bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrospinning formaldehyde‐crosslinked zein solutions
Authors: Selling Gordon W , Woods Kristen Kruger , Biswas Atanu
Published: January 2011

In order to develop zein fibers with improved physical properties and solvent resistance, formaldehyde was used as a crosslinking reagent before spinning. The crosslinking reaction was carried out in either acetic acid or ethanolic HCl where the amount of crosslinking reagent was between 1 and 6%. Reactions were carried out at various times and temperatures. When carried out in acetic acid, the maximum amount of formaldehyde that could be used was 1.5% as gelation occurred at higher levels. In ethanolic HCl, 6% formaldehyde could be incorporated into zein. All solutions were successfully electrospun, producing predominantly ribbon and round fibers; the morphology was strongly dependent on solvent and spinning solids. The formaldehyde‐crosslinked zein fabrics had double the tensile strength of control fabrics. SDS‐PAGE analysis clearly showed crosslinking had occurred. Electrospun fabrics from all formaldehyde‐treated zein solutions required an additional heating step in order to be resistant to dissolution in acetic acid, a known very good solvent for zein. Copyright © 2011 Society of Chemical Industry
Fracture behaviour of controlled‐rheology ethylene–propylene block copolymers
Authors: Salazar Alicia , Martín Tamara , Navarro José M , Rodríguez Jesús
Published: January 2011

The evolution of the molecular weight distribution and the thermal, mechanical and fracture behaviour of controlled‐rheology ethylene‐propylene block copolymers (ca 8 wt% ethylene content) has been analysed. Various concentrations of di‐tert‐butylperoxide were utilized. The melt flow index increased with the peroxide content due to the reduction of the molecular weight and the narrowing of the molecular weight distribution. However, the thermal behaviour and degree of crystallinity were not improved and some mechanical properties, such as the tensile strength and elongation at break, presented an anomalous behaviour. This trend can be explained by the presence of the elastomeric phase. The addition of peroxide influenced strongly the J–R curves obtained via the elastic–plastic fracture mechanics approach. The slope of these curves was markedly reduced with addition of peroxide to almost being flat for the highest concentration. This loss of ductility and the sudden decrease of the fracture toughness values with an increasing amount of peroxide were mainly due to the reduction in the molecular weight. Copyright © 2011 Society of Chemical Industry
Morphology and properties of stearate‐intercalated layered double hydroxide nanoplatelet‐reinforced thermoplastic polyurethane
Authors: Kotal Moumita , Srivastava Suneel Kumar , Bhowmick Anil Kumar , Chakraborty Sunity Kumar
Published: January 2011

In the past few years, layered double hydroxides (LDHs) with monolayer structure have been much studied for the development of polymer nanocomposites. LDHs with intercalated stearate anions form a bilayer structure with increased interlayer spacing and are expected to be better nanofillers in polymers. In the work reported, thermoplastic polyurethane (PU)/stearate‐intercalated LDH nanocomposites were prepared by solution intercalation and characterized. X‐ray diffraction and transmission electron microscopy confirmed the exfoliation at lower filler loading followed by intercalation at higher filler loading in PU matrix. As regards mechanical properties, these nanocomposites showed maximum improvements in tensile strength (45%) and elongation at break (53%) at 1 and 3 wt% loadings. Maximum improvements in storage and loss moduli (20%) with a shift of glass transition temperature (15 °C) and an increase in thermal stability (32 °C) at 50% weight loss were observed at 8 wt% loading in PU. Differential scanning calorimetry showed a shift of melting temperature of the soft segment in the nanocomposites compared to neat PU, possibly due to the nucleating effect of stearate‐intercalated LDH on the crystal structure of PU. All these findings are promising for the development of mechanically improved, thermally stable novel PU nanocomposites. Copyright © 2011 Society of Chemical Industry
α‐Amino acids as initiators of ε‐caprolactone and L,L‐lactide polymerization
Authors: Oledzka Ewa , Sokolowski Kamil , Sobczak Marcin , Kolodziejski Waclaw
Published: January 2011

Biodegradable polymers/oligomers were successfully synthesized through a ring‐opening polymerization of ε‐caprolactone and L,L‐lactide, initiated by L‐arginine and L‐citrulline. The α‐amino acid initiators are natural, operationally simple, inexpensive, environmentally friendly and safe for human health. The polymerizations were performed with no solvents and without introducing any metal impurities. The chemical structures of the polymers obtained were elucidated using 1H NMR, 13C NMR and Fourier transform infrared spectroscopies. In addition, incorporation of α‐amino acid molecules into the polymer chain was confirmed using matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry. Due to the significant biological activity of L‐arginine and L‐citrulline, these α‐amino acid initiators may open a new route for the synthesis of functional polymers especially for pharmaceutical applications. Copyright © 2011 Society of Chemical Industry
2‐Methyl‐2,4‐pentanediol induces spontaneous assembly of staphylococcal α‐hemolysin into heptameric pore structure
Authors: Tanaka Yoshikazu , Hirano Nagisa , Kaneko Jun , Kamio Yoshiyuki , Yao Min , Tanaka Isao
Published: January 2011

