bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computations on the Ã–X̃ transition of isoprene‐OH‐O2 peroxy radicals
Authors: Dibble Theodore S. 
Published: April 2005

AbstractCalculations are carried out on the Ã state of HO2, CH3O2, and CH3CH2O2 and 10 isomers and conformers of the isoprene‐OH‐O2 peroxy radicals derived from OH addition to isoprene (2‐methyl‐1,3‐butadiene). In addition to calculating vertical and adiabatic excitation energies, we consider the effect of excitation on molecular structure, and examine the OO stretching frequencies, which are known to be major features in the absorption spectra of the Ã states of the smaller radicals. The two methods used are the configuration interaction with single excitations (CIS) method and time‐dependent density functional theory (TD‐DFT), both with a range of basis sets up to 6‐311++G(2df,2pd). TD‐DFT overestimates excitation energies considerably, while CIS tends to underestimate them slightly. TD‐DFT does seem to capture the trend in excitation energy vs. size for the smaller peroxy radicals. Conformation and configuration strongly affect the excitation energies of the peroxy radicals from isoprene. CIS calculations indicate that the intramolecular OHO hydrogen bonds, present in the ground state of some peroxy radicals from isoprene, are weakened or broken in the excited state, while TD‐DFT calculations suggest they are retained. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 836–845, 2005
New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models
Authors: Oda Akifumi , Yamaotsu Noriyuki , Hirono Shuichi 
Published: April 2005

AbstractThe heme protein, cytochrome P450, is an oxidoreductase that plays an important role in drug metabolism. To model P450s using molecular mechanics methods and classical molecular dynamics simulations, force field parameters and atomic charges are required. Because these parameters are generally obtained by quantum chemical methods, an appropriate simplified model for the iron–porphyrin system was needed. In this study, two models with a five‐coordinated Fe(III) mimicking the sextet spin state of P450s are proposed, which are optimized by semiempirical and ab initio unrestricted Hartree–Fock methods. The results produced using the simpler of the two models were similar to those of the more complex model; therefore, the more simplified model of P450 can be used without a loss of accuracy. Furthermore, several quantum chemical calculations were carried out on the simpler model to investigate which method was most suitable for iron–porphyrin systems. The results calculated by hybrid density functional theory (DFT), with the MIDI basis set for iron, reproduced the three‐dimensional structures determined by X‐ray diffraction and extended X‐ray absorption fine‐structure experiments. From these results, atomic charges and force‐field parameters for molecular mechanics and molecular dynamics calculations were obtained. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 818–826, 2005
Interfaces between dendritic cells, other immune cells, and nerve fibres in mouse Peyer's patches: Potential sites for neuroinvasion in prion diseases
Authors: Defaweux Valérie , Dorban Gauthier , Demonceau Caroline , Piret Joëlle , Jolois Olivier , Thellin Olivier , Thielen Caroline , Heinen Ernst , Antoine Nadine 
Published: April 2005

AbstractIn this study, we examined where immune cells and nerve fibres are located in mouse Peyer's patches, with a view to identifying potential sites for neuroinvasion by prions. Special attention was paid to dendritic cells, viewed as candidate transporters of infectious prion. Double immunofluorescence labellings with anti‐CD11c antibody and marker for other immune cells (B cells, T cells, follicular dendritic cells) were carried out and analysed by confocal microscopy on Peyer's patch cryosections. To reveal the extensive ganglionated networks of the myenteric and submucosal plexi and the sparse meshworks of nerve strands, we used antibodies directed against different neurofilament subunits or against glial fibrillary acidic protein. In the suprafollicular dome, dendritic cells connect, via their cytoplasmic extensions, enterocytes with M cells of the follicle‐associated epithelium. They are also close to B and T cells. Nerve fibres are detected in the suprafollicular dome, notably in contact with dendritic cells. Similar connections between dendritic cells, T cells, and nerve fibres are seen in the interfollicular region. Germinal centres are not innervated; inside them dendritic cells establish contacts with follicular dendritic cells and with B cells. After immunolabelling of normal prion protein, dendritic cells of the suprafollicular dome are intensely positive labelled. Microsc. Res. Tech. 66:1–9, 2005. © 2005 Wiley‐Liss, Inc.
Influence of nitrogen and elemental‐sulfur fertilization on sulfur oxidation and mineralization in relation to soil moisture on a calcareous soil of the Inner Mongolia steppe of China
Authors: Wang Shiping , Wang Yanfen , Haneklaus Silvia , Xing Xuerong , Hu Zhengyi , Fan Xiaohui , Chen Zuozhong , Schnug Ewald 
Published: April 2005

