bluuebunny/crossref_metadata_2025 huggingface dataset:
Vegetated mixing layer around a finite‐size patch of submerged plants: 1. Theory and field experiments
Authors: Sukhodolova Tatiana A. , Sukhodolov Alexander N.
Published: September 2012

Dynamics of a vegetated mixing layer around a patch of submerged plants was examined theoretically and experimentally in a lowland river. Theoretical analysis explored analogy with hydrodynamic mixing layers and introduced equations that describe expansion of the layers and alterations in mean flow. Field experiments provided empirical data for validation of the theory and examination of the effects of population density on the mixing layer dynamics. Detailed measurements assessed the structure of turbulent flow, plant morphology, biomechanical properties, bending, and streamlining due to interaction with the flow. The theory was compared with the field experiments and an agreement was concluded. It was found that near the upstream edge of the patch, the vegetated mixing layer expands similar to the canonical mixing layers, although its statistics scale on the velocity differential characteristic for the stabilized part. Downstream mean momentum flux reduces in magnitude and reverses in direction, while turbulence became dominant. This was observed to stabilize the velocity differential and increase the mean velocity of the layer that result in its limited growth described by a logarithmic function. The population density of vegetation was found to control the flow. In dense vegetation, the analogy with mixing layers resembled best, while in sparse vegetation, the flow behaved similar to the boundary layers. This theory can be used for quantitative assessment of seasonal effects in natural vegetated rivers because the population density of vegetation varies during the vegetation season. The companion paper focuses on the structural properties of turbulence in the vegetated shear layers.
Effect of smectite dehydration on pore water geochemistry in the shallow subduction zone: An experimental approach
Authors: Hüpers A. , Kopf A. J.
Published: September 2012

The diagenetic smectite to illite transition is widely accepted to cause ubiquitous pore water freshening at convergent margins. However, experimental consolidation tests show that smectite also dehydrates partially with increasing effective stress. To shed light on this process three hydrothermal consolidation tests on a silty smectite‐rich claystone were conducted with stresses (P) up to 70 MPa and at constant temperatures (T) of 20°C, 60°C and 100°C. Fluids expelled during the tests were analyzed for major and trace elements to evaluate dehydration and fluid‐rock interaction with increasing PT conditions. The results document that fluid freshening starts when the effective stress exceeds 1.3 MPa. The smectite interlayer water content decreases from 27 wt‐% to ∼20 wt‐% during the experiments, which is equivalent to an interlayer collapse from 18.5 to ∼15.4 Å. The released interlayer H20 accounts for up to 17% of the total fluid volume released from the consolidating sediment. Major and volatile element geochemistry is influenced by temperature and smectite interlayer collapse. The interlayer collapse is characterized by K and Ca uptake while is B released from smectite. Application of experimental results to the Barbados accretionary margin shows that stress dependent smectite dehydration is an important fluid source mechanism and accounts for substantial fluid freshening. Modeled smectite dehydration suggests a decrease of smectite interlayer water content from 27 wt‐% at the surface down to ∼22 wt‐% at 2 km depth. This leads to chlorinity values as low as 460 mM.
The impact of the El Niño‐Southern Oscillation on maximum temperature extremes
Authors: Arblaster Julie M. , Alexander Lisa V.
Published: September 2012

The impact of the El Niño‐Southern Oscillation (ENSO) on temperature extremes is examined in both observations and coupled climate model simulations. HadEX2, a newly developed observed gridded dataset of climate extremes indices shows marked contrasts in seasonal composites of the monthly maximum value of daily maximum temperature during the cold and warm phases of ENSO. Extreme maximum temperatures are significantly cooler over Australia, southern Asia, Canada and South Africa during strong La Niña events compared to El Niño events and significantly warmer over the contiguous United States and southern South America. Two climate models are contrasted for their ability to capture these relationships given their very different simulations of ENSO. While both models capture some aspects of the observed patterns, the fidelity of the ENSO simulation appears to be crucial for simulating the magnitude and sign of the extreme maximum temperature relationships. The impact of future climate change on these patterns is also investigated.
Is cumulus convection the concertmaster of tropical cyclone activity in the Atlantic?
Authors: Stan Cristiana
Published: September 2012

The influence of the cloud representation in global climate models on the accuracy of the North Atlantic tropical cyclone simulations is investigated. The North Atlantic tropical cyclone activity is simulated with a standard climate model, CCSM. The conventional parameterization of cloud processes in CCSM is replaced by the “super‐parameterization” and the simulation is run again. The comparison of tropical cyclone statistics reveals that the model with explicit representation of cloud processes produces a larger number of events, with stronger intensity and longer life‐cycle. The results show that clouds have a significant impact on the mechanisms associated with tropical cyclone activity such as surface temperature and ocean subsurface processes, vertical wind shear, and the transport of moisture in the lower troposphere.
Dipolarization fronts and associated auroral activities: 1. Conjugate observations and perspectives from global MHD simulations
Authors: Ge Y. S. , Zhou X.‐Z. , Liang J. , Raeder J. , Gilson M. L. , Donovan E. , Angelopoulos V. , Runov A.
Published: September 2012