Staphylococcal α‐hemolysin is expressed as a water‐soluble monomeric protein and assembles on membranes to form a heptameric pore structure. The heptameric pore structure of α‐hemolysin can be prepared from monomer in vitro only in the presence of deoxycholate detergent micelles, artificially constructed phospholipid bilayers, or erythrocytes. Here, we succeeded in preparing crystals of the heptameric form of α‐hemolysin without any detergent but with 2‐methyl‐2,4‐pentanediol (MPD), and determined its structure. The structure of the heptameric pore was similar to that reported previously. In the structure, two molecules of MPD were bound around Trp179, around which phospholipid head groups were bound in the heptameric pore structure reported previously. Size exclusion chromatography showed that α‐hemolysin did not assemble spontaneously even when stored for 1 year. SDS‐PAGE analysis revealed that, among the compounds in the crystallizing buffer, MPD could induce heptamer formation. The concentration of MPD that most efficiently induced oligomerization was between 10 and 30%. Based on these observations, we propose MPD as a reagent that can facilitate heptameric pore formation of α‐hemolysin without membrane binding.
A structure‐based benchmark for protein–protein binding affinity
Authors: Kastritis Panagiotis L. , Moal Iain H. , Hwang Howook , Weng Zhiping , Bates Paul A. , Bonvin Alexandre M. J. J. , Janin Joël
Published: January 2011

We have assembled a nonredundant set of 144 protein–protein complexes that have high‐resolution structures available for both the complexes and their unbound components, and for which dissociation constants have been measured by biophysical methods. The set is diverse in terms of the biological functions it represents, with complexes that involve G‐proteins and receptor extracellular domains, as well as antigen/antibody, enzyme/inhibitor, and enzyme/substrate complexes. It is also diverse in terms of the partners' affinity for each other, with Kd ranging between 10−5 and 10−14M. Nine pairs of entries represent closely related complexes that have a similar structure, but a very different affinity, each pair comprising a cognate and a noncognate assembly. The unbound structures of the component proteins being available, conformation changes can be assessed. They are significant in most of the complexes, and large movements or disorder‐to‐order transitions are frequently observed. The set may be used to benchmark biophysical models aiming to relate affinity to structure in protein–protein interactions, taking into account the reactants and the conformation changes that accompany the association reaction, instead of just the final product.
Fic domain‐catalyzed adenylylation: Insight provided by the structural analysis of the type IV secretion system effector BepA
Authors: Palanivelu Dinesh V. , Goepfert Arnaud , Meury Marcel , Guye Patrick , Dehio Christoph , Schirmer Tilman
Published: January 2011

Numerous bacterial pathogens subvert cellular functions of eukaryotic host cells by the injection of effector proteins via dedicated secretion systems. The type IV secretion system (T4SS) effector protein BepA from Bartonella henselae is composed of an N‐terminal Fic domain and a C‐terminal Bartonella intracellular delivery domain, the latter being responsible for T4SS‐mediated translocation into host cells. A proteolysis resistant fragment (residues 10–302) that includes the Fic domain shows autoadenylylation activity and adenylyl transfer onto Hela cell extract proteins as demonstrated by autoradiography on incubation with α‐[32P]‐ATP. Its crystal structure, determined to 2.9‐Å resolution by the SeMet‐SAD method, exhibits the canonical Fic fold including the HPFxxGNGRxxR signature motif with several elaborations in loop regions and an additional β‐rich domain at the C‐terminus. On crystal soaking with ATP/Mg2+, additional electron density indicated the presence of a PPi/Mg2+ moiety, the side product of the adenylylation reaction, in the anion binding nest of the signature motif. On the basis of this information and that of the recent structure of IbpA(Fic2) in complex with the eukaryotic target protein Cdc42, we present a detailed model for the ternary complex of Fic with the two substrates, ATP/Mg2+ and target tyrosine. The model is consistent with an in‐line nucleophilic attack of the deprotonated side‐chain hydroxyl group onto the α‐phosphorus of the nucleotide to accomplish AMP transfer. Furthermore, a general, sequence‐independent mechanism of target positioning through antiparallel β‐strand interactions between enzyme and target is suggested.
Measuring rapid hydrogen exchange in the homodimeric 36 kDa HIV‐1 integrase catalytic core domain
Authors: Fitzkee Nicholas C. , Torchia Dennis A. , Bax Ad
Published: January 2011

Measurements of rapid hydrogen exchange (HX) of water with protein amide sites contain valuable information on protein structure and function, but current NMR methods for measuring HX rates are limited in their applicability to large protein systems. An alternate method for measuring rapid HX is presented that is well‐suited for larger proteins, and we apply the method to the deuterated, homodimeric 36 kDa HIV‐1 integrase catalytic core domain (CCD). Using long mixing times for water‐amide magnetization exchange at multiple pH values, HX rates spanning more than four orders of magnitude were measured, as well as NOE cross‐relaxation rates to nearby exchangeable protons. HX protection factors for the CCD are found to be large (>104) for residues along the dimer interface, but much smaller in many other regions. Notably, the catalytic helix (residues 152‐167) exhibits low HX protection at both ends, indicative of fraying at both termini as opposed to just the N‐terminal end, as originally thought. Residues in the LEDGF/p75 binding pocket also show marginal stability, with protection factors in the 10–100 range (∼1.4–2.7 kcal/mol). Additionally, elevated NOE cross‐relaxation rates are identified and, as expected, correspond to proximity of the amide proton to a rapidly exchanging proton, typically from an OH side chain. Indirect NOE transfer between H2O and the amide proton of I141, a residue in the partially disordered active site of the enzyme, suggests its proximity to the side chain of S147, an interaction seen in the DNA‐bound form for a homologous integrase.
Contributions of aromatic pairs to the folding and stability of long‐lived human γD‐crystallin
Authors: Kong Fanrong , King Jonathan
Published: January 2011

