bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimal structural requirements for root effect: Crystal structure of the cathodic hemoglobin isolated from the antarctic fish Trematomus newnesi
Authors: Mazzarella Lelio , Bonomi Giovanna , Lubrano Maria C. , Merlino Antonello , Riccio Antonio , Vergara Alessandro , Vitagliano Luigi , Verde Cinzia , di Prisco Guido 
Published: November 2005

AbstractThe cathodic hemoglobin component of the Antarctic fish Trematomus newnesi (HbCTn) is a Root‐effect protein. The interpretation of its functional properties in relation to its sequence is puzzling. Indeed, HbCTn sequence is characterized by an extremely low histidyl content, and in particular by the lack of His146β and His69β, which are believed to be important in Bohr and Root effects, respectively. Furthermore, previous analyses suggested that the local environment of Asp95α, Asp99β, and Asp101β should not be appropriate for the formation of Asp–Asp interactions, which are important for the Root effect. Here, we report the high‐resolution crystal structure of the deoxy form of HbCTn. Our data provide a structural interpretation for the very low oxygen affinity of the protein and insights into the structural determinants of the Root effect protein. The structure demonstrates that the presence of Ile41α and Ser97α at the α1β2 interface does not prevent the formation of the inter‐Asp interactions in HbCTn, as previous studies had suggested. The present data indicate that the hydrogen bond formed between Asp95α and Asp101β, which is stabilized by Asp99β, is per se sufficient to generate the Root effect, and it is the minimal structural requirement needed for the design of Root‐effect Hbs. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Similarity networks of protein binding sites
Authors: Zhang Ziding , Grigorov Martin G. 
Published: November 2005

AbstractAn increasing attention has been dedicated to the characterization of complex networks within the protein world. This work is reporting how we uncovered networked structures that reflected the structural similarities among protein binding sites. First, a 211 binding sites dataset has been compiled by removing the redundant proteins in the Protein Ligand Database (PLD) (http://www‐mitchell.ch.cam.ac.uk/pld/). Using a clique detection algorithm we have performed all‐against‐all binding site comparisons among the 211 available ones. Within the set of nodes representing each binding site an edge was added whenever a pair of binding sites had a similarity higher than a threshold value. The generated similarity networks revealed that many nodes had few links and only few were highly connected, but due to the limited data available it was not possible to definitively prove a scale‐free architecture. Within the same dataset, the binding site similarity networks were compared with the networks of sequence and fold similarity networks. In the protein world, indications were found that structure is better conserved than sequence, but on its own, sequence was better conserved than the subset of functional residues forming the binding site. Because a binding site is strongly linked with protein function, the identification of protein binding site similarity networks could accelerate the functional annotation of newly identified genes. In view of this we have discussed several potential applications of binding site similarity networks, such as the construction of novel binding site classification databases, as well as the implications for protein molecular design in general and computational chemogenomics in particular. Proteins 2006. © 2005 Wiley‐Liss, Inc.
The energy of tilt grain boundaries around 〈0001〉 in GaN
Authors: Chen Jun , Ruterana P. , Nouet G. 
Published: November 2005

AbstractThe energy of coincidence boundaries is investigated for rotations about the [0001] axis in wurtzite GaN. A boundary may have two types of interfaces corresponding to the edge or diagonal of the unit cell of the coincidence site lattice. Their energy is shown to be a function of the structural units in the unit period, and to have only two minima which are determined for the edge boundaries in the range 0–60°. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Identification of the aromatase inhibitor letrozole in urine by gas chromatography/mass spectrometry
Authors: Mareck U. , Sigmund G. , Opfermann G. , Geyer H. , Thevis M. , Schänzer W. 
Published: November 2005

