bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alteration zonation in the Loma Blanca kaolin deposit, Los Menucos, Province of Rio Negro, Argentina
Authors: Marfil S. A. , Maiza P. J. , Montecchiari N. 
Published: July 2010

AbstractThe Loma Blanca mine is in one of the northwest kaolinized zones of the Los Menucos area (Patagonia, Argentina). The parent rocks are andesites and andesitic tuffs from the Vera Formation, Los Menucos Group (Lower Triassic). Hayase & Maiza (1974) proposed a concentric zonation model. From the parent rock outward, four different alteration patterns were recognized: Zone 1, with sericite, chlorite and montmorillonite; Zone 2, with kaolinite and dickite; Zone 3, with dickite, pyrophyllite and alunite; and Zone 4, with quartz, disseminated sulphides and diaspore.The relationship between the chemical composition of major, minor and trace elements and the mineralogical alteration zonation was evaluated to confirm the genesis of the deposit. Fe2O3, CaO, Na2O and K2O contents decrease from Zone 1 to Zone 3, whereas Al2O3 and LOI increase in the kaolinite-alunite zone. In the chemical composition of alunite, Na > K. Large Ba, Sr, V and Zr contents were observed mainly in Zones 2 and 3. Co, Ni, Cu, Zn and Rb are more common in Zone 1. LREE are more abundant than HREE in Zones 2 and 3. In kaolinites, δ18O values range from 10.8% to 13.2%, and δD from –83% to –85%.The mineral assemblage (dickite-alunite-pyrophyllite-diaspore), the alteration zonation pattern (laterally concentric), the geochemistry of trace elements, the relation between LREE and HREE and the small δ18O values suggest that the Loma Blanca deposit was formed by hydrothermal processes.
Nano-size quartz accumulation in reservoir chalk, Ekofisk Formation, South Arne Field, North Sea
Authors: Lindgreen H. , Jakobsen F. , Springer N. 
Published: July 2010

AbstractIn the oil fields in the Central Graben of the North Sea, Maastrichtian chalk is an important hydrocarbon reservoir, but oil may also be found in the Danian chalk, consisting of white chalk interbedded with clay layers. Within the chalk section, discrete intervals appear like chalk but contain large amounts of quartz (up to 100%). The aim of the present investigation is to reveal the mechanism for formation of the quartz in these intervals and to discuss their regional distribution and importance for the reservoir properties. Samples of chalk, including quartz-rich intervals, and clay layers from three wells SA-1, Rigs-1 and Rigs-2 in the South Arne Field have been investigated. Calcite-free residues obtained using a buffered dissolution of calcite were investigated using X-ray diffraction, scanning electron microscopy and atomic force microscopy. The main silica phase in the Upper Cretaceous–Danian chalk in the three wells is a nano-size α-quartz. This has probably formed from Si dissolved from radiolarians in the free-water phase. The 600 Å diameter α-quartz spheres precipitated in the free-water phase with subsequent flocculation of the spheres and sedimentation of the flocs. Variations in the proportion of quartz in the chalk are attributed to variations in the amount of radiolarians in combination with variations in CO2 concentrations in the water; increased CO2 causes dissolution of coccoliths and thus a relative enrichment in quartz. This formation mechanism is regional and makes it probable that the layers rich in nano-quartz may be found over large areas provided that the chalk is authigenic. Quartz-rich layers are generally of low permeability and in areas with authigenic chalk these layers may act as internal seals in chalk reservoirs.
Noonkanbahite, BaKNaTi2(Si4O12)O2, a new mineral species: description and crystal structure
Authors: Uvarova Y. A. , Sokolova E. , Hawthorne F. C. , Liferovich R. P. , Mitchell R. H. , Pekov I. V. , Zadov A. E. 
Published: July 2010

