bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metallurgy Beyond Iron
Authors: Gallino Isabella , Busch Ralf 
Published: September 2009

AbstractMetallurgy is one of the oldest sciences. Its history can be traced back to 6000 BCE with the discovery of Gold, and each new discovery — Copper, Silver, Lead, Tin, Iron and Mercury — marked the beginning of a new era of civilization. Currently there are 86 known metals, but until the end of the 17th century, only 12 of these were known. Steel (Fe–C alloy) was discovered in the 11th century BCE; however, it took until 1709 CE before we mastered the smelting of pig-iron by using coke instead of charcoal and started the industrial revolution. The metallurgy of nowadays is mainly about discovering better materials with superior properties to fulfil the increasing demand of the global market. Promising are the Glassy Metals or Bulk Metallic Glasses (BMGs) — discovered at first in the late 50s at the California Institute of Technology — which are several times stronger than the best industrial steels and 10-times springier. The unusual structure that lacks crystalline grains makes BMGs so promising. They have a liquid-like structure that means they melt at lower temperatures, can be moulded nearly as easily as plastics, and can be shaped into features just 10 nm across. The best BMG formers are based on Zr, Pd, Pt, Ca, Au and, recently discovered, also Fe. They have typically three to five components with large atomic size mismatch and a composition close to a deep eutectic. Packing in such liquids is very dense, with a low content of free volume, resulting in viscosities that are several orders of magnitude higher than in pure metal melts.
Measuring Cosmic Elements with Gamma-Ray Telescopes
Authors: Diehl Roland 
Published: September 2009

AbstractGamma-ray telescopes are capable of measuring radioactive trace isotopes from cosmic nucleosynthesis events. Such measurements address new isotope production rather directly for a few key isotopes such as 44Ti, 26Al, 60Fe, and 56Ni, as well as positrons from the β+-decay variety. Experiments of the past decades have now established an astronomy with γ-ray lines, which is an important part of the study of nucleosynthesis environments in cosmic sources. For massive stars and supernovae, important constraints have been set: Co isotope decays in SN1987A directly demonstrated the synthesis of new isotopes in core-collapse supernovae, 44Ti from the 340-year-old Cas A supernova supports the concept of α-rich freeze-out, but results in interesting puzzles pursued by theoretical studies and future experiments. 26Al and 60Fe has been measured from superimposed nucleosynthesis within our Galaxy, and sets constraints on massive-star interior structure through its intensity ratio of ∼15%. The 26Al γ-ray line is now seen to trace current star formation and even the kinematics of interstellar medium throughout the Galaxy. Positron annihilation emission from nucleosynthesis throughout the plane of our Galaxy appears to be mainly from 26Al and other supernova radioactivity, but the striking brightness of the Galaxy's bulge region in positron annihilation γ-rays presents a puzzle involving several astrophysics issues beyond nuclear astrophysics. This paper focuses mainly on a discussion of 26Al and 60Fe from massive-star nucleosynthesis.
montage: AGB Nucleosynthesis with Full s-Process Calculations
Authors: Church R. P. , Cristallo S. , Lattanzio J. C. , Stancliffe R. J. , Straniero O. , Cannon R. C. 
Published: September 2009

AbstractWe present montage, a post-processing nucleosynthesis code that combines a traditional network for isotopes lighter than calcium with a rapid algorithm for calculating the s-process nucleosynthesis of the heavier isotopes. The separation of those parts of the network where only neutron-capture and beta-decay reactions are significant provides a substantial advantage in computational efficiency. We present the yields for a complete set of s-process isotopes for a 3-M⊙, Z = 0.02 stellar model, as a demonstration of the utility of the approach. Future work will include a large grid of models suitable for use in calculations of Galactic chemical evolution.
The Weil-Steinberg character of finite classical groups
Authors: Hiss G. , Zalesski A. 
Published: September 2009

Let GGbe one of the groupsGL⁡(n,q)\operatorname {GL}(n,q)orU(n,q)U(n,q), and let HHdenote the subgroupGL⁡(n−1,q)\operatorname {GL}({n-1},q)orU(n−1,q)U(n-1,q), respectively. We show that the restriction of the Steinberg character of GGto HHequals the product of the Weil character and the Steinberg character of HH.
SimCT: a generic tool to visualize ontology-based relationships for biological objects
Authors: Herrmann Carl , Bérard Sèverine , Tichit Laurent 
Published: September 2009