Earthward‐propagating dipolarization fronts (DFs) are often found to be associated with magnetic reconnection and bursty bulk flows (BBFs) in the magnetotail. Recent THEMIS (Time History of Events and Macroscale Interactions During Substorms) probe observations have shown a DF propagating over 10REfrom the mid‐tail region to the near‐Earth tail region, and THEMIS All‐Sky Imager data show a north‐south auroral form and intensification of westward auroral zone currents. In this study, we examine THEMIS in situ observations of DFs in the magnetotail and simultaneous observations of the proton aurora from ground‐based CANOPUS (the Canadian Auroral Network for the OPEN Program Unified Study) Meridian Scanning Photometers (MSPs). We find that earthward‐moving DFs are often associated with intensification of proton aurora when the THEMIS probes are conjugate to the meridian of the MSP. The proton auroral intensifications are transient and in some cases detached from the background proton precipitation. Just before the DFs, the ion distribution is anisotropic in the field‐aligned direction (mostly earthward) and the ion energy increases. These observations suggest that plasma sheet protons can be reflected and energized by earthward‐moving DFs as they propagate through the magnetotail. We postulate that this population of ions is the source of the proton auroral intensification observed on the ground. This conjecture is tested using our global MHD simulation results, where the proton precipitation is calculated with the field‐line curvature (FLC) model. The MHD simulation results show that proton precipitation enhancement can be caused by compression of plasma by approaching DFs/BBFs, which is consistent with ion reflection at DFs. Thus, using the conjugate observations from THEMIS spacecraft and MSP in this study, we are able to directly link the magnetotail dynamics, i.e., dipolarization fronts, with ground auroral activities. However, understanding of DF‐associated ion energization requires detailed test‐particle simulations with an analytical magnetotail model, such as those in our companion paper.
Electron source associated with dipolarization at the outer boundary of the radiation belts: Non‐storm cases
Authors: Lui A. T. Y. , Zong Q.‐G. , Wang C. , Dunlop M. W.
Published: September 2012

We examine the strength of the electron source associated with dipolarization at the outer boundary of the radiation belts using multisatellite observations from THEMIS. This topic is relevant to the determination on the relative roles of inward radial diffusion versus internal local acceleration for the origin of the relativistic electrons in the outer radiation belt. We focus on the electron phase space density (PSD) as a function of the first adiabatic invariant (μ) for equatorially mirroring population over a broad energy range. It is found that the source strength associated with dipolarization for non‐storm periods at the outer boundary of the radiation belts can be well above the observed fluxes of relativistic electrons inside the outer radiation belt. The PSD change due to the magnetic field strength variation dominates over PSD change from the energy flux increase with dipolarization, resulting in a strong anticorrelation between magnetic field strength and PSD values at a given μ. If observations from closely spaced satellites during the same event can be used to indicate radial transport of electrons with dipolarization, then the observed PSD at these satellites indicates frequent occurrence of non‐adiabatic process during their radial transport.
Azimuthal anisotropy of Lg attenuation in eastern Tibetan Plateau
Authors: Bao Xueyang , Sandvol Eric , Chen Yongshun John , Ni James , Hearn Thomas , Shen Yang
Published: September 2012

The Q of seismic phase Lg is measured to approach the crustal Qβ, which can be used to infer crustal rheology. A reverse two‐station/event method is used to measure the interstationQLg, which theoretically eliminates effects from the source and site response. Strong azimuthal anisotropy of 1/QLg in northern Tibet is observed, which approximately correlates with the seismic velocity anisotropy observed using both surface waves and teleseismic S waves. Both the intrinsic and scattering attenuation contribute the isotropic Q, whereas the anisotropic Q may be associated with the fractures and faults in the crust. Strong 1/QLgis observed in the northwestern Songpan‐Ganzi fold belt, where the high‐Qdirections correspond with the orientations of major strike‐slip faults. Intrinsic and scatteringQ values are estimated for different tectonic terranes in eastern Tibetan Plateau. The intrinsic Qvalues are approximately 500 in the northern Tibetan Plateau, which suggests a hot (∼700°C) crust, consistent with low seismic velocity measurements. Our result suggests that the crust of northwestern Songpan‐Ganzi fold belt may be hotter than that of the Qiangtang terrane, which may be related to the strain heating along the major strike slip fault zones that dominate the northernmost Tibet.
Improving sea level reconstructions using non‐sea level measurements
Authors: Hamlington B. D. , Leben R. R. , Kim K.‐Y.
Published: September 2012

