bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal protein‐RNA area, OPRA: A propensity‐based method to identify RNA‐binding sites on proteins
Authors: Pérez‐Cano Laura , Fernández‐Recio Juan 
Published: July 2009

AbstractProtein‐RNA interactions are essential in living organisms and they are involved in very different and important cellular processes. Thus, understanding protein‐RNA recognition at molecular level is a key goal not only from a basic biological point of view but also for biotechnological and therapeutic purposes. On basis of the most updated available set of nonredundant X‐ray structures of protein‐RNA complexes, we have computed protein‐RNA interface propensities for ribonucleotides and aminoacid residues. The results show several protein residues with high tendency to bind RNA, such as arginine, lysine, and histidine. However, we could not observe any clear preferences for protein binding among the different ribonucleotides. We applied these propensity values to predict RNA‐binding areas on proteins, using an ad hoc algorithm called OPRA (Optimal Protein‐RNA Area). First, for each protein residue, we derived a predictive score from its corresponding protein‐RNA interface propensity weighed by its accessible surface area (ASA). Then, optimal patch energy scores were computed for each residue by adding up the individual scores of the neighboring surface residues. The resulting patch scores correlate well with the known RNA‐binding sites on protein surfaces. The OPRA method has been benchmarked on a test set of 30 unbound proteins involved in protein‐RNA complexes of known structure, where it is able to successfully predict RNA‐binding sites on protein surfaces with around 80% positive predictive value. This can be useful for identifying potential RNA‐binding sites on proteins, and can help to model protein‐RNA interactions of biological and therapeutic interest. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Preface: Phys. Status Solidi B 246/7
Authors: Esser Norbert , Zahn Dietrich R.T. 
Published: July 2009

Abstractmagnified imageDr. Walter Braun inspecting a mirror device (construction of the TGM 2 beamline at BESSY I in 1982)The following collection of 15 publications is dedicated to Dr. Walter Braun on the occasion of his 60th birthday. The contributions were written by close friends and colleagues who collaborated with Walter Braun very often for a very long time. Since Walter Braun is known to many people as the key person at BESSY (now the Helmholtz‐Zentrum Berlin) who looks after the users and organises their beam times, the work presented, of course, all deals with synchrotron radiation research. The selected publications thus cover a wide range of synchrotron applications predominantly in the fields of surfaces, interfaces, semiconductors, and material science. So we believe that this collection also well mirrors the breadth of research fields which were and are influenced by Walter Braun's activities at BESSY. Everyone who ever visited BESSY I in Berlin‐Wilmersdorf or BESSY II in Adlershof as a user knows Walter Braun very well as he usually gets in touch with users and offers his support. But it is not just the usual user support or coordinating beam times, it is much more than this which distinguishes Walter Braun from many others. He formed and forms networks of researchers by setting up contacts and bringing people together. With his excellent judgement of people he has the right flair for those who can co‐operate well. It is fair to say that Walter Braun in such a way had and has great influence on the scientific development at BESSY and thus also on its success. Many of us are grateful to Walter Braun not only for his support for all these years and his permanent encouragement but also for his friendship (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A learning progression for deepening students' understandings of modern genetics across the 5th–10th grades
Authors: Duncan Ravit Golan , Rogat Aaron D. , Yarden Anat 
Published: July 2009

AbstractOver the past several decades, there has been a tremendous growth in our understanding of genetic phenomena and the intricate and complicated mechanisms that mediate genetic effects. Given the complexity of content in modern genetics and the inadequacy of current instructional methods and materials it seems that a more coherent and extensive approach to teaching modern genetics is needed. Learning progressions provide such an approach by describing the learning of core concepts in a domain as it unfolds over multiple grades and grade bands. In this paper we suggest a learning progression for modern genetics that spans grades 5–10. We describe the learning progression in terms of three key aspects of teaching and learning modern genetics: (1) the big ideas in modern genetics, and the knowledge and abilities that students should master by the end of compulsory education; and (2) the progression of learning that students are expected to make over several grades; and (3) the identification of learning performances and development of assessments for the proposed progression. We conclude by identifying the implications for instruction and research that stem from our analysis of the research base in genetics education, and our development of a theoretical progression for learning the big ideas in modern genetics. © 2009 Wiley Periodicals, Inc. J Res Sci Teach 46: 655–674, 2009
Image restoration
Authors: Qiu Peihua 
Published: July 2009

AbstractTrue images are usually degraded during image acquisition. Image restoration is for restoring true images from their observed but degraded versions; it is often used for preprocessing observed images so that subsequent image processing and analysis become more reliable. Among many different types of degradations, point degradations (or noise) and spatial degradations (or blurring) are most common in applications. This article introduces some fundamental image denoising and image deblurring methods. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:Data: Types and Structure > Image and Spatial Data
Service oriented architecture
Authors: Laskey Kathryn B. , Laskey Kenneth 
Published: July 2009

