bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of protein extraction and solubilization for mature grape berry clusters
Authors: Vincent Delphine , Wheatley Matthew D. , Cramer Grant R. 
Published: April 2006

AbstractProtein extraction from grape berries has been challenging, particularly in mature berries, which can have sugar concentrations as high as 26%. Grape skins and seeds contain large amounts of polyphenols, which can also interfere with efficient protein extraction. In plants, two extraction protocols, TCA/acetone‐based and phenol‐based methods, have been mainly used to extract proteins from different organs or tissues on many species. However, few results have been reported for grape berry clusters. We wanted to determine which of these protocols was optimal for berry clusters in order to achieve both efficient protein extraction and high spot resolution on 2‐D gels. Four protocols, derived from either TCA/acetone or phenol procedures, were tested on mature Cabernet Sauvignon whole berry clusters. The phenol‐based protocols were superior to the TCA/acetone methods, showing larger protein yields and greater spot resolution on 2‐D gels. One method was clearly superior to the rest, a phenol‐based extraction method combined with resuspension in the presence of both urea and thiourea as chaotropes. A total of 81 spots were excised and identified following MALDI‐TOF/TOF MS analyses. Their identification helped further characterize the specificity of each extraction procedure.
A new approach for separating low‐molecular‐weight RNA molecules by staircase electrophoresis in non‐sequencing gels
Authors: Velázquez Encarna , Rivas Raúl , Villar María del , Valverde Angel , Peix Alvaro , Mateos Pedro F. , Velázquez Enrique , Martínez‐Molina Eustoquio 
Published: April 2006

AbstractLow‐molecular‐weight (LMW) RNA profiles, which include ribosomal and transfer RNA molecules with similar small sizes, are molecular signatures of microorganisms with a great potential in microbial identification. The greatest resolution of these profiles was achieved by staircase electrophoresis in sequencing gels. Nevertheless, this technique is difficult to use because it takes 7 h, the gels have large sizes and it is necessary to heat the system and to recycle the buffer to maintain the denaturing conditions and avoid smile effects. Most available sequencing slabs have no internal temperature control or homogenizing devices, which by contrast are present in some newly designed non‐sequencing slabs. Nevertheless, these slabs present two important problems for separating LMW RNA molecules, the size of gels is only 20 cm (instead of 40 cm) and the maximum voltage that can be reached is only 840 V (instead 2400 V). Staircase electrophoresis follows a model in which the external polarization is incrementally modified with a constant time step value. In the present work, we experimentally confirmed that by reducing the time step and increasing the total number of steps a suitable resolution is achieved. Under these conditions, despite the smaller size of the gels and the lower values of the electric field, the intensity reaches higher values than in sequencing gels and the LMW RNA profiles are correctly separated in 5 h. The resolution of these profiles obtained in non‐sequencing gels is similar to that obtained in sequencing ones facilitating the analysis of large populations of microorganisms in any laboratory.
Electrophoretic mobility and molecular distribution studies of poly(amidoamine) dendrimers of defined charges
Authors: Shi Xiangyang , Bányai István , Rodriguez Keyla , Islam Mohammad T. , Lesniak Wojciech , Balogh Peter , Balogh Lajos P. , Baker James R. 
Published: April 2006

AbstractGeneration 5 ethylenediamine (EDA)‐cored poly(amidoamine) (PAMAM) dendrimers (E5, E denotes the EDA core and 5 the generation number) with different degrees of acetylation and carboxylation were synthesized and used as a model system to investigate the effect of charge and the influence of dendrimer surface modifications on electrophoretic mobility (EM) and molecular distribution. The surface‐modified dendrimers were characterized by size‐exclusion chromatography, 1H NMR, MALDI‐TOF‐MS, PAGE, and CE. The focus of our study was to determine how EM changes as a function of particle charge and molecular mass, and how the molecular distribution changes due to surface modifications. We demonstrate that partially modified dendrimers have much broader migration peaks than those of fully surface functionalized or unmodified E5 dendrimers due to variations in the substitution of individual dendrimer surfaces. EM decreased nonlinearly with increases in surface acetylation for both PAMAM acetamides and PAMAM succinamic acids, indicating a complex migration activity in CE separations that is not solely due to charge/mass ratio changes. These studies provide new insights into dendrimer properties under an electric field, as well as into the characterization of dendrimer‐based materials being developed for medical applications.
Evaluating erosion control measures for biorestoration between the time of soil reinstatement and vegetation establishment
Authors: Hann M. J. , Morgan R. P. C. 
Published: April 2006

