bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of some key geothermobarometers for pelitic metamorphic rocks
Authors: Holdaway M. J. 
Published: August 2004

AbstractI will consider mainly geothermobarometry in medium-grade pelitic rocks, including the garnet-biotite (GB) geothermometer, the Grossular-Al silicate-plagioclase (GASP) geobarometer, and the muscovite-almandine-biotite-sillimanite (MABS) geobarometer. For GB (Holdaway, 2000) experimental data and estimated biotite ΔWTi were used to optimize two exchange parameters and four biotite Margules parameters. Using stepwise linear regression, experimental vs. calculated T were constrained to lie on a line with slope of one and intercept of zero, maximizing r2. The best model involves experiments by Ferry and Spear (1978) and Perchuk and Lavrent’eva (1983), suggesting minimal viAl in the Ferry and Spear product biotite. For GASP (Holdaway, 2001), end-member experimental data do not adequately constrain the equilibrium. I used the GB model above, and allowed the end-member curve to rotate about the best-constrained part of the GASP end-member data. The end-member curve was further constrained with the kyanite-sillimanite (K-S) boundary using published chemical data on 76 pelitic schist samples from 11 localities, rejecting Low-Grs and low-An samples. The Fuhrman and Lindsley (1988) plagioclase model gives the best results. For MABS, work in progress involves 61 samples from the 11 localities which have muscovite analyses. Biotite Margules parameters were based on the GB model and McMullin et al. (1991). The MABS end-member curve was calibrated by comparison of P values determined using trial MABS data and GASP results. The P values for the 61 samples agree well with the K-S boundary, and sillimanite-bearing rocks of west-central Maine all fall in the sillimanite field. Preliminary biotite values are: GAnn = –5149198 – 412.05 T, WAlFe = –14023 + 28.14 T, WAlMg = –259582 + 308.44 T, WTiFe = 124842 – 98.67 T, WTiMg = –186148 + 271.72 T. For geobarometry, the Berman (1988, revised 1992) database was used with adjustable H and S of grossular for GASP and H and S of annite for MABS. The accuracy of currently available databases, activity models and mole fraction models is not adequate for good geothermobarometry, without further refinement. Adjustable parameters tend to compensate for error in activity models, mole fraction models and databases.
Arsenopyrite and As-bearing pyrite from the Roudný deposit, Bohemian Massif
Authors: Zachariáš J. , Frýda J. , Paterová B. , Mihaljevič M. 
Published: August 2004

AbstractThe major- and trace-element chemistry of pyrite and arsenopyrite from the mesothermal Roudný gold deposits was studied by electron microprobe and laser ablation ICP-MS techniques. In total, four generations of pyrite and two of arsenopyrite were distinguished. The pyrite is enriched in As through an Fe (AsxS1–x)2substitution mechanism. The As-rich zones of pyrite-2 (up to 4.5 wt.% As) are also enriched in gold (up to 20 ppm), lead (commonly up to 220 ppm, exceptionally up to 1500 ppm) and antimony (commonly <600 ppm, rarely up to 1350 ppm). Positive correlation of As and Au in the studied pyrites is not coupled with an Fe deficiency, in contrast to Au-rich As-bearing pyrites in Carlintype gold deposits. The As-rich pyrite-2 coprecipitated with the Sb-rich (1 –4.2 wt.%) and Au-rich (40 –150 ppm) arsenopyrite-1. The younger arsenopyrite-2 is significantly less enriched in these elements (0 –70 ppm of Au).The chemical zonality of pyrites in the Roudný gold deposits reflects the chemical evolution of orebearing fluids that are not observed in any other mineral phases. The data available suggest relatively high activity of sulphur and low activities of arsenic and gold during crystallization of the older pyrite generation (pyrite-1). Later, after particular dissolution of pyrite-1, Au-rich As-bearing pyrite-2 and arsenopyrite precipitated. These facts suggest a marked increase in the arsenic and gold activities in ore-bearing fluids. The As-content of pyrite-2 decreases in an oscillatory manner from the core to the rim, reflecting changes in the As activity or/and in theP-Tconditions. The As-bearing pyrites were formed at temperatures of at least 320–330°C, based on arsenopyrite thermometers and fluid inclusion data.
Thermodynamics of mixing and ordering in pyrope — grossular solid solution
Authors: Vinograd V. L. , Sluiter M. H. F. , Winkler B. , Putnis A. , Hålenius U. , D. Gale J. , Becker U. 
Published: August 2004

