bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dzhida island-arc system in the Paleoasian Ocean: structure and main stages of Vendian-Paleozoic geodynamic evolution
Authors: Gordienko I.V. , Filimonov A.V. , Minina O.R. , Gornova M.A. , Medvedev A.Ya. , Klimuk V.S. , Elbaev A.L. , Tomurtogoo O. 
Published: March 2007

Abstract
We propose a model of the geodynamic evolution of the Dzhida island-arc system of the Paleoasian Ocean margin which records transformation of an oceanic basin into an accretion-collision orogenic belt. The system includes several Vendian-Paleozoic complexes that represent a mature oceanic island arc with an accretionary prism, oceanic islands, marginal and remnant seas, and Early Ordovician collisional granitoids. We have revealed a number of subunits (sedimentary sequences and igneous complexes) in the complexes and reconstructed their geodynamic settings. The tectonic evolution of the Dzhida island-arc system comprises five stages: (1) ocean opening (Late Riphean); (2) subduction and initiation of an island arc (Vendian-Early Cambrian); (3) subduction and development of a mature island arc (Middle-Late Cambrian); (4) accretion and formation of local collision zones and remnant basins (Early Ordovician-Devonian); and (5) postcollisional strike-slip faulting (Carboniferous-Permian).
Ultrapotassic basites in the Central Chukchi region and their role in genesis of Sn-bearing granites
Authors: Efremov S.V. , Kozlov V.D. 
Published: March 2007

Abstract
Analysis of the genetic relationship of Sn-bearing granitoids with ultrapotassic basic magmatism showed that their metallogeny was determined by the geochemistry of a specific reservoir localized in the continental lithosphere mantle (metasomatized mantle). The granitoid formation is well explained by the binary model of mixing of primary melts (products of the metasomatized mantle) with the continental crustal material. Geochemical studies of basic magmatism of different ages showed that the specific lithosphere reservoir formed in the Middle-Late Jurassic and existed at least till the late Late Cretaceous, i.e., during both tin metallogenic epochs of the Chukchi region.
Prevalence, spatial distribution and the effect of control measures on louping-ill virus in the Forest of Bowland, Lancashire
Authors: LAURENSON M. K. , McKENDRICK I. J. , REID H. W. , CHALLENOR R. , MATHEWSON G. K. 
Published: March 2007

SUMMARYThe complex pathogen–host–vector system of the tick-borne louping-ill virus causes economic losses to sheep and red grouse in upland United Kingdom. This paper examines the spatial distribution, incidence and effect of control measures on louping-ill virus in the Bowland Fells of Lancashire. Seroprevalence in sheep at the beginning of the study varied within the area and was affected significantly by the frequency of acaricide treatment. There was a clear decrease over 5 years in the effective force of infection on farms implementing a vaccination programme, irrespective of acaricide treatment regime, however, only one third of farms apparently eliminated infection. On farms where vaccination did not occur or where vaccination was carried out intermittently, the estimated force of infection was variable or possibly increased. Thus, as befits a complex host–pathogen system, reductions in prevalence were not as dramatic as predicted; we discuss the potential explanations for these observations.
Prediction of epidemic cholera due toVibrio choleraeO1 in children younger than 10 years using climate data in Bangladesh
Authors: MATSUDA F. , ISHIMURA S. , WAGATSUMA Y. , HIGASHI T. , HAYASHI T. , FARUQUE A. S. G. , SACK D. A. , NISHIBUCHI M. 
Published: March 2007

SUMMARYTo determine if a prediction of epidemic cholera using climate data can be made, we performed autoregression analysis using the data recorded in Dhaka City, Bangladesh over a 20-year period (1983–2002) comparing the number of children aged <10 years who were infected withVibrio choleraeO1 to the maximum and minimum temperatures and rainfall. We formulated a simple autoregression model that predicts the monthly number of patients using earlier climate variables. The monthly number of patients predicted by this model agreed well with the actual monthly number of patients where the Pearson's correlation coefficient was 0·95. Arbitrarily defined, 39·4% of the predicted numbers during the study period were within 0·8–1·2 times the observed numbers. This prediction model uses the climate data recorded 2–4 months before. Therefore, our approach may be a good basis for establishing a practical early warning system for epidemic cholera.
MedicCyc: a biochemical pathway database forMedicago truncatula
Authors: Urbanczyk-Wochniak Ewa , Sumner Lloyd W. 
Published: March 2007