We present a new method for reconstructing sea level involving cyclostationary empirical orthogonal functions (CSEOFs). While we show results from a CSEOF reconstruction using basis functions computed from satellite altimetry and subsequently fit to tide gauge data, our focus is on how other ocean observations such as sea surface temperature can be leveraged to create an improved reconstructed sea level data set spanning the time period from 1900 to present. Basis functions are computed using satellite measurements of sea surface temperature, and using a simple regression technique, these basis functions are transformed to represent a similar temporal evolution to corresponding satellite altimeter‐derived sea level basis functions. The resulting sea level and sea surface temperature basis functions are fit to tide gauge data and historical sea surface temperature data, respectively, to produce a reconstructed sea level data set spanning the period from 1900 to present. We demonstrate the use of this reconstructed data set for climate monitoring, focusing primarily on climate signals in the Pacific Ocean. The CSEOF reconstruction technique can be used to create indices computed solely from sea level measurements for monitoring signals such as the eastern Pacific (EP) El Niño–Southern Oscillation (ENSO), central Pacific (CP) ENSO, and Pacific Decadal Oscillation (PDO). The EP ENSO, CP ENSO, and PDO signals are all well represented in the CSEOF reconstruction relying solely on sea level measurements from 1950 to present; however, significant improvement can be made in reconstructing these signals during the first half of the twentieth century by including sea surface temperature measurements in the sea level reconstruction procedure.
Ocean temperature variability for the past 60 years on the Norwegian‐Svalbard margin influences gas hydrate stability on human time scales
Authors: Ferré Bénédicte , Mienert Jürgen , Feseker Tomas
Published: September 2012

The potential impact of future climate change on methane release from oceanic gas hydrates is the subject of much debate. We analyzed World Ocean Database quality controlled data on the Norwegian‐Svalbard continental margin from the past 60 years to evaluate the potential effect of ocean temperature variations on continental margin gas hydrate reservoirs. Bottom water temperatures in the Norwegian‐Svalbard margin were subject to significant cooling until 1980 (by ∼2°C offshore NW‐Svalbard and in the Barents Sea) followed by a general bottom water temperature increase until 2010 (∼0.3°C in deep‐water areas offshore NW‐Svalbard and mid‐Norwegian margin and ∼2°C in the shallow areas of the Barents Sea and Prins Karls Forland). Bottom water warming in the shallow outer shelf areas triggered the Gas Hydrate Stability Zone (GHSZ) retreat toward upper continental slope areas, potentially increasing methane release due to gas hydrate dissociation. GHSZ responses to temperature changes on human time scales occur exclusively in shallow water and only if near‐surface gas hydrates exist. The responses are associated with a short time lag of less than 1 year. Temperatures in the bottom water column seem to be partly regulated by the North Atlantic Oscillation (NAO), with positive NAO associated with warm phases. However, cooling events in the surface water offshore NW‐Svalbard might be associated with El Niño events of 1976–1977, 1986–1987 and 1997–1998 in the Pacific. Such ocean cooling, if long enough, may delay ocean temperature driven gas hydrate dissociation and potential releases of methane to the ocean.
Potential for bias in 21st century semiempirical sea level projections
Authors: Jevrejeva S. , Moore J. C. , Grinsted A.
Published: September 2012

We examine the limitations of a semiempirical model characterized by a sea level projection of 73 cm with RCP4.5 scenario by 2100. Calibrating the model with data to 1990 and then simulating the period 1993–2009 produces sea level in close agreement with acceleration in sea level rise observed by satellite altimetry. Nonradiative forcing contributors, such as long‐term adjustment of Greenland and Antarctica ice sheets since Last Glacial Maximum, abyssal ocean warming, and terrestrial water storage, may bias model calibration which, if corrected for, tend to reduce median sea level projections at 2100 by 2–10 cm, though this is within the confidence interval. We apply the semiempirical approach to simulate individual contributions from thermal expansion and small glacier melting. Steric sea level projections agree within 3 cm of output from process‐based climate models. In contrast, semiempirical simulation of melting from glaciers is 26 cm, which is twice large as estimates from some process‐based models; however, all process models lack simulation of calving, which likely accounts for 50% of small glacier mass loss worldwide. Furthermore, we suggest that changes in surface mass balance and dynamics of Greenland ice sheet made contributions to the sea level rise in the early 20th century and therefore are included within the semiempirical model calibration period and hence are included in semiempirical sea level projections by 2100. Antarctic response is probably absent from semiempirical models, which will lead to a underestimate in sea level rise if, as is probable, Antarctica loses mass by 2100.
Improving the accuracy of SO2column densities and emission rates obtained from upward‐looking UV‐spectroscopic measurements of volcanic plumes by taking realistic radiative transfer into account
Authors: Kern Christoph , Deutschmann Tim , Werner Cynthia , Sutton A. Jeff , Elias Tamar , Kelly Peter J.
Published: September 2012

