bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geographical variation in climatic cues for mast seeding of Fagus crenata
Authors: Masaki Takashi , Oka Teruki , Osumi Katsuhiro , Suzuki Wajiro 
Published: August 2008

AbstractGeographical variation in climatic cues for masting of Fagus crenata Blume, which is the most dominant tree species in Japanese temperate forests, was investigated in the northern part of Japan, i.e., the Tohoku district of Honshu Island and the Oshima Peninsula of Hokkaido Island. The data obtained after an 18‐year assessment (1989–2006) of 163 stands, covering an area of ca. 200 × 500 km2 area, were used in this study. In all stands, mast seeding occurred three times (1995, 2000 and 2005) during the study period and the coefficient of annual variation (CV) in seedfall density was 0.94. Based on cluster analysis, the stands were classified into each of the seven groups, in which the seedfall density was temporally synchronized among the stands and showed higher values of CV (1.04–1.79). These groups were distributed spatially exclusively at the scale of 80–200 km. By selecting the tree model based on AIC values, lower temperature in spring, higher temperature in summer and seedfall density in a year were proved to have a decisive influence on the seedfall density in the subsequent year. The effects of the first two climatic cues overwhelm that of the seedfall density. Lower temperature in spring served as a cue mostly for the population in the Oshima Peninsula, while higher temperature in summer served as a cue for the populations in the Tohoku district. If this suggests a genetic variation in relation to cues, climatic changes (e.g., global warming) will have different impacts on seed production of different F. crenata populations. However, it remains to be tested in future studies whether multiple climatic cues simply reflect regionally variable climatic conditions or not.
Acculturation and Familiarity With, Attitudes Towards and Beliefs about Genetic Testing for Cancer Risk Within Latinas in East Harlem, New York City
Authors: Sussner Katarina M. , Thompson Hayley S. , Valdimarsdottir Heiddis B. , Redd William H. , Jandorf Lina 
Published: August 2008

AbstractRecent research underscores the need for increasing use of genetic testing for cancer risk in Latinos. This study examined the influence of acculturation on attitudes, beliefs about and familiarity with genetic testing for cancer risk in a community‐based sample of Latinas in East Harlem, New York City (N = 103). Multivariate linear regression models analyzed the relationship of acculturation to: (1) familiarity (2) perceived benefits (3) perceived barriers and (4) concerns about abuses of genetic testing for cancer risk. Controlling for sociodemographic factors, results revealed that with increasing acculturation Latinas were more familiar with genetic testing (β = 1.62, SE = 0.72, p = 0.03), more likely to cite perceived benefits (β = 1.67, SE = 0.79, p = 0.04), and less likely to report perceived barriers related to genetic testing (β = −2.76, SE = 1.64, p = 0.10). Study results may help inform the development of culturally‐appropriate health education outreach materials and programs targeted to increase awareness, knowledge and understanding about genetic testing for cancer risk within Latinas.
Benefit versus Numbers versus Helping the Worst-off: An Alternative to the Prevalent Approach to the Just Distribution of Resources
Authors: STARK ANDREW 
Published: August 2008

A central strand in philosophical debate over the just distribution of resources attempts to juggle three competing imperatives: helping those who are worst off, helping those who will benefit the most, and then – beyond this – determining when to aggregate such ‘worst off’ and ‘benefit’ claims, and when instead to treat no such claim as greater than that which any individual by herself can exert. Yet as various philosophers have observed, ‘we have no satisfactory theoretical characterization’ as to how to weigh each of the three imperatives against one another, we find it ‘difficult to state . . . precise or comprehensive conclusions’, and we do not yet have a ‘metric for integrating the three measures’. In what follows, I offer an approach to weighing the three criteria against one another that yields resolutions – in Hard Cases of the ‘saving one infant's life versus replacing ten elderly people's hips’ sort – that are cardinally definitive, intuitively satisfactory and theoretically justified.
Outbreak of Invasive Methicillin-ResistantStaphylococcus aureusInfection Associated With Acupuncture and Joint Injection
Authors: Murray R. J. , Pearson J. C. , Coombs G. W. , Flexman J. P. , Golledge C. L. , Speers D. J. , Dyer J. R. , McLellan D. G. , Reilly M. , Bell J. M. , Bowen S. F. , Christiansen K. J. 
Published: August 2008