Human γD‐crystallin (HγD‐Crys) is a highly stable protein that remains folded in the eye lens for the majority of an individual's lifetime. HγD‐Crys exhibits two homologous crystallin domains, each containing two Greek key motifs with eight β‐strands. Six aromatic pairs (four Tyr/Tyr, one Tyr/Phe and one Phe/Phe) are present in the β‐hairpin sequences of the Greek keys. Ultraviolet damage to the aromatic residues in lens crystallins may contribute to the genesis of cataract. Mutant proteins with these aromatic residues substituted with alanines were constructed and expressed inE. coli. All mutant proteins except F115A and F117A had lower thermal stability than the WT protein. In equilibrium experiments in guanidine hydrochloride (GuHCl), all mutant proteins had lower thermodynamic stability than the WT protein. N‐terminal domain (N‐td) substitutions shifted the N‐td transition to lower GuHCl concentration, but the C‐terminal domain (C‐td) transition remained unaffected. C‐td substitutions led to a more cooperative unfolding/refolding process, with both the N‐td and C‐td transitions shifted to lower GuHCl concentration. The aromatic pairs conserved for each Greek key motif (Greek key pairs) had larger contributions to both thermal stability and thermodynamic stability than the other pairs. Aromatic‐aromatic interaction was estimated as 1.5–2.0 kcal/mol. In kinetic experiments, N‐td substitutions accelerated the early phase of unfolding, while C‐td substitutions accelerated the late phase, suggesting independent domain unfolding. Only substitutions of the second Greek key pair of each crystallin domain slowed refolding. The second Greek keys may provide nucleation sites during the folding of the double‐Greek‐key crystallin domains.
The structure of human ubiquitin in 2‐methyl‐2,4‐pentanediol: A new conformational switch
Authors: Huang Kuo Ying , Amodeo Gabriele A. , Tong Liang , McDermott Ann
Published: January 2011

A new crystal structure of human ubiquitin is reported at 1.8 Å resolution. Compared with the other known crystal structure or the solution NMR structure of monomeric human ubiquitin, this new structure is similar in its overall fold but differs with respect to the conformation of the backbone in a surface‐exposed region. The conformation reported here resembles conformations previously seen in complex with deubiquinating enzymes, wherein the Asp52/Gly53 main chain and Glu24 side chain move. This movement exposes the backbone carbonyl of Asp52 to the exterior of the molecule, making it possible to engage in hydrogen‐bond contacts with neighboring molecules, rather than in an internal hydrogen bond with the backbone of Glu24. This particular crystal form of ubiquitin has been used in a large number of solid state NMR studies. The structure described here elucidates the origin of many of the chemical shift differences comparing solution and solid state studies.
On the analysis of protein–protein interactions via knowledge‐based potentials for the prediction of protein–protein docking
Authors: Feliu Elisenda , Aloy Patrick , Oliva Baldo
Published: January 2011

Development of effective methods to screen binary interactions obtained by rigid‐body protein–protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein–protein binding. We have derived empirical knowledge‐based potential functions for selecting rigid‐body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state‐of‐art benchmark dataset and on a decoy dataset of permanent interactions. Our results were compared with a residue‐pair potential scoring function (RPScore) and an atomic‐detailed scoring function (Zrank). We have combined knowledge‐based potentials to score protein–protein poses of decoys of complexes classified either as transient or as permanent protein–protein interactions. Being defined from residue‐pair statistical potentials and not requiring of an atomic level description, our method surpassed Zrank for scoring rigid‐docking decoys where the unbound partners of an interaction have to endure conformational changes upon binding. However, when only moderate conformational changes are required (in rigid docking) or when the right conformational changes are ensured (in flexible docking), Zrank is the most successful scoring function. Finally, our study suggests that the physicochemical properties necessary for the binding are allocated on the proteins previous to its binding and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid‐body docking methods.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures
Authors: Bernard Aymeric , Vranken Wim F. , Bardiaux Benjamin , Nilges Michael , Malliavin Thérèse E.
Published: January 2011

The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal choices for potential shape (bounds‐free log‐harmonic shape) and restraints weights. We compare the classical protocol with the Bayesian approach for more than 300 protein structures. We analyze the conformation similarity to the corresponding X‐ray crystal structure, the distribution of the conformations around their average, and independent validation criteria. On average, the log‐harmonic potential reduces the difference to the X‐ray crystal structure. If the log‐harmonic potential is used, the constant weighting tightens the distribution around the average conformation, with respect to the distributions obtained with Bayesian weighting. Conversely, the structure quality is improved by the Bayesian weighting over the classical procedure, whereas constant weighting worsens some criteria. The quality improvement obtained with the log‐harmonic potential coupled to Bayesian weighting validates this approach on a representative set of protein structures. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Rational design of new agrochemical fungicides using substructural descriptors
Authors: Speck‐Planche Alejandro , Guilarte‐Montero Lisvey , Yera‐Bueno Reider , Rojas‐Vargas Julio A , García‐López América , Uriarte Eugenio , Molina‐Pérez Enrique
Published: January 2011

BACKGROUND:The increasing resistance of several phytopathogenic fungal species to existing agrochemical fungicides has alarmed the worldwide scientific community. In an attempt to overcome this problem, a discriminant model based on substructural descriptors was developed from a heterogeneous database of compounds for the design of, search for and prediction of agrochemical fungicides.

