bluuebunny/crossref_metadata_2025 huggingface dataset:
Toward a mechanistic understanding of the decadal trends in the Southern Ocean carbon sink
Authors: Lovenduski Nicole S. , Gruber Nicolas , Doney Scott C.
Published: August 2008

We investigate the multidecadal and decadal trends in the flux of CO2 between the atmosphere and the Southern Ocean using output from hindcast simulations of an ocean circulation model with embedded biogeochemistry. The simulations are run with NCEP‐1 forcing under both preindustrial and historical atmospheric CO2 concentrations so that we can separately analyze trends in the natural and anthropogenic CO2 fluxes. We find that the Southern Ocean (<35°S) CO2 sink has weakened by 0.1 Pg C a−1 from 1979–2004, relative to the expected sink from rising atmospheric CO2 and fixed physical climate. Although the magnitude of this trend is in agreement with prior studies (Le Quéré et al., 2007), its size may not be entirely robust because of uncertainties associated with the trend in the NCEP‐1 atmospheric forcing. We attribute the weakening sink to an outgassing trend of natural CO2, driven by enhanced upwelling and equatorward transport of carbon‐rich water, which are caused by a trend toward stronger and southward shifted winds over the Southern Ocean (associated with the positive trend in the Southern Annular Mode (SAM)). In contrast, the trend in the anthropogenic CO2 uptake is largely unaffected by the trend in the wind and ocean circulation. We regard this attribution of the trend as robust, and show that surface and interior ocean observations may help to solidify our findings. As coupled climate models consistently show a positive trend in the SAM in the coming century [e.g., Meehl et al., 2007], these mechanistic results are useful for projecting the future behavior of the Southern Ocean carbon sink.
Interaction of propagating magnetosonic and Alfvén waves in a longitudinally inhomogeneous plasma
Authors: Pilipenko V. A. , Mazur N. G. , Fedorov E. N. , Engebretson M. J.
Published: August 2008

The field line resonance theory has turned out to be very successful in the interpretation of the occurrence of narrow‐band ULF waves at middle and auroral latitudes. However, observational evidence has emerged (such as the occurrence of monochromatic Pc3 waves deep in the polar cap, Pi1B pulsations associated with tail plasma flows, and ULF waves in the magnetospheres of giant planets) which indicates that some basic assumptions of this theory may be insufficient in regions with open or very extended field lines. To interpret these observations, we suggest a model describing the interaction of propagating magnetosonic and Alfvén waves in longitudinally inhomogeneous plasma. A set of equations for the amplitudes of the interacting modes with account of finite frequency effect is obtained and investigated in the WKB approximation. In the synchronization region, where the wave vectors of the two modes approach one another, a substantial part of the fast magnetosonic wave energy is converted into the Alfvén wave energy. The phases of the waves are matched in such a way that the phase difference is most favorable for wave conversion. This conversion has a resonant character which may explain the occurrence of monochromatic waves with frequencies much higher than the field line eigenfrequency.
Observations of sea surface fCO2 distributions and estimated air‐sea CO2 fluxes in the Hudson Bay region (Canada) during the open water season
Authors: Else Brent G. T. , Papakyriakou Tim N. , Granskog Mats A. , Yackel John J.
Published: August 2008

The lack of baseline estimates of air‐sea CO2 exchange in Arctic and sub‐Arctic regions represents a major shortfall in our ability to understand how climate change may affect CO2 fluxes at high latitudes. The 2005 ArcticNet cruise of Hudson Bay (Canada) provided a rare comprehensive oceanographic survey of one such region. Ship‐based observations of sea‐surface fugacity of CO2 (fCO2sw) were made at 56 locations between 15 September and 26 October and were found to range from 259 μatm in Hudson Strait to 425 μatm at the entrance to James Bay. Strong relationships between fCO2sw and river discharge were identified, with coastal waters observed to be supersaturated with respect to the atmosphere, while offshore waters were undersaturated. High correlations of fCO2sw with salinity, sea surface temperature, and colored dissolved organic matter suggest that thermodynamic effects and the oxidation of riverine carbon are driving supersaturation in the coastal zone. Calculated instantaneous fluxes of CO2 ranged from +16.5 mmol m−2 d−1 in James Bay to −19.6 mmol m−2 d−1 in Foxe Channel. Using National Centers for Environmental Prediction wind speed climatologies, a net sink in Hudson Bay of −0.73 (±0.4) mmol m−2 d−1 was estimated for study period, substantially lower compared to many other Arctic shelf environments. This initial study provides a preliminary examination of fCO2sw dynamics in Hudson Bay; future analyses and field measurements will be necessary to properly constrain CO2 fluxes in this season and over an annual cycle.
Simulated impact of double‐diffusive mixing on physical and biogeochemical upper ocean properties
Authors: Glessmer Mirjam S. , Oschlies Andreas , Yool Andrew
Published: August 2008

