bluuebunny/crossref_metadata_2025_split huggingface dataset:
The importance of synthesis: A suggestion for international research efforts
Authors: Akasofu Syun‐Ichi 
Published: June 2007

In a scientific discipline, it is common to deal with a system that consists of many elements or subsystems. Most of us engage in the study of system components and their elements by dividing and subdividing them, leading to the trend of infinite specialization. However, at a certain point during the course of the development of a scientific discipline, a grand synthesis enables the distillation and coalescence of disparate results into a coherent understanding of the system as a whole.Synthesis also allows us to test and validate hypotheses, understand key processes, and better design future research efforts. Indeed, when a discipline succeeds in synthesis, it can make distinct, often epoch‐making progress, leading the discipline to higher levels of understanding of the system being studied. The concept of plate tectonics is an outstanding example of synthesis in the geosciences [Stewart, 1990].
Web-based GeneChip analysis system for large-scale collaborative projects
Authors: Dai Manhong , Wang Pinglang , Jakupovic Elvis , Watson Stanley J. , Meng Fan 
Published: June 2007

Abstract
Summary: The Web-Based GeneChip Analysis System (WGAS) is developed to overcome limitations in analysis setup efficiency, data and procedure sharing, as well as security issues in existing commercial and public domain solutions. It also incorporates unique functions and resources for more accurate and flexible GeneChip analysis.
Availability: WGAS is freely available at: http://arrayanalysis.mbni.med.umich.edu/arrayanalysis.html
Contact: mengf@umich.edu
TASSEL: software for association mapping of complex traits in diverse samples
Authors: Bradbury Peter J. , Zhang Zhiwu , Kroon Dallas E. , Casstevens Terry M. , Ramdoss Yogesh , Buckler Edward S. 
Published: June 2007

AbstractSummary: Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components.Availability: The TASSEL executable, user manual, example data sets and tutorial document are freely available at http://www.maizegenetics.net/tassel. The source code for TASSEL can be found at http://sourceforge.net/projects/tassel.Contact: pjb39@cornell.edu
beadarray: R classes and methods for Illumina bead-based data
Authors: Dunning Mark J. , Smith Mike L. , Ritchie Matthew E. , Tavaré Simon 
Published: June 2007

Abstract
Summary: The R/Bioconductor package beadarray allows raw data from Illumina experiments to be read and stored in convenient R classes. Users are free to choose between various methods of image processing, background correction and normalization in their analysis rather than using the defaults in Illumina's; proprietary software. The package also allows quality assessment to be carried out on the raw data. The data can then be summarized and stored in a format which can be used by other R/Bioconductor packages to perform downstream analyses. Summarized data processed by Illumina's; BeadStudio software can also be read and analysed in the same manner.
Availability: The beadarray package is available from the Bioconductor web page at www.bioconductor.org. A user's; guide and example data sets are provided with the package.
Contact: md392@cam.ac.uk
HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies
Authors: Laramie Jason M. , Wilk Jemma B. , DeStefano Anita L. , Myers Richard H. 
Published: June 2007

Abstract
Summary: We have created a program that searches densely genotyped regions for associated non-contiguous haplotypes using a standard family based haplotype association test. This program was designed to expand upon the ‘sliding window’ methodologies commonly used for haplotype construction by allowing the association of subsets of single nucleotide polymorphisms (SNPs) to drive the construction of the haplotype. This strategy permits HaploBuild to construct more biologically relevant haplotypes that are not constrained by arbitrary length and contiguous orientation.
Availability: http://snp.bumc.bu.edu
Contact: laramiej@bu.edu
BiVisu: software tool for bicluster detection and visualization
Authors: Cheng K.O. , Law N.F. , Siu W.C. , Lau T.H. 
Published: June 2007