AbstractStatic lattice energy calculations have been combined with cluster expansion formalism to predict pairwise ordering interactions in the pyrope–grossular solid solution. The ordering interactions, the Js, have been then used to calculate the activity-composition relations over a wide temperature range with the help of the Cluster Variation Method. It is shown that short-range ordering in the system is driven by size mismatch. The prediction of the right signs and magnitudes of the ordering interaction energies requires separation of the mixing enthalpy into the configuration-dependent (chemical) and the configuration-independent (elastic) components. The study predicts the existence of a miscibility gap below 500°C.
Heat capacity of lazulite, MgAl2(PO4)2(OH)2, from 35 to 298 K and a (S–V) value for P2O5 to estimate phosphate entropy
Authors: Brunet F. , Morineau D. , Schmid-Beurmann P. 
Published: August 2004

AbstractThe heat capacity of synthetic lazulite, MgAl2(PO4)2(OH)2, has been measured between 35 and 298 K by means of low-temperature adiabatic calorimetry. A lazulite third-law entropy (S2980) value of 204(3) J K–1 mol–1 was retrieved after extrapolation of the lazulite heat capacity by a cubic temperature function, down to absolute temperature. Identical measurements on α-Al2O3 yielded S2980 = 51.2 J mol–1 K–1 instead of the recommended 50.94 J mol–1 K–1 value. This new lazulite third-law entropy along with other phosphate entropy data either derived from low-temperature adiabatic calorimetry or experimental phase equilibria under pressure and temperature, were computed to retrieve a (S–V)P2O5 value of 57.4(2.9) to predict phosphate entropies from oxide summation. The predicted third-law entropy for trolleite, Al4(PO4)3(OH)3, amounts to 285.4(8.5) J mol–1 K–1 ~13% higher than the previously published value. We propose a new formation enthalpy from the elements of –6504.2 kJ mol–1 and a new third-law entropy of 281.7 J mol–1 K–1 for trolleite, compatible with the predicted entropy from oxide summation as well as with the published brackets on the trolleite = berlinite + corundum + water reaction.
Characterization of ammonioleucite (NH4)[AlSi2O6] and ND4-ammonioleucite (ND4)[AlSi2O6] using IR spectroscopy and Rietveld refinement of XRD spectra
Authors: Andrut M. , E. Harlov D. , Najorka J. 
Published: August 2004

AbstractAmmonioleucite, (NH4)[AlSi2O6], and its deuterated analogue ND4-ammonioleucite (ND4)[AlSi2O6] have been synthesized in 20–150 mg amounts at 300°C and 500 MPa in 5 mm wide, 4 cm long Au capsules using Rene’ metal hydrothermal autoclaves. The resultant product consists of 20–30 mm-size single tetragonal crystals as well as 50 –100 mm wide clumps of ingrown crystals. Infrared (IR) spectra obtained from powdered samples are assigned on the basis of Td symmetry for both the ammonium and deutero-ammoniumion. They show triply degenerate vibrational bands (i.e. v3 and v4), some overtones, and combination modes from NH4+ and ND4+. While Td symmetry for NH4+ in ammonioleucite is not strictly correct due to distortion of the NH+4 molecule, the non-cubic field is not large enough at room temperature to cause a substantial splitting in the bands. However, this perturbation is documented in the IR spectra by a substantial increase in the FWHH as well as the occurrence of shoulders on the broadened bands. In contrast, at lower temperatures, the observed band splittings in the former triply degenerated states of v3 and v4 could be explained by an effective local field with D2 symmetry.Rietveld refinement indicates that ammonioleucite, like leucite, has a tetragonal structure with space group symmetry I41/a. Here the NH4+ molecule replaces the K+ cation on the 8-fold co-ordinated W site, which has m symmetry. Substitution of NH4+ for K+ in the leucite structure results in an increase of the cell parameter a, whereas c is slightly reduced. The mean <W–O> bond length of ammonioleucite is increased in comparison to leucite from 3.00 to 3.12 Å whereas the mean <T–O> bond length of 1.65 Å remains unchanged. This results in an increase in the volume of the polyhedron hosting the NH4+ molecule as well as a decrease in distortion for structural channels parallel to the <111> direction, formed by the arrangement of the six-fold rings, on which the W cations are located. The same effect is also observed, in general, when Rb+ or Cs+ is substituted for K+ in leucite.
Pb-Si ordering in sheet-oxychloride minerals: the super-structure of asisite, nominally Pb7SiO8Cl2
Authors: Welch M. D. 
Published: August 2004