AbstractA modified Universal Soil Loss Equation is used to evaluate the performance of erosion control measures along pipeline rights‐of‐way in Colombia and Georgia in a ten‐year return‐period storm occurring during the first year following pipeline installation. An erosion mat is the most effective way of reducing erosion until a sufficient vegetation cover has been established. On steep slopes and where climate restricts the rate of vegetation growth, it may be necessary to supplement the mat with diverter berms. Although the method cannot be validated in the study areas because of a lack of appropriate data, the results conform to local experience. Copyright © 2006 John Wiley & Sons, Ltd.
Genetic mapping of a putative tumor suppressor locus that influences tumorigenesis and metastasis in mice
Authors: Ayanga Bernard , Price Roger , Gu Xiangjun , Lozano Guillermina , Evans Susan C. 
Published: April 2006

AbstractThe tumor suppressor TP53 is mutated in ∼70% of Li‐Fraumeni syndrome (LFS) families; however, other genes may lead to the predisposition to tumors in other families. We developed a mouse model to search for other tumor suppressors that may be involved in the syndrome. Inbred CE/J mice, which succumb to multiple types of tumors similar to those found in LFS, were crossed with the Trp53‐null 129‐Trp53tm1Tyj mouse. We monitored the tumor onset and type and found a significant earlier tumor onset in the CE/J:129‐Trp53tm1Tyj mice compared with 129‐Trp53tm1Tyj mice with a Trp53‐null allele. Additionally, in CE/J:129‐Trp53tm1Tyj‐Trp53+/− mice, the tumors metastasize, which does not occur in other strains of mice. Using simple‐sequence length polymorphism analysis for loss of heterozygosity in tumors, we identified a putative tumor suppressor locus within 1 cM on mouse chromosome 11, which encompasses 12 mapped genes. © 2006 Wiley‐Liss, Inc.
An evaluation of the replicate pool method: quick estimation of genome‐wide linkage peak p‐values
Authors: Wigginton Janis E. , Abecasis Gonçalo R. 
Published: April 2006

AbstractThe calculation of empirical p‐values for genome‐wide non‐parametric linkage tests continues to present significant computational challenges for many complex disease mapping studies. The gold standard approach is to use gene dropping to simulate null genome scans. Unfortunately, this approach is too computationally expensive for many data sets of interest. An alternative, more efficient method for sampling null genome scans is to pre‐calculate pools of family‐specific statistics and then resample from these replicate pools to generate “pseudo‐replicate” genome scans. In this study, we use simulations to explore properties of the replicate pool p‐value estimator p̂RP and show that it provides an excellent approximation to the traditional gene‐dropping estimator for significantly less computational effort. While the computational efficiency of the replicate pool estimator is noticeable in almost all data sets, by applying the replicate pool method to several previously characterized data sets we show that savings in computational effort can be especially significant (on the order of 10,000‐fold or more) when one or more large families are analyzed. We also estimate replicate pool p‐values for the schizophrenia data described by Abecasis et al. and show that p̂RP closely approximates gene‐drop p‐values for all linkage peaks reported for this study. Lastly, we expand upon Song et al.'s previous work by deriving a conservative estimator of the variance for p̂RP that can easily be computed in practical settings.We have implemented the replicate pool method along with our variance estimator in a new program called Pseudo, which is the first widely available automated implementation of the replicate pool method. Genet. Epidemiol. 30, 2006. © 2006 Wiley‐Liss, Inc.
Testing for genetic heterogeneity in the genome search meta‐analysis method
Authors: Lewis Cathryn M. , Levinson Douglas F. 
Published: April 2006