AbstractMotivation: There is an imperative need to integrate functional genomics data to obtain a more comprehensive systems-biology view of the results. We believe that this is best achieved through the visualization of data within the biological context of metabolic pathways. Accordingly, metabolic pathway reconstruction was used to predict the metabolic composition for Medicago truncatula and these pathways were engineered to enable the correlated visualization of integrated functional genomics data.Results: Metabolic pathway reconstruction was used to generate a pathway database for M. truncatula (MedicCyc), which currently features more than 250 pathways with related genes, enzymes and metabolites. MedicCyc was assembled from more than 225 000 M. truncatula ESTs (MtGI Release 8.0) and available genomic sequences using the Pathway Tools software and the MetaCyc database. The predicted pathways in MedicCyc were verified through comparison with other plant databases such as AraCyc and RiceCyc. The comparison with other plant databases provided crucial information concerning enzymes still missing from the ongoing, but currently incomplete M. truncatula genome sequencing project. MedicCyc was further manually curated to remove non-plant pathways, and Medicago-specific pathways including isoflavonoid, lignin and triterpene saponin biosynthesis were modified or added based upon available literature and in-house expertise. Additional metabolites identified in metabolic profiling experiments were also used for pathway predictions. Once the metabolic reconstruction was completed, MedicCyc was engineered to visualize M. truncatula functional genomics datasets within the biological context of metabolic pathways.Availability: freely accessible at http://www.noble.org/MedicCyc/Contact: lwsumner@noble.org
From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycle
Authors: Steuer Ralf , Nesi Adriano Nunes , Fernie Alisdair R. , Gross Thilo , Blasius Bernd , Selbig Joachim 
Published: March 2007

AbstractMotivation: Mitochondrial metabolism, dominated by the reactions of the tricarboxylic acid (TCA) cycle, is of vital importance for a wide range of metabolic processes. In particular for autotrophic tissue, such as plant leaves, the TCA cycle marks the point of divergence of anabolic pathways and plays an essential role in biosynthesis. However, despite extensive knowledge about its stoichiometric properties, the function and the dynamical capabilities of the TCA cycle remain largely unknown.Methods and Results: Based on a recently proposed formalism, we investigate the dynamic and functional properties of the mitochondrial TCA cycle of plants. Starting with the structural properties, as described by the elementary flux modes of the system, we aim for the transition from structure to the dynamics of the TCA cycle. Using a parametric description of the system, encompassing all possible differential equations and parameter values, we detect and quantify regimes of different dynamic behavior. Optimizing the system with respect to dynamic stability, we demonstrate that maximal stability is associated with specific (relative) metabolite concentrations and flux values that are subsequently compared to the experimental literature. Our analysis also serves as a general example how to elucidate the transition from the structure to the dynamics of metabolic pathways.Contact: steuer@agnld.uni-potsdam.deSupplementary information: Supplementary data are available at Bioinformatics online.
Codelink: an R package for analysis of GE healthcare gene expression bioarrays
Authors: Diez Diego , Alvarez Rebeca , Dopazo Ana 
Published: March 2007

AbstractMotivation: Microarray-based expression profiles have become a standard methodology in any high-throughput analysis. Several commercial platforms are available, each with its strengths and weaknesses. The R platform for statistical analysis and graphics is a powerful environment for the analysis of microarray data, because it has many integrated statistical methods available as well as the specialized microarray analysis project Bioconductor. Many packages have been added in the last few years increasing the range of possible analysis. Here, we report the availability of a package for reading and analyzing data from GE Healthcare Gene Expression Bioarrays within the R environment.Availability: The software is implemented in the R language, is open source and available for download free of charge through the Bioconductor (http://www.bioconductor.org) project.Contact: diez@kuicr.kyoto-u.ac.jpSupplementary information: Supplementary data are available at Bioinformatics online.
Analyzing microarray data using CLANS
Authors: Frickey Tancred , Weiller Georg 
Published: March 2007