Objective.To describe an outbreak of invasive methicillin-resistantStaphylococcus aureus(MRSA) infection after percutaneous needle procedures (acupuncture and joint injection) performed by a single medical practitioner.Setting.A medical practitioner's office and 4 hospitals in Perth, Western Australia.Patients.Eight individuals who developed invasive MRSA infection after acupuncture or joint injection performed by the medical practitioner.Methods.We performed a prospective and retrospective outbreak investigation, including MRSA colonization surveillance, environmental sampling for MRSA, and detailed molecular typing of MRSA isolates. We performed an infection control auditofthe medical practitioner's premises and practices and administered MRSA decolonization therapy to the medical practitioner.Results.Eight cases of invasive MRSA infection were identified. Seven cases occurred as a cluster in May 2004; another case (identified retrospectively) occurred approximately 15 months earlier in February 2003. The primary sites of infection were the neck, shoulder, lower back, and hip: 5 patients had septic arthritis and bursitis, and 3 had pyomyositis; 3 patients had bacteremia, including 1 patient with possible endocarditis. The medical practitioner was found to be colonized with the same MRSA clone [ST22-MRSA-IV (EMRSA-15)] at 2 time points: shortly after the first case of infection in March 2003 and again in May 2004. After the medical practitioner's premises and practices were audited and he himself received MRSA decolonization therapy, no further cases were identified.Conclusions.This outbreak most likely resulted from a breakdown in sterile technique during percutaneous needle procedures, resulting in the transmission of MRSA from the medical practitioner to the patients. This report demonstrates the importance of surveillance and molecular typing in the identification and control of outbreaks of MRSA infection.
N-PARAMETRIC CANONICAL PERTURBATION METHOD BASED ON LIE TRANSFORMS
Authors: Andrade M. 
Published: August 2008

ABSTRACT
In the dynamical analysis of multiple stellar systems, one usually has to deal with problems involving several perturbations: more than two bodies, mass loss, nonspherical shape, rotation, and such. In order to take into account all of them, we have derived a multiparametric theory based on Lie transforms. It allows us to solve perturbation problems involving an arbitrary number of small parameters in the Hamiltonian formulation. Based on the Lie transforms theory, a complete generalization of the Hori–Deprit method is obtained for N parameters—with N arbitrary—and general expressions are explicitly provided. This method is used to solve the classical Gyldén–Meščerskij problem—the relative motion of a binary system the components of which are losing mass over time—when the primary's oblateness, as well as relativistic effects, is taken into account. Besides this, speed and accuracy comparisons between this analytical method and a numerical one are accomplished.
Optimizing amino acid groupings for GPCR classification
Authors: Davies Matthew N. , Secker Andrew , Freitas Alex A. , Clark Edward , Timmis Jon , Flower Darren R. 
Published: August 2008

Abstract
Motivation: There is much interest in reducing the complexity inherent in the representation of the 20 standard amino acids within bioinformatics algorithms by developing a so-called reduced alphabet. Although there is no universally applicable residue grouping, there are numerous physiochemical criteria upon which one can base groupings. Local descriptors are a form of alignment-free analysis, the efficiency of which is dependent upon the correct selection of amino acid groupings.
Results: Within the context of G-protein coupled receptor (GPCR) classification, an optimization algorithm was developed, which was able to identify the most efficient grouping when used to generate local descriptors. The algorithm was inspired by the relatively new computational intelligence paradigm of artificial immune systems. A number of amino acid groupings produced by this algorithm were evaluated with respect to their ability to generate local descriptors capable of providing an accurate classification algorithm for GPCRs.
Contact: m.davies@mail.cryst.bbk.ac.uk
Large-scale computation of elementary flux modes with bit pattern trees
Authors: Terzer Marco , Stelling Jörg 
Published: August 2008