RESULTS:The discriminant model classifies correctly 81.95% of the fungicides and 81.54% of the inactive compounds in the training series, with an accuracy of 81.72%. In the prediction series, the percentage of correct classification was 80.59 and 85.56% for fungicides and inactive compounds respectively, with an accuracy of 83.44%. Some fragments were extracted and their contributions were calculated. From the fragments that were determined to make positive contributions to the fungicidal activity, new molecules such as pyrrole derivatives were designed and the probabilities of their being fungicides were calculated. These molecules were correctly classified as potential fungicides.

CONCLUSION:The discriminant model based on substructural descriptors provides a promising methodology for the development of molecular patterns to be used in the design of, search for and prediction of agrochemical fungicides of wide spectrum. This constitutes an alternative for the discovery of compounds that are able to decrease crop losses caused by phytopathogenic fungal species. Copyright © 2011 Society of Chemical Industry
Field control of Fusarium ear rot, Ostrinia nubilalis (Hübner), and fumonisins in maize kernels
Authors: Mazzoni Emanuele , Scandolara Andrea , Giorni Paola , Pietri Amedeo , Battilani Paola
Published: January 2011

BACKGROUND: A 6 year study was conducted to evaluate the possible support of pesticides in mitigating mycotoxin contamination in maize grown in northern Italy. Different pesticides to control Ostrinia nubilalis (Hübner) (ECB), Fusarium verticillioides (Sacc.) Nirenb. and Aspergillus flavus Link were considered to check their efficacy and the best schedule to reduce fumonisin and aflatoxin contamination.

RESULTS: Fumonisin B1 (FB1) contamination at harvest has been reduced by ECB control, while the addition of ingredients targeted to F. verticillioides gave a limited advantage, mainly with low FB1 contamination; nevertheless, fusaria control is relevant in high‐risk conditions, when FB1 is likely to exceed the legal limit. The combination of fungal and pest control in a single spray at silk browning stage (BBCH 67) is the best way of application. These results are robust because they were obtained in a 6 year trial, with relevant differences in meteorological conditions, ECB and fungal presence and mycotoxin contamination.

CONCLUSION: Insecticides have been shown to give advantages in their application, while the low FB1 contamination in the final years of the study did not lead to conclusive data on the advantage of adding a fungicide. Chemicals applied did not modify A. flavus incidence or aflatoxin contamination (only detected in trace amounts). Copyright © 2011 Society of Chemical Industry
The relevance of background‐error covariance matrix localization: an application to the variational retrieval of vertical profiles from SEVIRI observations
Authors: Di Giuseppe F. , Marsigli C. , Paccagnella T.
Published: January 2011

A method to select local statistics for background‐error covariance matrix (B) determination is presented and applied to the 1D‐Var+nudging assimilation of SEVIRI radiances in the COSMO model. The system is designed as a post‐processing algorithm of an ensemble forecast system based on multi‐model initial and boundary conditions and perturbations of physical parametrization parameters. Ensemble spread maps are combined to identify regions (‘islands’) inside the model domain of uniform and large error. Thereafter B matrices are calculated using local statistics from the identified islands assuming the ensemble spread to be representative of the background‐error dispersion. This calculation is repeated at the beginning of each assimilation cycle to ensure the time evolution of the selected regions and thus the flow‐dependency of the background‐error covariance matrix statistics.

The benefit of calculating B using local statistics is then quantified by comparison to background covariance errors evaluated from global domain statistics. This is done using the same ensemble members over the whole domain, i.e. without applying the localization procedure. The standard NMC approach, which uses long time series of model departures calculated at different forecast times, is also compared for reference. Model departure statistics and comparison of the final analysis to independent observations from surface stations and satellite products highlight the relevance of the localization procedure even though the noisy structure of the variance profiles produces a substantial reduction in the number of valid retrieved profiles. The final findings show that the selective identification of areas of homogeneous spread/error is a suitable approach to characterize local error growth which can bring about sensible improvements in the forecast scores. Copyright © 2011 Royal Meteorological Society
The water vapour intercomparison effort in the framework of the Convective and Orographically‐induced Precipitation Study: airborne‐to‐ground‐based and airborne‐to‐airborne lidar systems
Authors: Bhawar R. , Di Girolamo P. , Summa D. , Flamant C. , Althausen D. , Behrendt A. , Kiemle C. , Bosser P. , Cacciani M. , Champollion C. , Di Iorio T. , Engelmann R. , Herold C. , Müller D. , Pal S. , Wirth M. , Wulfmeyer V.
Published: January 2011

An intensive water vapour intercomparison effort, involving airborne and ground‐based water vapour lidar systems, was carried out in the framework of the COPS experiment. The main objective of this paper is to provide accurate error estimates for these systems.