AbstractSummary: BiVisu is an open-source software tool for detecting and visualizing biclusters embedded in a gene expression matrix. Through the use of appropriate coherence relations, BiVisu can detect constant, constant-row, constant-column, additive-related as well as multiplicative-related biclusters. The biclustering results are then visualized under a 2D setting for easy inspection. In particular, parallel coordinate (PC) plots for each bicluster are displayed, from which objective and subjective cluster quality evaluation can be performed.Availability: BiVisu has been developed in Matlab and is available at http://www.eie.polyu.edu.hk/~nflaw/Biclustering/Contact: k.o.cheng@polyu.edu.hk
The effect of diet on Paraoxonase 1/Arylesterase activities in patients with disorders of galactose metabolism
Authors: Schulpis Kleopatra H. , Karikas George A. , Bartzeliotou Anastasia , Papakonstantinou Evangelos D. , Kalogerakou Maria , Tsakiris Stylianos 
Published: June 2007

SummaryObjective  To investigate the effects of diet on the antiatherogenic enzyme Paraoxonase 1/Arylesterase (PON1/Aryl) activities in patients with disorders of galactose metabolism.Patients and methods  Eleven poorly dietary controlled children with classical galactosaemia (GALT deficiency), 7 with epimerase deficiency and 12 with duarte 1 variant ‘off diet’ underwent clinical and laboratory investigations before and after 10 days on galactose restricted diet whereas controls (N = 20) were examined once. Serum lipids, lipoproteins and apolipoprotein A1 (ApoA1) were measured with routine methods, PON1/Aryl activities and total antioxidant status (TAS) spectrophotometrically, and galactose‐1‐phosphate (Gal‐1‐P) enzymatically.Results  Lipids, lipoproteins, ApoA1, PON1/Aryl, TAS remained unaltered in all groups, except in those with classical galactosaemia pre‐ versus postdiet. In patients with classical galactosaemia, TAS, PON1, Aryl (0·98 ± 0·2 mmol/l, 60 ± 12 U/min/ml, 56 ± 16 KU/min/ml, respectively) were significantly reduced prediet as compared with those postdiet (1·63 ± 0·2 mmol/l, 136 ± 15 U/min/ml, 112 ± 18 KU/min/ml, respectively; P < 0·001) and controls. The enzyme activities positively correlated with TAS (r = 0·56, P < 0·001) in all groups and negatively with Gal‐1‐P (r = –0·54, P < 0·001) in group with GALT deficiency.Conclusions  Low TAS and high Gal‐1‐P levels may reduce PON1/Aryl activities. Patients with classical galactosaemia, when on strict diet, may benefit with a generous antiatherogenic capacity.
Soil organic matter chemistry in allophanic soils: a pyrolysis‐GC/MS study of a Costa Rican Andosol catena
Authors: Buurman P. , Peterse F. , Almendros Martin G. 
Published: June 2007

SummarySoil organic matter (SOM) in allophanic soils is supposed to accumulate due to protection caused by binding to allophane, aluminium and iron. We investigated a catena of allophanic and non‐allophanic soils in Costa Rica to determine the effect of such binding mechanisms on SOM chemistry. These soils contain no contribution of black carbon. Molecular characterization of litter, extractable and dispersed organic matter was done by Curie‐point pyrolysis‐GC/MS. The molecular chemistry of the organic fractions indicates a strong decomposition of plant‐derived organic matter and a strong contribution of microbial sugars and N‐compounds to SOM. Both the decomposition of plant‐derived SOM – including that of relatively recalcitrant compounds – and the relative contribution of microbial SOM were greater in allophanic samples than in non‐allophanic ones. This suggests that chemical protection does not act on primary OM, although it may influence the accumulation of secondary OM in these soils. The effect of allophane on SOM contents in such perhumid soils is probably through incorporation of decomposition products and microbial SOM in very fine aggregates that – in a perhumid environment – remain saturated with water during much of the year. Greater concentrations of aliphatics are found in allophanic residues, but there is no evidence of any specific mineral‐organic binding. The results do not support the existing theory of chemical protection of plant‐derived components through binding to allophane, iron and aluminium.
Sulphate adsorption at the Fe (hydr)oxide–H2O interface: comparison of cluster and periodic slab DFT predictions
Authors: Paul K. W. , Kubicki J. D. , Sparks D. L. 
Published: June 2007