AbstractThe original structure determination of asisite, nominally Pb7SiO8Cl2, has been re-evaluated in the light of electron-diffraction data (TEM) on the original sample material. Electron diffraction patterns indicate a super-structure based upon a metrically tetragonal 26-cation-site super-sheet motif (14x14x23 Å). Given the strong ordering of elements substituting for Pb in closely-related litharge-based oxychlorides (parkinsonite, symesite, kombatite, schwartzembergite), the asisite superstructure is inferred to be due to strong ordering of Si within the PbO sheet. The original chemical analyses of asisite given by Rouse et al. (1988) are shown to be consistent with such a super-structure, which has a 12Pb:1Si cation ratio. A new formula for asisite is proposed that is based upon this superstructure: Pb12(SiO4)O8Cl4 (Z = 8). The structure of asisite determined by Rouse et al. (1988) is that of the average Pb/Si-disordered tetragonal sub-cell (I4/mmm: 4x4x23 Å) and belies the highly ordered real state. The structure of the tetragonal sub-cell has been re-determined here: R = 5.6% for 178 unique Fo > 4σFo and an anisotropic model. A significantly reduced 72% occupancy of the Pb(2) site was found that implies the nominal formula Pb7SiO8Cl2, thus confirming the findings of Rouse et al. (1988). Comparisons with kombatite and symesite support the assignment of Si to Pb(2) and imply that Si in asisite is also likely to be in tetrahedral coordination, with the apical oxygen cross-linking PbO sheets. However, because most of the key information relating to the location of Si is provided by the super-lattice reflections, the inability of X-ray diffraction to register these reflections introduces a significant ambiguity into the interpretation of Pb/Si ordering behaviour in this mineral.
Refractory gold ores in Archaean greenstones,Western Australia: mineralogy, gold paragenesis, metallurgical characterization and classification
Authors: Vaughan J. P. , Kyin A. 
Published: August 2004

AbstractMesothermal gold ores in the Archaean Yilgarn Craton of Western Australia are dominated by a pyrite ± arsenopyrite ± pyrrhotite sulphide assemblage. Many of these ores are refractory to varying degrees and require treatment by roasting, bacterial oxidation or finer milling. The most common sulphide ore types can be sub-divided broadly into pyritic (pyrite±pyrrhotite) and arsenical types (pyrite+arsenopyrite± pyrrhotite). Arsenical ores vary from highly refractory to free-milling. Arsenopyrite in highly refractory ores is finer grained, As-deficient (27 –32.5 at.% As), contains high average concentrations of submicroscopic gold (60 –270 ppm), but does not contain inclusions of particulate gold. Arsenopyrite in free-milling ores is coarser grained, less As-deficient to slightly As-rich (30 –35 at.% As), contains low or negligible concentrations of submicroscopic gold, but contains inclusions and fracture fillings of particulate gold. In some refractory arsenical ores, pyrite also contains moderately high levels of submicroscopic gold (20 –40 ppm), the concentration of which is directly related to As content of the pyrite.Pyritic ores are free-milling to mildly refractory, or rarely moderately refractory. Pyrite in pyritic ores contains negligible to low levels of submicroscopic gold (<5 ppm). Other reasons for refractory behaviour in pyritic ores include very fine-grained native gold inclusions in pyrite, or the presence of gold-bearing tellurides.It is concluded that submicroscopic gold is incorporated into the crystal lattices of arsenopyite and arsenical pyrite at sub-greenschist to lower greenschist-facies temperatures, and is progressively expelled as inclusions and fracture fillings of native gold in sulphides, and ultimately into the gangue, as recrystallization proceeds through upper greenschist- into amphibolite-facies temperatures, during deformation and burial. Submicroscopic gold is expelled more rapidly from pyrite than arsenopyrite.Pyrrhotite progressively replaces primary pyrite at higher temperatures, but rarely contains gold. Finally, a metallurgical classification scheme for refractory ores is presented which incorporates the above mineralogical conclusions.
Acid leaching and dissolution of major sulphide ore minerals: processes and galvanic effects in complex systems
Authors: Abraitis P. K. , D. Pattrick R. A. , Kelsall G. H. , Vaughan D. J. 
Published: August 2004