Comparisons between the ground‐based Raman lidar BASIL and the airborne CNRS DIAL (Differential Absorption Lidar) indicate a mean relative bias between the two sensors, calculated with respect to the mean value of −2.13% (−0.034 g kg−1) in the altitude region 0.5–3.5 km, while comparisons between BASIL and the airborne DLR DIAL lead to a mean relative bias of 1.87% (0.018 g kg−1) in this same altitude region.

Comparisons between the ground‐based UHOH DIAL and the CNRS DIAL indicate a bias of −3.2% (−0.37 × 1022 m−3) in the altitude range 1.5–4.5 km, while comparisons between the UHOH DIAL and the DLR DIAL indicate a bias of 0.83% (0.06 × 1022 m−3) in this same altitude range. Based on the available comparisons between the ground‐based Raman lidar BERTHA and the CNRS DIAL, the mean relative bias is found to be −4.37% (−0.123 g kg−1) in the altitude region 0.5–4.5 km. Comparisons between the ground‐based IGN Raman lidar and the CNRS DIAL indicate a bias of 3.18% (0.55 g kg−1) in the altitude range from 0.5 to 4.5 km, while comparisons between the CNRS DIAL and DLR DIAL result in a mean relative bias of 3.93% (1.1 × 1022 m−3) in the altitude interval 0.5–4.0 km. Based on the available statistics of comparisons, benefiting from the fact that the CNRS DIAL was able to be compared with all other lidar systems, and putting equal weight on the data reliability of each instrument, overall relative values for BASIL, BERTHA, IGN Raman lidar, UHOH DIAL, DLR DIAL, and CNRS DIAL, with respect to the mean value, are found to be −0.38, −2.60, 4.90, −1.43, −2.23 and 1.72%, respectively. Copyright © 2011 Royal Meteorological Society
Initiation of deep convection at marginal instability in an ensemble of mesoscale models: a case‐study from COPS
Authors: Barthlott Christian , Burton Ralph , Kirshbaum Daniel , Hanley Kirsty , Richard Evelyne , Chaboureau Jean‐Pierre , Trentmann Jörg , Kern Bastian , Bauer Hans‐Stefan , Schwitalla Thomas , Keil Christian , Seity Yann , Gadian Alan , Blyth Alan , Mobbs Stephen , Flamant Cyrille , Handwerker Jan
Published: January 2011

The present study investigates the initiation of precipitating deep convection in an ensemble of convection‐resolving mesoscale models. Results of eight different model runs from five non‐hydrostatic models are compared for a case of the Convective and Orographically‐induced Precipitation Study (COPS). An isolated convective cell initiated east of the Black Forest crest in southwest Germany, although convective available potential energy was only moderate and convective inhibition was high. Measurements revealed that, due to the absence of synoptic forcing, convection was initiated by local processes related to the orography. In particular, the lifting by low‐level convergence in the planetary boundary layer is assumed to be the dominant process on that day. The models used different configurations as well as different initial and boundary conditions. By comparing the different model performance with each other and with measurements, the processes which need to be well represented to initiate convection at the right place and time are discussed. Besides an accurate specification of the thermodynamic and kinematic fields, the results highlight the role of boundary‐layer convergence features for quantitative precipitation forecasts in mountainous terrain. Copyright © 2011 Royal Meteorological Society
Forecasting summer convection over the Black Forest: a case study from the Convective and Orographically‐induced Precipitation Study (COPS) experiment
Authors: Richard E. , Chaboureau J.‐P. , Flamant C. , Champollion C. , Hagen M. , Schmidt K. , Kiemle C. , Corsmeier U. , Barthlott C. , Di Girolamo P.
Published: January 2011

In the mid‐afternoon of 15 July 2007, during the Convective and Orographically‐induced Precipitation Study (COPS), in a very warm and dry environment, an isolated, short‐lived, deep convective system developed over the southern Black Forest. Most of the high‐resolution, convection‐permitting models involved in COPS were unable to capture this event whereas the Meso‐NH forecast was quite skilful. To assess the Meso‐NH performance further, the model results were carefully checked against the various and numerous COPS observations. In full agreement with clear‐air radar observations, model results underlined the triggering role of a low‐level convergence line that developed in the lee of the Feldberg. The main departure from the observations was found to be in the low‐level moisture fields, which appeared significantly moister in the model than in the observations and also slightly moister than in the other models. Sensitivity studies showed that this departure from the observations was strongly controlled by the initial surface moisture conditions. When the surface moisture was reduced by 20% or replaced by the value derived from a different analysis, the evolution of the planetary boundary layer was more accurately represented while the storm evolution was still correctly captured. These results demonstrate that the quality of the initial forecast cannot be ascribed to the moist bias of the model. It could therefore be hypothesized that the key parameters for a satisfactory forecast of this event lie more in the ability of the model to reproduce the dynamical forcing accurately than in the characteristics of the air‐mass instability. Copyright © 2011 Royal Meteorological Society
Unified treatment of dry convective and stratocumulus‐topped boundary layers in the ECMWF model
Authors: Köhler M. , Ahlgrimm M. , Beljaars A.
Published: January 2011