Sulfur dioxide (SO2) is monitored using ultraviolet (UV) absorption spectroscopy at numerous volcanoes around the world due to its importance as a measure of volcanic activity and a tracer for other gaseous species. Recent studies have shown that failure to take realistic radiative transfer into account during the spectral retrieval of the collected data often leads to large errors in the calculated emission rates. Here, the framework for a new evaluation method which couples a radiative transfer model to the spectral retrieval is described. In it, absorption spectra are simulated, and atmospheric parameters are iteratively updated in the model until a best match to the measurement data is achieved. The evaluation algorithm is applied to two example Differential Optical Absorption Spectroscopy (DOAS) measurements conducted at Kīlauea volcano (Hawaii). The resulting emission rates were 20 and 90% higher than those obtained with a conventional DOAS retrieval performed between 305 and 315 nm, respectively, depending on the different SO2 and aerosol loads present in the volcanic plume. The internal consistency of the method was validated by measuring and modeling SO2absorption features in a separate wavelength region around 375 nm and comparing the results. Although additional information about the measurement geometry and atmospheric conditions is needed in addition to the acquired spectral data, this method for the first time provides a means of taking realistic three‐dimensional radiative transfer into account when analyzing UV‐spectral absorption measurements of volcanic SO2 plumes.
Influence of large scale oscillations on upwelling‐favorable coastal wind off central Chile
Authors: Rahn David A.
Published: September 2012

Along the central coast of Chile is typically equatorward, upwelling‐favorable wind associated with the southeast Pacific anticyclone. A coastal low‐level jet often develops, and its wind speed is mostly controlled by the meridional pressure gradient. While the low‐level jet is a mesoscale feature forced by an interaction between synoptic conditions and coastal topography, regional sea level pressure anomalies are associated with changes of the Antarctic, Madden Julian, and El Niño–Southern Oscillation. The connection between the alongshore wind and changes to the large‐scale circulation is examined and quantified using 31 years of the Climate Forecast System Reanalysis, which resolves coastal features better than previous, coarser analyses. Composites based on each index reveal the modulation of the sea level pressure and significant alongshore wind anomalies of ±0.5–1.5 m s−1 that correlate well to meridional surface pressure gradient changes and are centered near 35°S. Constructive and destructive interference exists between the three indices that either enhance or cancel the alongshore wind anomaly. During favorable upwelling conditions the distribution of meridional wind is generally clustered around positive anomalies with a tail toward negative values, representing a stronger and persistent anticyclone. During unfavorable upwelling conditions the anomalies are generally more normally distributed, representing a weaker anticyclone and the passage of more cyclones.
Human cystathionine β-synthase (CBS) contains two classes of binding sites for S-adenosylmethionine (SAM): complex regulation of CBS activity and stability by SAM
Authors: Pey Angel L. , Majtan Tomas , Sanchez-Ruiz Jose M. , Kraus Jan P.
Published: September 2012

CBS (cystathionine β-synthase) is a multidomain tetrameric enzyme essential in the regulation of homocysteine metabolism, whose activity is enhanced by the allosteric regulator SAM (S-adenosylmethionine). Missense mutations in CBS are the major cause of inherited HCU (homocystinuria). In the present study we apply a novel approach based on a combination of calorimetric methods, functional assays and kinetic modelling to provide structural and energetic insight into the effects of SAM on the stability and activity of WT (wild-type) CBS and seven HCU-causing mutants. We found two sets of SAM-binding sites in the C-terminal regulatory domain with different structural and energetic features: a high affinity set of two sites, probably involved in kinetic stabilization of the regulatory domain, and a low affinity set of four sites, which are involved in the enzyme activation. We show that the regulatory domain displays a low kinetic stability in WT CBS, which is further decreased in many HCU-causing mutants. We propose that the SAM-induced stabilization may play a key role in modulating steady-state levels of WT and mutant CBS in vivo. Our strategy may be valuable for understanding ligand effects on proteins with a complex architecture and their role in human genetic diseases and for the development of novel pharmacological strategies.
Small dense LDL is more susceptible to glycation than more buoyant LDL in Type 2 diabetes
Authors: Younis Nahla N. , Soran Handrean , Pemberton Philip , Charlton-Menys Valentine , Elseweidy Mohamed M. , Durrington Paul N.
Published: September 2012

Glycation of apoB (apolipoprotein B) of LDL (low-density lipoprotein) increases its atherogenicity. Concentrations of both serum glyc-apoB (glycated apoB) and SD-LDL (small dense LDL) (syn LDL3; D=1.044–1.063 g/ml) are increased in diabetes and are closely correlated. We studied whether SD-LDL is more susceptible to glycation in vitro than more buoyant LDL in statin- and non-statin-treated Type 2 diabetes mellitus. Serum SD-LDL apoB and glyc-apoB on statins was 20±2 (means±S.D.) and 3.6±0.41 compared with 47±3 and 5.89±0.68 mg/dl in those not receiving statins (P<0.001 and <0.01, respectively). There was a dose-dependent increase in glycation on incubation of LDL subfractions with glucose, which was accompanied by an increase in LPO (lipid peroxide) and electrophoretic mobility and a decrease in free amino groups. SD-LDL was more susceptible to these changes than more buoyant LDL. Both SD-LDL and more buoyant LDL from statin-treated patients were less susceptible to glycation. There were fewer free amino groups on LDL subfractions from statin-treated patients, which may contribute to this resistance. In conclusion, greater susceptibility of SD-LDL to glycation is likely to contribute to the raised levels of circulating glyc-apoB in diabetes. Statins are associated with lower levels of both SD-LDL and glyc-apoB.
Perspectives From General Education Teachers, Students and Their Parents: Including Students With Robust Communication Devices in General Education Classrooms
Authors: Kramlich Christine
Published: September 2012