AbstractSummary: Analysis of microarray experiments is complicated by the huge amount of data involved. Searching for groups of co-expressed genes is akin to searching for protein families in a database as, in both cases, small subsets of genes with similar features are to be found within vast quantities of data. CLANS was originally developed to find protein families in large sets of amino acid sequences where the amount of data involved made phylogenetic approaches overly cumbersome. We present a number of improvements that greatly extend the previous version of CLANS and show its application to microarray data as well as its ability of incorporating additional information to facilitate interactive analysis.Availability: The program is available for download from: http://bioinfoserver.rsbs.anu.edu.au/downloads/clans/Contact: Georg.Weiller@anu.edu.auSupplementary information: http://bioinfoserver.rsbs.anu.edu.au/programs/clans
ABCGrid: Application for Bioinformatics Computing Grid
Authors: Sun Ying , Zhao Shuqi , Yu Huashan , Gao Ge , Luo Jingchu 
Published: March 2007

AbstractSummary: We have developed a package named Application for Bioinformatics Computing Grid (ABCGrid). ABCGrid was designed for biology laboratories to use heterogeneous computing resources and access bioinformatics applications from one master node. ABCGrid is very easy to install and maintain at the premise of robustness and high performance. We implement a mechanism to install and update all applications and databases in worker nodes automatically to reduce the workload of manual maintenance. We use a backup task method and self-adaptive job dispatch approach to improve performance. Currently, ABCGrid integrates NCBI_BLAST, Hmmpfam and CE, running on a number of computing platforms including UNIX/Linux, Windows and Mac OS X.Availability: The source code, executables and documents can be downloaded from http://abcgrid.cbi.pku.edu.cnContact: abcgrid@mail.cbi.pku.edu.cn
Glycan classification with tree kernels
Authors: Yamanishi Yoshihiro , Bach Francis , Vert Jean-Philippe 
Published: March 2007

AbstractMotivation: Glycans are covalent assemblies of sugar that play crucial roles in many cellular processes. Recently, comprehensive data about the structure and function of glycans have been accumulated, therefore the need for methods and algorithms to analyze these data is growing fast.Results: This article presents novel methods for classifying glycans and detecting discriminative glycan motifs with support vector machines (SVM). We propose a new class of tree kernels to measure the similarity between glycans. These kernels are based on the comparison of tree substructures, and take into account several glycan features such as the sugar type, the sugar bound type or layer depth. The proposed methods are tested on their ability to classify human glycans into four blood components: leukemia cells, erythrocytes, plasma and serum. They are shown to outperform a previously published method. We also applied a feature selection approach to extract glycan motifs which are characteristic of each blood component. We confirmed that some leukemia-specific glycan motifs detected by our method corresponded to several results in the literature.Availability: Softwares are available upon request.Contact: yoshi@kuicr.kyoto-u.ac.jpSupplementary information: Datasets are available at the following website: http://web.kuicr.kyoto-u.ac.jp/supp/yoshi/glycankernel/
Social Mixing with Other Children during Infancy Enhances Antibody Response to a Pneumococcal Conjugate Vaccine in Early Childhood
Authors: Salt Penny , Banner Carly , Oh Sarah , Yu Ly-mee , Lewis Susan , Pan Dingxin , Griffiths David , Ferry Berne , Pollard Andrew 
Published: March 2007

ABSTRACTChildren who have siblings and/or who attend day care have higher rates of nasopharyngeal colonization with pneumococci than lone children do. Pneumococcal colonization is usually asymptomatic but is a prerequisite for invasive disease. We studied the effect of social mixing with other children on immunity to a pneumococcal vaccine. One hundred sixty children aged 1 year were immunized with a 7-valent conjugate pneumococcal vaccine. A blood sample was obtained before and 9 to 11 days after the vaccine. The concentration and avidity of antibody against vaccine pneumococcal serotypes (4, 6B, 9V, 14, 18C, 19F, and 23F) were studied in relation to pneumococcal carriage rate and measures of social mixing. Children with increased social mixing had higher antibody concentrations against serotypes 4, 9V, 14, and 23F than lone children did. The least-carried serotype, serotype 4, was the one of the most immunogenic. This contrasts with serotype 6B, the most common nasopharyngeal isolate but the least immunogenic. Social mixing in infancy enhances the immune response to aStreptococcus pneumoniaepolysaccharide-protein conjugate vaccine at 1 year of age. Exposure to pneumococci in the first year of life may induce immunological priming. An alternative explanation is that differences in immunological experience, such as increased exposure to respiratory viral infections in early childhood, alters the response to vaccines perhaps by affecting the balance between Th1 and Th2 cytokines. The low immunogenicity of serotype 6B polysaccharide might make conditions more favorable for carriage of the 6B organism and explain why 6B pneumococci were more frequently isolated than other serotypes.
Borreliacidal OspC Antibody Response of Canines with Lyme Disease Differs Significantly from That of Humans with Lyme Disease
Authors: Lovrich Steven D. , La Fleur Rhonda L. , Jobe Dean A. , Johnson Jennifer C. , Asp Krista E. , Schell Ronald F. , Callister Steven M. 
Published: March 2007