AbstractThe Genome Search Meta‐Analysis (GSMA) method is widely used to detect linkage by pooling results of previously published genome‐wide linkage studies. The GSMA uses a non‐parametric summed rank statistic in 30 cM bins of the genome. Zintzaras and Ioannidis ([2005] Genet. Epidemiol. 28:123–137) developed a method of testing for heterogeneity of evidence for linkage in the GSMA, with three heterogeneity statistics (Q, Ha, B). They implement two testing procedures, restricted versus unrestricted for the summed rank within the bin. We show here that the rank‐unrestricted test provides a conservative test for high heterogeneity and liberal test for low heterogeneity in linked regions. The rank‐restricted test should therefore be used, despite the extensive simulations needed. In a simulation study, we show that the power to detect heterogeneity is low. For 20 studies of affected sib pairs, simulated assuming linkage in all studies to a gene with sibling relative risk of 1.3, the power to detect low heterogeneity using the Q statistic was 14%. With linkage present in 50% of the studies (to a gene with sibling relative risk of 1.4), the Q heterogeneity statistic had power of 29% to detect high heterogeneity. The power to detect linkage using the summed rank was high in both of these situations, at 98% and 79%, respectively. Although testing for heterogeneity in the GSMA is of interest, the currently available method provides little additional information to that provided by the summed rank statistic. Genet. Epidemiol. 2006. © 2006 Wiley‐Liss, Inc.
Facies development, depositional settings and sequence stratigraphy across the Ordovician–Silurian boundary: a new perspective from the Barrandian area of the Czech Republic
Authors: Štorch Petr 
Published: April 2006

AbstractThe Hirnantian and Llandovery sedimentary succession of the Barrandian area has been assigned to middle and outer clastic‐shelf depositional settings, respectively. Deposition was influenced by the remote Gondwanan glaciation and subsequent, long‐persisting, post‐glacial anoxia triggered by a current‐driven upwelling system. High‐resolution graptolite stratigraphy, based upon 19 formally defined biozones—largely interval zones—and five subzones, enabled a detailed correlation between 42 surface sections and boreholes, and enabled linking of the sedimentary record, graptoloid fauna dynamics, organic‐content fluctuations and spectral gamma‐ray curves. The Hirnantian and Llandovery succession has been subdivided into four biostratigraphically dated third‐order sequences (units 1–4). Time–spatial facies distribution recorded early and late Hirnantian glacio‐eustatic sea‐level lowstands separated by a remarkable mid‐Hirnantian rise in sea‐level. A major part of the post‐glacial sea‐level rise took place within the late Hirnantian. The highstand of Unit 2 is apparently at the base of the Silurian succession. Short‐term relative sea‐level drawdown and a third‐order sequence boundary followed in the early Rhuddanian upper acuminatus Zone. Early Aeronian and late Telychian sea‐level highstands and late Aeronian drawdown of likely eustatic origin belong to units 3 and 4. Sea‐level rise culminated in the late Telychian, which may also be considered as a highstand episode of a second‐order Hirnantian–early Silurian cycle. Facies and sequence‐stratigraphic analysis supports recent interpretations on nappe structures in the core part of the Ordovician–Middle Devonian Prague Synform of the Barrandian. Copyright © 2006 John Wiley & Sons, Ltd.
Stratigraphy and volcanology of the Türkbükü volcanics: products of a stratovolcano in the Bodrum Peninsula, SW Anatolia
Authors: Karacik Zekiye 
Published: April 2006