AbstractNoonkanbahite, ideally BaKNaTi2(Si4O12)O2, is described as a new mineral species. At Liley [Löhley], Eifel Mountains, Germany (the holotype locality), it occurs as sprays of prismatic crystals (up to 8 mm) or single prismatic crystals (up to 4 mm) on walls of cavities in alkaline igneous rocks. At Murun, Siberia, Russia, noonkanbahite forms coarse lamellar crystals up to 0.05 cm × 0.7 cm × 1.5 cm embedded in kalsilite syenite. Noonkanbahite is brittle, H = 6, Dobs. = 3.39(1), Dcalc. = 3.49 g/cm3, has a vitreous lustre and does not fluoresce in ultraviolet light. It has poor cleavage on {010} and {100} and weak parting on {011}. Noonkanbahite is biaxial positive with 2Vobs. = 75(2)°, 2Vcalc. = 72.7(9)°, α 1.730(5), β 1.740(5) and γ 1.765(5), dispersion is medium, r < v. In transmitted plane-polarized light, noonkanbahite is strongly pleochroic, with X colourless, Y yellowish, Z straw-yellow; X = a, Y = b, Z = c. Noonkanbahite is orthorhombic, space group Imma, a = 8.0884(4), b = 10.4970(5), c = 13.9372(6) Å, V = 1183.3(1) Å3, Z = 4. The strongest ten X-ray diffraction lines in the powder pattern [d in Å (I)(hkl)] are: 2.907(100)(222), 8.353(50)(001), 3.196(50)(220), 2.097(50)(242), 2.241(40)(215), 2.179(40)(035), 3.377(30)(031), 2.694(30)(015), 2.304(30)(233), and 1.564(30)(064). Electron microprobe analysis gives SiO2 37.82, TiO2 15.54, ZrO2 0.42, Nb2O5 3.18, Al2O3 0.17, Fe2O3 (recalculated from FeO) 5.63, MnO 0.32, MgO 0.53, BaO 20.60, CaO 1.36, K2O 5.32, Na2O 6.14, F 0.78, H2O 0.58, sum 98.39 wt.%, (H2O determined by SIMS). The formula unit, calculated on the basis of 14 anions (O+OH+F), is (Ba0.85K0.13)Σ0.98(K0.59Na0.26Ca0.15)Σ1.00Na(Ti1.23Fe0.453+Nb0.15Mg0.08Mn0.03Zr0.02Al0.01)Σ1.97 (Si3.99Al0.01O12)(O1.33OH0.41F0.26)Σ2.00, Z = 4.The crystal structure was refined to R1 = 2.8% for 970 unique (F0 > 4σF) reflections collected on a Bruker single-crystal P4 diffractometer with a CCD detector and MoKα X-radiation. The crystal structure of noonkanbahite is isostructural with that of batisite, ideally BaNa2Ti2(Si4O12)O2, and scherbakovite, ideally K2NaTi2(Si4O12)O(OH). There are two octahedrally coordinated sites, M(1) and M(2), occupied by (Ti1.23Fe0.453+Nb0.15Mg0.08Mn0.03Zr0.02Al0.01), ideally Ti2 a.p.f.u. There are three interstitial A sites, [9]A(1), [8]A(2) and [6]A(3), occupied by Ba, K and Na, respectively. Si tetrahedra and M octahedra form a framework with interstitial cages occupied by Ba, K and Na atoms at the A sites. Noonkanbahite, BaKNaTi2(Si4O12)O2, is a K analogue of batisite, BaNa2Ti2(Si4O12)O2, and a Ba analogue of shcherbakovite, K2NaTi2(Si4O12)O(OH).
Complex impedance spectroscopy and ionic transport properties of natural leucite, K0.90Na0.08[Al0.98Si2.02]O6, as a function of temperature and pressure
Authors: Jones R. L. , Thrall M. , Henderson C. M. B. 
Published: July 2010

AbstractThe temperature (T) and pressure (P) dependence of dielectric and conductivity properties of natural leucite were determined using complex impedance spectroscopy at frequencies from 103 to 106 Hz. Experiments were carried out in a Walker multi-anvil cell at 1 atm and P from 2.5 to 6 GPa and at T from 350 to 800°C. At pressure >6 GPa and temperature >790°C the leucite broke down to kalsilite+sanidine and dielectric properties for this phase assemblage are given at 6.0–7.0 GPa and T to 1050°C.Leucite conductivity increases with increasing T and decreases with increasing P reflecting their different effects on migration of K cations within the channels in the leucite aluminosilicate framework. Activation energies for K+ migration in leucite increase with increasing pressure (0.74–0.97 eV; 70.0–93.2 kJ/mol) and activation volumes for leucite increase with increasing T (6.42–9.51 cm3/mol; 400–700°C). The latter data provide model K+ cation diameters increasing from 2.7 Å at 400°C to 3.2 Å at 700°C. These values are consistent with the earlier suggestion of Palmer and Salje that the ionic mobility mechanism consists of diffusion along <110> rather than along the main channels parallel to <111>.
Treatment and prognosis of mature T-cell and NK-cell lymphoma: an analysis of patients with T-cell lymphoma treated in studies of the German High-Grade Non-Hodgkin Lymphoma Study Group
Authors: Schmitz Norbert , Trümper Lorenz , Ziepert Marita , Nickelsen Maike , Ho Anthony D. , Metzner Bernd , Peter Norma , Loeffler Markus , Rosenwald Andreas , Pfreundschuh Michael 
Published: July 2010

