bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying cysteines and histidines in transition‐metal‐binding sites using support vector machines and neural networks
Authors: Passerini Andrea , Punta Marco , Ceroni Alessio , Rost Burkhard , Frasconi Paolo 
Published: August 2006

AbstractAccurate predictions of metal‐binding sites in proteins by using sequence as the only source of information can significantly help in the prediction of protein structure and function, genome annotation, and in the experimental determination of protein structure. Here, we introduce a method for identifying histidines and cysteines that participate in binding of several transition metals and iron complexes. The method predicts histidines as being in either of two states (free or metal bound) and cysteines in either of three states (free, metal bound, or in disulfide bridges). The method uses only sequence information by utilizing position‐specific evolutionary profiles as well as more global descriptors such as protein length and amino acid composition. Our solution is based on a two‐stage machine‐learning approach. The first stage consists of a support vector machine trained to locally classify the binding state of single histidines and cysteines. The second stage consists of a bidirectional recurrent neural network trained to refine local predictions by taking into account dependencies among residues within the same protein. A simple finite state automaton is employed as a postprocessing in the second stage in order to enforce an even number of disulfide‐bonded cysteines. We predict histidines and cysteines in transition‐metal‐binding sites at 73% precision and 61% recall. We observe significant differences in performance depending on the ligand (histidine or cysteine) and on the metal bound. We also predict cysteines participating in disulfide bridges at 86% precision and 87% recall. Results are compared to those that would be obtained by using expert information as represented by PROSITE motifs and, for disulfide bonds, to state‐of‐the‐art methods. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Prediction of flammability speciation for the lower alkanes, carboxylic acids, and esters
Authors: Palucis M. , Glowienka T. , Van Brunt V. , Ervin R. , Chastain W. , Kline R. , Lodal P. 
Published: August 2006

AbstractA Gibbs energy minimization procedure is used to predict the flammability envelopes of alkanes, carboxylic acids, and acetates. In addition to providing the calculated adiabatic flame temperature (CAFT), the product profiles reveal regions of incomplete combustion products and the onset of methane formation above 0.0001 mole fraction. Temperatures at the predicted onset of methane production appear to be closely related to the temperature at the upper flammability limit (UFL). Although a fixed CAFT value could be related to the lower flammability limit (LFL), it was found that this was not the case with the UFL and only for acetic acid could a single CAFT value of 1200K be used to conservatively predict the flammable region. Rather, in general, a single CAFT value could not conservatively predict the upper flammable region. The predictions also reveal local maxima and minima in the concentrations of reaction products. These maps of incomplete combustion products for the flammability region predict that incomplete combustion products are produced at fuel/oxygen ratios significantly below the fuel/oxygen stoichiometric ratio. This region decreases as the limiting oxygen concentration is approached. © 2006 American Institute of Chemical Engineers Process Saf Prog, 2006
Retracted: Spatial distribution of beetle pests in precision integrated pest management in a food processing mill
Authors: Trematerra Pasquale , Gentile Paolo 
Published: August 2006

AbstractRetracted: P. Trematerra and P. Gentile. Spatial distribution of beetle pests in precision integrated Pest Management in a food processing mill, Pest Management Science. [DOI: 10.1002/ps.1250].
The above article, published online in EarlyView on 28 June 2006, has been retracted for legal reasons. Copyright © 2006 Society of Chemical Industry
On‐farm management practices to minimise off‐site movement of pesticides from furrow irrigation
Authors: Oliver Danielle P , Kookana Rai S 
Published: August 2006