AbstractThe Middle‐Upper Miocene Bodrum magmatic complex of the Aegean region, southwestern Turkey, is mainly represented by intermediate stocks, lavas, pyroclastic and volcaniclastic deposits. Monzonitic stocks and connected porphyry intrusions and extrusions are the first products of the magmatism. These are followed by a volcanic succession consisting of andesitic‐latitic lavas, autobrecciated lavas, pyroclastic and volcaniclastic deposits. The final stage is represented by basaltic and basaltic andesitic flows and dykes intruded into previous units.The volcanic succession crops out in the northern part of the Bodrum peninsula. In the lower part of this succession are widespread pyroclastic deposits, composed of pyroclastic fall and flow units, alternating with epiclastic deposits. Grain size, volume and thickness of the pyroclastic deposits were mainly controlled by the type, magnitude and intensity of the eruption. Further up the section, there are two horizons of debris avalanche deposits forming the coarsest and thickest deposits of the volcaniclastic succession. The debris avalanche deposits indicate at least two different flank collapses coeval with the volcanism. The stratigraphy and map pattern of these volcanic units imply that the northern part of the Bodrum peninsula was the north‐facing flank of a stratovolcano during the mid‐Late Miocene. Copyright © 2006 John Wiley & Sons, Ltd.
Analytical solution of water table fluctuations above an inclined leaky layer due to ditch recharge
Authors: Hung Chien‐Jen , Tan Yih‐Chi , Chen Chu‐Hui , Chen Jiann‐Mou , Chang Po‐Wen 
Published: April 2006

AbstractDitch recharge is a method used for raising a water table. However, if the aquifer lies above a leaky layer, then the leaky bed will have an effect on the height of the water table. This paper attempts to provide an analytical solution of the transient state to the linearized Boussinesq equation. The solution proposed in this paper is intended for a generalized form of the leaky layer, with the boundary condition of the water level moving according to an exponential form. The results of theoretical analysis and experimental studies can provide a much better explanation of ditch recharge on an inclined leaky layer. Copyright © 2006 John Wiley & Sons, Ltd.
Regionalizing mean annual flow and daily flow variability for basin‐scale sediment and nutrient modelling
Authors: Wilkinson Scott N. , Young William J. , DeRose Ron C. 
Published: April 2006

AbstractRiver discharges vary strongly through time and space, and quantifying this variability is fundamental to understanding and modelling river processes. The river basin is increasingly being used as the unit for natural resource planning and management; to facilitate this, basin‐scale models of material supply and transport are being developed. For many basin‐scale planning activities, detailed rainfall‐runoff modelling is neither necessary nor tractable, and models that capture spatial patterns of material supply and transport averaged over decades are sufficient. Nevertheless, the data to describe the spatial variability of river discharge across large basins for use in such models are often limited, and hence models to predict river discharge at the basin scale are required. We describe models for predicting mean annual flow and a non‐dimensional measure of daily flow variability for every river reach within a drainage network. The models use sparse river gauging data, modelled grid surfaces of mean annual rainfall and mean annual potential evapotranspiration, and a network accumulation algorithm. We demonstrate the parameterization and application of the models using data for the Murrumbidgee basin, in southeast Australia, and describe the use of these predictions in modelling sediment transport through the river network. The regionalizations described contain less uncertainty, and are more sensitive to observed spatial variations in runoff, than regionalizations based on catchment area and rainfall alone. Copyright © 2006 John Wiley & Sons, Ltd.
Groundwater quality in Mesogea basin in eastern Attica (Greece)
Authors: Stamatis G. , Lambrakis N. , Alexakis D. , Zagana E. 
Published: April 2006