Abstract
To evaluate outcome and prognosis of patients with T-cell lymphoma we analyzed 343 patients treated within trials of the German High-Grade Non-Hodgkin Lymphoma Study Group (DSHNHL). Two hundred eighty-nine patients belonged to 1 of the 4 major T-cell lymphoma subtypes: anaplastic large cell lymphoma (ALCL), anaplastic large cell lymphoma kinase (ALK)–positive (n = 78); ALCL, ALK-negative (n = 113); peripheral T-cell lymphoma, unspecified (PTCLU; n = 70); and angioimmunoblastic T-cell lymphoma (AITL; n = 28). Treatment consisted of 6-8 courses of CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone/prednisolone) or etoposide plus (CHOEP). Three-year event-free survival (EFS) and overall survival were 75.8% and 89.8% (ALK-positive ALCL), 50.0% and 67.5% (AITL), 45.7% and 62.1% (ALK-negative ALCL), and 41.1% and 53.9% (PTCLU), respectively. The International Prognostic Index (IPI) was effective in defining risk groups with significantly different outcomes. For patients, ≤ 60 years with lactate dehydrogenase ≤ upper normal value (UNV), etoposide improved improved 3-year EFS: 75.4% versus 51.0%, P = .003. In patients > 60 years 6 courses of CHOP administered every 3 weeks remains the standard therapy. Patients with ALK-negative ALCL, PTCLU, or AITL presenting with IPI > 1 have a poor prognosis and should be considered candidates for novel treatment strategies.
Targeting CK2 overexpression and hyperactivation as a novel therapeutic tool in chronic lymphocytic leukemia
Authors: Martins Leila R. , Lúcio Paulo , Silva Milene C. , Anderes Kenna L. , Gameiro Paula , Silva Maria G. , Barata João T. 
Published: July 2010

Abstract
Expression of protein kinase CK2 is frequently deregulated in cancer and mounting evidence implicates CK2 in tumorigenesis. Here, we show that CK2 is overexpressed and hyperactivated in chronic lymphocytic leukemia (CLL). Inhibition of CK2 induces apoptosis of CLL cells without significantly affecting normal B and T lymphocytes. Importantly, this effect is not reversed by coculture with OP9 stromal cells, which are otherwise capable of rescuing CLL cells from in vitro spontaneous apoptosis. CLL cell death upon CK2 inhibition is mediated by inactivation of PKC, a PI3K downstream target, and correlates with increased PTEN activity, indicating that CK2 promotes CLL cell survival at least in part via PI3K-dependent signaling. Although CK2 antagonists induce significant apoptosis of CLL cells in all patient samples analyzed, sensitivity to CK2 blockade positively correlates with the percentage of CLL cells in the peripheral blood, β2 microglobulin serum levels and clinical stage. These data suggest that subsets of patients with aggressive and advanced stage disease may especially benefit from therapeutic strategies targeting CK2 function. Overall, our study indicates that CK2 plays a critical role in CLL cell survival, laying the groundwork for the inclusion of CK2 inhibitors into future therapeutic strategies.
Deriving enzymatic and taxonomic signatures of metagenomes from short read data
Authors: Weingart Uri , Persi Erez , Gophna Uri , Horn David 
Published: July 2010

Abstract

Background
We propose a method for deriving enzymatic signatures from short read metagenomic data of unknown species. The short read data are converted to six pseudo-peptide candidates. We search for occurrences of Specific Peptides (SPs) on the latter. SPs are peptides that are indicative of enzymatic function as defined by the Enzyme Commission (EC) nomenclature. The number of SP hits on an ensemble of short reads is counted and then converted to estimates of numbers of enzymatic genes associated with different EC categories in the studied metagenome. Relative amounts of different EC categories define the enzymatic spectrum, without the need to perform genomic assemblies of short reads.

Results
The method is developed and tested on 22 bacteria for which there exist many EC annotations in Uniprot. Enzymatic signatures are derived for 3 metagenomes, and their functional profiles are explored.
We extend the SP methodology to taxon-specific SPs (TSPs), allowing us to estimate taxonomic features of metagenomic data from short reads. Using recent Swiss-Prot data we obtain TSPs for different phyla of bacteria, and different classes of proteobacteria. These allow us to analyze the major taxonomic content of 4 different metagenomic data-sets.