Abstract
Motivation: Elementary flux modes (EFMs)—non-decomposable minimal pathways—are commonly accepted tools for metabolic network analysis under steady state conditions. Valid states of the network are linear superpositions of elementary modes shaping a polyhedral cone (the flux cone), which is a well-studied convex set in computational geometry. Computing EFMs is thus basically equivalent to extreme ray enumeration of polyhedral cones. This is a combinatorial problem with poorly scaling algorithms, preventing the large-scale analysis of metabolic networks so far.
Results: Here, we introduce new algorithmic concepts that enable large-scale computation of EFMs. Distinguishing extreme rays from normal (composite) vectors is one critical aspect of the algorithm. We present a new recursive enumeration strategy with bit pattern trees for adjacent rays—the ancestors of extreme rays—that is roughly one order of magnitude faster than previous methods. Additionally, we introduce a rank updating method that is particularly well suited for parallel computation and a residue arithmetic method for matrix rank computations, which circumvents potential numerical instability problems. Multi-core architectures of modern CPUs can be exploited for further performance improvements. The methods are applied to a central metabolism network of Escherichia coli, resulting in ≈26 Mio. EFMs. Within the top 2% modes considering biomass production, most of the gain in flux variability is achieved. In addition, we compute ≈5 Mio. EFMs for the production of non-essential amino acids for a genome-scale metabolic network of Helicobacter pylori. Only large-scale EFM analysis reveals the &gt;85% of modes that generate several amino acids simultaneously.
Availability: An implementation in Java, with integration into MATLAB and support of various input formats, including SBML, is available at http://www.csb.ethz.ch in the tools section; sources are available from the authors upon request.
Contact: joerg.stelling@inf.ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Predicting pathway membership via domain signatures
Authors: Fröhlich Holger , Fellmann Mark , Sültmann Holger , Poustka Annemarie , Beißbarth Tim 
Published: August 2008

AbstractMotivation: Functional characterization of genes is of great importance for the understanding of complex cellular processes. Valuable information for this purpose can be obtained from pathway databases, like KEGG. However, only a small fraction of genes is annotated with pathway information up to now. In contrast, information on contained protein domains can be obtained for a significantly higher number of genes, e.g. from the InterPro database.Results: We present a classification model, which for a specific gene of interest can predict the mapping to a KEGG pathway, based on its domain signature. The classifier makes explicit use of the hierarchical organization of pathways in the KEGG database. Furthermore, we take into account that a specific gene can be mapped to different pathways at the same time. The classification method produces a scoring of all possible mapping positions of the gene in the KEGG hierarchy. Evaluations of our model, which is a combination of a SVM and ranking perceptron approach, show a high prediction performance. Moreover, for signaling pathways we reveal that it is even possible to forecast accurately the membership to individual pathway components.Availability: The R package gene2pathway is a supplement to this article.Contact: h.froehlich@dkfz-heidelberg.deSupplementary Information: Supplementary data are available at Bioinformatics online.
Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps
Authors: Latino Diogo A. R. S. , Zhang Qing-You , Aires-de-Sousa João 
Published: August 2008