AbstractLetrozole (1‐(bis‐(4‐cyanophenyl)methyl)‐1,2,4‐triazole) is used therapeutically as a non‐steroidal aromatase inhibitor (Femara®) to treat hormone‐sensitive breast cancer in postmenopausal women. For doping purposes it may be used to counteract the adverse effects of an extensive abuse of anabolic androgenic steroids (gynaecomastia) and to increase the testosterone concentration by stimulation of the testosterone biosynthesis. The use of aromatase inhibitors has been prohibited by IOC/WADA regulations for male and female athletes since September 2001 and January 2005, respectively. Spot urine samples from women suffering from metastatic breast cancer and being treated with letrozole were collected and analysed to develop/optimise the detection system for metabolites of letrozole to allow the identification of athletes who do not comply with the internationally prohibited use of this cancer drug. The assay was based on gas chromatography/mass spectrometry (GC/MS) and the main metabolite of letrozole (bis‐4‐cyanophenylmethanol) was identified by comparison of its mass spectrum and retention time with that of a bis‐4‐cyanophenylmethanol reference. The full‐scan spectrum, diagnostic ions and a validation of the method for the analysis of bis‐4‐cyanophenylmethanol are presented. Copyright © 2005 John Wiley & Sons, Ltd.
Quantitative liquid chromatography/tandem mass spectrometry determination of chloramphenicol residues in food using sub‐2 µm particulate high‐performance liquid chromatography columns for sensitivity and speed
Authors: Kaufmann Anton , Butcher Patrick 
Published: November 2005

AbstractThe use of chloramphenicol (CAP) — a highly effective broad‐spectrum antibiotic used in animal husbandry — is banned in many countries. Therefore, a very low minimum required performance limit (MRPL) of 0.3 µg/kg CAP in meat for human consumption has been defined. Analytical methods capable of quantifying and confirming such low residue levels require sophisticated instrumentation. Preferably sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) or gas chromatography/mass spectrometry (GC/MS) methods have been used. This paper suggests the use of sub‐2 µm particulate high‐performance liquid chromatography (HPLC) columns to gain additional sensitivity and improve resolution as well as speed. Depending on the operating conditions, higher chromatographic resolution and speed can be obtained at the price of a significantly increased operating pressure, requiring dedicated LC equipment. A 3–4‐fold overall improvement of the signal‐to‐noise ratio for CAP was obtained compared to more classical 5 µm particulate HPLC columns. The proposed analytical methodology includes an enzymatic digestion, which liberates glucuronide‐bound CAP from kidney tissue. The extracts obtained after an Extrelut® clean‐up are sufficiently pure to permit routine injection of biological samples into the sub‐2 µm particulate HPLC column, without observing rapid deterioration of peak shape or column clogging problems. The time for one chromatographic run was 4.2 min. The described method was validated for two particularly difficult matrices (kidney and honey). Decision limits (CCα) were 0.007 µg/kg (honey) und 0.011 µg/kg (kidney), which are significantly below the current MRPL. Copyright © 2005 John Wiley & Sons, Ltd.
Electrospray‐assisted laser desorption/ionization mass spectrometry for direct ambient analysis of solids
Authors: Shiea Jentaie , Huang Min‐Zon , HSu Hsiu‐Jung , Lee Chi‐Yang , Yuan Cheng‐Hui , Beech Iwona , Sunner Jan 
Published: November 2005

AbstractA new method of electrospray‐assisted laser desorption/ionization (ELDI) mass spectrometry, which combines laser desorption with post‐ionization by electrospray, was applied to rapid analysis of solid materials under ambient conditions. Analytes were desorbed from solid metallic and insulating substrata using a pulsed nitrogen laser. Post‐ionization produced high‐quality mass spectra characteristic of electrospray, including protein multiple charging. For the first time, mass spectra of intact proteins were obtained using laser desorption without adding a matrix. Bovine cytochrome c and an illicit drug containing methaqualone were chosen in this study to demonstrate the applicability of ELDI to the analysis of proteins and synthetic organic compounds. Copyright © 2005 John Wiley & Sons, Ltd.
High sensitivity determination of valproic acid in mouse plasma using semi‐automated sample preparation and liquid chromatography with tandem mass spectrometric detection
Authors: Pucci Vincenzo , Monteagudo Edith , Bonelli Fabio 
Published: November 2005