A global ocean circulation model coupled with a simple marine ecosystem model including the biogeochemical cycles and air–sea fluxes of oxygen and carbon dioxide is used to investigate the impact of double‐diffusive mixing on upper ocean physical and biogeochemical properties. By comparing results for two different parameterizations of double‐diffusive mixing, we also examine the sensitivity of our estimates to the particular representation of this process in general circulation models. Differences between the two parameterizations considered turned out to be much smaller than the difference with respect to a model run without double‐diffusive mixing. For both parameterizations, the impact on upper ocean temperatures and salinities is relatively small (±1°C, ±0.25 psu regionally and 0.04°C, 0.01 psu as global rms difference over the top 50 m) and changes in surface heat flux amount to 0.05 W m−2 globally. However primary production and export production in the oligotrophic subtropics are found to increase by up to 80% and 120%, respectively, when double diffusion is switched on in the model. Double‐diffusive nutrient supply generates an additional oceanic carbon uptake of about 0.4 g C m−2 year−1, amounting to 0.14 Gt C year−1 globally.
The dependence of aerosol effects on clouds and precipitation on cloud‐system organization, shear and stability
Authors: Lee Seoung Soo , Donner Leo J. , Phillips Vaughan T. J. , Ming Yi
Published: August 2008

Precipitation suppression due to an increase of aerosol number concentration in stratiform cloud is well‐known. It is not certain whether the suppression applies for deep convection. Recent studies have suggested increasing precipitation from deep convection with increasing aerosols under some, but not all, conditions. Increasing precipitation with increasing aerosols can result from strong interactions in deep convection between dynamics and microphysics. High cloud liquid, due to delayed autoconversion, provides more evaporation, leading to more active downdrafts, convergence fields, condensation, collection of cloud liquid by precipitable hydrometeors, and precipitation. Evaporation of cloud liquid is a primary determinant of the intensity of the interactions. It is partly controlled by wind shear modulating the entrainment of dry air into clouds and transport of cloud liquid into unsaturated areas. Downdraft‐induced convergence, crucial to the interaction, is weak for shallow clouds, generally associated with low convective available potential energy (CAPE). Aerosol effects on cloud and precipitation can vary with CAPE and wind shear. Pairs of idealized numerical experiments for high and low aerosol cases were run for five different environmental conditions to investigate the dependence of aerosol effect on stability and wind shear. In the environment of high CAPE and strong wind shear, cumulonimbus‐ and cumulus‐type clouds were dominant. Transport of cloud liquid to unsaturated areas was larger at high aerosol, leading to stronger downdrafts. Because of the large vertical extent of those clouds, strong downdrafts and convergence developed for strong interactions between dynamics and microphysics. These led to larger precipitation at high aerosol. Detrainment of cloud liquid and associated evaporation were less with lower CAPE and wind shear, where dynamically weaker clouds dominated. Transport of cloud liquid to unsaturated areas was not as active as in the environment of high CAPE and strong shear. Also, evaporatively driven differences in downdrafts at their level of initial descent were not magnified in clouds with shallow depth as much as in deep convective clouds as they accelerated to the surface over shorter distances. Hence the interaction between dynamics and microphysics was reduced, leading to precipitation suppression at high aerosol. These results demonstrate that increasing aerosol can either decrease or increase precipitation for an imposed large‐scale environment supporting cloud development. The implications for larger‐scale aspects of the hydrological cycle will require further study with larger‐domain models and cumulus parameterizations with advanced microphysics.
Simulating the impact of glaciations on continental groundwater flow systems: 2. Model application to the Wisconsinian glaciation over the Canadian landscape
Authors: Lemieux J.‐M. , Sudicky E. A. , Peltier W. R. , Tarasov L.
Published: August 2008

A 3‐D groundwater flow and brine transport numerical model of the entire Canadian landscape up to a depth of 10 km is constructed in order to capture the impacts of the Wisconsinian glaciation on the continental groundwater flow system. The numerical development of the model is presented in the companion paper of Lemieux et al. (2008b). Although the scale of the model prevents the use of a detailed geological model, commonly occurring geological materials that exhibit relatively consistent hydrogeological properties over the continent justify the simplifications while still allowing the capture of large‐scale flow system trends. The model includes key processes pertaining to coupled groundwater flow and glaciation modeling, such a density‐dependent (i.e., brine) flow, hydromechanical loading, subglacial infiltration, isostasy, and permafrost development. The surface boundary conditions are specified with the results of a glacial system model. The significant impact of the ice sheet on groundwater flow is evident by increases in the hydraulic head values below the ice sheet by as much as 3000 m down to a depth of 1.5 km into the subsurface. Results also indicate that the groundwater flow system after glaciation did not fully revert to its initial condition and that it is still recovering from the glaciation perturbation. This suggests that the current groundwater flow system cannot be interpreted solely on the basis of present‐day boundary conditions and it is likely that several thousands of years of additional equilibration time will be necessary for the system to reach a new quasi‐steady state. Finally, we find permafrost to have a large impact on the rate of dissipation of high hydraulic heads that build at depth and capturing its accurate distribution is important to explain the current hydraulic head distribution across the Canadian landscape.
Empirical modeling of light availability in rivers
Authors: Julian J. P. , Doyle M. W. , Stanley E. H.
Published: August 2008