AbstractGrassland‐livestock farming is the main agricultural activity in the Inner Mongolia steppe of China. It has been estimated that more than 80% of the grasslands suffer from sulfur (S) deficiency in this region. In an incubation study and a greenhouse experiment with alfalfa, the influence of soil moisture (40% and 70% water‐holding capacity, WHC), nitrogen (0 and 200 mg N (kg soil)–1 as NH4NO3), and elemental sulfur (eS; 0 and 300 mg S (kg soil)–1) amendments on the apparent eS oxidation, eS‐oxidation rate, net S‐mineralization rate, and S uptake of alfalfa were studied. After 28 d of incubation, the eS‐oxidation rate was four times higher at 70% than at 40% WHC if no N was applied. With N application, soil moisture had only minor effects on eS oxidation during the whole incubation period. In the greenhouse experiment, lower values for eS‐oxidation rate and net S‐mineralization rate were found if no N was applied. Application of N and eS significantly increased alfalfa growth and S uptake. The results of both experiments suggest that combined N and eS applications are the best way to alleviate S deficiency on these calcareous soils.
Adaptation of Medicago sativa cv. Gabès to long‐term NaCl stress
Authors: Boughanmi Néziha , Michonneau Philippe , Daghfous Doraïd , Fleurat‐Lessard Pierrette 
Published: April 2005

AbstractThe perennial Medicago sativa cv. Gabès is widely grown on saline soils in Tunisian oases. The mechanisms by which this NaCl‐tolerant cultivar maintains a positive growth balance were analyzed. In this plant of considerable agronomic interest, biochemical analyses were conducted in order to study the effects of salinity on mature leaves. Free‐radical detoxification mechanisms and changes induced by the accumulation of reactive oxygen species (ROS) in response to the NaCl stress were compared between the upper (young) and lower (old) carbohydrate source leaves. Long‐term NaCl (150 mM) treatment significantly reduced the size of source leaves supporting growth. Salinity damage was greater in the lower than in the upper leaves. This damage was associated with a high Na+ : K+ ratio and a decrease in the activity of H2O2‐scavenging enzymes, leading to lipid peroxidation. In lower source leaves that were mainly affected by ionic stress, superoxide dismutase (SOD) was overexpressed and guaiacol peroxidase (GPX) activity increased. In contrast, in upper source leaves that were mainly exposed to water deficit, catalase and ascorbate peroxidase (APX) activities increased whereas GPX activity was unchanged. The upper source leaves maintained adequate ionic and water status and an efficient ROS detoxification, allowing sinks to be supplied with photoassimilates and maintaining a positive growth balance in this cultivar of alfalfa.
Medium‐ and short‐term available organic matter, microbial biomass, and enzyme activities in soils under Pinus sylvestris L. and Robinia pseudoacacia L. in a sandy soil in NE Saxony, Germany
Authors: Landgraf Dirk , Wedig Sven , Klose Susanne 
Published: April 2005

AbstractTotal, mobile, and easily available C and N fractions, microbial biomass, and enzyme activities in a sandy soil under pine (Pinus sylvestris L.) and black locust (Robinia pseudoacacia L.) stands were investigated in a field study near Riesa, NE Germany. Samples of the organic layers (Oi and Oe‐Oa) and the mineral soil (0–5, 5–10, 10–20, and 10–30 cm) were taken in fall 1999 and analyzed for their contents of organic C and total N, hot‐water‐extractable organic C and N (HWC and HWN), KCl‐extractable organic C and N (Corg(KCl) and Norg(KCl)), NH$ _4^+ $‐N and NO$ _3^- $‐N, microbial‐biomass C and N, and activities of β‐glucosidase and L‐asparaginase. With exception of the HWC, all investigated C and N pools showed a clear response to tilling, which was most pronounced in the Oi horizon. Compared to soils under pine, those under black locust had higher contents of medium‐ and short‐term available C (HWC, Corg(KCl)) and N (HWN, Norg(KCl)), mineral N (NH$ _4^+ $‐N, NO$ _3^- $‐N), microbial‐biomass C and N, and enzyme activities in the uppermost horizons of the soil. The strong depth gradient found for all studied parameters was most pronounced in soils under black locust. Microbial‐biomass C and N and enzyme activities were closely related to the amounts of readily mineralizable organic C (HWC and Corg(KCl)). However, the presented results implicate a faster C and N turnover in the top‐soil layers under black locust caused by higher N‐input rates by symbiotic N2 fixation.
Bodensystematik und Bodenklassifikation Teil II: Zur Situation in der deutschen Bodenkunde
Authors: Albrecht Christoph , Jahn Reinhold , Huwe Bernd 
Published: April 2005