Conclusions
The SP methodology can be successfully extended to applications on short read genomic and metagenomic data. This leads to direct derivation of enzymatic signatures from raw short reads. Furthermore, by employing TSPs, one obtains valuable taxonomic information.
Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra)
Authors: Rodríguez Fernando , Pérez Trinidad , Hammer Sabine E , Albornoz Jesús , Domínguez Ana 
Published: July 2010

AbstractBackgroundThe chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species,Rupicapra pyrenaicafrom southwestern Europe andR. rupicaprafrom eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region) and microsatellites (20 loci) to include all subspecies and cover its entire distribution range.ResultsWe found discordant microsatellite (μsat) and mitochondrial (mt) DNA phylogenies. Mitochondrial phylogenies form three clades, West, Central and East (mtW, mtC and mtE), at variance with taxonomic classification. Our divergence age estimates indicate an initial separation into branches mtW-mtC and mtE 1.7 million years ago (mya), in the late Pliocene-early Pleistocene, quickly followed by the split of clades mtW and mtC. Clade mtW contains haplotypes from the Iberian peninsula and the western Alps, Clade mtC includes haplotypes from the Apennines and the Massif of Chartreuse and Clade mtE comprises populations to the east of the Alps. Divergence among populations within these three major clades is recent (< 0.5 mya). New microsatellite multilocus genotypes added to previously published data revealed differences between every pair of subspecies, forming three well defined groups (μsatW, μsatC and μsatE) also with a strong geographic signature. Grouping does not correspond with the mitochondrial lineages but is closer to morphology and taxonomic classification. Recent drastic reductions in population size can be noted for the subspeciesornataas an extremely low diversity.ConclusionsThe phylogeographic patterns for mtDNA and microsatellites suggest an evolutionary history with limited range contractions and expansions during the Quaternary period and reflect a major effect of the Alpine barrier on west-east differentiation. The contrasting phylogenies for mtDNA and microsatellites indicate events of hybridization among highly divergent lineages in the central area of distribution. Our study points to the importance of reticulate evolution, with periods of isolation and reduction of population size followed by expansions and hybridizations, in the diversification at the level of close species or subspecies.
Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis: additional molecular markers for a tapeworm genus of human and animal health significance
Authors: Jia Wan-Zhong , Yan Hong-Bin , Guo Ai-Jiang , Zhu Xing-Quan , Wang Yu-Chao , Shi Wan-Gui , Chen Hao-Tai , Zhan Fang , Zhang Shao-Hua , Fu Bao-Quan , Littlewood D Timothy J , Cai Xue-Peng 
Published: July 2010

Abstract

Background
Mitochondrial genomes provide a rich source of molecular variation of proven and widespread utility in molecular ecology, population genetics and evolutionary biology. The tapeworm genus Taenia includes a diversity of tapeworm parasites of significant human and veterinary importance. Here we add complete sequences of the mt genomes of T. multiceps, T. hydatigena and T. pisiformis, to a data set of 4 published mtDNAs in the same genus. Seven complete mt genomes of Taenia species are used to compare and contrast variation within and between genomes in the genus, to estimate a phylogeny for the genus, and to develop novel molecular markers as part of an extended mitochondrial toolkit.

Results
The complete circular mtDNAs of T. multiceps, T. hydatigena and T. pisiformis were 13,693, 13,492 and 13,387 bp in size respectively, comprising the usual complement of flatworm genes. Start and stop codons of protein coding genes included those found commonly amongst other platyhelminth mt genomes, but the much rarer initiation codon GTT was inferred for the gene atp 6 in T. pisiformis. Phylogenetic analysis of mtDNAs offered novel estimates of the interrelationships of Taenia. Sliding window analyses showed nad 6, nad 5, atp 6, nad 3 and nad 2 are amongst the most variable of genes per unit length, with the highest peaks in nucleotide diversity found in nad 5. New primer pairs capable of amplifying fragments of variable DNA in nad 1, rrn S and nad 5 genes were designed in silico and tested as possible alternatives to existing mitochondrial markers for Taenia.

Conclusions
With the availability of complete mtDNAs of 7 Taenia species, we have shown that analysis of amino acids provides a robust estimate of phylogeny for the genus that differs markedly from morphological estimates or those using partial genes; with implications for understanding the evolutionary radiation of important Taenia. Full alignment of the nucleotides of Taenia mtDNAs and sliding window analysis suggests numerous alternative gene regions are likely to capture greater nucleotide variation than those currently pursued as molecular markers. New PCR primers developed from a comparative mitogenomic analysis of Taenia species, extend the use of mitochondrial markers for molecular ecology, population genetics and diagnostics.
Contrasting predictors of poor antiretroviral therapy outcomes in two South African HIV programmes: a cohort study
Authors: Dahab Mison , Charalambous Salome , Karstaedt Alan S , Fielding Katherine L , Hamilton Robin , La Grange Lettie , Churchyard Gavin J , Grant Alison D 
Published: July 2010