While the influence of hydrology and geomorphology on ecosystem‐limiting factors in rivers has been well studied, particularly habitat availability and nutrient cycling, the more fundamental limitation of light availability has received much less attention. Characterizing light regimes in rivers is optically complex and requires consideration of five hydrogeomorphic controls: topography, riparian vegetation, channel geometry, optical water quality, and hydrologic regime. To generalize and quantify these hydrogeomorphic controls, we developed an empirical model that predicts both spatial and temporal variability of photosynthetically active radiation reaching the riverbed (benthic PAR). We applied this benthic light availability model (BLAM) to two dissimilar systems: a large, turbid river and a small, optically clear river. Comparisons between the two systems revealed that the dominant control on temporal light availability for the large river was discharge, which accounted for 90% of the variation. A dominant temporal control for the small river did not emerge, but instead was found to be a function of both above‐canopy PAR and discharge. Spatially, water depth accounted for 99% of the variation in benthic PAR for the large river, and riparian shading accounted for 93% of the variation for the small river. Channel orientation also had a major influence, where an E‐W configuration increased benthic PAR by as much as 108% relative to a N‐S configuration. BLAM predictions agreed well with measured benthic PAR, within 39% on average over a 9‐d period. BLAM is the first model to quantify benthic PAR using all five hydrogeomorphic controls, and thus provides a new tool for investigating the role of light in fluvial ecosystem dynamics and for establishing light availability targets in water resource management.
Formulation of reduced surface integral equations for the electromagnetic wave scattering from three‐dimensional layered dielectric bodies
Authors: Ciric I. R.
Published: August 2008

A reduction procedure is developed for an arbitrarily shaped layered dielectric body using for each interface a single unknown function to which the classical surface electric and magnetic currents are related by some surface operators. These operators and single functions are determined recursively from one interface to the next. This allows us to derive the field everywhere from the solution of a surface integral equation in only one vector function relative to only the interface between the layered body and the source region. Since the reduction operators are independent of the structure of the outside region and of the given field source, and also invariant under translation and rotation, the analysis of the three‐dimensional electromagnetic wave scattering and propagation for systems of multilayered or/and multiply nested dielectric bodies based on reduced single integral equations is substantially more efficient than that based on existing coupled integral equation formulations using electric and magnetic currents on all the interfaces, especially for configurations with identical such bodies arbitrarily located and oriented with respect to each other.
Modeling coupled degradation, sorption, and transport of 17β‐estradiol in undisturbed soil
Authors: Fan Zhaosheng , Casey Francis X. M. , Hakk Heldur , Larsen Gerald L.
Published: August 2008

The presence of 17β‐estradiol in the environment, even at parts‐per‐trillion concentrations, raises significant concern regarding the health of aquatic organisms. Once 17β‐estradiol is released into the environment from human and animal sources, its fate and transport is controlled by factors such as sorption and transformation, which need to be understood to fully assess potential exposures. The objective of this study was first to discern, through controlled batch experiments, the simultaneous transformation (i.e., chemical and biological) of natural estrogenic compounds and their mass exchange between the aqueous and solid phase (i.e., reversible and irreversible sorption sites). In addition, a model was developed that used a series of first‐order expressions to describe the various fate and transport processes of parent and metabolite estrogens in the nonequilibrium batch experiments. A global optimization method was used to estimate the parameters of this nonequilibrium batch model. The model provided a good description of the data, and the parameter estimates were reliable. The batch studies parameter estimates were then incorporated into a convective‐dispersive model to describe two undisturbed column experiments. The consistency of parameter estimates between the batch and column experiments indicated a high capability and reliability of this model and the parameter values.
Southeastern Pacific Coupled Climate Field Experiment
Authors: Wood Robert , Mechoso C. Roberto
Published: August 2008

During October and November 2008, some 150 scientists from 40 institutions in eight nations will take part in the Variability of the American Monsoon Systems' (VAMOS) Ocean‐Cloud‐Atmosphere‐Land Study Regional Experiment (VOCALS‐REx). VOCALS‐REx is an international field program designed to make observations of critical components of the coupled climate system of the southeastern Pacific that are poorly understood and poorly represented in global climate models. The region is dominated by strong coastal upwelling and extensive cold sea surface temperatures (SSTs) and home to the largest subtropical deck of stratocumulus clouds on Earth.
Direct evidence from anisotropy of magnetic susceptibility for lateral melt migration at superfast spreading centers
Authors: Varga Robert J. , Horst Andrew J. , Gee Jeffrey S. , Karson Jeffrey A.
Published: August 2008

Rare, fault‐bounded escarpments expose natural cross sections of ocean crust in several areas and provide an unparalleled opportunity to study the end products of tectonic and magmatic processes that operated at depth beneath oceanic spreading centers. We mapped the geologic structure of ocean crust produced at the East Pacific Rise (EPR) and now exposed along steep cliffs of the Pito Deep Rift near the northern edge of the Easter microplate. The upper oceanic crust in this area is typified by basaltic lavas underlain by a sheeted dike complex comprising northeast striking, moderately to steeply southeast dipping dikes. Paleomagnetic remanence of oriented blocks of dikes collected with both Alvin and Jason II indicate clockwise rotation of ∼61° related to rotation of the microplate indicating structural coupling between the microplate and crust of the Nazca Plate to the north. The consistent southeast dip of dikes formed as the result of tilting at the EPR shortly after their injection. Anisotropy of magnetic susceptibility of dikes provides well‐defined magmatic flow directions that are dominantly dike‐parallel and shallowly plunging. Corrected to their original EPR orientation, magma flow is interpreted as near‐horizontal and parallel to the ridge axis. These data provide the first direct evidence from sheeted dikes in ocean crust for along‐axis magma transport. These results also suggest that lateral transport in dikes is important even at fast spreading ridges where a laterally continuous subaxial magma chamber is present.
Eastern margin variability of the South Pacific Convergence Zone
Authors: Lintner Benjamin R. , Neelin J. David
Published: August 2008