AbstractService oriented architecture (SOA) is a paradigm for organizing a set of capabilities, often distributed across the network and possibly under the control of different ownership domains. The organized capabilities can be used to provide solutions to business problems. A business problem is broadly defined as any problem, in any domain of interest, encountered by an individual or organization as it goes about its business. SOA is applied to business problems that are amenable to information technology solutions. Services are made visible to potential users, interact with users through a series of information exchanges, and produce real‐world effects. Invocation and information exchange rely on standard languages and protocols that facilitate interoperability. From a user's perspective, invoking a service to produce an intended effect is experienced as a single, atomic operation. The detailed sequence of actions carried out by the service may involve any number of operations such as database queries, data transformations, execution of models, and formatting of displays. These operations may themselves be composed of lower level operations. The data and/or software modules required to perform the operations may reside at different physical locations and be controlled by different organizations. The details of composing the sequence of actions that produces the real world effect are transparent to the user interacting with the service. SOA frees users to concentrate on their business problem, leaving the details of the solution to the service. Copyright © 2009 John Wiley & Sons, Inc.This article is categorized under:

Software for Computational Statistics > Software/Statistical Software
Arbitrage‐free construction of the swaption cube
Authors: Johnson Simon , Nonas Bereshad 
Published: July 2009

AbstractIn this paper we look at two areas in the interest rate options market where arbitrage could be hiding. In the first section we derive a no‐arbitrage condition for swaption prices with complementary expiry dates and tenors within the swaption cube. In the second section we propose an alternative European option approximation for the widely used SABR dynamics that reduces the possibility of arbitrage for long maturities and low strikes. Copyright © 2009 Wilmott Magazine Ltd
Mucobilia: current aspects in the management of a rare cause of malignant biliary obstruction
Authors: Brown Melanie‐Antonietta , Sakpal Sujit Vijay , Chamberlain Ronald Scott 
Published: July 2009

AbstractMucobilia is a rare pathologic condition characterized by the abnormal secretion and accumulation of abundant mucus within the biliary tree. It is usually seen in association with mucin‐producing hepatobiliary and pancreatic tumors. Neoplastic transformation of these tumors can range from low‐grade dysplasia to invasive adenocarcinoma. Mucobilia usually presents with signs and symptoms of biliary obstruction, which may span from jaundice to cholangitis with progression to septic complications in severe cases. Occurrence of hepatolithiasis has also been attributed to mucobilia, which raises the concern of an increased risk for the development of cholangiocarcinoma. Precise radiological evaluation and detailed histopathological tissue diagnosis followed by execution of appropriate surgical therapy is vital in the integrated management of mucin‐producing biliary neoplasms. This review will address the etiologies and symptomatology of mucobilia as well as discuss current aspects in the management of mucobilia and its causative etiologies.
Meniscal ossicle
Authors: Rohilla Seema , Yadav Rohtas K. , Singh Raj , Devgan Ashish , Dhaulakhandi Dhara B. 
Published: July 2009

Abstract
Meniscal ossicle, or bone within the substance of meniscus, is a rare entity and commonly confused with a loose body both clinically and radiologically. MRI is the modality that can definitely diagnose meniscal ossicle and avoid unnecessary diagnostic arthroscopy. Here we report one such case diagnosed using MRI; this patient is doing well without surgery one year after diagnosis.
Menstrual knowledge and practices of female adolescents in urban Karachi, Pakistan
Authors: Ali Tazeen Saeed , Rizvi Syeda Naghma 
Published: July 2009

ABSTRACTMenstruation is a normal physiological process that is managed differently according to various social and cultural understandings. Therefore, this cross‐sectional study was conducted to explore the menstrual practices among 1275 female adolescents of urban Karachi, Pakistan from April to October 2006 by using interviews. Data was entered and analyzed in Epi Info Version 9 and SPSS Version 10. Descriptive findings showed that 50% of the girls lacked an understanding of the origin of menstrual blood and those with a prior knowledge of menarche had gained it primarily through conversations with their mothers. Many reported having fear at the first experience of bleeding. Nearly 50% of the participants reported that they did not take baths during menstruation. In univariate analysis, factors of using unhygienic material, using washcloths, and not drying under sun were found to be significant in the Chi square test among those going and not going to schools. This study concludes that there are unhygienic practices and misconceptions among girls requiring action by health care professionals.
Understanding the Australian Environmental Volunteering Market: A Basis for Behavioural Change and a Sustainable Future
Authors: Randle Melanie , Dolnicar Sara 
Published: July 2009