ABSTRACT

Humans reliably produce high concentrations of borreliacidal OspC antibodies specific for the seven C-terminal amino acids shortly after infection with
Borrelia burgdorferi
. We show that dogs also produce OspC borreliacidal antibodies but that their frequencies, intensities, and antigenicities differ significantly. The findings therefore confirm a major difference between the borreliacidal antibody responses of humans and canines with Lyme disease.
Inadequacy of Colominic Acid as an Absorbent Intended To Facilitate Use of Complement-Preserved Baby Rabbit Serum in theNeisseria meningitidisSerogroup B Serum Bactericidal Antibody Assay
Authors: Findlow Jamie , Holland Ann , Martin Diana , Oster Philipp , Balmer Paul , Borrow Ray 
Published: March 2007

ABSTRACTThe surrogate of protection againstNeisseria meningitidisserogroup B (MenB) is the serum bactericidal antibody (SBA) assay, which measures the functional activity of antibody by using an exogenous complement source. Despite baby rabbit complement having been used in meningococcal serogroup A, C, Y, and W135 SBA assays, it is not recommended for use in the MenB SBA assay due to elevated SBA titers caused by low-avidity anti-MenB capsular antibody in test sera. Therefore, the possibility of absorbing anti-MenB capsular antibody from test sera to enable the use of baby rabbit complement in the MenB SBA assay was investigated by comparing the results with those gained using human complement. Colominic acid fromEscherichia coliK1, which shares the same linkage residue as MenB polysaccharide, was used as an absorbent due to the commercial unavailability of purified MenB polysaccharide. Inclusion of soluble colominic acid as an absorbent with baby rabbit complement resulted in a general reduction in SBA titers compared with those obtained using baby rabbit complement alone. However, these were not comparable to human SBA titers for all samples. Further optimization and investigations demonstrated that for some samples, colominic acid reduced titers to less than those achieved with human complement, and for others, it was not possible to inhibit titers by using colominic acid. The results suggested that the use of colominic acid will not result in the ability to use baby rabbit complement in the MenB SBA assay, thus not alleviating the difficulties in procuring human complement. However, alternative absorbents, such as purified MenB polysaccharide, may warrant further evaluation.
Carotenoid Biosynthesis in the Primitive Red Alga
Cyanidioschyzon merolae
Authors: Cunningham Francis X. , Lee Hansel , Gantt Elisabeth 
Published: March 2007

ABSTRACT

Cyanidioschyzon merolae
is considered to be one of the most primitive of eukaryotic photosynthetic organisms. To obtain insights into the origin and evolution of the pathway of carotenoid biosynthesis in eukaryotic plants, the carotenoid content of
C. merolae
was ascertained, genes encoding enzymes of carotenoid biosynthesis in this unicellular red alga were identified, and the activities of two candidate pathway enzymes of particular interest, lycopene cyclase and β-carotene hydroxylase, were examined.
C. merolae
contains perhaps the simplest assortment of chlorophylls and carotenoids found in any eukaryotic photosynthetic organism: chlorophyll
a
, β-carotene, and zeaxanthin. Carotenoids with ε-rings (e.g., lutein), found in many other red algae and in green algae and land plants, were not detected, and the lycopene cyclase of
C. merolae
quite specifically produced only β-ringed carotenoids when provided with lycopene as the substrate in
Escherichia coli
. Lycopene β-ring cyclases from several bacteria, cyanobacteria, and land plants also proved to be high-fidelity enzymes, whereas the structurally related ε-ring cyclases from several plant species were found to be less specific, yielding products with β-rings as well as ε-rings.
C. merolae
lacks orthologs of genes that encode the two types of β-carotene hydroxylase found in land plants, one a nonheme diiron oxygenase and the other a cytochrome P450. A
C. merolae
chloroplast gene specifies a polypeptide similar to members of a third class of β-carotene hydroxylases, common in cyanobacteria, but this gene did not produce an active enzyme when expressed in
E. coli
. The identity of the
C. merolae
β-carotene hydroxylase therefore remains uncertain.
Posaconazole Treatment for
Apophysomyces elegans
Rhino-Orbital Zygomycosis following Trauma for a Male with Well-Controlled Diabetes
Authors: Ferguson T. D. , Schniederjan S. D. , Dionne-Odom J. , Brandt M. E. , Rinaldi M. G. , Nolte F. S. , Langston A. , Zimmer S. M. 
Published: March 2007