AbstractIn Deutschland werden Böden mit einem Ordnungssystem beschrieben, welches eine Mischung aus einer Systematik und einer Klassifikation ist. Damit wird versucht, gleichzeitig auf wissenschaftliche und praktische Anforderungen zu reagieren. Die Definitionen der Bodenhorizonte und ‐profile haben eine Struktur, mit der subjektive Interpretationen und ein relativ freier Umgang mit vorhandenen Grenzwerten möglich sind. Infolgedessen kommt es zu Inkonsequenzen beim Aufbau des Bodenordnungssystems und zu Problemen bei der Bodenansprache. Den bodensystematischen Angaben fehlt dann oft die Qualität, die für die Nutzung in weiteren Anwendungen nötig wäre.Mit Fallbeispielen werden Probleme bei der Identifikation von Horizonten und Böden aufgezeigt. Zur Problemlösung wird vorgeschlagen, sowohl eine wissenschaftlich‐beschreibende Bodensystematik als auch einfach und objektiv anwendbare Bestimmungsschlüssel für Horizonte und Böden zu entwickeln bzw. weiter zu entwickeln. Seit längerem ist in der deutschen Bodenkunde eine Entwicklung weg von der deskriptiven Systematik zu einer grenzwertbasierten Klassifikation zu erkennen, obwohl beide Ordnungssysteme parallel verwendet werden sollten. Diese Tendenz zeigt sich auch in der 5. Auflage der Bodenkundlichen Kartieranleitung, die einen Bestimmungsschlüssel für die Abteilungen, Klassen und Typen der deutschen Bodensystematik enthält. Eigenschaften und Bedeutung des Schlüssels werden kurz betrachtet und weitere Notwendigkeiten für die Strukturierung bodenkundlichen Wissens und deren Weitergabe an die Praxis erörtert.
Ability of different soil extraction methods to predict potassium release from soil in ley over three consecutive years
Authors: Øgaard Anne Falk , Krogstad Tore 
Published: April 2005

AbstractTo avoid over‐fertilization of potassium (K) and thereby a mineral composition in the grass crop not optimal for animal health, estimation of K release from soil is important. The analytical methods should therefore predict the total K release. Furthermore, to minimize costs for the farmers they should provide information which remains valid over a period of several years.The relationship between different soil extraction procedures for K and K uptake in ley for three subsequent years after soil sampling was studied in 19 field experiments on a range of mineral soil types in Norway. Potassium determined with solutions that extracted exchangeable K or parts of exchangeable K (0.01 M CaCl2, 0.5 M NaHCO3, 1 M NH4oAc, or ammonium acetate lactate) was significantly (p < 0.05) related to the K yield only in the 1st yr after soil sampling. Potassium extracted with boiling in 1 M or 2 M HNO3 was significantly related to the K yield only in the 2nd and 3rd yr. Potassium extracted with cold 2 M HCl, boiling 0.1 M HNO3 or 0.5 M HNO3 was significantly related to the K yield in all 3 yr after soil sampling. Among these extractants, 0.1 M and 0.5 M HNO3‐extractable K were better predictors of K uptake than 2 M HCl‐extractable K. These three extractants release some non‐exchangeable K in addition to exchangeable K. The fraction of 1 M HNO3‐K extractable with 0.1 M HNO3 varied from 4% to 45%, whereas from 15% to 78% of 1 M HNO3‐K was extractable with 0.5 M HNO3. Consequently, the more easily releasable fraction of K extracted by boiling with 1 M HNO3 varied considerably between different sites.
Effects of rice‐straw and phosphorus application on production and emission of methane from tropical rice soil
Authors: Rath Arun Kumar , Ramakrishnan B. , Rao V. R. , Sethunathan N. 
Published: April 2005