The influence of low‐level inflow wind and its high‐frequency variability on the spatial characteristics of the eastern margin of the South Pacific Convergence Zone (SPCZ) is examined. Compositing daily and 5‐day mean low‐level wind, precipitation, and tropospheric moisture data reveals a clear relationship between high‐frequency zonal inflow variations and the eastern SPCZ margin, with relaxation of trade wind intensity associated with increased moisture near the mean eastern SPCZ margin and an eastward displacement of the convection. An idealized 2‐dimensional model demonstrates that variations in dry air inflow cause tropospheric moisture and precipitation variations akin to those observed. In this prototype, factors affecting the extent of SPCZ variability are also important to the mean margin position. SPCZ margin shifts under natural variability thus offer an observational target against which to evaluate simulated interactions of inflow air mass characteristics with convection.
Summertime “ozone valley” over the Tibetan Plateau derived from ozonesondes and EP/TOMS data
Authors: Tobo Yutaka , Iwasaka Yasunobu , Zhang Daizhou , Shi Guangyu , Kim Yoon‐Suk , Tamura Koichi , Ohashi Tetsuya
Published: August 2008

During the Asian summer monsoon period, total ozone over the Tibetan Plateau is much lower than that over the surrounding areas when compared at the same latitudes. This phenomenon called the “ozone valley” was investigated continuously with the use of ozonesondes and Earth Probe/Total Ozone Mapping Spectrometer (EP/TOMS). These measurements reveal that although relatively low ozone mixing ratios extend from the troposphere to the lower stratosphere, those near the tropopause (between about 150 and 70 hPa) largely contribute to lower total ozone over the Tibetan Plateau. Temperatures near the tropopause appear to be correlated with the observed ozone changes. Meteorological analyses show that this phenomenon is accompanied by the upper level monsoon anticyclone, which is characterized by deep convection over South Asia. These results suggest that lower ozone mixing ratios and colder temperatures near the tropopause are primarily due to convection, which is linked to the Asian summer monsoon.
Anticorrelated intensity change of the quasi‐biweekly and 30–50‐day oscillations over the South China Sea
Authors: Yang Jing , Wang Bin , Wang Bin
Published: August 2008

Over the South China Sea, the year‐to‐year variations in the intensity of the quasi‐biweekly (QBW) and 30–50‐day oscillations during June–July are anti‐correlated. An explanation is offered for the out‐of‐phase relationship. We found during strong QBW years, the June–July mean convection and easterly vertical shear are enhanced over the equatorial western‐central Pacific, with corresponding low‐level cyclonic meridional shear to the northwest. These conditions, concurring with the equatorial eastern Pacific warming, are favorable for emanation of moist Rossby waves from the equatorial western Pacific. On the other hand, the 30–50 day becomes active when the mean convection is enhanced over the eastern Indian Ocean and maritime continent where this mode stems from and develops, which often corresponds to cold western IO. One of these two large‐scale settings often occurs in the absence of the other, so that when one mode is strong during June–July the other mode tends to be weak.
Mantle plumes: Thin, fat, successful, or failing? Constraints to explain hot spot volcanism through time and space
Authors: Kumagai Ichiro , Davaille Anne , Kurita Kei , Stutzmann Eléonore
Published: August 2008

Density heterogeneities in the mantle influence the dynamics of mantle upwellings and therefore modify plume characteristics. Using analog laboratory experiments, we explore the dynamics of “thermo‐chemical” plumes containing both thermal and chemical density anomalies inherited from a stratified boundary layer at the base of the mantle. Because all plumes cool by thermal diffusion as they rise, a chemically composite thermal plume will eventually attain a level of neutral buoyancy, at which it will begin to “fail”. Separation within the plume will occur, whereby the chemically denser material will start to sink back while the heated surrounding mantle keeps rising. It more generally implies that 1) mantle plumes are not necessarily narrow and continuous throughout the mantle but can be fat and patchy such as Iceland, 2) a hot mantle region may not be buoyant and rising, but on contrary may be sinking, and 3) mantle plumes dynamics are strongly time‐dependent.
One‐dimensional hybrid simulations of planetary ion pickup: Effects of variable plasma and pickup conditions
Authors: Cowee M. M. , Russell C. T. , Strangeway R. J.
Published: August 2008

The one‐dimensional hybrid simulation technique using massless fluid electrons and kinetic ions has been shown to successfully reproduce the growth of electromagnetic plasma waves generated by ion populations with a ring velocity distributions (T⊥ > T∥). Such populations are found at Jupiter and Saturn, where newborn ions are picked up into corotating plasma flows that are nearly perpendicular to the background magnetic field. In previous simulation work, which focused on pickup ion generated waves near Io, we considered all the pickup ions to be present in the simulation at the start of the run (initial value). For a more realistic treatment of ion pickup, we now modify the simulation to include continuous ion injection over time. There are several important differences between the initial value and the injection simulations, namely that when ions are injected, the generated waves eventually reach a quasi‐steady level, which is proportional to the injection rate. The results indicate that less than 20% of the pickup ion energy resides in the waves at any given time. Indeed, for certain conditions, the ion cyclotron waves observed at Io may represent only a few percent of the initial pickup ion energy. We carry out simulations varying the plasma and pickup conditions, including the background plasma density and temperature, pickup rate, and multiple pickup ion species to see how the wave amplitudes are affected. We also briefly look at the oblique propagation of the waves to estimate group velocities.
Gas hydrate occurrence from pore water chlorinity and downhole logs in a transect across the northern Cascadia margin (Integrated Ocean Drilling Program Expedition 311)
Authors: Malinverno A. , Kastner M. , Torres M. E. , Wortmann U. G.
Published: August 2008