ABSTRACT

We report a case of rhino-orbital zygomycosis in a 43-year-old male with well-controlled diabetes mellitus. The patient initially received liposomal amphotericin B, but the infection continued to progress, so posaconazole treatment was begun and eventually led to the cure of his infection. The causative agent was identified as
Apophysomyces elegans
, an emerging cause of zygomycosis in immunocompetent hosts.
Variation in the Number of Tandem Repeats and Profile of Surface Protein Genes among Invasive Group B Streptococci Correlates with Patient Age
Authors: Ho Yueh-Ren , Li Chien-Ming , Su Hsin-Pi , Wu Jane-Hong , Tseng Yu-Ching , Lin Yuh-Jyh , Wu Jiunn-Jong 
Published: March 2007

ABSTRACT

The average number of tandem repeats of the
rib
gene (which encodes the Rib surface protein) in invasive group B streptococci from 29 neonates was smaller than that from 20 adults (6.8 and 8.6, respectively;
P
< 0.05), implying a distinct contribution of immunity toward this age-related variation.
Prevalence and Characteristics of Heteroresistant Vancomycin-Intermediate
Staphylococcus aureus
Bacteremia in a Tertiary Care Center
Authors: Maor Yasmin , Rahav Galia , Belausov Natasha , Ben-David Debby , Smollan Gill , Keller Nathan 
Published: March 2007

ABSTRACT

Infections with
S. aureus
with heterogeneous intermediate resistance to vancomycin (hVISA) are occurring more frequently. The detection of these infections, their prevalence, clinical characteristics, and significance are controversial. During 2003 and 2004, all blood culture isolates of methicillin-resistant
Staphylococcus aureus
(264 patients) at the Sheba Medical Center, Tel Hashomer, Israel, were assessed for hVISA by using the Etest macromethod. A total of 16 patients (6%) were positive for hVISA. Resistance to teicoplanin alone and to vancomycin alone using the Etest macromethod was found in 14 and 10 patients, respectively. Standard MICs to vancomycin were between 1 to 4 mg/ml. Most of these isolates (12 of 16 [75%]) would have been missed without specific testing. The median number of bacteremic days was 4. Seven patients had positive blood cultures for more than 5 days. Twelve patients died, and for eight of these the deaths were directly related to hVISA sepsis. We found that hVISA bacteremia was prevalent in our institution, and we suggest seeking hVISA in patients with persistent
S. aureus
bacteremia.
Characterization of the Epidemic European Fusidic Acid-Resistant Impetigo Clone of
Staphylococcus aureus
Authors: O'Neill A. J. , Larsen A. R. , Skov R. , Henriksen A. S. , Chopra I. 
Published: March 2007

ABSTRACT

Resistance to the antibiotic fusidic acid in European strains of
Staphylococcus aureus
causing impetigo has increased in recent years. This increase appears to have resulted from clonal expansion of a strain we have designated the epidemic European fusidic acid-resistant impetigo clone (EEFIC), which carries the fusidic acid resistance determinant
fusB
on its chromosome. To understand better the properties of the EEFIC responsible for its success, we have performed detailed phenotypic and genotypic characterization of this clone. Molecular typing revealed the EEFIC to be ST123,
spa
type t171, and
agr
type IV and therefore unrelated to earlier prevalent
fusB
+
strains found in the United Kingdom. EEFIC strains exhibited resistance to fusidic acid, penicillin, and, in some cases, erythromycin, which are all used in the treatment of impetigo. PCR analysis of the EEFIC and complete DNA sequencing of the 39.3 Kb plasmid it harbors identified genes encoding several toxins previously implicated in impetigo (exfoliative toxins A and B and EDIN-C). The location of
fusB
was mapped on the chromosome and found to be associated with a novel 16.6-kb genomic island integrated downstream of
groEL
. Although this element is related to classical staphylococcal pathogenicity islands, it does not encode any known virulence factors and consequently has been designated SaRI

fusB

(for “
S. aureus
resistance island carrying
fusB
”).