AbstractThe kinetics and mechanisms of dissolution of the major base metal sulphide minerals, pyrite, chalcopyrite, galena and sphalerite in acidic (chloride) media have been investigated. Minerals were ground in air, then dissolved in air-equilibrated solutions at pH 2.5, while monitoring the redox potential. Solution samples were analysed by ICP-AES and HPLC, and surfaces of residual sulphides analysed using XPS. Dissolution of aerial oxidation products on pyrite particles in the first 15 min apparently led to a sulphur-rich surface, and was followed by slower dissolution of pyrite itself, driven by oxygen reduction, and resulting in net production of protons. Chalcopyrite dissolution resulted in a Cu, S-rich (near) surface layer, accompanied by net consumption of protons. Apparently incongruent dissolution of galena and sphalerite may reflect the formation of elemental S at the surface. The rates of dissolution of chalcopyrite, galena and sphalerite in the presence of pyrite were determined, respectively, as 18, 31 and 1.5 times more rapid than in single-mineral experiments. These data were consistent with galvanically-promoted mineral oxidation of the other sulphides in the presence of pyrite. In the case of galena, the experimental data suggested extensive release of Pb ions and development of a sulphur-rich surface during galvanically-promoted dissolution.
Applying Support Vector Machines for Gene ontology based gene function prediction
Authors: Vinayagam Arunachalam , König Rainer , Moormann Jutta , Schubert Falk , Eils Roland , Glatting Karl-Heinz , Suhai Sándor 
Published: August 2004

Abstract
Background
The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate sequences on a large scale. However, these methods can either only be applied for specific subsets, or their results are not formalised, or they do not provide precise confidence estimates for their predictions.

Results
We have developed a large-scale annotation system that tackles all of these shortcomings. In our approach, annotation was provided through Gene Ontology terms by applying multiple Support Vector Machines (SVM) for the classification of correct and false predictions. The general performance of the system was benchmarked with a large dataset. An organism-wise cross-validation was performed to define confidence estimates, resulting in an average precision of 80% for 74% of all test sequences. The validation results show that the prediction performance was organism-independent and could reproduce the annotation of other automated systems as well as high-quality manual annotations. We applied our trained classification system to Xenopus laevis sequences, yielding functional annotation for more than half of the known expressed genome. Compared to the currently available annotation, we provided more than twice the number of contigs with good quality annotation, and additionally we assigned a confidence value to each predicted GO term.

Conclusions
We present a complete automated annotation system that overcomes many of the usual problems by applying a controlled vocabulary of Gene Ontology and an established classification method on large and well-described sequence data sets. In a case study, the function for Xenopus laevis contig sequences was predicted and the results are publicly available at ftp://genome.dkfz-heidelberg.de/pub/agd/gene_association.agd_Xenopus.
Cloning and expression analysis of cDNAs corresponding to genes activated in cucumber showing systemic acquired resistance after BTH treatment
Authors: Bovie Catherine , Ongena Marc , Thonart Philippe , Dommes Jacques 
Published: August 2004

Abstract
Background
Infection of plants by necrotizing pathogens can lead to the rapid and localized induction of a complex set of defense responses resulting in a restriction of pathogen growth and spread. Subsequently, an increase of plant resistance against a broad spectrum of pathogens is observed systemically. This plant immunity is known as Systemic Acquired Resistance. To identify components of the transduction pathway, we cloned and analysed the expression pattern of several mRNAs accumulating in cucumber plants after induction of Systemic Acquired Resistance.

Results
We tested on cucumber different compounds known to induce systemic acquired resistance. Among these, BTH (benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester) proved to be very effective. mRNA RT-PCR differential display was used to identify mRNA sequences induced 24 hours after the application of 10 μM BTH to cucumber plants. A cDNA library constructed from cucumber plants sprayed with 10 μM BTH was screened to get corresponding full length cDNAs. Among the identified cDNAs were those coding for a putative ras-related GTP-binding protein, a putative beta-1,4-N-Acetylglucosaminyltranferase III and a putative pathogenesis related protein. The time course of accumulation of the three corresponding mRNAs was analysed by northern blotting in plants treated by BTH or in plants infected by Colletotrichum lagenarium.