The world is facing an environmental crisis. Long-term environmental sustainability requires social change: individuals need to take personal responsibility for the environment and change their behaviour. Environmental volunteering organisations play a key role in this process: they create opportunities for individuals to improve their natural environment, they facilitate behavioural change. Successful facilitation of behavioural change requires in-depth understanding of the environmental volunteering market to identify those individuals most likely to volunteer, compete successfully and create targeted, motivating marketing campaigns. The present study (1) assesses the usefulness of a novel method (PBMS) to explore volunteering markets, and (2) provides insight into the Australian environmental volunteering market structure. Results indicate PBMS analysis provides unique insights into the volunteering market with respect to image, competition and suitable market segments. The environmental volunteering organisation considered in this study, Bushcare, is perceived as “outdoorsy”, “Aussie” and “supporting local community” and competes primarily with Surf Life Saving and the Rural Fire Service for volunteers.
Prenatal methamphetamine exposure affects the mesolimbic dopaminergic system and behavior in adult offspring
Authors: Bubenikova‐Valesova Vera , Kacer Petr , Syslova Kamila , Rambousek Lukas , Janovsky Martin , Schutova Barbora , Hruba Lenka , Slamberova Romana 
Published: July 2009

AbstractMethamphetamine is a commonly abused psychostimulant that causes addiction and is often abused by pregnant women. Acute or chronic administration of methamphetamine elevates the levels of the extracellular monoamine neurotransmitters, such as dopamine.The aim of the present study was to show whether prenatal exposure to methamphetamine (5 mg/kg, entire gestation) or saline in Wistar rats induces changes in dopamine levels and its metabolites in the nucleus accumbens, and in behavior (locomotor activity, rearing, and immobility) after the administration of a challenge dose of methamphetamine (1 mg/kg) or saline in male offspring.We found that adult offspring prenatally exposed to methamphetamine had higher basal levels of dopamine (about 288%), dihydroxyphenylacetic acid (about 67%) and homovanillic acid (about 74%) in nucleus accumbens. An increased basal level of dopamine corresponds to lower basal immobility in offspring prenatally exposed to methamphetamine. The acute injection of methamphetamine in adulthood increased the level of dopamine in the nucleus accumbens, which is related to an increase of locomotion and rearing (exploration). In addition, prenatally methamphetamine‐exposed rats showed higher response to the challenge dose of methamphetamine, when compared to prenatally saline‐exposed rats.In conclusion, rats exposed to methamphetaminein uterohave shown changes in the mesolimbic dopaminergic system and were more sensitive to the administration of the acute dose of methamphetamine in adulthood.
DNA Copy Number Aberrations in Breast Cancer by Array Comparative Genomic Hybridization
Authors: Li Jian , Wang Kai , Li Shengting , Timmermans-Wielenga Vera , Rank Fritz , Wiuf Carsten , Zhang Xiuqing , Yang Huanming , Bolund Lars 
Published: July 2009

Abstract
Array comparative genomic hybridization (CGH) has been popularly used for analyzing DNA copy number variations in diseases like cancer. In this study, we investigated 82 sporadic samples from 49 breast cancer patients using 1-Mb resolution bacterial artificial chromosome CGH arrays. A number of highly frequent genomic aberrations were discovered, which may act as “drivers” of tumor progression. Meanwhile, the genomic profiles of four “normal” breast tissue samples taken at least 2 cm away from the primary tumor sites were also found to have some genomic aberrations that recurred with high frequency in the primary tumors, which may have important implications for clinical therapy. Additionally, we performed class comparison and class prediction for various clinicopathological parameters, and a list of characteristic genomic aberrations associated with different clinicopathological phenotypes was compiled. Our study provides clues for further investigations of the underlying mechanisms of breast carcinogenesis.
Bioinformatic Comparison of Bacterial Secretomes
Authors: Song Catharine , Kumar Aseem , Saleh Mazen 
Published: July 2009

Abstract
The rapid increasing number of completed bacterial genomes provides a good opportunity to compare their proteomes. This study was undertaken to specifically compare and contrast their secretomes—the fraction of the proteome with predicted N-terminal signal sequences, both type I and type II. A total of 176 theoretical bacterial proteomes were examined using the ExProt program. Compared with the Gram-positives, the Gram-negative bacteria were found, on average, to contain a larger number of potential Sec-dependent sequences. In the Gram-negative bacteria but not in the others, there was a positive correlation between proteome size and secretome size, while there was no correlation between secretome size and pathogenicity. Within the Gram-negative bacteria, intracellular pathogens were found to have the smallest secretomes. However, the secretomes of certain bacteria did not fit into the observed pattern. Specifically, the secretome of Borrelia burgdoferi has an unusually large number of putative lipoproteins, and the signal peptides of mycoplasmas show closer sequence similarity to those of the Gram-negative bacteria. Our analysis also suggests that even for a theoretical minimal genome of 300 open reading frames, a fraction of this gene pool (up to a maximum of 20%) may code for proteins with Sec-dependent signal sequences.
A Method for Identification of Selenoprotein Genes in Archaeal Genomes
Authors: Li Mingfeng , Huang Yanzhao , Xiao Yi 
Published: July 2009