A transect of four sites drilled by Integrated Ocean Drilling Program Expedition 311 provides an ideal data set to investigate the distribution of gas hydrates across the northern Cascadia convergent margin. We quantify gas hydrate saturation (fraction of pore space occupied by gas hydrate) in a joint interpretation of pore water chlorinity data and downhole logs of porosity and electrical resistivity. The estimated saturation profiles define a gas hydrate occurrence zone (GHOZ), the depth interval where gas hydrates are actually found. In three of the Expedition 311 transect sites (U1326, U1325, and U1327), the top of the GHOZ systematically deepens moving landward of the deformation front of the Cascadia accretionary wedge. The farthest site from the deformation front (U1329) shows no clear evidence of gas hydrates. We apply a simple diagenetic model to explain the observed landward deepening of the GHOZ. The model computes the methane concentration in the pore fluid for a given in situ bacterial methane production, sedimentation rate, and fluid advection velocity. Model results show that lower rates of sedimentation or fluid advection result in slower increases in methane concentration with depth and deeper tops of the GHOZ. Sedimentation rates in the Expedition 311 sites decrease landward, and fluid advection rates due to the dewatering of the accretionary wedge are expected to decrease moving landward of the deformation front as well. A combination of these two mechanisms can explain the deepening of the top of the GHOZ observed in the Expedition 311 transect sites.
p38α MAPK inhibits JNK activation and collaborates with IκB kinase 2 to prevent endotoxin‐induced liver failure
Authors: Heinrichsdorff Jan , Luedde Tom , Perdiguero Eusebio , Nebreda Angel R , Pasparakis Manolis
Published: August 2008

Activation of c‐Jun amino‐terminal kinase (JNK) facilitates tumour necrosis factor (TNF)‐induced cell death. The p38 mitogen‐activated protein kinase pathway is induced by TNF stimulation, but it has not been implicated in TNF‐induced cell death. Here, we show that hepatocyte‐specific ablation of p38α in mice results in excessive activation of JNK in the liver after in vivo challenge with bacterial lipopolysaccharide (LPS). Despite increased JNK activity, p38α‐deficient hepatocytes were not sensitive to LPS/TNF toxicity showing that JNK activation was not sufficient to mediate TNF‐induced liver damage. By contrast, LPS injection caused liver failure in mice lacking both p38α and IκB kinase 2 (IKK2) in hepatocytes. Therefore, when combined with partial nuclear factor‐κB inhibition, p38α deficiency sensitizes the liver to cytokine‐induced damage. Collectively, these results reveal a new function of p38α in collaborating with IKK2 to protect the liver from LPS/TNF‐induced failure by controlling JNK activation.
The Atg8 and Atg12 ubiquitin‐like conjugation systems in macroautophagy
Authors: Geng Jiefei , Klionsky Daniel J.
Published: August 2008

As a lysosomal/vacuolar degradative pathway that is conserved in eukaryotic organisms, autophagy mediates the turnover of long‐lived proteins and excess or aberrant organelles. The main characteristic of autophagy is the formation of a double‐membrane vesicle, the autophagosome, which envelops part of the cytoplasm and delivers it to the lysosome/vacuole for breakdown and eventual recycling of the degradation products. Among the approximately 30 autophagy‐related (Atg) genes identified so far, there are two ubiquitin‐like proteins, Atg12 and Atg8. Analogous to ubiquitination, Atg12 is conjugated to Atg5 by Atg7—an E1‐like protein—and Atg10—an E2‐like protein. Similarly, Atg7 and Atg3 are the respective E1‐like and E2‐like proteins that mediate the conjugation of Atg8 to phosphatidylethanolamine. Both Atg12–Atg5 and Atg8 localize to the developing autophagosome. The Atg12–Atg5 conjugate facilitates the lipidation of Atg8 and directs its correct subcellular localization. Atg8–phosphatidylethanolamine is probably a scaffold protein that supports membrane expansion and the amount present correlates with the size of autophagosomes.
ESG: Extended Similarity Group method for automated protein function prediction
Authors: Chitale Meghana , Hawkins Troy , Park Changsoon , Kihara Daisuke
Published: August 2008