AbstractA high‐throughput liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS) assay using automated sample preparation has been developed for the determination of valproic acid (VPA) in mouse plasma. A liquid‐handling system was programmed to prepare calibration standard solutions in plasma, as well as quality controls and clinical samples. Plasma protein precipitation was performed on a 96‐well plate, and the collected supernatant was directly injected into a reversed‐phase LC/ESI‐MS/MS system in the negative ionization mode. The calibration curve for VPA was linear over a dynamic range of 0.15–100 µg/mL. The limit of detection was 75 ng/mL and the lower limit of quantitation was 150 ng/mL. Intra‐ and inter‐day validation assays of the semi‐automated plasma analysis showed satisfactory accuracy and precision. Copyright © 2005 John Wiley & Sons, Ltd.
Radio resource management across multiple protocol layers in satellite networks: a tutorial overview
Authors: Barsocchi Paolo , Celandroni Nedo , Davoli Franco , Ferro Erina , Giambene Giovanni , Castaño Francisco Javier González , Gotta Alberto , Moreno Jose Ignacio , Todorova Petia 
Published: November 2005

AbstractSatellite transmissions have an important role in telephone communications, television broadcasting, computer communications, maritime navigation, and military command and control. Moreover, in many situations they may be the only possible communication set‐up. Trends in telecommunications indicate that four major growth market/service areas are messaging and navigation services (wireless and satellite), mobility services (wireless and satellite), video delivery services (cable and satellite), and interactive multimedia services (fibre/cable, satellite).When using geostationary satellites (GEO), the long propagation delay may have great impact, given the end‐to‐end delay user's requirements of relevant applications; moreover, atmospheric conditions may seriously affect data transmission. Since satellite bandwidth is a relatively scarce resource compared to the terrestrial one (e.g. in optical transport networks), and the environment is harsher, resource management of the radio segment plays an important role in the system's efficiency and economy. The radio resource management (RMM) entity is responsible for the utilization of the air interface resources, and covers power control, handover, admission control, congestion control, bandwidth allocation, and packet scheduling. RRM functions are crucial for the best possible utilization of the capacity. RRM functions can be implemented in different ways, thus having an impact on the overall system efficiency.This tutorial aims to provide an overview of satellite transmission aspects at various OSI layers, with emphasis on the MAC layer; some cross‐layer solutions for bandwidth allocation are also indicated. Far from being an exhaustive survey (mainly due to the extensive nature of the subject), it offers the readers an extensive bibliography, which could be used for further research on specific aspects. Copyright © 2005 John Wiley & Sons, Ltd.
Vegetation responses along environmental gradients on the Ordos plateau, China
Authors: Zheng Yuanrun , Xie Zhixiao , Jiang Lianhe , Shimizu Hideyuki , Rimmington Glyn M. , Zhou Guangsheng 
Published: November 2005

AbstractThe Ordos plateau is a unique ecotone and is a focal region for the campaign to reduce or reverse desertification in China. This paper explores the relationship between vegetation and environmental gradients on the Ordos plateau based on a field survey of species distribution, vegetation distribution patterns, plant community structure, ecophysiological properties, and soil water content along an environmental gradient. The vegetation on the Ordos plateau may be divided into three types from east to west: steppe (eastern part), desert steppe (middle part) and steppe desert (western part). From east to west, precipitation declines significantly (from 400 mm to 150 mm). The spatial distribution pattern of vegetation at different sites was random. The density of shrub islands decreased from east to west, and their height and diameter were negatively correlated with precipitation. From east to west, the transpiration rate increased as temperature increased. Stomatal conductance was positively correlated with percentage of sunshine hours and negatively correlated with temperature. Water‐use efficiency was positively correlated with average annual precipitation but negatively correlated with increasing percentage of sunshine hours. The results suggest that for effective revegetation, highly drought‐tolerant species, such as Caragana tibetica and C. stenophylla, should be used and a lower percentage of vegetation cover expected (30–40%) in the western half of the Ordos plateau. In the eastern half, moderately drought‐tolerant species, such as Artemisia ordosica and C. korshinskii, could be used and a higher percentage vegetation cover expected (40–50%).
Parenting processes and dating violence: The mediating role of self‐esteem in low‐ and high‐SES adolescents
Authors: Pflieger Jacqueline C. , Vazsonyi Alexander T. 
Published: November 2005