Abstract
Summary: We present a web-based service, SimCT, which allows to graphically display the relationships between biological objects (e.g. genes or proteins) based on their annotations to a biomedical ontology. The result is presented as a tree of these objects, which can be viewed and explored through a specific java applet designed to highlight relevant features. Unlike the numerous tools that search for overrepresented terms, SimCT draws a simplified representation of biological terms present in the set of objects, and can be applied to any ontology for which annotation data is available. Being web-based, it does not require prior installation, and provides an intuitive, easy-to-use service.
Availability: http://tagc.univ-mrs.fr/SimCT
Contact: carl.herrmann@univmed.fr
Supplementary information: Supplementary data are available at Bioinformatics online
In response to ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’
Authors: Faust Karoline , Croes Didier , van Helden Jacques 
Published: September 2009

Abstract
Motivation: In their article entitled ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’ de Figueiredo and co-authors assess the performance of three pathway prediction tools (METATOOL, PathFinding and Pathway Hunter Tool) using the synthesis of glucose-6-phosphate (G6P) from acetyl-CoA in humans as a test case. We think that this article is biased for three reasons: (i) the metabolic networks used as input for the respective tools were of very different sizes; (ii) the ‘assessment’ is restricted to two study cases; (iii) developers are inherently more skilled to use their own tools than those developed by other people. We extended the analyses led by de Figueiredo and clearly show that the apparent superior performance of their tool (METATOOL) is partly due to the differences in input network sizes. We also see a conceptual problem in the comparison of tools that serve different purposes. In our opinion, metabolic path finding and elementary mode analysis are answering different biological questions, and should be considered as complementary rather than competitive approaches.
Contact: kfaust@ulb.ac.be
Supplementary information: Supplementary data are available at Bioinformatics online.
Capture efficiency and size selectivity of hydraulic clam dredges used in fishing for ocean quahogs (Arctica islandica): simultaneous estimation in the SELECT model
Authors: Thorarinsdóttir Gudrun G. , Jacobson Larry , Ragnarsson Stefan Áki , Garcia Elena Guijarro , Gunnarsson Karl 
Published: September 2009

AbstractThorarinsdóttir, G. G., Jacobson, L., Ragnarsson, S. Á., Garcia, E. G., and Gunnarsson, K. 2010. Capture efficiency and size selectivity of hydraulic clam dredges used in fishing for ocean quahogs (Arctica islandica): simultaneous estimation in the SELECT model. – ICES Journal of Marine Science, 67: 345–354. Estimates of capture efficiency and size selectivity for commercial dredges are important in estimating stock biomass and setting catch limits for the ocean quahog off Iceland and the United States. Ocean quahogs are long-lived, slow-growing, and sensitive to overharvest resulting from poor estimates of capture efficiency and stock biomass. Capture efficiency and size selectivity were estimated simultaneously in mixed-effect SELECT models using diver and commercial dredge experiment data from the shallow-water habitats off Iceland. Estimated capture efficiency for the commercial dredge E = 92% (CV = 8%) was high for large [107.5 mm shell length (SL)] ocean quahogs. Size selectivity followed an ascending logistic curve, with L50 = 70.5 mm SL (CV 4%), a selectivity range of 17.6 mm SL, and substantial variability among experimental dredge tows. Estimated capture efficiency was higher than that for ocean quahogs in US waters, possibly because of the deep habitats off the United States or uncertainty about dredge position during US depletion experiments. Scaling maximum selectivity from the SELECT model to one reduces correlations between size-selectivity and capture-efficiency parameters and may enhance the utility of selectivity estimates in stock assessment modelling. Our experimental and modelling approach may be useful for studies with other non-mobile benthic species.
LIN, a Novel Type of U-Box/WD40 Protein, Controls Early Infection by Rhizobia in Legumes
Authors: Kiss Ernö , Oláh Boglárka , Kaló Péter , Morales Monica , Heckmann Anne B. , Borbola Andrea , Lózsa Anita , Kontár Katalin , Middleton Patrick , Downie J. Allan , Oldroyd Giles E.D. , Endre Gabriella 
Published: September 2009