SummaryThe transport and bioavailability of sulphate in soils are significantly affected by adsorption reactions at the mineral–H2O interface. Therefore, an understanding of the mechanisms and kinetics of sulphate adsorption is of fundamental importance in soil chemistry. In this investigation, the binding geometries of bidentate bridging and monodentate sulphate complexes at the Fe (hydr)oxide–H2O interface were predicted with static cluster and periodic slab density functional theory (DFT) calculations. The cluster calculations were performed with edge‐sharing dioctahedral Fe3+ models, using the unrestricted PBE0 exchange‐correlation functional and a combination of effective core potential (LanL2DZ – Fe atoms) and all‐electron (6–311+G(d,p) or 6–311+G(3df,p) – S, O, and H atoms) basis sets. The periodic slab calculations were performed with a (3 × 2) slab of the (100) α‐FeOOH surface, by means of the projector‐augmented wave method and a plane‐wave basis set. For the periodic slab DFT calculations, the spin‐polarized (SP) PBE exchange‐correlation functional, with and without explicit consideration of an on‐site Coulomb interaction parameter (i.e. SP‐PBE and SP‐PBE+U methods), was used. Despite the lack of long‐range order, cluster model predictions of the interatomic distances and angles of bidentate bridging and monodentate sulphate were in good agreement with the periodic slab model predictions. Quantitative analysis of the cluster and periodic slab DFT predictions is expected to result from theoretical fitting of extended X‐ray absorption fine structure measurements. The application of computational chemistry methods to soil chemistry research is anticipated to provide novel insight into the mechanisms and kinetics of ion sorption.
Long‐term use of Swedish moist snuff and the risk of myocardial infarction amongst men
Authors: Hergens M.‐P. , Alfredsson L. , Bolinder G. , Lambe M. , Pershagen G. , Ye W. 
Published: June 2007

Abstract.Background.  The scientific evidence on cardiovascular risks associated with long‐term use of snuff is limited and inconclusive. The use of this smokeless tobacco has increased in recent decades, and adverse health effects associated with snuff use could be of great public health concern.Objective.  We aimed to study whether long‐term use of snuff affects the risk of myocardial infarction.Design.  Between 1978 and 1993 all construction workers in Sweden were offered repeated health check‐ups by the Swedish Construction Industry's Organization for Working Environment Safety and Health. A cohort was created with information on tobacco use and other risk factors, collected through questionnaires.Setting.  In total, 118 395 nonsmoking men without a history of myocardial infarction were followed through 2004. Information on myocardial infarction morbidity and mortality was obtained from national registers. Relative risk estimates were derived from Cox proportional hazards regression model, with adjustment for age, body mass index and region of residence.Results.  Almost 30% of the men had used snuff. In total, 118 395 nonsmoking men without a history of myocardial infarction were followed through 2004. The multivariable‐adjusted relative risks for ever snuff users were 0.91 (95% confidence interval, 0.81–1.02) for nonfatal cases and 1.28 (95% confidence interval, 1.06–1.55) for fatal cases. Heavy users (≥50 g day−1) had a relative risk of fatal myocardial infarction of 1.96 (95% confidence interval, 1.08–3.58). Snuff use increased the probability of mortality from cardiovascular disease amongst nonfatal myocardial infarction patients.Conclusion.  Our results indicate that snuff use is associated with an increased risk of fatal myocardial infarction.
Impaired cortisol response to acute stressors in patients with coronary disease. Implications for inflammatory activity
Authors: Nijm J. , Kristenson M. , Olsson A. G. , Jonasson L. 
Published: June 2007

Abstract.Objectives. Inflammation is assumed to play a major role in the progress of atherosclerotic disease. We hypothesized that an altered hypothalamic‐pituitary adrenal (HPA) axis activity was linked to a disinhibited inflammatory activity in patients with coronary artery disease (CAD).Methods. Thirty CAD patients were assessed 12–14 weeks after a first‐time acute coronary syndrome. Serum samples were assayed for C‐reactive protein (CRP) and interleukin‐6. Free cortisol was measured in a 24‐h urine sample and in repeated saliva samples 30 min after awakening and at bedtime. The levels of inflammatory markers and cortisol were also determined before and after standardized physical and psychological stress tests.Results. The CAD patients had a higher 24‐h cortisol secretion and a flattened diurnal slope, resulting from significantly higher cortisol levels at bedtime, compared to clinically healthy controls. The levels of evening cortisol were strongly related to inflammatory markers in serum. When exposed to acute physical and psychological stressors, the CAD patients showed a significantly blunted cortisol response compared to controls. In addition, a stress‐induced increase in CRP was only observed in the patient group.Conclusions. Patients with CAD exhibited a cortisol pattern that markedly differed from controls. The data indicate that a dysfunctional HPA axis response involves a failure to contain inflammatory activity in CAD patients, thus providing a possible link between stress and inflammation in disease.
Matrix metalloproteinase‐1 and its inhibitor, TIMP‐1, in systolic heart failure: relation to functional data and prognosis
Authors: Jordán A. , Roldán V. , García M. , Monmeneu J. , De Burgos F. G. , Lip G. Y. H. , Marín F. 
Published: June 2007