Teachers face a number of challenges with regard to including students, but especially when including those who have complex communication needs and use speech-generating devices (SGDs). Parents are interested in collaborating with teachers, but may find themselves with differing opinions than school and staff. Students using SGDs want to be part of the class, not just physically in the classroom. Finding ways to communicate and work together is critical to overcoming these challenges and facilitating inclusion. In this process, it is important to consider the perspectives of the general education teacher, the parent of the student using the SGD, classmates, and, most important, the student using the SGD.
Making It A Reality: Using Standards-Based General Education Science and Math Curriculum To Teach Vocabulary and Language Structures to Students Who Use AAC
Authors: Boruta Michele Caputo , Bidstrup Kara
Published: September 2012

Students who use AAC to access vocabulary and language typically receive much of their language intervention in a classroom environment. Given this, it is important to teach emerging vocabulary and language concepts as well as academic content when delivering curriculum to students who use AAC. In this article, we will focus on identifying the language level of the student, providing him or her with a linguistically based AAC system, and delivering language intervention within the context of standards-based science and math curriculum. In addition, we will show how a standards-based science and math curriculum can serve as an excellent platform for language instruction. We will also discuss and demonstrate backwards planning as a method to create authentic and meaningful lessons for students who use AAC. The sample lessons will include a national standard, that standard reframed into an appropriate language target, assessment tools, strategies for teaching and learning, and an instructional activity and materials.
Providing School-Based Speech-Language Therapy Services by Telepractice: A Brief Tutorial
Authors: Grogan-Johnson Sue
Published: September 2012

Speech-language pathologists (SLPs) are increasingly turning to technologies such as the Internet and videoconferencing for service provision (Dudding & Justice, 2004). Many school-based SLPs are recognizing the potential applications of telepractice for students with communication impairments, but may be uncertain about how to put telepractice into action. The purpose of this article is to describe one approach to implementing telepractice in the public school setting.
Complexity of Images: Experimental and Computational Estimates Compared
Authors: Chikhman Valeriy , Bondarko Valeriya , Danilova Marina , Goluzina Anna , Shelepin Yuri
Published: September 2012

We tested whether visual complexity can be modeled through the use of parameters relevant to known mechanisms of visual processing. In psychophysical experiments observers ranked the complexity of two groups of stimuli: 15 unfamiliar Chinese hieroglyphs and 24 outline images of well-known common objects. To predict image complexity, we considered: (i) spatial characteristics of the images, (ii) spatial-frequency characteristics, (iii) a combination of spatial and Fourier properties, and (iv) the size of the image encoded as a JPEG file. For hieroglyphs the highest correlation was obtained when complexity was calculated as the product of the squared spatial-frequency median and the image area. This measure accounts for the larger number of lines, strokes, and local periodic patterns in the hieroglyphs. For outline objects the best predictor of the experimental data was complexity estimated as the number of turns in the image, as Attneave (1957 Journal of Experimental Psychology53 221–227) obtained for his abstract outlined images. Other predictors of complexity gave significant but lower correlations with the experimental ranking. We conclude that our modeling measures can be used to estimate the complexity of visual images but for different classes of images different measures of complexity may be required.
Studies of the Angular Function of a Duncker-Type Induced Motion Illusion
Authors: Farrell-Whelan Max , Wenderoth Peter , Wiese Mark
Published: September 2012

Duncker (1929/1955, Source Book of Gestalt Psychology, pp 161–172) demonstrated a laboratory version of induced motion. He showed that, when a stationary spot of light in a dark laboratory is enclosed in an oscillating rectangular frame, the frame is perceived as stationary and the dot appears to move in the direction opposite the true motion of the frame. Zivotofsky (2004, Investigative Ophthalmology & Visual Science45 2867–2872) studied a more complex variant of the Duncker illusion, in which both the inducing and the test stimuli moved: a single red test dot moved horizontally left or right while a dense background set of black dots on a white background moved vertically up or down. When the background inducing dots moved up (down), the truly horizontally translating test dot appeared to drift at an angle down (up) from the horizontal. In experiment 1, we used two methods to measure the complete angular function of the Zivotofsky effect and found it to peak with an inducer-test direction separation of approximately 30°, similar to the inducing angle that has been found to maximise other direction illusions. Experiment 2 tested and confirmed predictions regarding the effects of relative test and inducer speeds based on the vectorial subtraction of the inducing velocity from the test velocity.
The Composite-Face Effect Survives Asymmetric Face Distortions
Authors: de Heering Adélaïde , Wallis Jessica , Maurer Daphne
Published: September 2012