Abstract
The formation of a nitrogen-fixing nodule requires the coordinated development of rhizobial colonization and nodule organogenesis. Based on its mutant phenotype, lumpy infections (lin), LIN functions at an early stage of the rhizobial symbiotic process, required for both infection thread growth in root hair cells and the further development of nodule primordia. We show that spontaneous nodulation activated by the calcium- and calmodulin-dependent protein kinase is independent of LIN; thus, LIN is not necessary for nodule organogenesis. From this, we infer that LIN predominantly functions during rhizobial colonization and that the abortion of this process in lin mutants leads to a suppression of nodule development. Here, we identify the LIN gene in Medicago truncatula and Lotus japonicus, showing that it codes for a predicted E3 ubiquitin ligase containing a highly conserved U-box and WD40 repeat domains. Ubiquitin-mediated protein degradation is a universal mechanism to regulate many biological processes by eliminating rate-limiting enzymes and key components such as transcription factors. We propose that LIN is a regulator of the component(s) of the nodulation factor signal transduction pathway and that its function is required for correct temporal and spatial activity of the target protein(s).
Altered Architecture and Enhanced Drought Tolerance in Rice via the Down-Regulation of Indole-3-Acetic Acid by TLD1/OsGH3.13 Activation
Authors: Zhang Sheng-Wei , Li Chen-Hui , Cao Jia , Zhang Yong-Cun , Zhang Su-Qiao , Xia Yu-Feng , Sun Da-Ye , Sun Ying 
Published: September 2009

Abstract
Plant architecture is determined by genetic and developmental programs as well as by environmental factors. Sessile plants have evolved a subtle adaptive mechanism that allows them to alter their growth and development during periods of stress. Phytohormones play a central role in this process; however, the molecules responsible for integrating growth- and stress-related signals are unknown. Here, we report a gain-of-function rice (Oryza sativa) mutant, tld1-D, characterized by (and named for) an increased number of tillers, enlarged leaf angles, and dwarfism. TLD1 is a rice GH3.13 gene that encodes indole-3-acetic acid (IAA)-amido synthetase, which is suppressed in aboveground tissues under normal conditions but which is dramatically induced by drought stress. The activation of TLD1 reduced the IAA maxima at the lamina joint, shoot base, and nodes, resulting in subsequent alterations in plant architecture and tissue patterning but enhancing drought tolerance. Accordingly, the decreased level of free IAA in tld1-D due to the conjugation of IAA with amino acids greatly facilitated the accumulation of late-embryogenesis abundant mRNA compared with the wild type. The direct regulation of such drought-inducible genes by changes in the concentration of IAA provides a model for changes in plant architecture via the process of drought adaptation, which occurs frequently in nature.
Mesalazine inhibits the β‐catenin signalling pathway acting through the upregulation of μ‐protocadherin gene in colo‐rectal cancer cells
Authors: PARENTI S. , FERRARINI F. , ZINI R. , MONTANARI M. , LOSI L. , CANOVI B. , FERRARI S. , GRANDE A. 
Published: September 2009

SummaryBackground  Several reports indicate that mesalazine (5‐aminosalicylic acid, 5‐ASA) is a promising candidate for the chemoprevention of colo‐rectal cancer because of its ability to reach the purpose avoiding the unwanted side effects usually associated with prolonged administration of nonsteroidal anti‐inflammatory drugs. This activity of 5‐ASA is probably the consequence of a number of effects determined on colo‐rectal cancer cells, consisting of reduced proliferation, increased apoptosis and activation of cell cycle checkpoints and DNA repair processes. A recent observation has suggested that inhibition of β‐catenin signalling could induce these cellular effects.Aim  To characterize better the capacity of 5‐ASA to inhibit the β‐catenin signalling pathway.Methods  Genes belonging to the β‐catenin signalling pathway were analysed in colo‐rectal cancer cell lines treated with 5‐ASA using a combination of laboratory assays that are able to detect their phenotypic expression and functional activity.Results  The results obtained indicated that 5‐ASA induces the expression of a protein called μ‐protocadherin that belongs to the cadherin superfamily and is able to sequester β‐catenin on the plasmatic membrane of treated cells hampering its function.Conclusion  These findings suggest that μ‐protocadherin might be employed as a biological marker to monitor the chemopreventive efficacy of 5‐ASA.
A comparison of the acid‐inhibitory effects of esomeprazole and pantoprazole in relation to pharmacokinetics and CYP2C19 polymorphism
Authors: HUNFELD N. G. , TOUW D. J. , MATHOT R. A. , MULDER P. G. H. , VAN SCHAIK R. H. , KUIPERS E. J. , KOOIMAN J. C. , GEUS W. P. 
Published: September 2009