AbstractRice‐straw amendment increased methane production by 3‐fold over that of unamended control. Application of P as single superphosphate at 100 μg (g soil)–1 inhibited methane (CH4) production distinctly in flooded alluvial rice soil, in the absence more than in the presence of rice straw. CH4 emission from rice plants (cv. IR72) from alluvial soil treated with single superphosphate as basal application, in the presence and absence of rice straw, and held under non‐flooded and flooded conditions showed distinct variations. CH4 emission from non‐flooded soil amended with rice straw was high and almost similar to that of flooded soil without rice‐straw amendment. The cumulative CH4 efflux was highest (1041 mg pot–1) in rice‐straw‐amended flooded soil. Appreciable methanogenic reactions in rice‐straw‐amended soils were evident under both flooded and non‐flooded conditions. Rice‐straw application substantially altered the balance between total aerobic and anaerobic microorganisms even in non‐flooded soil. The mitigating effects of single‐superphosphate application or low‐moisture regime on CH4 production and emission were almost nullified due to enhanced activities of methanogenic archaea in the presence of rice straw.
Hepatomegaly in transgenic mice expressing the homeobox gene Cux‐1
Authors: Vanden Heuvel Gregory B. , Brantley Jennifer G. , Alcalay Neal I. , Sharma Madhulika , Kemeny Gabor , Warolin Joshua , Ledford Aric W. , Pinson David M. 
Published: April 2005

AbstractCux‐1 is a member of a family of homeobox genes structurally related to Drosophila Cut. Mammalian Cut proteins function as transcriptional repressors of genes specifying terminal differentiation in multiple cell lineages. In addition, mammalian Cut proteins serve as cell‐cycle‐dependent transcriptional factors in proliferating cells, where they function to repress expression of the cyclin kinase inhibitors p21 and p27. Previously we showed that transgenic mice expressing Cux‐1 under control of the CMV immediate early gene promoter develop multiorgan hyperplasia. Here we show that mice constitutively expressing Cux‐1 exhibit hepatomegaly correlating with an increase in cell proliferation. In addition, the increase in Cux‐1 expression in transgenic livers was associated with a decrease in p21, but not p27, expression. Within transgenic livers, Cux‐1 was ectopically expressed in a population of small cells, but not in mature hepatocytes, and many of these small cells expressed markers of proliferation. Transgenic livers showed an increase in α‐smooth muscle actin, indicating activation of hepatic stellate cells, and an increase in cells expressing chromogranin‐A, a marker for hepatocyte precursor cells. Morphological analysis of transgenic livers revealed inflammation, hepatocyte swelling, mixed cell foci, and biliary cell hyperplasia. These results suggest that increased expression of Cux‐1 may play a role in the activation of hepatic stem cells, possibly through the repression of the cyclin kinase inhibitor p21. © 2005 Wiley‐Liss, Inc.
Hyperplastic perilobar nephroblastomatosis: Long‐term survival of 52 patients
Authors: Perlman Elizabeth J. , Faria Paulo , Soares Andreia , Hoffer Fred , Sredni Simone , Ritchey Michael , Shamberger Robert C. , Green Daniel , Beckwith J.B. 
Published: April 2005

AbstractBackgroundThis study provides insight into the clinical behavior, diagnostic complexities, and long‐term management of patients with hyperplastic perilobar nephroblastomatosis (HPLN).ProcedureFifty‐two patients with HPLN with available long‐term follow‐up were retrospectively analyzed for pathologic, radiologic, and clinical features.ResultsThe mean age at diagnosis was 16 months; the lesions were bilateral in 49 patients. Of 33 patients who initially underwent diagnostic biopsy and adjuvant chemotherapy, 18 (55%) developed Wilms tumor (WT) at a mean of 35 months from diagnosis. Of 16 patients whose initial therapy included nephrectomy and adjuvant therapy, three (19%) developed WT at a mean of 36 months from diagnosis. All three patients who underwent initial diagnostic biopsy and received no adjuvant therapy during their initial course developed WT 4, 4, and 10 months following diagnosis. 24/52 patients developed either a single (13 patients) or multiple (11 patients) WT throughout their course; 8/24 (33%) of WT were anaplastic. The time from initial diagnosis to the development of the last WT ranged from 13 to 116 months (mean 42 months). Three children with HPLN died of WT at 3, 5, and 6 years of age; 2/3 were anaplastic.ConclusionsHPLN is a self‐limited, pre‐neoplastic proliferative process associated with a high risk of developing WT. The accurate diagnosis and the choices of therapy during the often‐complex course of HPLN depend on the availability and accurate interpretation of a combination of pathologic, radiologic, and clinical information. When such information is appropriately obtained, the long‐term survival of patients with HPLN is excellent. © 2005 Wiley‐Liss, Inc.
Comparative molecular dynamics simulations of HIV‐1 integrase and the T66I/M154I mutant: Binding modes and drug resistance to a diketo acid inhibitor
Authors: Brigo Alessandro , Lee Keun Woo , Fogolari Federico , Mustata Gabriela Iurcu , Briggs James M. 
Published: April 2005