ABSTRACTThe current investigation tested a model in which low self‐esteem mediated the effects by parenting processes (monitoring, closeness, and support) on measures of dating violence (victimization, perpetration, attitudes, and perceptions) in a sample of adolescents (; mean age=16.4 years) from both low‐ and high‐socioeconomic (SES) backgrounds. Hierarchical regression analyses provided evidence that low self‐esteem partially mediated the link between parenting processes and dating violence, with unique differences observed between low‐ and high‐SES youth. Specifically, in low‐SES youth, low self‐esteem mediated the relationship between closeness as well as support and dating violence behaviours, while in high‐SES youth, it only mediated the relationship between maternal support and dating violence attitudes.
Total antioxidant capacity is impaired in different structures from aged rat brain
Authors: Siqueira Ionara Rodrigues , Fochesatto Cíntia , de Andrade Aline , Santos Melissa , Hagen Martine , Bello‐Klein Adriane , Netto Carlos Alexandre 
Published: November 2005

AbstractOur data support a disproportion between free radicals levels and scavenging systems activity in different cerebral regions of the aging rat. We investigated the total reactive antioxidant potential and reactivity levels, which represent the total antioxidant capacity, in different cerebral regions of the aging rat (cortex, striatum, hippocampus and the cerebellum). In addition, we have determined several oxidative stress parameters, specifically the free radicals levels, the macromolecules damage (lipid peroxidation and carbonyl content), as well as the antioxidant enzymes activities in different cerebral areas from young (2 months‐old), mature adult (6 months‐old) and old (24 months‐old) male Wistar rats. Free radicals levels, determined by 2′,7′‐dichlorofluorescein diacetate probe, were higher in striatum, cerebellum and hippocampus from aged rats. There was an age‐related increase in lipoperoxidation in hippocampus and cerebral cortex. In the cerebellum, a high activity of superoxide dismutase and a decrease of catalase activity were observed. The striatum exhibited a significant catalase activity decrease; and glutathione peroxidase activity was diminished in the hippocampus of mature and aged rats. There was a marked decrease of total antioxidant capacity in hippocampus in both reactivity and potential levels, whereas striatum and cerebral cortex displayed a reduction on reactivity assay. We suggest that age‐related variations of total antioxidant defenses in brain may predispose structures to oxidative stress‐related neurodegenerative disorders.
End‐of‐life decisions in delivery room and neonatal intensive care unit
Authors: ARLETTAZ ROMAINE , MIETH DIETO , BUCHER HANS‐ULRICH , DUC GABRIEL , FAUCHÈRE JEAN‐CLAUDE 
Published: November 2005

AbstractBackground: The increase in neonatal survival in recent decades has been followed by an increase in later disabilities. This has given rise to many new ethical issues. In different countries, efforts are being made to define ethical guidelines regarding withholding or withdrawing intensive care and end‐of‐life decisions in critically ill newborn infants. These guidelines have to be differentiated from ethical decision‐making models which structure the process of decision making for an individual child. Such a framework has been in existence in our clinic for 10 years. Aim: The aims of this study were to evaluate how end‐of‐life decisions are taken in our perinatal centre and to analyse whether these decisions are consistent with our framework for structured ethical decision making.Methods: 199 consecutive neonatal deaths over 5 y were evaluated.Results: In 157 cases (79%), end‐of‐life decisions were taken according to our ethical framework; in the remaining 42 cases (21%), the baby died before this could be done. In 92% of cases, parents were involved in the decision and, in all cases but one, agreed with the decision. A patient's life was never intentionally and actively terminated.Conclusion: In contrast to earlier years, in‐hospital death in our clinic is nowadays usually preceded by structured and documented medical end‐of‐life decisions.
Comparison between Japanese and Swedish schoolchildren in regards to physical symptoms and psychiatric complaints
Authors: TANAKA HIDETAKA , MÖLLBORG PER , TERASHIMA SHIGENORI , BORRES MAGNUS P. 
Published: November 2005