Conclusions
The mRNA RT-PCR differential display technique allowed the identification of three genes possibly involved in Systemic Acquired Resistance in cucumber. Pathogenesis-related proteins are known to be involved in plant defence against pathogens. GTP-binding protein and N-acetylglucosaminyltranferase III have been reported to be components of signal transduction pathways in mammals and plants.
External decontamination of wild leeches with hypochloric acid
Authors: Aydin Atakan , Nazik Hasan , Kuvat Samet Vasfi , Gurler Nezahat , Ongen Betigul , Tuncer Serdar , Hocaoglu Emre , Kesim Sinan Nur 
Published: August 2004

Abstract
Background
Medicinal leech, Hirudo medicinalis, has been used in plastic and reconstructive surgery, to relieve venous congestion and to improve the microrevascularization of flaps. In many countries, wild leeches are still provided from local markets and utilised with antibiotic prophylaxies. In this research, results of identification of bacteria in the transport fluid is reported, oral and intestinal floras and the antibiograms of the identified microorganisms are investigated. Also, to avoid possible infections, the ability of hypochloric acid, a disinfectant, to suppress the relevant microorganisms without changing the life style and behavior of leeches in terms of sucking function, is investigated.

Methods
Bacterial identifications and antibiograms of oral and intestinal flora and transport medium were performed for 10 leeches. The optimum concentration of hypochloric acid which eliminated microorganisms without affecting the viability and sucking function of the leeches were determined by dilution of hypochloric acid to 100, 50, 25, 12.5, 6.25 ppm concentrations in different groups of 25 leeches. Finally, 20 leeches were applied atraumatically to the bleeding areas of rats, the duration of suction was determined and compared statistically between the leeches treated and not treated with hypochloric acid solution.

Results
Aeromonas hydrophilia was the most commonly identified microorganism and found to be resistant to first generation cephalosporins, frequently used in prophylaxis at surgical wards. In the next stages of the study, the leeches were subjected to a series of diluted hypochloric acid solutions. Although disinfection of the transport material and suppression of the oral flora of hirudo medicinalis were successful in 100, 50, 25, 12.5, 6.25 ppm concentrations; 12.5 ppm solution was the greatest concentration in which hirudo medicinalis could survive and sucking function was not affected significantly.

Conclusions
External decontamination of wild leeches with 12.5 ppm hypochloric acid enables bacterial suppression without causing negative effects on leech sucking function and life.
No evidence for involvement of SDHD in neuroblastoma pathogenesis
Authors: De Preter Katleen , Vandesompele Jo , Hoebeeck Jasmien , Vandenbroecke Caroline , Smet Jöel , Nuyts Annick , Laureys Geneviève , Combaret Valérie , Van Roy Nadine , Roels Frank , Van Coster Rudy , Praet Marleen , De Paepe Anne , Speleman Frank 
Published: August 2004

Abstract
Background
Deletions in the long arm of chromosome 11 are observed in a subgroup of advanced stage neuroblastomas with poor outcome. The deleted region harbours the tumour suppressor gene SDHD that is frequently mutated in paraganglioma and pheochromocytoma, which are, like neuroblastoma, tumours originating from the neural crest. In this study, we sought for evidence for involvement of SDHD in neuroblastoma.

Methods
SDHD was investigated on the genome, transcriptome and proteome level using mutation screening, methylation specific PCR, real-time quantitative PCR based homozygous deletion screening and mRNA expression profiling, immunoblotting, functional protein analysis and ultrastructural imaging of the mitochondria.

Results
Analysis at the genomic level of 67 tumour samples and 37 cell lines revealed at least 2 bona-fide mutations in cell lines without allelic loss at 11q23: a 4bp-deletion causing skip of exon 3 resulting in a premature stop codon in cell line N206, and a Y93C mutation in cell line NMB located in a region affected by germline SDHD mutations causing hereditary paraganglioma. No evidence for hypermethylation of the SDHD promotor region was observed, nor could we detect homozygous deletions. Interestingly, SDHD mRNA expression was significantly reduced in SDHD mutated cell lines and cell lines with 11q allelic loss as compared to both cell lines without 11q allelic loss and normal foetal neuroblast cells. However, protein analyses and assessment of mitochondrial morphology presently do not provide clues as to the possible effect of reduced SDHD expression on the neuroblastoma tumour phenotype.

Conclusions
Our study provides no indications for 2-hit involvement of SDHD in the pathogenesis of neuroblastoma. Also, although a haplo-insufficient mechanism for SDHD involvement in advanced stage neuroblastoma could be considered, the present data do not provide consistent evidence for this hypothesis.