AbstractOff‐site movement of pesticides from furrow‐irrigated agriculture has been a concern in the Ord River Irrigation Area, Western Australia. This paper reports on the effectiveness of incorporation of pesticides by cultivator or power harrows before irrigating, and spraying pesticides only onto beds to minimise off‐site transport. Incorporation of pesticides by power harrows prior to irrigation was found to be more effective in decreasing the off‐site transport of a more strongly sorbed pesticide, endosulfan. The average load of total endosulfan (α + β + sulfate) decreased by 74% (P < 0.01) from 11.41 g ha−1 from the conventionally treated bays to 2.96 g ha−1 from the incorporated irrigation bays. The total average load of atrazine leaving the irrigation bays was decreased by 81% (P < 0.05) from 87.82 g ha−1 under the conventional practice of spraying the whole field to 16.95 g ha−1 by spraying the beds only. A reduction of 52% in total average load of metolachlor was observed following incorporation with power harrows, but this was not significant. Incorporation by cultivator or by power harrows decreased the total load of atrazine or metolachlor leaving the irrigation bays over the whole irrigation period, but these treatments were not shown to be statistically significant, which may have been due to the limited number of field replicates. Incorporation of strongly sorbed pesticides (e.g. endosulfan) prior to irrigation significantly decreased the off‐site transport of these pesticides in a furrow irrigation system and may be a useful practice to minimise off‐site transport of other similar pesticides. Minimising off‐site transport of weakly sorbed pesticides (e.g. atrazine and metolachlor) from a furrow irrigation system is more difficult. The nature of furrow irrigation makes it highly conducive to pesticide transport, particularly of weakly sorbed pesticides, and further work is needed to develop strategies to minimise the movement of this group of pesticides to water bodies. Copyright © 2006 Society of Chemical Industry
Use of crop residues for the control of Meloidogyne incognita under laboratory conditions
Authors: PiedraBuena Ana , García‐Álvarez Avelino , Díez‐Rojo Miguel Á , Bello Antonio 
Published: August 2006

AbstractThis laboratory study evaluates the biofumigant effect of different organic materials with the aim of developing non‐chemical alternatives for the management of Meloidogyne incognita (Kofoid & White) Chitwood populations. Sources of organic material from the production system were selected with the aim of reducing agricultural residue accumulation problems as well as decreasing the costs due to the use of chemical fertilizers and pesticides. The selected materials were residues from pepper, strawberry, tomato and cucumber crops, orange juice industry residues, commercial manure and sheep manure, applied at different dosages. Two biofumigation assays were performed under laboratory conditions, using alkaline soils from the Torreblanca area (Murcia, Spain) and acidic soils from the Villa del Prado area (Madrid, Spain). The assays evaluated the effect of the treatments on M. incognita juveniles and other soil organisms, the nematode galling index on tomato roots (susceptible cv. Marmande) grown in the biofumigated soil and soil fertility parameters. The results showed that all biofumigant materials significantly decreased M. incognita populations and galling indices in tomato cv. Marmande. A greater effect was observed on galling indices when applying crop residues together with manure than with the residues alone. Biofumigation had a general beneficial effect on soil fertility, generally increasing nitrogen, organic carbon, pH and potassium levels, and also calcium levels when crop residues of pepper and strawberry were applied. There were no important variations in the number of saprophagous nematodes, dorylaimids and enchytraeids. Copyright © 2006 Society of Chemical Industry
Relationship between esterase activity and acrinathrin and methiocarb resistance in field populations of western flower thrips, Frankliniella occidentalis
Authors: Maymó Ana C , Cervera Amelia , Dolores Garcerá M , Bielza Pablo , Martínez‐Pardo Rafael 
Published: August 2006

AbstractThe western flower thrips, Frankliniella occidentalis (Pergande), is a serious pest in the south‐east of Spain owing to its direct feeding on crops, transmission of the tomato spotted wilt virus and its very high level of resistance to insecticides. Mechanisms of resistance were examined using field populations of F. occidentalis with different susceptibilities to acrinathrin, methiocarb (selective insecticides), endosulfan, metamidophos and deltamethrin (broad‐spectrum insecticides). Esterase activity towards α‐naphthyl acetate and p‐nitrophenyl acetate in resistant strains was significantly higher than in the reference strain (MLFOM) for both model substrates. This higher activity was significantly correlated with acrinathrin and methiocarb resistance. Copyright © 2006 Society of Chemical Industry
Advances in serviceability and strength of normal‐ and high‐strength concrete structures
Authors: Loo Yew‐Chaye , Huq Chowdhury Sanaul 
Published: August 2006