Abstract.Background.  Structural remodelling of left ventricle is a common feature in the progression of congestive heart failure (CHF). Matrix metalloproteinases (MMPs) have been directly implicated as they degrade extracellular proteins. To test the hypothesis that MMP‐and its inhibitor, tissue type inhibitor of matrix metalloproteinases (TIMP‐1), could be related to functional status and prognosis in CHF, we examined the relationship of MMP‐1 and TIMP‐1 to peak oxygen consumption (VO2) and peak minute ventilation/carbon dioxide production relationship (VE/VCO2), and assessed their prognostic value.Methods.  We studied 50 patients with CHF, who were compared with 53 controls echocardiogram and ergoespirometry were performed, and serum levels of MMP‐1 and TIMP‐1 were assayed by ELISA. Patients were followed up for 17.5 ± 8.9 months, and total mortality, readmissions for heart failure and cardiac transplantation were recorded.Results.  Patients with CHF had lower levels of MMP‐1 (P = 0.027), and higher levels of TIMP‐1 and TIMP‐1/MMP‐1 ratio (both P < 0.01) than controls. TIMP‐1 levels and the TIMP‐1/MMP‐1 ratio correlated negatively with peak VO2 (Spearman, r:−0.51; P = 0.001 and r: −0.42; P = 0.030, respectively). During the follow‐up period, 23 patients (47.9%) suffered endpoints – these patients had higher baseline peak VE/VCO2 (P = 0.001), TIMP‐1 (P = 0.004), and TIMP‐1/MMP‐1 ratio values (P = 0.002), whereas MMP‐1 levels were lower (P = 0.027). On multivariate analysis, VE/VCO2, MMP‐1 levels and age were the only variables independently related to prognosis (all P < 0.05).Conclusion.  Poor functional capacity in CHF can be related to abnormal extracellular matrix turnover. Patients who suffered endpoints had more abnormal indices of matrix turnover, where MMP‐1 levels showed independent prognostic value.
Strong population structure despite evidence of recent migration in a selfing hermaphroditic vertebrate, the mangrove killifish (Kryptolebias marmoratus)
Authors: TATARENKOV ANDREY , GAO HONG , MACKIEWICZ MARK , TAYLOR D. SCOTT , TURNER BRUCE J. , AVISE JOHN C. 
Published: June 2007

AbstractWe employ a battery of 33 polymorphic microsatellite loci to describe geographical population structure of the mangrove killifish (Kryptolebias marmoratus), the only vertebrate species known to have a mixed‐mating system of selfing and outcrossing. Significant population genetic structure was detected at spatial scales ranging from tens to hundreds of kilometres in Florida, Belize, and the Bahamas. The wealth of genotypic information, coupled with the highly inbred nature of most killifish lineages due to predominant selfing, also permitted treatments of individual fish as units of analysis. Genetic clustering algorithms, neighbour‐joining trees, factorial correspondence, and related methods all earmarked particular killifish specimens as products of recent outcross events that could often be provisionally linked to specific migration events. Although mutation is the ultimate source of genetic diversity in K. marmoratus, our data indicate that interlocality dispersal and outcross‐mediated genetic recombination (and probably genetic drift also) play key proximate roles in the local ‘clonal’ dynamics of this species.
A sharper view of the outer Galaxy at 1420 and 408 MHz from the Canadian Galactic Plane Survey II: the catalogue of extended radio sources
Authors: Kerton C. R. , Murphy J. , Patterson J. 
Published: June 2007