The unified parametrization of the dry boundary layer and stratocumulus in the ECMWF model is described using the eddy diffusivity mass‐flux framework. Model simulations are compared to observations at a few selected research field experiments, to ISCCP cloud cover, to LIDAR from space cloud observations, to SYNOP observations over Europe and to the climatology. It is shown that the new stratocumulus formulation improved the quality of the stratocumulus simulations rather dramatically. The key ingredients are: (i) mixing in moist conserved variables, (ii) diffusion related to cloud‐top cooling, (iii) an additional mass‐flux term, (iv) an entrainment parametrization and (v) a switching between shallow cumulus and stratocumulus based on lower tropospheric stability. To illustrate the relevance of various aspects, the sensitivity to different parameters is also presented. Copyright © 2011 Royal Meteorological Society
Cortisol outcomes among caucasian and latina/hispanic women caring for a family member with dementia: a preliminary examination of psychosocial predictors and effects of a psychoeducational intervention
Authors: Holland Jason M. , Thompson Larry W. , Cucciare Michael A. , Tsuda Akira , Okamura Hisayoshi , Spiegel David , Rasgon Natalie L. , Gallagher‐Thompson Dolores
Published: January 2011

A host of interventions are now known to be helpful to alleviate subjective distress and improve well‐being in dementia caregivers. However, few intervention studies have focused on measures of physical health, and none have examined cortisol as an outcome—despite the fact that cortisol is regarded as a crucial biological intermediary by which chronic stress leads to disease. In this study, we examined demographic and psychosocial factors as predictors of salivary cortisol at a baseline assessment, among a sample of 175 Latino/Hispanic and Caucasian women caring for a family member with dementia. We also examined the influence of a cognitive–behaviour‐based psychoeducational intervention (Coping with Caregiving) on cortisol at a post‐treatment assessment, compared with a minimal support condition. Results revealed that caregivers with high intensity caregiving situations, characterized by long hours of care and co‐residence with the care recipient, tended to have less adaptive cortisol patterns. However, these ‘at‐risk’ caregivers benefited most from the Coping with Caregiving intervention and had more normal cortisol patterns at post‐treatment, compared with caregivers in the control condition. Copyright © 2011 John Wiley & Sons, Ltd.
Imposing resolved turbulence in CFD simulations
Authors: Gilling L. , Sørensen N. N.
Published: January 2011

In large‐eddy simulations, the inflow velocity field should contain resolved turbulence. This paper describes and analyzes two methods for imposing resolved turbulence in the interior of the domain in Computational Fluid Dynamics simulations. The intended application of the methods is to impose resolved turbulence immediately upstream of the region or structure of interest. Comparing to the alternative of imposing the turbulence at the inlet, there is a large potential to reduce the computational cost of the simulation by reducing the total number of cells. The reduction comes from a lower demand for mesh resolution in the upstream part of the domain. The first method uses a modification of the source terms in the discrete Navier‐Stokes equations. In the second method, an actuator is used to impose the turbulence. The methods are tested, and the most accurate is shown to be the approach of modifying the source terms. None of the two methods can impose synthetic turbulence with good results, but it is shown that by running the turbulence field through a short precursor simulation, very good results are obtained. Copyright © 2011 John Wiley & Sons, Ltd.
Multivariate random forests
Authors: Segal Mark , Xiao Yuanyuan
Published: January 2011

Random forests have emerged as a versatile and highly accurate classification and regression methodology, requiring little tuning and providing interpretable outputs. Here, we briefly outline the genesis of, and motivation for, the random forest paradigm as an outgrowth from earlier tree‐structured techniques. We elaborate on aspects of prediction error and attendant tuning parameter issues. However, our emphasis is on extending the random forest schema to the multiple response setting. We provide a simple illustrative example from ecology that showcases the improved fit and enhanced interpretation afforded by the random forest framework. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 80‐87 DOI: 10.1002/widm.12

This article is categorized under:

Algorithmic Development > Hierarchies and Trees

Algorithmic Development > Ensemble Methods

Technologies > Machine Learning

Technologies > Prediction
Multivariate image mining
Authors: Herold Julia , Loyek Christian , Nattkemper Tim W.
Published: January 2011

Because of recent advances in sensor technology and a rapid increase in storage capacities, a growing number of intensity values can be recorded and associated with pixel coordinates using new imaging technologies. This growth in dimension can be observed in different scientific areas and this new category of images is referred to as multivariate images (MVIs). In these images, an almost arbitrary number of variables is associated with each pixel that represent, for instance, signal values at different time points or for different spectral bands or for different imaging parameters or modalities. Thus, these images can no longer be interpreted as gray value images or red, green, blue color images, and new information technologies are needed. In this review article, we summarize the different imaging technologies and recently published approaches to MVI mining with a special focus on biomedical applications. © 2011 John Wiley & Sons, Inc.WIREs Data Mining Knowl Discov2011 1 2‐13 DOI: 10.1002/widm.4

This article is categorized under:

Algorithmic Development > Biological Data Mining

Algorithmic Development > Spatial and Temporal Data Mining

Application Areas > Health Care

Technologies > Structure Discovery and Clustering
Classification and regression trees
Authors: Loh Wei‐Yin
Published: January 2011