AbstractServiceability and strength of concrete structures have been a topic of intense research for many years. Reported herein is the work conducted in this area, especially in the past decade, which ranges from the development of the layered finite element method and the associated theoretical studies to elaborate laboratory tests of high‐strength concrete elements. In particular, serviceability studies reviewed include natural frequency, cracking and crack patterns, deflection and damping characteristics; strength investigations reviewed cover beams, slabs and walls, as well as the punching shear strength of flat plates. A long‐term on‐site study of column shortening in an 80‐storey residential building recently completed at Gold Coast in Southeast Queensland, Australia is also reported. In addition, a separate section discusses the serviceability studies specific for high‐strength concrete structures. Summarized herein is the review of research findings published during the period spanning mainly from 1995 to 2005. Relevant formulas and analytical procedures which may assist practising engineers in the design of concrete structures are reported for completion. Copyright © 2006 John Wiley & Sons, Ltd.
Electric transport perpendicular to the planes
Authors: Herper H. C. 
Published: August 2006

AbstractSince the discovery of the giant magnetoresistance (GMR) in magnetic multilayers, several theoretical descriptions have been used to determine the resistivity of such layered structures. The resistance for the current in direction of the planes of layers can easily be measured, and has been intensively studied theoretically. However, the investigation of the GMR for the current perpendicular to the planes (CPP) is slightly more difficult. Here, a microscopic formalism for the study of the CPP GMR is reported by making use of the Kubo–Greenwood equation. Within this method perturbations of the interfaces like interdiffusion, alloy formation, or impurities can easily be included, which is of importance, because the discussion of the GMR is always related to the structure of the interfaces. The presentation of the Kubo–Greenwood formalism for CPP transport is complemented by a brief discussion of some exemplary results. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Cover picture: Extrinsic defect structure of RE3Al5O12 garnets
Authors: Stanek C. R. , McClellan K. J. , Levy M. R. , Grimes R. W. 
Published: August 2006

AbstractThe cover picture of Rapid Research Letters refers to the article [1] by Chris Stanek et al. The image visually describes the results of calculations pertaining to the defect structure in rare earth aluminum garnet corresponding to Me2+ and Me4+ dopants. In particular, this result aids the development of garnet scintillators.
Scientific Highlights from the Ψk Network: Towards Atomistic Materials Design
Authors: Dederichs P. H. , Szotek Z. (Dzidka) , Ordejon P. 
Published: August 2006

AbstractThe Ψk network aims at encompassing the whole community of European groups working in the area of ab‐initio materials modelling, including very many small groups and isolated researchers. Historically, the activities started in the 1980s in Trieste with the workshop series entitled “Total Energies and Forces”. Since then, it has operated on the European level in various forms, with funding from various EC/EU and ESF sources, beginning more than 10 years ago with the EC's Human Capital and Mobility Programme. In that time, Ψk has done much to make Europe the leading area in the world for research in atomic‐scale ab‐initio computer simulation of all types of materials, their structures, properties, and processes. To a large extent, this has been done by nurturing scientific excellence and collaboration in what might be called “the Ψk family”. The Ψk Network is presently organized around 15 topical working groups. Over the years, the Ψk network organized three large scale conferences in Schwäbisch Gmünd, Germany (1996, 2000, 2005), attended by hundreds of scientists from all over the world. The next Ψk Conference is to be organized in Berlin in 2010. These Ψk Conferences are unique events fully dedicated to the ab‐initio research. In addition, the network organizes a variety of meetings and topical workshops every year.The core activities of the Ψk network involve editing every two months a Ψk newsletter with typically more than 100 pages, which contains a “Scientific Highlight”, announcements of conferences, workshops and vacant positions, news of various ESF and EU funded networks, including reports on workshops, and abstracts of submitted papers. The Ψk has its own web pages (http://psi‐k.dl.ac.uk) which inform about the Network, its structure, and how to get involved in Ψk activities. These web pages are also the repository of the Ψk newsletters and Scientific Highlights and details about the Ψk Workshops of the most recent years. The Ψk mailing list contains about 1700 e‐mail addresses from across the world, and all the important information about a variety of activities of the network is distributed across this list on a daily basis.The “Scientific Highlights” of the Ψk newsletters reflect the scientific activities of the network and aim at presenting reviews and current developments in the field. This special issue of physica status solidi (b) gives a collection of some of the most recent Highlight contributions to the Ψk newsletter. All manuscripts originally posted on the Ψk server were peer‐reviewed by two referees and accepted according to the standards of pss. They are published here partly in revised or updated version. We hope that the readership of the journal will benefit from the quality of the research they report on and the high level of the presentations.
Power and sample size considerations in clinical trials with competing risk endpoints
Authors: Maki Ellen 
Published: August 2006