In two experiments, we investigated whether adults use holistic processing even for faces that are grossly distorted because their eyes have been moved asymmetrically to violate the common layout of a face (distorting its first-order relations). To this end we used a compelling demonstration that faces are processed as wholes, the composite-face effect. Specifically, adults judged the similarity of sequentially presented top halves of normal (original condition) and distorted faces with one eye (one-eye condition) or two eyes (two-eyes condition) shifted up by an abnormal amount. Trials were either blocked by type of distortion (experiment 1) or intermixed within the experiment (experiment 2). In both experiments, participants demonstrated a composite-face effect of the same magnitude in the three conditions, a pattern suggesting that they processed holistically even faces whose first-order relations were violated.
Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits
Authors: Hill Sean L. , Wang Yun , Riachi Imad , Schürmann Felix , Markram Henry
Published: September 2012

It is well-established that synapse formation involves highly selective chemospecific mechanisms, but how neuron arbors are positioned before synapse formation remains unclear. Using 3D reconstructions of 298 neocortical cells of different types (including nest basket, small basket, large basket, bitufted, pyramidal, and Martinotti cells), we constructed a structural model of a cortical microcircuit, in which cells of different types were independently and randomly placed. We compared the positions of physical appositions resulting from the incidental overlap of axonal and dendritic arbors in the model (statistical structural connectivity) with the positions of putative functional synapses (functional synaptic connectivity) in 90 synaptic connections reconstructed from cortical slice preparations. Overall, we found that statistical connectivity predicted an average of 74 ± 2.7% (mean ± SEM) synapse location distributions for nine types of cortical connections. This finding suggests that chemospecific attractive and repulsive mechanisms generally do not result in pairwise-specific connectivity. In some cases, however, the predicted distributions do not match precisely, indicating that chemospecific steering and aligning of the arbors may occur for some types of connections. This finding suggests that random alignment of axonal and dendritic arbors provides a sufficient foundation for specific functional connectivity to emerge in local neural microcircuits.
Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells
Authors: Ruiz Sergio , Diep Dinh , Gore Athurva , Panopoulos Athanasia D. , Montserrat Nuria , Plongthongkum Nongluk , Kumar Sachin , Fung Ho-Lim , Giorgetti Alessandra , Bilic Josipa , Batchelder Erika M. , Zaehres Holm , Kan Natalia G. , Schöler Hans Robert , Mercola Mark , Zhang Kun , Izpisua Belmonte Juan Carlos
Published: September 2012

Generation of human induced pluripotent stem cells (hiPSCs) by the expression of specific transcription factors depends on successful epigenetic reprogramming to a pluripotent state. Although hiPSCs and human embryonic stem cells (hESCs) display a similar epigenome, recent reports demonstrated the persistence of specific epigenetic marks from the somatic cell type of origin and aberrant methylation patterns in hiPSCs. However, it remains unknown whether the use of different somatic cell sources, encompassing variable levels of selection pressure during reprogramming, influences the level of epigenetic aberrations in hiPSCs. In this work, we characterized the epigenomic integrity of 17 hiPSC lines derived from six different cell types with varied reprogramming efficiencies. We demonstrate that epigenetic aberrations are a general feature of the hiPSC state and are independent of the somatic cell source. Interestingly, we observe that the reprogramming efficiency of somatic cell lines inversely correlates with the amount of methylation change needed to acquire pluripotency. Additionally, we determine that both shared and line-specific epigenetic aberrations in hiPSCs can directly translate into changes in gene expression in both the pluripotent and differentiated states. Significantly, our analysis of different hiPSC lines from multiple cell types of origin allow us to identify a reprogramming-specific epigenetic signature comprised of nine aberrantly methylated genes that is able to segregate hESC and hiPSC lines regardless of the somatic cell source or differentiation state.
Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5′ processing
Authors: Howard Michael J. , Lim Wan Hsin , Fierke Carol A. , Koutmos Markos
Published: September 2012

Ribonuclease P (RNase P) catalyzes the maturation of the 5′ end of tRNA precursors. Typically these enzymes are ribonucleoproteins with a conserved RNA component responsible for catalysis. However, protein-only RNase P (PRORP) enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of
Arabidopsis thaliana
. PRORP enzymes are nuclear encoded and conserved among many eukaryotes, having evolved recently as yeast mitochondrial genomes encode an RNase P RNA. Here we report the crystal structure of PRORP1 from
A. thaliana
at 1.75 Å resolution, revealing a prototypical metallonuclease domain tethered to a pentatricopeptide repeat (PPR) domain by a structural zinc-binding domain. The metallonuclease domain is a unique high-resolution structure of a Nedd4-BP1, YacP Nucleases (NYN) domain that is a member of the PIN domain-like fold superfamily, including the FLAP nuclease family. The structural similarity between PRORP1 and the FLAP nuclease family suggests that they evolved from a common ancestor. Biochemical data reveal that conserved aspartate residues in PRORP1 are important for catalytic activity and metal binding and that the PPR domain also enhances activity, likely through an interaction with pre-tRNA. These results provide a foundation for understanding tRNA maturation in organelles. Furthermore, these studies allow for a molecular-level comparison of the catalytic strategies used by the only known naturally evolved protein and RNA-based catalysts that perform the same biological function, pre-tRNA maturation, thereby providing insight into the differences between the prebiotic RNA world and the present protein-dominated world.
Stream Conductivity: Relationships to Land Use, Chloride, and Fishes in Maryland Streams
Authors: Morgan Raymond P. , Kline Kathleen M. , Kline Matthew J. , Cushman Susan F. , Sell Matthew T. , Weitzell Roy E. , Churchill John B.
Published: September 2012