SummaryBackground Esomeprazole and pantoprazole are metabolized in the liver and the polymorphic CYP2C19 enzyme is involved in that process. This genetic polymorphism determines fast (70% of Caucasians), intermediate (25–30% of Caucasians) and slow (2–5% of Caucasians) metabolism of PPIs.Aim To compare the acid‐inhibitory effects of esomeprazole 40 mg and pantoprazole 40 mg at 4, 24 and 120 h after oral administration in relation to CYP2C19 genotype and pharmacokinetics.Methods CYP2C19*2, *3, *4, *5 and *17 genotypes were determined in healthyHelicobacter pylori‐negative Caucasian subjects. 7 wt/wt, 7 wt/*2, 2 wt/*17, 2 *2/*17 and 1 *2/*2 were included in a randomized investigator‐blinded cross‐over study with esomeprazole 40 mg and pantoprazole 40 mg. Intragastric 24‐h pH‐monitoring was performed on days 0, 1 and 5 of oral dosing.Results A total of 19 subjects (mean age 24 years, 7 male) completed the study. At day 1 and 5, acid‐inhibition with esomeprazole was significantly greater and faster than with pantoprazole. Differences in acid‐inhibition and pharmacokinetics between wt/wt and wt/*2 genotype were significant for pantoprazole at day 1 and 5.Conclusions Esomeprazole provides acid‐inhibition faster than and superior to pantoprazole after single and repeated administration. The acid‐inhibitory effect and the kinetics of pantoprazole are influenced by CYP2C19 genotype.
An investigation of medication adherence to 5‐aminosalicylic acid therapy in patients with ulcerative colitis, using self‐report and urinary drug excretion measurements
Authors: MOSHKOVSKA T. , STONE M. A. , CLATWORTHY J. , SMITH R. M. , BANKART J. , BAKER R. , WANG J. , HORNE R. , MAYBERRY J. F. 
Published: September 2009

SummaryBackground Non‐adherence to 5‐aminosalicylic acid (5‐ASA) medication can limit the established benefits of this therapy in ulcerative colitis (UC).Aim To determine rates and predictors of non‐adherence to 5‐ASA therapy in UC patients.Methods Medication adherence was assessed using self‐report data and urinary drug excretion measurements. Participants completed a study‐specific questionnaire and two validated questionnaires: Beliefs about Medicine Questionnaire (BMQ)‐Specific and Satisfaction with Information about Medicines Scale.Results A total of 169 participants provided self‐report adherence data; 151 also provided urine samples. Adherence rates were 111/151 (68%) according to self‐report and 90/151 (60%) according to urine analysis, but the two measures were not correlated (χ2 = 0.12,P = 0.725). Logistic regression identified a significant association between self‐reported non‐adherence and younger age [odds ratio (OR) for increased age 0.954, 95% confidence interval (CI) 0.932–0.976] and also doubts about personal need for medication (OR for BMQ – Specific Necessity scores 0.578, 95% CI 0.366–0.913). For non‐adherence based on urine analysis, only South Asian ethnicity was independently associated with non‐adherence (OR 2.940, 95% CI 1.303–6.638).Conclusions Our observations confirm the difficulty of accurately assessing medication adherence. Nonmodifiable (younger age, South Asian ethnicity) and potentially modifiable (medication beliefs) predictors of non‐adherence were identified.
Effects of DGAT1 and GHR on milk yield and milk composition in the Chinese dairy population
Authors: Sun D. , Jia J. , Ma Y. , Zhang Y. , Wang Y. , Yu Y. , Zhang Y. 
Published: September 2009