AbstractIn clinical trials with a time‐to‐event endpoint, subjects are often at risk for events other than the one of interest. When the occurrence of one type of event precludes observation of any later events or alters the probably of subsequent events, the situation is one of competing risks. During the planning stage of a clinical trial with competing risks, it is important to take all possible events into account. This paper gives expressions for the power and sample size for competing risks based on a flexible parametric Weibull model. Nonuniform accrual to the study is considered and an allocation ratio other than one may be used. Results are also provided for the case where two or more of the competing risks are of primary interest. Copyright © 2006 John Wiley & Sons, Ltd.
A case study comparing a randomized withdrawal trial and a double‐blind long‐term trial for assessing the long‐term efficacy of an antidepressant
Authors: Mallinckrodt Craig , Chuang‐Stein Christy , McSorley Paul , Schwartz Jeffrey , Archibald Donald G. , Perahia David G. , Detke Michael J. , Alphs Larry 
Published: August 2006

AbstractAssessing long‐term efficacy in psychiatric drugs involves a number of complex questions, and the priaority of these questions is different for different disorders and for different stakeholders. Therefore, it is essential that we not adopt a one‐method‐fits‐all approach, but rather adapt the specific details of the designs and analysis of data from long‐term trials to individual disease states. Randomized withdrawal (RW) designs, even though addressing a specific question of particular interest, face some difficult methodological and ethical challenges. A less common alternative design, termed the double‐blind long‐term efficacy (DBLE) design, is logistically similar to traditional responder extension designs. However, use of an analytic approach that includes all randomized patients rather than only the selected subset that continued beyond acute treatment avoids the major criticism of the extender design. The present paper illustrates the attributes of the RW and DBLE designs by analyzing data from trials adopting these designs. The RW and DBLE designs address different questions, and are thus not directly comparable. Potential benefits of the DBLE design include: (1) the parsimonious use of patients and the resultant reduced exposure to placebo as each patient can contribute to multiple developmental objectives; (2) the results are generalizable to actual clinical practice as the design matches treatment guidelines; and, (3) results of safety assessments are meaningful as they involve all randomized patients. Our case study suggests that the DBLE design can provide definitive answers to important questions and may be a useful design for assessing long‐term treatment effects. Copyright © 2006 John Wiley & Sons, Ltd.
Effect of rosmarinus officinalis in modulating 7,12‐dimethylbenz(a)anthracene induced skin tumorigenesis in mice
Authors: Sancheti Garima , Goyal P. K. 
Published: August 2006

AbstractThe chemopreventive potential of rosemary (Rosmarinus officinalis) on 7,12‐dimethlybenz(a)anthracene (DMBA) initiated and croton oil promoted mouse skin tumorigenesis was assessed. The modulatory effects of R. officinalis was monitored on the basis of the average latency period, tumor incidence, tumor burden, tumor yield, tumor weight and diameter as well as lipid peroxidation and glutathione level. The results indicate that R. officinalis leaves extract could prolong the latency period of tumor occurrence, decrease the tumor incidence, tumor burden and tumor yield. The average weight and diameter of tumors recorded were comparatively lower in the rosemary extract treated mouse groups. The level of lipid peroxidation was significantly reduced in blood serum and liver. Furthermore, depleted levels of glutathione were restored in RE‐administered animal groups. Thus, at a dose rate of 500 mg/kg body wt/mouse, the oral administration of rosemary extract was found to be significantly protective against two‐stage skin tumorigenesis. Copyright © 2006 John Wiley & Sons, Ltd.
A review of the bioactivity of south African herbal teas: rooibos (Aspalathus linearis) and honeybush (Cyclopia intermedia)
Authors: McKay Diane L. , Blumberg Jeffrey B. 
Published: August 2006