Abstract
Motivation: The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer-aided validation of classification systems, to genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Comparison of metabolic reactions has been mostly based on Enzyme Commission (EC) numbers, which are extremely useful and widespread, but not always straightforward to apply, and often problematic when an enzyme catalyzes several reactions, when the same reaction is catalyzed by different enzymes, when official full EC numbers are unavailable or when reactions are not catalyzed by enzymes. Different methods should be available to compare metabolic reactions. Simultaneously, methods are required for the automatic assignment of EC numbers to reactions still not officially classified.
Results: We have proposed the MOLMAP reaction descriptors to numerically encode the structural transformations resulting from a chemical reaction. Here, such descriptors are applied to the mapping of a genome-scale database of almost 4000 metabolic reactions by Kohonen self-organizing maps (SOMs), and its screening for inconsistencies in EC numbers. This approach allowed for the SOMs to assign EC numbers at the class, subclass and sub-subclass levels for reactions of independent test sets with accuracies up to 92, 80 and 70%, respectively. Different levels of similarity between training and test sets were explored. The approach also led to the identification of a number of similar reactions bearing differences at the EC class level.
Availability: The programs to generate MOLMAP descriptors from atomic properties included in SDF files are available upon request for evaluation.
Contact: jas@fct.unl.pt
Supplementary information: Supplementary data are available at Bioinformatics online.
Protein-ligand interaction prediction: an improved chemogenomics approach
Authors: Jacob Laurent , Vert Jean-Philippe 
Published: August 2008

AbstractMotivation: Predicting interactions between small molecules and proteins is a crucial step to decipher many biological processes, and plays a critical role in drug discovery. When no detailed 3D structure of the protein target is available, ligand-based virtual screening allows the construction of predictive models by learning to discriminate known ligands from non-ligands. However, the accuracy of ligand-based models quickly degrades when the number of known ligands decreases, and in particular the approach is not applicable for orphan receptors with no known ligand.Results: We propose a systematic method to predict ligand–protein interactions, even for targets with no known 3D structure and few or no known ligands. Following the recent chemogenomics trend, we adopt a cross-target view and attempt to screen the chemical space against whole families of proteins simultaneously. The lack of known ligand for a given target can then be compensated by the availability of known ligands for similar targets. We test this strategy on three important classes of drug targets, namely enzymes, G-protein-coupled receptors (GPCR) and ion channels, and report dramatic improvements in prediction accuracy over classical ligand-based virtual screening, in particular for targets with few or no known ligands.Availability: All data and algorithms are available as Supplementary Material.Contact: laurent.jacob@ensmp.frSupplementary information: Supplementary data are available at Bioinformatics online.
Applicability of the trophic index TRIX in two transitional ecosystems: the Mar Menor lagoon (Spain) and the Mondego estuary (Portugal)
Authors: Salas Fuensanta , Teixeira Heliana , Marcos Concepción , Marques João Carlos , Pérez-Ruzafa Angel 
Published: August 2008

Abstract
Salas, F., Teixeira, H., Marcos, C., Marques, J. C., and Pérez-Ruzafa, A. 2008. Applicability of the trophic index TRIX in two transitional ecosystems: the Mar Menor lagoon (Spain) and the Mondego estuary (Portugal). – ICES Journal of Marine Science, 65: 1442–1448. Ecological indicators are commonly used to provide synoptic information about the state of ecosystems. Their main attribute is that they combine a range of environmental factors in a single value, which is thought useful for management and for making ecological-quality concepts easily understandable by the general public. In some European countries, the trophic state of marine and coastal waters is characterized using the trophic index TRIX. We used TRIX in the studies of the Mar Menor coastal lagoon (southeast Spain) and the Mondego estuary (northwest Portugal). These areas are under environmental stress, and eutrophication processes have been monitored in recent years. The results demonstrate the inefficacy of TRIX as a trustworthy tool to classify eutrophication status in estuarine waters. The causes of the malfunction of the index are discussed, and we suggest that, if the index is to be applied over wide areas, the classification criteria will have to be adapted to specific environments.
Tigecycline for the treatment of multidrug-resistant Enterobacteriaceae: a systematic review of the evidence from microbiological and clinical studies
Authors: Kelesidis Theodoros , Karageorgopoulos Drosos E. , Kelesidis Iosif , Falagas Matthew E. 
Published: August 2008