AbstractBackgroundMany national antiretroviral therapy (ART) programmes encourage providers to identify and address baseline factors associated with poor treatment outcomes, including modifiable adherence-related behaviours, before initiating ART. However, evidence on such predictors is scarce, and providers judgement may often be inaccurate. To help address this evidence gap, this observational cohort study examined baseline factors potentially predictive of poor treatment outcomes in two ART programmes in South Africa, with a particular focus on determinants of adherence.MethodsTreatment-naïve patients starting ART were enrolled from a community and a workplace ART programme. Potential baseline predictors associated with poor treatment outcomes (defined as viral load > 400 copies/ml or having discontinued treatment by six months) were assessed using logistic regression. Exposure variables were organised for regression analysis using a hierarchical framework.Results38/227 (17%) of participants in the community had poor treatment outcomes compared to 47/117 (40%) in the workplace. In the community, predictors of worse outcomes included: drinking more than 20 units of alcohol per week, having no prior experience of chronic medications, and consulting a traditional healer in the past year (adjusted odds ratio [aOR] 15.36, 95% CI 3.22-73.27; aOR 2.30, 95%CI 1.00-5.30; aOR 2.27, 95% CI 1.00-5.19 respectively). Being male and knowing someone on ART were associated with better outcomes (aOR 0.25, 95%CI 0.09-0.74; aOR 0.44, 95%CI 0.19-1.01 respectively). In the workplace, predictors of poor treatment outcomes included being uncertain about the health effects of ART and a traditional healer's ability to treat HIV (aOR 7.53, 95%CI 2.02-27.98; aOR 4.40, 95%CI 1.41-13.75 respectively). Longer pre-ART waiting time (2-12 weeks compared to <2 weeks) predicted better treatment outcomes (aOR 0.13, 95% CI 0.03-0.56).ConclusionBaseline predictors of poor treatment outcomes were largely unique to each programme, likely reflecting different populations and pathways to HIV care. In the workplace, active promotion of HIV testing may have extended ART to individuals who, without provider initiation, would not have spontaneously sought care. As provider-initiated testing makes ART available to individuals less motivated to seek care, patients may need additional adherence support, especially addressing uncertainty about the health benefits of ART.
Fusion of EML4 and ALK is associated with development of lung adenocarcinomas lacking EGFR and KRAS mutations and is correlated with ALK expression
Authors: Zhang Xuchao , Zhang Shirley , Yang Xuening , Yang Jinji , Zhou Qing , Yin Lucy , An Shejuan , Lin Jiaying , Chen Shiliang , Xie Zhi , Zhu Mike , Zhang Xiaolin , Wu Yi-long 
Published: July 2010

Abstract

Background
The anaplastic lymphoma kinase (ALK) gene is frequently involved in translocations that lead to gene fusions in a variety of human malignancies, including lymphoma and lung cancer. Fusion partners of ALK include NPM, EML4, TPM3, ATIC, TFG, CARS, and CLTC. Characterization of ALK fusion patterns and their resulting clinicopathological profiles could be of great benefit in better understanding the biology of lung cancer.

Results
RACE-coupled PCR sequencing was used to assess ALK fusions in a cohort of 103 non-small cell lung carcinoma (NSCLC) patients. Within this cohort, the EML4-ALK fusion gene was identified in 12 tumors (11.6%). Further analysis revealed that EML4-ALK was present at a frequency of 16.13% (10/62) in patients with adenocarcinomas, 19.23% (10/52) in never-smokers, and 42.80% (9/21) in patients with adenocarcinomas lacking EGFR and KRAS mutations. The EML4-ALK fusion was associated with non-smokers (P = 0.03), younger age of onset (P = 0.03), and adenocarcinomas without EGFR/KRAS mutations (P = 0.04). A trend towards improved survival was observed for patients with the EML4-ALK fusion, although it was not statistically significant (P = 0.20). Concurrent deletion in EGFR exon 19 and fusion of EML4-ALK was identified for the first time in a Chinese female patient with an adenocarcinoma. Analysis of ALK expression revealed that ALK mRNA levels were higher in tumors positive for the EML-ALK fusion than in negative tumors (normalized intensity of 21.99 vs. 0.45, respectively; P = 0.0018). However, expression of EML4 did not differ between the groups.

Conclusions
The EML4-ALK fusion gene was present at a high frequency in Chinese NSCLC patients, particularly in those with adenocarcinomas lacking EGFR/KRAS mutations. The EML4-ALK fusion appears to be tightly associated with ALK mRNA expression levels. RACE-coupled PCR sequencing is a highly sensitive method that could be used clinically for the identification of EML4-ALK-positive patients.