AbstractRooibos (Aspalathus linearis) and honeybush (Cyclopia intermedia) are popular tisanes in their native South Africa and have a growing worldwide market. Both herbal teas are used traditionally for medicinal purposes and are rich in polyphenols with rooibos a rare source of the dietary dihydrochalcones, aspalathin and nothofagin. The principal polyphenols in honeybush include the xanthone mangiferin and the flavonones hesperitin and isokuranetin. Despite their divergent phytochemical and nutrient compositions, rooibos and honeybush share potent antioxidant and antimutagenic activities in vitro. Animal model studies indicate both herbal teas possess potent antioxidant, immune‐modulating and chemopreventive actions. However, human studies of rooibos are limited and of honeybush are absent. No adverse effects of rooibos or honeybush consumption as tisanes have been reported. Copyright © 2006 John Wiley & Sons, Ltd.
QSAR Prediction of the Penetration of Drugs Across a Polydimethylsiloxane Membrane
Authors: Ma Weiping , Luan Feng , Zhao Chunyan , Zhang Xiaoyun , Liu Mancang , Hu Zhide , Fan Botao 
Published: August 2006

AbstractA quantitative structure–activity relationship was developed by the Heuristic Method (HM) to study the penetration of 245 drugs across a polydimethylsiloxane membrane. The descriptors in this study were calculated by the software CODESSA. HM was used both for preselecting molecular descriptors and for developing the linear model. Logarithms of the maximum steady‐state flux (J) values are correlated with four descriptors, with a squared correlation coefficient (R2) of 0.844 and root‐mean‐square error of 0.438, respectively. These four theoretical molecular descriptors are count of H‐acceptor sites, gravitation index, H‐donors charged surface area, and weighted positive‐charged partial surface area. The rationality of the descriptors was evaluated by similarity analysis, while the stability and validity of the model was evaluated by validation. This paper provides a simple and straightforward way to predict the log J values of the drugs from their structures alone and gives some insight into structural features related to the penetration of drugs.
Theory of chemical bonds in metalloenzymes III: Full geometry optimization and vibration analysis of ferredoxin‐type [2Fe–2S] cluster
Authors: Shoji Mitsuo , Koizumi Kenichi , Taniguchi Takeshi , Kitagawa Yasutaka , Yamanaka Shusuke , Okumura Mitsutaka , Yamaguchi Kizashi 
Published: August 2006

AbstractThe nature of chemical bonds in a ferredoxin‐type [2Fe–2S] cluster has been investigated on the basis of natural orbitals and several bond indices developed in Parts I and II of this study. The broken‐symmetry hybrid density functional theory (BS‐HDFT) with spin projection approach has been applied to elucidate the natural orbitals and occupation numbers for a model compound [Fe2S2(SCH3)4] (1), which is used to calculate the indices. The molecular structure, vibration frequencies, electronic structures, and magnetic properties in both oxidized and reduced forms of 1 have been calculated and compared with the experimental values. The optimized molecular structures after approximate spin projection have been in good agreement with experimental data. The structure changes upon one‐electron reduction have been slight (<0.1 Å) and only limited around one side of the Fe atom. Raman and infrared (IR) spectra have been calculated, and their vibration modes have been assigned using the bridging34S isotope substitution. Their magnetic properties have been examined in terms of spin Hamiltonians that contain exchange interactions and double exchange interactions. The BS‐HDFT methods have provided the magnetic parameters; i.e., effective exchange integral (J) values and valence delocalization (B) values, which agree with the experimental results. It is found that large charge transfer (CT) from the bridging sulfur to the iron atoms has led to the strong antiferromagnetic interactions between iron atoms. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007