Classification and regression trees are machine‐learning methods for constructing prediction models from data. The models are obtained by recursively partitioning the data space and fitting a simple prediction model within each partition. As a result, the partitioning can be represented graphically as a decision tree. Classification trees are designed for dependent variables that take a finite number of unordered values, with prediction error measured in terms of misclassification cost. Regression trees are for dependent variables that take continuous or ordered discrete values, with prediction error typically measured by the squared difference between the observed and predicted values. This article gives an introduction to the subject by reviewing some widely available algorithms and comparing their capabilities, strengths, and weakness in two examples. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 14‐23 DOI: 10.1002/widm.8

This article is categorized under:

Technologies > Classification

Technologies > Machine Learning

Technologies > Prediction

Algorithmic Development > Statistics
Accelerating data mining workloads: current approaches and future challenges in system architecture design
Authors: Choudhary Alok N. , Honbo Daniel , Kumar Prabhat , Ozisikyilmaz Berkin , Misra Sanchit , Memik Gokhan
Published: January 2011

Conventional systems based on general‐purpose processors cannot keep pace with the exponential increase in the generation and collection of data. It is therefore important to explore alternative architectures that can provide the computational capabilities required to analyze ever‐growing datasets. Programmable graphics processing units (GPUs) offer computational capabilities that surpass even high‐end multi‐core central processing units (CPUs), making them well‐suited for floating‐point‐ or integer‐intensive and data parallel operations. Field‐programmable gate arrays (FPGAs), which can be reconfigured to implement an arbitrary circuit, provide the capability to specify a customized datapath for any task. The multiple granularities of parallelism offered by FPGA architectures, as well as their high internal bandwidth, make them suitable for low complexity parallel computations. GPUs and FPGAs can serve as coprocessors for data mining applications, allowing the CPU to offload computationally intensive tasks for faster processing. Experiments have shown that heterogeneous architectures employing GPUs or FPGAs can result in significant application speedups over homogenous CPU‐based systems, while increasing performance per watt. © 2011 John Wiley & Sons, Inc.WIREs Data Mining Knowl Discov2011 1 41‐54 DOI: 10.1002/widm.9

This article is categorized under:

Application Areas > Data Mining Software Tools

Fundamental Concepts of Data and Knowledge > Key Design Issues in Data Mining

Technologies > Computer Architectures for Data Mining
Expression and Function of a Large Non‐coding RNA Gene XIST in Human Cancer
Authors: Weakley Sarah M. , Wang Hao , Yao Qizhi , Chen Changyi
Published: January 2011

Background

X inactive‐specific transcript (XIST) RNA is involved in X chromosome silencing in female cells and allows X chromosome equilibration with males. X inactive‐specific transcript expression has been found to be dysregulated in a variety of human cancers when compared to normal cells; meanwhile, the inactivated X chromosome has been noted to be conspicuously absent in human cancer specimens, whereas X chromosome duplications are widely noted. The specific pathways whereby changes in X chromosome status and XIST expression occur in cancer remain incompletely described. Nevertheless, a role for XIST in BRCA1‐mediated epigenetic activity has been proposed.

Methods

Here we review the data regarding XIST expression and X chromosome status in a variety of female, male, and non–sex‐related human cancers.

Conclusions

It is not yet known whether X chromosome duplication, XIST dysregulation, and over‐expression of X‐linked genes represent important factors in tumorgenesis or are simply a consequence of overall epigenetic instability in these cancers.
Shifting sources of soil labile organic carbon after termination of plant carbon inputs in a subtropical moist forest of southwest China
Authors: Feng Wenting , Schaefer Douglas A. , Zou Xiaoming , Zhang Min
Published: January 2011

Labile organic carbon (LOC) is a critical component of soil organic carbon (C) because of its intimate association with soil heterotrophic respiration and role in the decomposition of resistant soil organic matter. In a subtropical moist evergreen broad‐leaved forest of southwest China, we examined changes of LOC and its potential turnover time, microbial biomass C (MBC), and soil microbial activity of the organic and the 0–10 cm mineral soil layers with aboveground plant litter and belowground root treatments. In February of 2004, removal of organic layer, root‐trenching, and tree‐girdling treatments were applied alone and in combination to manipulate plant‐C inputs. In 2006, root‐trenching and tree‐girdling treatments did not significantly change LOC in the organic layer. In the 0–10 cm mineral soil layer, LOC increased substantially due to tree‐girdling treatment, especially in the plots of tree‐girdling and the combinations of three treatments, but this increase was absent in 2007. Soil MBC in these two layers generally did not change markedly after plant‐C inputs manipulations except significant increase under tree‐girdling treatment in 2006. The potential turnover times of LOC increased in all plots with the plant‐C inputs manipulations. The lack of influence of plant‐C inputs manipulations on LOC pools is likely due to high total soil organic C here, while insignificant changes of MBC suggest the soil microbes are not C limited in this forest. The changes of the potential turnover time of LOC imply that the sources of LOC have been shifted from fresh plant litter or root exudates to old soil organic C. Our results suggest that LOC recently derived from plants is preferred by microbes when available, but microbes can also use LOC from soil organic matter when fresh plant C is not available.
Dorsal Tangential View of the Wrist to Detect Screw Penetration to the Dorsal Cortex of the Distal Radius after Volar Fixed-Angle Plating
Authors: Ozer Kagan , Toker Serdar
Published: January 2011

Background

Extensor tendon irritation and attritional tendon ruptures are well-recognized complications, secondary to dorsal screw penetration following volar plating of the distal radius. Lateral and oblique views of the wrist have limited ability to detect such penetration, particularly at the ulnar side of the Lister's tubercle. In this report, we conducted an intraoperative fluoroscopic study to determine dorsal screw penetration in various positions of the wrist/forearm and compared the standard radiographic views (lateral, supination, and pronation views) with dorsal tangential view of the wrist.