Stream conductivity reflects both landscape and anthropogenic interactions, although increasing chloride inputs from road salt in eastern North America is also important. Employing a spatially extensive database derived from the Maryland Biological Stream Survey (MBSS), we examined relationships of stream conductivity to landscape attributes and determined relationships between stream MBSS fish metrics, abundance, and biomass as well as fish assemblages by means of conductivity (as a chloride surrogate) to estimate potential effects. Background stream conductivity for the MBSS strata and Maryland L3 ecoregions ranged from 51 to 150 μS/cm, with the Piedmont having the highest background conductivity (145–160 μS/cm). For MBSS sites there were strong relationships of stream conductivity and chloride with both impervious surface and road density, and 0.26% of the MBSS sites exceeded the U.S. Environmental Protection Agency's acute chloride criterion and 1.5% the chronic chloride criterion. For the Maryland Piedmont species assemblage, observed conductivity values between 230 and 540 μS/cm caused important alterations in the biotic community as measured by the series of fish metrics, and thus affected fish species assemblages associated with chloride concentrations between 33 and 108 mg/L. Maryland coastal, coldwater, and highland species assemblages displayed variable responses of conductivity to fish metrics, abundance, and biomass. If regional conductivity and chloride levels continue to increase or remain high from road deicing owing to an increase in urbanization in a watershed or climatic changes, differences in stream fish assemblages and therefore fish diversity may become more apparent. Because of the linkage between salt usage and impervious road surfaces resulting from urbanization, it is important to manage effectively the use of road salt to protect biotic resources.

Received January 24, 2012; accepted June 5, 2012
Weak Fubini property and infinity harmonic functions in Riemannian and sub-Riemannian manifolds
Authors: Dragoni Federica , Manfredi Juan , Vittone Davide
Published: September 2012

We examine the relationship between infinity harmonic functions, absolutely minimizing Lipschitz extensions, strong absolutely minimizing Lipschitz extensions, and absolutely gradient minimizing extensions in Carnot-Carathéodory spaces. Using the weak Fubini property we show that absolutely minimizing Lipschitz extensions are infinity harmonic in any sub-Riemannian manifold.
Quality of life and survival in patients with heart failure
Authors: Hoekstra Tialda , Jaarsma Tiny , van Veldhuisen Dirk J. , Hillege Hans L. , Sanderman Robbert , Lesman‐Leegte Ivonne
Published: September 2012

Aims

To examine whether self‐rated disease‐specific and generic quality of life predicts long‐term mortality, independent of brain natriuretic peptide (BNP) levels, and to explore factors related to low quality of life in a well‐defined heart failure (HF) population.

Methods and results

A cohort of 661 patients (62% male; age 71 years; left ventricular ejection fraction 34%) was followed prospectively for 3 years. Quality of life questionnaires (Ladder of Life, RAND36, and Minnesota Living with Heart Failure Questionnaire) and BNP levels were assessed at discharge after a hospital admission for HF. Three‐year mortality was 42%. After adjustment for demographic variables, clinical variables, and BNP levels, poor quality of life scores predicted higher mortality; per 10 units on the physical functioning [hazard ratio (HR) 1.08, 95% confidence interval (CI) 1.02–1.14] and general health (HR 1.08, 95% CI 1.01–1.16) dimensions of the RAND36. Patients with low scores on these dimensions were more likely to be in New York Heart Association class III–IV, diagnosed with co‐morbidities, have suffered longer from HF, have lower estimated glomerular filtration rates, and have fewer beta‐blocker prescriptions.

Conclusion

Quality of life was independently related to survival in a cohort of hospitalized patients with HF.

Trial registration:

NCT 98675639.
Prevention of Intraoperative Awareness with Explicit Recall in an Unselected Surgical Population
Authors: Mashour George A. , Shanks Amy , Tremper Kevin K. , Kheterpal Sachin , Turner Christopher R. , Ramachandran Satya Krishna , Picton Paul , Schueller Christa , Morris Michelle , Vandervest John C. , Lin Nan , Avidan Michael S.
Published: September 2012

Background

Intraoperative awareness with explicit recall occurs in approximately 0.15% of all surgical cases. Efficacy trials based on the Bispectral Index® (BIS) monitor (Covidien, Boulder, CO) and anesthetic concentrations have focused on high-risk patients, but there are no effectiveness data applicable to an unselected surgical population.