AbstractStudies on the hydrogeological conditions of the Mesogea basin in east Attica reveal that the aquifers developed on the post‐alpine formations at the inner part of the coastal brackish zone exhibit positive hydraulic head. These Neogene and Quaternary deposits present high salt concentrations. Selected points were sampled (total 85: 51 wells and 34 boreholes) in order to obtain hydrogeological and hydrochemical data for a better understanding of the structure, operation and dynamics of the aquifer of the area. Statistical methods, R‐mode factor analysis and scatter‐plot diagrams were used for the hydrochemical analysis and presentation of the data. The groundwater resources are relatively weak and there is significant quality degradation due to the geological structure of the greater area, as well as the bad management of the aquifer and anthropogenic activities. Groundwater is characterized by high salt concentrations. Electrical conductivity values range between 260 and 6970 µS cm−1. High salt concentrations at the coastal aquifers are due to sea intrusion, whereas they are attributed to the dissolution of minerals of the geological environment in the inland area. The groundwaters of the study area can be classified into five water types: Ca–HCO3, Mg–HCO3, Na–HCO3, Na–Cl and Mg–Cl. They are saturated in dolomite and calcite, whereas they are unsaturated in anhydrite. High ion concentrations, e.g. $\hbox{NO}_{3}^{-}$] (0‐221 mg l−1), $\hbox{NH}_{4}^{+}$] (0·01‐1·88 mg l−1), $\hbox{PO}_{4}^{3-}$] (0·01‐6·75 mg l−1), as well as high heavy metals concentrations are attributed to anthropogenic impacts. Copyright © 2006 John Wiley & Sons, Ltd.
Uncertainties in DRAINMOD predictions of subsurface drain flow for an Indiana silt loam using the GLUE methodology
Authors: Wang X. , Frankenberger J. R. , Kladivko E. J. 
Published: April 2006

AbstractGood modelling practice requires the incorporation of uncertainty analysis into hydrologic/water quality models. The generalized likelihood uncertainty estimation procedure was used to evaluate the uncertainty in DRAINMOD predictions of daily, monthly, and yearly subsurface drain flow. A variance‐based sensitivity analysis technique, the extended Fourier amplitude sensitivity test, was used to identify the main sources of prediction uncertainty. The analysis was conducted for the experimental drainage field at the Southeast Purdue Agricultural Center in Indiana. Six years of data were used and the uncertainties in eight model parameters were considered to analyse how uncertainties in input parameters propagate to model outputs. The width of 90% confidence interval bands of drain flow ranged from 0 to 0·6 cm day−1for daily predictions, from 0 to 3·1 cm month−1for the monthly predictions, and from 7·6 to 12·4 cm year−1for yearly predictions. Annual drain flow predicted by DRAINMOD fell well within the 90% confidence bounds. Model results were most sensitive to the vertical saturated hydraulic conductivity of the restrictive layer and the lateral hydraulic conductivity of the deepest soil layer, followed by the lateral hydraulic conductivity of the top soil layer and surface micro‐storage. Parameter interactions also contributed to the prediction uncertainty. Copyright © 2006 John Wiley & Sons, Ltd.
Multiple injected and natural conservative tracers quantify mixing in a stream confluence affected by acid mine drainage near Silverton, Colorado
Authors: Schemel Laurence E. , Cox Marisa H. , Runkel Robert L. , Kimball Briant A. 
Published: April 2006

AbstractThe acidic discharge from Cement Creek, containing elevated concentrations of dissolved metals and sulphate, mixed with the circumneutral‐pH Animas River over a several hundred metre reach (mixing zone) near Silverton, CO, during this study. Differences in concentrations of Ca, Mg, Si, Sr, and SO42− between the creek and the river were sufficiently large for these analytes to be used as natural tracers in the mixing zone. In addition, a sodium chloride (NaCl) tracer was injected into Cement Creek, which provided a Cl− ‘reference’ tracer in the mixing zone. Conservative transport of the dissolved metals and sulphate through the mixing zone was verified by mass balances and by linear mixing plots relative to the injected reference tracer. At each of seven sites in the mixing zone, five samples were collected at evenly spaced increments of the observed across‐channel gradients, as determined by specific conductance. This created sets of samples that adequately covered the ranges of mixtures (mixing ratios, in terms of the fraction of Animas River water, %AR). Concentratis measured in each mixing zone sample and in the upstream Animas River and Cement Creek were used to compute %AR for the reference and natural tracers. Values of %AR from natural tracers generally showed good agreement with values from the reference tracer, but variability in discharge and end‐member concentrations and analytical errors contributed to unexpected outlier values for both injected and natural tracers. The median value (MV) %AR (calculated from all of the tracers) reduced scatter in the mixing plots for the dissolved metals, indicating that the MV estimate reduced the effects of various potential errors that could affect any tracer. Copyright © 2006 John Wiley & Sons, Ltd.