Materials and Method

Standard lateral, oblique (in pronation and supination), and dorsal tangential views were obtained in 27 consecutive patients undergoing fixation a distal radius fractures using a volar plate. The number of penetrating screws in each dorsal compartment (second, third, fourth) was recorded in each view. Dorsal tangential view was obtained using a mini C-arm intraoperatively and sending the beam parallel to the dorsal aspect of the wrist in transverse plane.

Results

Of the 125 distal screws, 8 screws were seen to be penetrating the dorsal cortex in lateral and oblique views, whereas 11 screws were detected in dorsal tangential view.

Conclusion

The screw penetration to the third dorsal compartment was missed in standard views, but visualized in dorsal tangential view. We recommend the use of dorsal tangential view in addition to standard lateral and oblique views during volar plating of the distal radius.
Pilot Plant Recovery of Soybean Oleosome Fractions by an Enzyme‐Assisted Aqueous Process
Authors: Towa Lili T. , Kapchie Virginie N. , Hauck Catherine , Wang Hui , Murphy Patricia A.
Published: January 2011

An aqueous enzymatic procedure for oleosome fractionation from 25 g of soy flour was developed in our laboratory. This fractionation procedure was evaluated with 75 kg using pilot plant equipment to evaluate the effect of the scale‐up on the recovery, proximate composition, soybean storage protein profiles, and subcellular microstructure of oleosome fractions. The process included enzymatic hydrolysis, grinding, and centrifugation, respectively. Pilot‐scale grinding and centrifugation of the slurry were accomplished with a Stephan® Microcut mill grinder and a three phase decanter. A blender and swinging bucket rotor were used for the laboratory‐scale fractionation. The oleosome fractions recovered in the pilot plant were similar in oil and protein content to those obtained in the laboratory. The pilot‐scale process resulted in a significantly higher oil yield of 93.40% as total oleosomes compared to that of 76.83% achieved in the laboratory. Urea–SDS gel electrophoresis of proteins extracted from the oleosomes and supernatant from the pilot‐scale fractionation had similar profiles to those obtained in the laboratory. Electron microscopy verified that the structure of isolated oleosomes was virtually identical with that of in situ oleosomes. This work confirms that large‐scale fractionation of oleosomes from full fat soybean flour can be accomplished.
Age of picrite and picrodolerite magmatism in western Mongolia
Authors: Izokh A.E. , Vishnevskii A.V. , Polyakov G.V. , Shelepaev R.A.
Published: January 2011

The paper presents 39Ar/40Ar and UPb (SHRIMP zircon method) geochronological data on minor picrodolerite intrusions from western Mongolia. Picrodolerite magmatism in western Mongolia took place within different age intervals and in different geodynamic settings: accretionary–collisional Ꞓ1-2, ~510 Ma (Üüreg Nuur association, Hayrhan intrusion), intraplate D1, 410–390 Ma (Tsagaan Shuvuut Range, Mor’t Uula intrusion), intraplate D3–C1, 345–360 Ma (Altan Gadas, Tavtyn Hundiyn, and Hu Tsan Bulak intrusions), island-arc C2, 315–335 Ma (Dzahuy, Yaryn Had, and Javhlant intrusions), and intraplate P1, ~270 Ma (Dzaraa Uula intrusion).

Petrographic, mineralogical, and geochemical data permit distinguishing derivates of picrobasaltic (12–14 wt.% MgO) (Üüreg Nuur association, Tsagaan Shuvuut, Javhlant, Yaryn Had) and melabasaltic melts (7–10 wt.% MgO) (Mor’t Uula, Altan Gadas, Dzahuy, Dzaraa Uula) among picrodolerite magmatism in western Mongolia. Picritoids in these associations resulted from early olivine fractionation.

The Early Devonian picrites and picrodolerites of the Tsagaan Shuvuut Range and the olivine dolerites of the Mor’t Uula intrusion can be assigned to mafic magmatism in the Devonian large igneous province (LIP) in the North Mongolian megablock. The Late Devonian–Early Carboniferous picrodolerite intrusions in the Baruun Huuray zone (Altan Gadas) and Mongolian Altay (Tavtyn Hundiyn) are related to the Tien Shan LIP. Bimodal volcanism on the southern margin of the Hangayn Mts. (Dzaraa Uula), in the eastern segment of the Hanhöhiy Ridge (Dzagday Nuur, Hara Teg), and in the Argalantu trough (Tegshiyn Gol, Muhur Shurgah, and Deed Shurgah massifs) may be related to the Tarim LIP, where they are part of an Early Permian volcanoplutonic association. Carboniferous picrodolerite intrusions in the South Mongolian megablock and the Trans-Altai Gobi formed in subduction-related settings (Dzahuy, Yaryn Had, Javhlant).