Methods

We conducted a randomized controlled trial of unselected surgical patients at three hospitals of a tertiary academic medical center. Surgical cases were randomized to alerting algorithms based on either BIS values or anesthetic concentrations. The primary outcome was the incidence of definite intraoperative awareness; prespecified secondary outcomes included postanesthetic recovery variables.

Results

The study was terminated because of futility. At interim analysis the incidence of definite awareness was 0.12% (11/9,376) (95% CI: 0.07-0.21%) in the anesthetic concentration group and 0.08% (8/9,460) (95% CI: 0.04-0.16%) in the BIS group (P = 0.48). There was no significant difference between the two groups in terms of meeting criteria for recovery room discharge or incidence of nausea and vomiting. By post hoc secondary analysis, the BIS protocol was associated with a 4.7-fold reduction in definite or possible awareness events compared with a cohort receiving no intervention (P = 0.001; 95% CI: 1.7-13.1).

Conclusion

This negative trial could not detect a difference in the incidence of definite awareness or recovery variables between monitoring protocols based on either BIS values or anesthetic concentration. By post hoc analysis, a protocol based on BIS monitoring reduced the incidence of definite or possible intraoperative awareness compared with routine care.
Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species
Authors: Wiens John J. , Hutter Carl R. , Mulcahy Daniel G. , Noonan Brice P. , Townsend Ted M. , Sites Jack W. , Reeder Tod W.
Published: September 2012

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.
Lung collapse in the diving sea lion: hold the nitrogen and save the oxygen
Authors: McDonald Birgitte I. , Ponganis Paul J.
Published: September 2012

Lung collapse is considered the primary mechanism that limits nitrogen absorption and decreases the risk of decompression sickness in deep-diving marine mammals. Continuous arterial partial pressure of oxygen

profiles in a free-diving female California sea lion (
Zalophus californianus
) revealed that (i) depth of lung collapse was near 225 m as evidenced by abrupt changes in

during descent and ascent, (ii) depth of lung collapse was positively related to maximum dive depth, suggesting that the sea lion increased inhaled air volume in deeper dives and (iii) lung collapse at depth preserved a pulmonary oxygen reservoir that supplemented blood oxygen during ascent so that mean end-of-dive arterial

was 74 ± 17 mmHg (greater than 85% haemoglobin saturation). Such information is critical to the understanding and the modelling of both nitrogen and oxygen transport in diving marine mammals.
Combined Simulated Annealing Algorithm for the Discrete Facility Location Problem
Authors: Qin Jin , Ni Ling-lin , Shi Feng
Published: September 2012

The combined simulated annealing (CSA) algorithm was developed for the discrete facility location problem (DFLP) in the paper. The method is a two-layer algorithm, in which the external subalgorithm optimizes the decision of the facility location decision while the internal subalgorithm optimizes the decision of the allocation of customer's demand under the determined location decision. The performance of the CSA is tested by 30 instances with different sizes. The computational results show that CSA works much better than the previous algorithm on DFLP and offers a new reasonable alternative solution method to it.
The γ-Carbonic Anhydrase Subcomplex of Mitochondrial Complex I Is Essential for Development and Important for Photomorphogenesis of Arabidopsis
Authors: Wang Qin , Fristedt Rikard , Yu Xuhong , Chen Zugen , Liu Hongtao , Lee Yurhee , Guo Hongwei , Merchant Sabeeha S. , Lin Chentao
Published: September 2012

Complex I (NADH:ubiquinone oxidoreductase) is the entry point for electrons into the respiratory electron transport chain; therefore, it plays a central role in cellular energy metabolism. Complex I from different organisms has a similar basic structure. However, an extra structural module, referred to as the γ-carbonic anhydrase (γCA) subcomplex, is found in the mitochondrial complex I of photoautotrophic eukaryotes, such as green alga and plants, but not in that of the heterotrophic eukaryotes, such as fungi and mammals. It has been proposed that the γCA subcomplex is required for the light-dependent life style of photoautotrophic eukaryotes, but this hypothesis has not been successfully tested. We report here a genetic study of the genes γCAL1 and γCAL2 that encode two subunits of the γCA subcomplex of mitochondrial complex I. We found that mutations of γCAL1 and γCAL2 in Arabidopsis (Arabidopsis thaliana) result in defective embryogenesis and nongerminating seeds, demonstrating the functional significance of the γCA subcomplex of mitochondrial complex I in plant development. Surprisingly, we also found that reduced expression of γCAL1 and γCAL2 genes altered photomorphogenic development. The γcal1 mutant plant expressing the RNA interference construct of the γCAL2 gene showed a partial constitutive photomorphogenic phenotype in young seedlings and a reduced photoperiodic sensitivity in adult plants. The involvement of the γCA subcomplex of mitochondrial complex I in plant photomorphogenesis and the possible evolutionary significance of this plant-specific mitochondrial protein complex are discussed.