefined by J. Du. As a consequence, we give a new hypothesis which implies James’ conjecture.
AnnTools: a comprehensive and versatile annotation toolkit for genomic variants
Authors: Makarov Vladimir , O'Grady Tina , Cai Guiqing , Lihm Jayon , Buxbaum Joseph D. , Yoon Seungtai
Published: January 2012

Summary: AnnTools is a versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions/deletions (INDEL) and structural variants/copy number variation (SV/CNV). The variants are interpreted by interrogating data compiled from 15 constantly updated sources. In addition to detailed functional characterization of the coding variants, AnnTools searches for overlaps with regulatory elements, disease/trait associated loci, known segmental duplications and artifact prone regions, thereby offering an integrated and comprehensive analysis of genomic data. The tool conveniently accepts user-provided tracks for custom annotation and offers flexibility in input data formats. The output is generated in the universal Variant Call Format. High annotation speed makes AnnTools suitable for high-throughput sequencing facilities, while a low-memory footprint and modest CPU requirements allow it to operate on a personal computer. The application is freely available for public use; the package includes installation scripts and a set of helper tools.

Availability:  http://anntools.sourceforge.net/

Contact:  vladimir.makarov@mssm.edu; chris.yoon@mssm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Statistical Analysis of List Experiments
Authors: Blair Graeme , Imai Kosuke
Published: January 2012

The validity of empirical research often relies upon the accuracy of self-reported behavior and beliefs. Yet eliciting truthful answers in surveys is challenging, especially when studying sensitive issues such as racial prejudice, corruption, and support for militant groups. List experiments have attracted much attention recently as a potential solution to this measurement problem. Many researchers, however, have used a simple difference-in-means estimator, which prevents the efficient examination of multivariate relationships between respondents' characteristics and their responses to sensitive items. Moreover, no systematic means exists to investigate the role of underlying assumptions. We fill these gaps by developing a set of new statistical methods for list experiments. We identify the commonly invoked assumptions, propose new multivariate regression estimators, and develop methods to detect and adjust for potential violations of key assumptions. For empirical illustration, we analyze list experiments concerning racial prejudice. Open-source software is made available to implement the proposed methodology.
Is more better? Polyploidy and parasite resistance
Authors: King K. C. , Seppälä O. , Neiman M.
Published: January 2012

Ploidy-level variation is common and can drastically affect organismal fitness. We focus on the potential consequences of this variation for parasite resistance. First, we elucidate connections between ploidy variation and key factors determining resistance, including allelic diversity, gene expression and physiological condition. We then argue that systems featuring both natural and artificially manipulated ploidy variation should be used to evaluate whether ploidy level influences host–parasite interactions.
On the rigorous foundations of the Fokas method for linear elliptic partial differential equations
Authors: Ashton A. C. L.
Published: January 2012

In this paper, we address some of the rigorous foundations of the Fokas method, confining attention to boundary value problems for linear elliptic partial differential equations on bounded convex domains. The central object in the method is the global relation, which is an integral equation in the spectral Fourier space that couples the given boundary data with the unknown boundary values. Using techniques from complex analysis of several variables, we prove that a solution to the global relation provides a solution to the corresponding boundary value problem, and that the solution to the global relation is unique. The result holds for any number of spatial dimensions and for a variety of boundary value problems.
Pathogenicity of a natural reassortant hantavirus CGRn9415 in newborn rats and newborn mice
Authors: Chen Xiao-Ping , Yu Juan , Li Ming-Hui , Zhao Gao-Yu , Wang Wen , Guo Wen-Ping , Deng Xiao-Zhao , Zhang Yun , Fu Zhen F. , Qin Xin-Cheng , Zhang Yong-Zhen
Published: January 2012

To better understand the pathogenicity and infectivity of a natural reassortant CGRn9415 generated from Hantaan virus (HTNV) and Seoul virus (SEOV), CGRn9415, HTNV 76–118 and SEOV L99 were used to infect newborn Kunming (KM) mice and newborn Wistar rats. In KM mice, there was no statistical difference between the death rate with CGRn9415 and that of L99, while 76–118 killed all mice even at low dosage; CGRn9415 killed all infected rats similar to L99 at the dosage of 105 f.f.u., while no death occurred in rats infected with 76–118 even as high as 2×105 f.f.u., suggesting that the reassortant CGRn9415 possesses similar pathogenicity as L99. Furthermore, the reassortant CGRn9415 could establish a persistent infection in both KM mice and Wistar rats more easily than 76–118 or L99. These data suggest that the reassorted hantavirus behaves more like SEOV as far as the pathogenicity is concerned.
Routes to the Tonoplast: The Sorting of Tonoplast Transporters in Arabidopsis Mesophyll Protoplasts
Authors: Wolfenstetter Susanne , Wirsching Petra , Dotzauer Dorina , Schneider Sabine , Sauer Norbert
Published: January 2012

Vacuoles perform a multitude of functions in plant cells, including the storage of amino acids and sugars. Tonoplast-localized transporters catalyze the import and release of these molecules. The mechanisms determining the targeting of these transporters to the tonoplast are largely unknown. Using the paralogous Arabidopsis thaliana inositol transporters INT1 (tonoplast) and INT4 (plasma membrane), we performed domain swapping and mutational analyses and identified a C-terminal di-leucine motif responsible for the sorting of higher plant INT1-type transporters to the tonoplast in Arabidopsis mesophyll protoplasts. We demonstrate that this motif can reroute other proteins, such as INT4, SUCROSE TRANSPORTER2 (SUC2), or SWEET1, to the tonoplast and that the position of the motif relative to the transmembrane helix is critical. Rerouted INT4 is functionally active in the tonoplast and complements the growth phenotype of an int1 mutant. In Arabidopsis plants defective in the β-subunit of the AP-3 adaptor complex, INT1 is correctly localized to the tonoplast, while sorting of the vacuolar sucrose transporter SUC4 is blocked in cis-Golgi stacks. Moreover, we demonstrate that both INT1 and SUC4 trafficking to the tonoplast is sensitive to brefeldin A. Our data show that plants possess at least two different Golgi-dependent targeting mechanisms for newly synthesized transporters to the tonoplast.