We present here the Extended Similarity Group (ESG) method, which annotates query sequences with Gene Ontology (GO) terms by assigning probability to each annotation computed based on iterative PSI-BLAST searches. Conventionally sequence homology based function annotation methods, such as BLAST, retrieve function information from top hits with a significant score (E-values). In contrast, the PFP method, which we have presented previously, goes one step ahead in utilizing a PSI-BLAST result by considering very weak hits even an E-value of up to 100 and also by incorporating the functional association between GO terms (FAM matrix) computed using term co-occurrence frequencies in the UniProt database. PFP is very successful which is evidenced by the top rank in the function prediction category in CASP7 competition. Our new approach, ESG method, further improves the accuracy of PFP by essentially employing PFP in an iterative fashion. An advantage of ESG is that it is built in a rigorous statistical framework: Unlike PFP method that assigns a weighted score to each GO term, ESG assigns a probability based on weights computed using the E-value of each hit sequence on the path between the original query sequence and the current hit sequence.
Ordered Stratification to Reduce Heterogeneity in Linkage to Diabetes‐related Quantitative Traits
Authors: Meigs James B. , Manning Alisa K. , Dupuis Josée , Liu Chunyu , Florez Jose C. , Cupples L. Adrienne
Published: August 2008

Phenotypic heterogeneity complicates detection of genomic loci predisposing to type 2 diabetes, potentially obscuring or unmasking specific loci. We conducted ordered‐subsets linkage analyses (OSAs) for diabetes‐related quantitative traits (fasting insulin and glucose, hemoglobin A1c (HbA1c), and 28‐year‐time‐averaged fasting plasma glucose (FPG)) from 330 families of the Framingham Offspring Study. We calculated mean BMI, waist circumference (WC), and a diabetes “age‐of‐onset score” for each family. We constructed subsets by adding one family at a time in increasing (lean family to obese) or decreasing (obese to lean) adiposity order, or increasing or decreasing propensity to develop diabetes at a younger age, with the OSA LOD reported as the maximum LOD observed in any subset. Permutation P values tested the hypothesis that phenotypic ordering showed stronger linkage than random ordering. On chromosome 1, ordering by increasing family mean WC increased linkage to time‐averaged FPG at 256 cM from LOD = 2.4 to 3.5 (permuted P = 0.02) and to HbA1c at 180 cM from LOD = 2.0 to 3.3 (P = 0.01). On chromosome 19, ordering by decreasing WC increased linkage to fasting insulin at 68 cM from LOD = 2.7 to 4.6 (P = 0.002), and ordering by decreasing propensity to develop diabetes at a young age increased linkage to fasting insulin at 73 cM from LOD = 2.7 to 4.0 (P = 0.046). We conclude that chromosomes 1 and 19 could harbor adiposity‐interacting diabetes susceptibility genes. Such interactions might also influence trait‐locus associations and may be useful to consider in diabetes genome‐wide association studies.
Synthesis, Characterization, and Cation-Induced Supramolecular Structures of Photochromic Bisthienylethene-Tetraazaporphyrin Hybrids (BTE-TAPs) Bearing Crown Ether Moieties
Authors: Li Lei , Sun Xuan
Published: August 2008

A series of novel tetraazaporphyrinato (TAP) copper compounds 1–5 substituted with different numbers of 15-crown-5 voids and photochromic 1,2-bisthienylethenes (BTEs) were synthesized by ‘one-pot’ reaction and characterized by spectroscopic methods as well as elemental analysis. The effects of BTE and 15-crown-5 substituent number and molecular symmetry on the electronic absorption spectra, infrared spectra, photochromic performance and supramolecular structure formation induced by K+ ions have been systematically investigated. All the BTE-TAP hybrids presented photocyclization and cycloreversion with different quantum yields by irradiation with 365 and 700 nm light in CHCl3 solution, respectively. The steric hindrance derived from the BTE substituents prevents the cofacial dimerization of the compounds, and only linear dimers formed as a result.
Lewis Acid-Promoted Suzuki Reaction using Palladium Chloride Anchored on a Polymer as a Catalyst
Authors: Fan Guozhi , Zhang Hanjun , Cheng Siqing , Ren Zhandong , Hu Zhijun , Wang Zilan
Published: August 2008

Palladium chloride anchored on polystyrene modified by 5-amino-1,10-phenanthroline was prepared and used as an efficient recoverable catalyst for Suzuki cross-coupling reactions. The heterogeneous catalysts can be easily separated from the reaction mixture and reused for five cycles without significant Pd leaching and loss of catalytic activity. Rate enhancement in the Suzuki reaction by Lewis acids was also studied.
Solution-Phase Peptide Synthesis; Synthesis of 'North-Western' and 'South-Eastern' Fragments of the Antifungal Cyclodepsipeptide Petriellin A
Authors: Aurelio Luigi , Brownlee Robert T. C. , Hughes Andrew B.
Published: August 2008

The solution-phase synthesis of two highly modified peptides, a hexamer and a heptamer, that constitute the two halves of the antifungal cyclic depsipeptide, Petriellin A, is reported.
Facile Photochemical Synthesis of 1,1?-Binaphthyls
Authors: Wessig Pablo , Müller Gunnar
Published: August 2008

The photochemical synthesis of highly functionalized 1,1′-binaphthyls 9 by photodehydro-Diels–Alder reaction of esters 8 is reported. It was found that π-stacking interactions between a naphthyl moiety already present in the reactants 8 and an aryl group tethered in the propargyl position of these esters clearly influence the regio- and diastereoselectivity of the reaction. The formation of undesired phenanthrenes 10 could be suppressed by introduction of a blocking methoxy group in the 2-position of the naphthyl moiety. In one case, a diastereomeric ratio of 32:68 was achieved. This is the first example of an atropselective synthesis of biaryls by a photodehydro-Diels–Alder reaction.
pH-Controlled Supramolecular Enantiodifferentiating Photocyclodimerization of 2-Anthracenecarboxylate with Capped ?-Cyclodextrins
Authors: Yang Cheng , Ke Chenfeng , Kahee Fujita , Yuan De-Qi , Mori Tadashi , Inoue Yoshihisa
Published: August 2008