AbstractObjectivesAntimicrobial drug resistance is spreading among Enterobacteriaceae, limiting the utility of traditionally used agents. We sought to systematically review the microbiological activity and clinical effectiveness of tigecycline for multidrug-resistant (MDR) Enterobacteriaceae, including those resistant to broad-spectrum β-lactams due to the expression of extended-spectrum β-lactamases (ESBLs), AmpC enzymes and carbapenemases (including metallo-β-lactamases).MethodsPubMed was searched for articles including relevant data.ResultsTwenty-six microbiological and 10 clinical studies were identified. Tigecycline was active against more than 99% of 1936 Escherichia coli isolates characterized by any of the above resistance patterns (including 1636 ESBL-producing isolates) using the US Food and Drug Administration (FDA) breakpoint of susceptibility (MIC ≤ 2 mg/L). Findings were not different using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoint (≤1 mg/L). Susceptibility rates for Klebsiella spp. with any of the above resistance patterns were 91.2% for 2627 isolates by the FDA criteria and 72.3% for 1504 isolates by the EUCAST criteria (92.3% for 2030 and 72.3% for 1284 ESBL-producing isolates, by the FDA and EUCAST criteria, respectively). The degree of microbiological activity of tigecycline against 576 MDR Enterobacter spp. isolates was moderate. In clinical studies, 69.7% of the 33 reported patients treated with tigecycline achieved resolution of an infection caused by a carbapenem-resistant or ESBL-producing or MDR Enterobacteriaceae.ConclusionsTigecycline is microbiologically active against almost all of the ESBL or MDR E. coli isolates and the great majority of ESBL or MDR Klebsiella spp. isolates. Further evaluation of its clinical utility against such resistant Enterobacteriaceae, particularly regarding non-labelled indications, is warranted.
European collectors and Japanese merchants of lacquer in ‘Old Japan’
Authors: Bincsik Monika 
Published: August 2008

Abstract
During the Meiji period, following the opening of Japan's borders to foreign trade, not only did the Japanese lacquer trading system and the market undergo a marked change but so too did almost all the factors affecting collecting activities: the European reception of the aesthetics and history of Japanese lacquer art, the taste of the collectors, the structure of private collections, the systematization of museum collections, along with changes in the art canon in the second half of the nineteenth century. The patterns of collecting Japanese lacquer art in the second half of the nineteenth century cannot be understood in depth without discussing shortly its preliminaries in the seventeenth and eighteenth centuries, focusing also on the art historical reception of Japanese lacquer in Europe. Supplementary material relating to this article in the form of a list of dealers and distributors of lacquer in Japan during the Meiji period (1868–1912) is available online.
Molecular interactions of ASPP1 and ASPP2 with the p53 protein family and the apoptotic promoters PUMA and Bax
Authors: Patel Seema , George Roger , Autore Flavia , Fraternali Franca , Ladbury John E. , Nikolova Penka V. 
Published: August 2008

AbstractThe apoptosis stimulating p53 proteins, ASPP1 and ASPP2, are the first two common activators of the p53 protein family that selectively enable the latter to regulate specific apoptotic target genes, which facilitates yes yet unknown mechanisms for discrimination between cell cycle arrest and apoptosis. To better understand the interplay between ASPP- and p53-family of proteins we investigated the molecular interactions between them using biochemical methods and structure-based homology modelling. The data demonstrate that: (i) the binding of ASPP1 and ASPP2 to p53, p63 and p73 is direct; (ii) the C-termini of ASPP1 and ASPP2 interact with the DNA-binding domains of p53 protein family with dissociation constants, Kd, in the lower micro-molar range; (iii) the stoichiometry of binding is 1:1; (iv) the DNA-binding domains of p53 family members are sufficient for these protein-protein interactions; (v) EMSA titrations revealed that while tri-complex formation between ASPPs, p53 family of proteins and PUMA/Bax is mutually exclusive, ASPP2 (but not ASPP1) formed a complex with PUMA (but not Bax) and displaced p53 and p73. The structure-based homology modelling revealed subtle differences between ASPP2 and ASPP1 and together with the experimental data provide novel mechanistic insights.