Abstract
A new catalogue of extended radio sources has been prepared based on arcminute-resolution 1420-MHz images from the Canadian Galactic Plane Survey (CGPS). The new catalogue provides both 1420- and 408-MHz flux density measurements on sources found near the Galactic plane in the second quadrant of our Galaxy. In addition cross-identifications are made with other major radio catalogues and information is provided to facilitate the recovery of CGPS image data associated with each catalogued source. Numerous new radio sources are identified and the catalogue provides a comprehensive summary of both newly discovered and previously known H ii regions and supernova remnants in the outer Galaxy. The catalogue should be of use both for synoptic studies of Galactic structure and for placing higher resolution observations, at radio and other wavelengths, in context.
phyB‐1 sorghum maintains responsiveness to simulated shade, irradiance and red light : far‐red light
Authors: FINLAYSON SCOTT A. , HAYS DIRK B. , MORGAN PAGE W. 
Published: June 2007

ABSTRACTThe sorghum [Sorghum bicolor (L.) Moench]phyB‐1 mutant exhibits a constitutive shade‐avoidance phenotype including excessive shoot elongation. It was previously shown that this mutant also overproduces ethylene. Although phytochrome B (phyB) is assumed to be the pigment most important in sensing and transducing shade signals, the sorghum phyB‐1 mutant still responds to light signals characteristic of shade. Specifically, it was determined that the leaf blade : leaf sheath elongation of phyB‐1 is responsive to red : far red (R : FR), but this response is opposite that of wild type (WT). Reducing the photosynthetic photon flux density (PPFD) strongly reduced the leaf blade : leaf sheath of WT but did not affect phyB‐1, demonstrating a role for phyB in sensing PPFD. Using light‐emitting diode (LED) lighting, it was found that WT ethylene production was increased with low R : FR while PPFD had no effect. Conversely, phyB‐1 ethylene production increased only with high PPFD, high R : FR which was the treatment resulting in the least ethylene production by WT. Elevated ethylene production inhibits shoot elongation, but may contribute to shade avoidance by reducing leaf blade : leaf sheath elongation. Ethylene responses to light treatments designed to promote or reduce phytochrome A (phyA) activity, and the analysis of PHYA levels in the two cultivars suggests that phyA could be involved in transducing shade signals in light‐grown sorghum. Responses potentially tranduced by phyA are elevated in phyB‐1 which also over‐expresses PHYA.
An annual cycle of dimethylsulfoniopropionate‐sulfur and leucine assimilating bacterioplankton in the coastal NW Mediterranean
Authors: Vila‐Costa Maria , Pinhassi Jarone , Alonso Cecilia , Pernthaler Jakob , Simó Rafel 
Published: June 2007

SummaryThe contribution of major phylogenetic groups to heterotrophic bacteria assimilating sulfur from dissolved dimethylsulfoniopropionate (DMSP) and assimilating leucine was analysed in surface seawaters from Blanes Bay (NW Mediterranean) over an annual study between March 2003 and April 2004. The percentage of bacteria assimilating DMSP‐S showed a strong seasonal pattern, with a steady increase from winter (8 ± 5%) to summer (23 ± 3%). The same seasonal pattern was observed for the rate of DMSP‐S assimilation. The annual average percentage of DMSP‐S‐assimilating bacteria (16 ± 8%) was lower than the corresponding percentage of leucine‐assimilating cells (35 ± 16%), suggesting that not all bacteria synthesizing protein incorporated DMSP‐S. Smaller differences between both percentages were recorded in summer. Members of the Alphaproteobacteria (Roseobacter and SAR11) and Gammaproteobacteria groups accounted for most of bacterial DMSP‐S‐assimilating cells over the year. All major bacterial groups showed an increase of the percentage of cells assimilating DMSP‐S during summer, and contributed to the increase of the DMSP‐S assimilation rate in this period. In these primarily P‐limited waters, enrichment with P + DMSP resulted in a stimulation of bacterial heterotrophic production comparable to, or higher than, that with P + glucose in summer, while during the rest of the year P + glucose induced a stronger response. This suggested that DMSP was more important a S and C source for bacteria in the warm stratified season. Overall, our results suggest that DMSP‐S assimilation is controlled by the contribution of DMSP to S (and C) sources rather than by the phylogenetic composition of the bacterioplankton.