γ-Cyclodextrins capped with p-cresolbisbenzimidazole at the primary rim were synthesized and used as chiral hosts for mediating the enantiodifferentiating [4 + 4] photocyclodimerization of 2-anthracenecarboxylate. The use of 6A,6E-capped γ-cyclodextrin led to the formation of the anti-head-to-head photodimer in –5% enantiomeric excesses (ee) at pH 11 but in 28% ee at pH 6 with accompanying switching of product chirality, for which a pH-responsive conformational change of the capping moiety is likely to be responsible.
Chirality Control in Photochemical Reactions: Enantioselective Formation of Complex Photoproducts in Solution
Authors: Müller Christiane , Bach Thorsten
Published: August 2008

In recent years, new methods have been developed that allow for the photochemical formation of enantiomerically pure or enantiomerically enriched compounds in solution. Major strategies presented in this review rely on the use of chiral complexing agents either in a supermolecular assembly or in a defined 1:1 substrate-template complex. In addition, organocatalytic approaches and a chirality transfer from inherently chiral substrates obtained by spontaneous crystallization are discussed. Synthetic applications show that the area of enantioselective photochemistry has left the state of infancy and is about to become a mature but continuously challenging area of modern chemistry.
1H-1,3-Diazepines and Ketenimines from Cyanotetrazolopyridines
Authors: Addicott Chris , Wentrup Curt
Published: August 2008

Cyano-substituted tetrazolo[1,5-a]pyridines/2-azidopyridines 8T and 15T undergo thermal ring opening to the azides 8A and 15A. Solution photolysis causes nitrogen elimination and ring expansion to 1,3-diazacyclohepta-1,2,4,6-tetraenes 10 and 17, which react with alcohols to afford 2-alkoxy-1H-1,3-diazepines, with secondary amines to 2-dialkylamino-5H-1,3-diazepines, and with water to 1,3-diazepin-2-ones (12–14, 19, 21). Argon matrix photolysis of the azides affords the diazacycloheptatetraenes 10 and 17 as principal products together with ring-opened dicyanovinylketenimines 11 and 18. The matrix-isolated species were identified on the basis of comparison of the infrared spectra with those calculated at the B3LYP/6–31+G* level.
Influence of the Crystallization Solvent on the Molecular Structures of Copper(II) Saccharinato Complexes with Pyridazine: Synthesis, X-Ray Crystallography, Spectroscopy, Photoluminescence, and Thermal Properties
Authors: Yilmaz Veysel T. , Senel Evrim , Kazak Canan
Published: August 2008

X-Ray structural analysis has shown that the products of the reaction of [Cu(sac)2(H2O)4]·2H2O (sac = saccharinate) with pyridazine (pydz) are markedly dependent on the solvent used in the crystallization. The mononuclear complex [Cu(sac)2(H2O)(pydz)2] is obtained by slow evaporation of a 1:2 H2O/methanol solution at room temperature, whereas liquid-phase diffusion of diethyl ether into the same reaction solution produces the polymeric complex [Cu(μ-OH)(μ-sac)(μ-pydz)]n. The individual molecules of [Cu(sac)2(H2O)(pydz)2] are doubly bridged into dimers by O–H…O hydrogen bonds. All ligands in [Cu(sac)2(H2O)(pydz)2] are monodentate, whereas copper(ii) ions in [Cu(μ-OH)(μ-sac)(μ-pydz)]n are triply bridged by all ligands, leading to a one-dimensional chain structure, which is further assembled to form a three-dimensional framework by non-covalent π–π and CH–π stacking interactions. Complex [Cu(sac)2(H2O)(pydz)2] is paramagnetic, whereas complex [Cu(μ-OH)(μ-sac)(μ-pydz)]n exhibits a significantly low μeffective value due to very strong exchange coupling between the copper atoms with a relatively short Cu–Cu distance of 3.360(3) Å. In addition, the full spectroscopic, luminescence, and thermal properties of the complexes are reported.
Swinging the Pendulum: World War II History, Politics, National Identity and Difficulties of Reconciliation in Croatia and Serbia
Authors: Cvijic Srdjan
Published: August 2008

The downfall of communist Yugoslavia and the democratization process that followed at the end of the 1980s have led to the fragmentation of the country, which was accompanied by several wars of different intensity and duration (1991–1999). From the ashes of what once was the Socialist Federal Republic of Yugoslavia raised six independent states: Slovenia, Croatia, Bosnia and Herzegovina, Montenegro, Macedonia and Serbia. The situation relating to the southern Serbian province of Kosovo, after its unilateral declaration of independence at the beginning of 2008, and subsequent recognition by parts of the international community, remains unclear. Slovenia is already in the EU, while the rest of the former Yugoslav republics, within the framework of the Stabilization and Association Process of the European Union, have the status of EU Candidate or Potential Candidate countries and are slowly moving towards EU membership.
Conceptualizing Paradoxes of Post-Socialist Education in Kyrgyzstan
Authors: DeYoung Alan J.
Published: August 2008