AbstractBackground: Physical symptoms are an increasing problem among Japanese children and adolescents, and the symptoms seem to be related to their school situation. These symptoms are prevalent in Sweden, and a comparison with Japan is of interest due to the differences in the educational system and school climate. Objective and methods: To compare physical symptoms and psychiatric complaints in school pupils from Japan and Sweden, using a questionnaire that also addressed life satisfaction and stressful life events. The study population comprised 742 Japanese children and 1120 Swedish children attending public compulsory schools, grades 4–9 (10–15 y). Physical symptom and psychiatric complaint scores were calculated for each pupil.Results: The Japanese children had significantly higher physical symptom and psychiatric complaint scores than did the Swedish children. Both the physical symptom and psychiatric complaint scores were significantly higher in adolescents than in preadolescents in Japan; this trend was less apparent in Swedish children. In addition, Japanese children were found to have considerably lower life satisfaction. Loss of appetite was the only physical symptom more prevalent in the Swedish population compared to the Japanese population.Conclusion: We conclude that Japanese schoolchildren have more physical symptoms and psychiatric complaints and less life satisfaction than Swedish schoolchildren of corresponding ages.
Enhanced recognition of protein transmembrane domains with prediction-based structural profiles
Authors: Cao Baoqiang , Porollo Aleksey , Adamczak Rafal , Jarrell Mark , Meller Jaroslaw 
Published: November 2005

Abstract
Motivation: Membrane domain prediction has recently been re-evaluated by several groups, suggesting that the accuracy of existing methods is still rather limited. In this work, we revisit this problem and propose novel methods for prediction of alpha-helical as well as beta-sheet transmembrane (TM) domains. The new approach is based on a compact representation of an amino acid residue and its environment, which consists of predicted solvent accessibility and secondary structure of each amino acid. A recently introduced method for solvent accessibility prediction trained on a set of soluble proteins is used here to indicate segments of residues that are predicted not to be accessible to water and, therefore, may be ‘buried’ in the membrane. While evolutionary profiles in the form of a multiple alignment are used to derive these simple ‘structural profiles’, they are not used explicitly for the membrane domain prediction and the overall number of parameters in the model is significantly reduced. This offers the possibility of a more reliable estimation of the free parameters in the model with a limited number of experimentally resolved membrane protein structures.
Results: Using cross-validated training on available sets of structurally resolved and non-redundant alpha and beta membrane proteins, we demonstrate that membrane domain prediction methods based on such a compact representation outperform approaches that utilize explicitly evolutionary profiles and multiple alignments. Moreover, using an external evaluation by the TMH Benchmark server we show that our final prediction protocol for the TM helix prediction is competitive with the state-of-the-art methods, achieving per-residue accuracy of ∼89% and per-segment accuracy of ∼80% on the set of high resolution structures used by the TMH Benchmark server. At the same time the observed rates of confusion with signal peptides and globular proteins are the lowest among the tested methods. The new method is available online at .
Contact: jmeller@chmcc.org
Supplementary information: Supplementary data are available at Bioinformatics online and at
Gene Time Eχpression Warper: a tool for alignment, template matching and visualization of gene expression time series
Authors: Criel Jo , Tsiporkova Elena 
Published: November 2005

Abstract
Summary: An application tool for alignment, template matching and visualization of gene expression time series is presented. The core algorithm is based on dynamic time warping techniques used in the speech recognition field. These techniques allow for non-linear (elastic) alignment of temporal sequences of feature vectors and consequently enable detection of similar shapes with different phases.
Availability: The Java program, examples and a tutorial are available at
Contact: eltsi@psb.ugent.be