AbstractHIV‐1 IN is an essential enzyme for viral replication and an interesting target for the design of new pharmaceuticals for use in multidrug therapy of AIDS. L‐731,988 is one of the most active molecules of the class of β‐diketo acids. Individual and combined mutations of HIV‐1 IN at residues T66, S153, and M154 confer important degrees of resistance to one or more inhibitors belonging to this class. In an effort to understand the molecular mechanism of the resistance of T66I/M154I IN to the inhibitor L‐731,988 and its specific binding modes, we have carried out docking studies, explicit solvent MD simulations, and binding free energy calculations. The inhibitor was docked against different protein conformations chosen from prior MD trajectories, resulting in 2 major orientations within the active site. MD simulations have been carried out for the T66I/M154I DM IN, DM IN in complex with L‐731,988 in 2 different orientations, and 1QS4 IN in complex with L‐731,988. The results of these simulations show a similar dynamical behavior between T66I/M154I IN alone and in complex with L‐731,988, while significant differences are observed in the mobility of the IN catalytic loop (residues 138–149). Water molecules bridging the inhibitor to residues from the active site have been identified, and residue Gln62 has been found to play an important role in the interactions between the inhibitor and the protein. This work provides information about the binding modes of L‐731,988, as well as insight into the mechanism of inhibitor–resistance in HIV‐1 integrase. Proteins 2005. © 2005 Wiley‐Liss, Inc.
The CCPN data model for NMR spectroscopy: Development of a software pipeline
Authors: Vranken Wim F. , Boucher Wayne , Stevens Tim J. , Fogh Rasmus H. , Pajon Anne , Llinas Miguel , Ulrich Eldon L. , Markley John L. , Ionides John , Laue Ernest D. 
Published: April 2005

AbstractTo address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR community (CCPN) created a “Data Model” that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high‐throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Quantum chemical and statistical study of megazol‐derived compounds with trypanocidal activity
Authors: Rosselli F. P. , Albuquerque C. N. , da Silva A. B. F. 
Published: April 2005

AbstractIn this work we performed a structure–activity relationship (SAR) study with the aim to correlate molecular properties of the megazol compound and 10 of its analogs with the biological activity against Trypanosoma cruzi (trypanocidal or antichagasic activity) presented by these molecules. The biological activity indication was obtained from in vitro tests and the molecular properties (variables or descriptors) were obtained from the optimized chemical structures by using the PM3 semiempirical method. It was calculated ∼80 molecular properties selected among steric, constitutional, electronic, and lipophilicity properties. In order to reduce dimensionality and investigate which subset of variables (descriptors) would be more effective in classifying the compounds studied, according to their degree of trypanocidal activity, we employed statistical methodologies (pattern recognition and classification techniques) such as principal component analysis (PCA), hierarchical cluster analysis (HCA), K‐nearest neighbor (KNN), and discriminant function analysis (DFA). These methods showed that the descriptors molecular mass (MM), energy of the second lowest unoccupied molecular orbital (LUMO+1), charge on the first nitrogen at substituent 2 (qN′), dihedral angles (D1 and D2), bond length between atom C4 and its substituent (L4), Moriguchi octanol‐partition coefficient (MLogP), and length‐to‐breadth ratio (L/Bw) were the variables responsible for the separation between active and inactive compounds against T. cruzi. Afterwards, the PCA, KNN, and DFA models built in this work were used to perform trypanocidal activity predictions for eight new megazol analog compounds. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005