SummaryPrevious studies have demonstrated that the p.Lys232Ala substitution in the acylCoA: diacylglycerol acyltransferase (DGAT1) gene and the p.Phe279Tyr mutation in the growth hormone receptor (GHR) gene are the causative quantitative trait loci underlying milk yield and composition on BTA14 and BTA20 respectively. To examine their applications in the genetic improvement of Chinese dairy cattle productivity, we herein investigated the effects of the DGAT1 p.Lys232Ala and GHR p.Phe279Tyr mutations on milk, fat and protein yield, as well as fat and protein percentage in the milk of 1222 Holstein cows. Genotyping was performed using PCR‐RFLP for DGAT1 or primer‐introduced restriction analysis (PCR‐PIRA) for GHR. With a mixed animal model, the significant associations of the DGAT1 p.Lys232Ala substitution with 305‐day milk, fat and protein yield were identified (P = 0.0001). The DGAT1 allele that encode lysine at position 232 was associated with increased 305‐day milk fat yield, but with decreased 305‐day milk and protein yield, whereas the GHR p.Phe279Tyr mutation was found to be significantly associated with protein percentage (P = 0.0014). The allele substitution effect of p.279Phe by p.279Tyr may lead to a significant increase in protein percentage. Our findings indicate that DGAT1 p.232Ala and GHR p.279Phe could be used to increase milk yield and protein yield of Chinese Holstein cows.
How should we manage patients with mildly increased serum thyrotrophin concentrations?
Authors: Vanderpump Mark P. J. 
Published: September 2009

SummaryA mildly increased serum thyrotrophin (TSH) is usually because of mild thyroid failure, and the most common aetiology in iodine‐replete communities is chronic autoimmune thyroiditis. It is more common in women, and the prevalence increases with age in both men and women and is associated with the presence of antithyroid antibodies. The majority will have serum TSH levels between 5–10 mIU/l, normal free thyroxine (T4) levels and relatively few symptoms. In 2004, US evidence‐based consensus guidelines concluded that there were no adverse outcomes of a mildly increased serum TSH other than a risk of progression to overt hypothyroidism and few data to justify levothyroxine therapy. There is still debate as to what constitutes an increased serum TSH, particularly in older subjects. Although some subjects will progress to overt hypothyroidism, recent data suggest a significant proportion revert to a serum TSH within the reference range without treatment. Two recent meta‐analyses have suggested that the possible cardiovascular risks may be more significant in younger adults. Other data suggest that mild thyroid failure may be the only reversible cause of left ventricular diastolic dysfunction. No appropriately powered prospective, randomized, controlled, double‐blinded interventional trial of levothyroxine therapy for a mildly increased serum TSH exists. However, treatment in subjects who are symptomatic, pregnant or preconception, aged less than 65 years and older subjects with evidence of heart failure appear justified.
Responses of fungal root colonization, plant cover and leaf nutrients to long‐term exposure to elevated atmospheric CO2 and warming in a subarctic birch forest understory
Authors: OLSRUD MARIA , CARLSSON BENGT Å. , SVENSSON BRITA M. , MICHELSEN ANDERS , MELILLO JERRY M. 
Published: September 2009

AbstractResponses of the mycorrhizal fungal community in terrestrial ecosystems to global change factors are not well understood. However, virtually all land plants form symbiotic associations with mycorrhizal fungi, with approximately 20% of the plants' net primary production transported down to the fungal symbionts. In this study, we investigated how ericoid mycorrhiza (ErM), fine endophytes (FE) and dark septate endophytes (DSE) in roots responded to elevated atmospheric CO2 concentrations and warming in the dwarf shrub understory of a birch forest in the subarctic region of northern Sweden. To place the belowground results into an ecosystem context we also investigated how plant cover and nutrient concentrations in leaves responded to elevated atmospheric CO2 concentrations and warming. The ErM colonization in ericaceous dwarf shrubs increased under elevated atmospheric CO2 concentrations, but did not respond to warming following 6 years of treatment. This suggests that the higher ErM colonization under elevated CO2 might be due to increased transport of carbon belowground to acquire limiting resources such as N, which was diluted in leaves of ericaceous plants under enhanced CO2. The elevated CO2 did not affect total plant cover but the plant cover was increased under warming, which might be due to increased N availability in soil. FE colonization in grass roots decreased under enhanced CO2 and under warming, which might be due to increased root growth, to which the FE fungi could not keep up, resulting in proportionally lower colonization. However, no responses in aboveground cover of Deschampsia flexuosa were seen. DSE hyphal colonization in grass roots significantly increased under warmer conditions, but did not respond to elevated CO2. This complex set of responses by mycorrhizal and other root‐associated fungi to global change factors of all the fungal types studied could have broad implications for plant community structure and biogeochemistry of subarctic ecosystems.