Abstract
The genetic codon UGA has a dual function: serving as a terminator and encoding selenocysteine. However, most popular gene annotation programs only take it as a stop signal, resulting in misannotation or completely missing selenoprotein genes. We developed a computational method named Asec-Prediction that is specific for the prediction of archaeal selenoprotein genes. To evaluate its effectiveness, we first applied it to 14 archaeal genomes with previously known selenoprotein genes, and Asec-Prediction identified all reported selenoprotein genes without redundant results. When we applied it to 12 archaeal genomes that had not been researched for selenoprotein genes, Asec-Prediction detected a novel selenoprotein gene in Methanosarcina acetivorans. Further evidence was also collected to support that the predicted gene should be a real selenoprotein gene. The result shows that Asec-Prediction is effective for the prediction of archaeal selenoprotein genes.
GALT Protein Database, a Bioinformatics Resource for the Management and Analysis of Structural Features of a Galactosemia-Related Protein and Its Mutants
Authors: d’Acierno Antonio , Facchiano Angelo , Marabotti Anna 
Published: July 2009

Abstract
We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.
Field-scale dispersal ofAphodiusdung beetles (Coleoptera: Scarabaeidae) in response to avermectin treatments on pastured cattle
Authors: Webb L. , Beaumont D.J. , Nager R.G. , McCracken D.I. 
Published: July 2009

AbstractVery few studies have examined, at the field scale, the potential for faecal residues in the dung of avermectin-treated cattle to affect dung-breeding insects. The current study examined populations of dung beetles (Scarabaeidae:Aphodius) using pitfall traps baited with dung from untreated cattle on 26 fields across eight farms in southwest Scotland. The fields were grazed either by untreated cattle or by cattle treated with an avermectin product, i.e. doramectin or ivermectin. During the two-year study, significantly more beetles were trapped in fields grazed by treated cattle (n=9377 beetles) than in fields where cattle remained untreated (n=2483 beetles). Additional trials showed that beetles preferentially colonised dung of untreated versus doramectin-treated cattle. This may explain the higher captures of beetles in traps baited with dung of untreated cattle, which were located in fields of treated cattle. Given thatAphodiusbeetles avoided dung of treated cattle in the current study, the potential harmful effects of avermectin residues in cattle dung could be reduced through livestock management practices that maximise the availability of dung from untreated livestock in areas where avermectins are being used.
Pheromone communication channels in tortricid moths: lower specificity of alcohol vs. acetate geometric isomer blends
Authors: Witzgall P. , Trematerra P. , Liblikas I. , Bengtsson M. , Unelius C.R. 
Published: July 2009

AbstractDiscrimination of conspecific and heterospecific signals is a key element in the evolution of specific mate recognition systems. Lepidopteran pheromone signals are typically composed of several compounds that synergize attraction of conspecific and inhibit attraction of heterospecific males. Blends convey specificity, but not their single components, that are typically shared by several species. Many sex pheromones are blends of geometric or positional isomers of straight-chain acetates, while species-specific blends of analogous alcohols have not been described. We have, therefore, studied the attraction of tortricid moths to the geometric isomers (E,E)-, (E,Z)-, (Z,E)- and (Z,Z)-8,10-dodecadien-1-ol. Only one species responding to these alcohols seemed to be attracted to a blend of two isomers, while most species are attracted to only one alcohol isomer. Lack of a pronounced synergist or antagonist effect of the other geometric isomers explains the lack of specific attraction to isomer blends and reduces accordingly the number of specific communication signals composed of these alcohols. In comparison, many more species respond to the analogous (E,E)-, (E,Z)-, (Z,E)- and (Z,Z)-8,10-dodecadienyl acetates and their binary blends. The acetate isomers all play a behavioural role, either as attractants, attraction synergists or antagonists, and thus promote specific communication with acetate blends. Male moths seem to discriminate the acetate isomers with greater precision than the analogous alcohols. It is proposed that discrimination is facilitated by steric differences between the four acetate isomers, as compared to the more uniform steric properties of the alcohols.