Official government educational pronouncements and policy in the Kyrgyz Republic have called for wider access and participation in higher education as an essential part of the general strategy to build democracy and a market economy. The number of higher education institutions (vuzy) has increased from approximately 10 at the end of the Soviet period to 50 institutions, with over 200,000 students now in attendance. Various international statistical sources show that higher education enrollments peaked above 70% of secondary school graduates in the early 1990s. For the past decade, these figures are lower yet still substantial. UNDP reports between 53% and 63%, while the World Bank and UNESCO report between 41% and 45%. In any of these calculations, however, higher education enrollments in Kyrgyzstan have at least trebled since independence, which is even more remarkable considering that the Kyrgyz system of higher education has become almost entirely paid for by students and parents rather than by the national government.
GIMSAN: a Gibbs motif finder with significance analysis
Authors: Ng Patrick , Keich Uri
Published: August 2008

Summary: We present GIMSAN (GIbbsMarkov with Significance ANalysis): a novel tool for de novo motif finding. GIMSAN combines GibbsMarkov, our variant of the Gibbs Sampler, described here for the first time, with our recently introduced significance analysis.

Availability: GIMSAN is currently available as a web application and a stand-alone application on Unix and PBS (Portable Batch System) cluster through links from http://www.cs.cornell.edu/~keich.

Contact:  keich@cs.cornell.edu
Motor and Somatosensory Evoked Potentials Are Well Maintained in Patients Given Dexmedetomidine during Spine Surgery
Authors: Bala Endrit , Sessler Daniel I. , Nair Dileep R. , McLain Robert , Dalton Jarrod E. , Farag Ehab
Published: August 2008

Background

Many commonly used anesthetic agents produce a dose-dependent amplitude reduction and latency prolongation of evoked responses, which may impair diagnosis of intraoperative spinal cord injury. Dexmedetomidine is increasingly used as an adjunct for general anesthesia. Therefore, the authors tested the hypothesis that dexmedetomidine does not have a clinically important effect on somatosensory and transcranial motor evoked responses.

Methods

Thirty-seven patients were enrolled and underwent spinal surgery with instrumentation during desflurane and remifentanil anesthesia with dexmedetomidine as an anesthetic adjunct. Upper- and lower-extremity transcranial motor evoked potentials and somatosensory evoked potentials were recorded during four defined periods: baseline without dexmedetomidine; two periods with dexmedetomidine (0.3 and 0.6 ng/ml), in a randomly determined order; and a final period 1 h after drug discontinuation. The primary outcomes were amplitude and latency of P37/N20, and amplitude, area under the curve, and voltage threshold for transcranial motor evoked potential stimulation.

Results

Of the total, data from 30 patients were evaluated. Use of dexmedetomidine, as an anesthetic adjunct, did not have an effect on the latency or amplitude of sensory evoked potentials greater than was prespecified as clinically relevant, and though the authors were unable to claim equivalence on the amplitude of transcranial motor evoked responses due to variability, recordings were made throughout the study in all patients.

Conclusion

Use of dexmedetomidine as an anesthetic adjunct at target plasma concentrations up to 0.6 ng/ml does not change somatosensory or motor evoked potential responses during complex spine surgery by any clinically significant amount.
Ambulatory Continuous Posterior Lumbar Plexus Nerve Blocks after Hip Arthroplasty
Authors: Ilfeld Brian M. , Ball Scott T. , Gearen Peter F. , Le Linda T. , Mariano Edward R. , Vandenborne Krista , Duncan Pamela W. , Sessler Daniel I. , Enneking F Kayser , Shuster Jonathan J. , Theriaque Douglas W. , Meyer R Scott
Published: August 2008

Background

The authors tested the hypotheses that after hip arthroplasty, ambulation distance is increased and the time required to reach three specific readiness-for-discharge criteria is shorter with a 4-day ambulatory continuous lumbar plexus block (cLPB) than with an overnight cLPB.

Methods

A cLPB consisting of 0.2% ropivacaine was provided from surgery until the following morning. Patients were then randomly assigned either to continue ropivacaine or to be switched to normal saline. Primary endpoints included (1) time to attain three discharge criteria (adequate analgesia, independence from intravenous analgesics, and ambulation > or = 30 m) and (2) ambulatory distance in 6 min the afternoon after surgery. Patients were discharged with their cLPB and a portable infusion pump, and catheters were removed on the fourth postoperative day.

Results

Patients given 4 days of perineural ropivacaine (n = 24) attained all three discharge criteria in a median (25th-75th percentiles) of 29 (24-45) h, compared with 51 (42-73) h for those of the control group (n = 23; estimated ratio = 0.62; 95% confidence interval, 0.45-0.92; P = 0.011). Patients assigned to receive ropivacaine ambulated a median of 34 (9-55) m the afternoon after surgery, compared with 20 (6-46) m for those receiving normal saline (estimated ratio = 1.3; 95% confidence interval, 0.6-3.0; P = 0.42). Three falls occurred in subjects receiving ropivacaine (13%), versus none in subjects receiving normal saline.

Conclusions

Compared with an overnight cLPB, a 4-day ambulatory cLPB decreases the time to reach three predefined discharge criteria by an estimated 38% after hip arthroplasty. However, the extended infusion did not increase ambulation distance to a statistically significant degree.