bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnetic resonance imaging (MRI) of heavy-metal transport and fate in an artificial biofilm
Authors: Phoenix V. R. , Holmes W. M. , Ramanan B. 
Published: August 2008

AbstractUnlike planktonic systems, reaction rates in biofilms are often limited by mass transport, which controls the rate of supply of contaminants into the biofilm matrix. To help understand this phenomenon, we investigated the potential of magnetic resonance imaging (MRI) to spatially quantify copper transport and fate in biofilms. For this initial study we utilized an artificial biofilm composed of a 50:50 mix of bacteria and agar. MRI successfully mapped Cu2+ uptake into the artificial biofilm by mapping T2 relaxation rates. A calibration protocol was used to convert T2 values into actual copper concentrations. Immobilization rates in the artificial biofilm were slow compared to the rapid equilibration of planktonic systems. Even after 36 h, the copper front had migrated only 3 mm into the artificial biofilm and at this distance from the copper source, concentrations were very low. This slow equilibration is a result of (1) the time it takes copper to diffuse over such distances and (2) the adsorption of copper onto cell surfaces, which further impedes copper diffusion. The success of this trial run indicates MRI could be used to quantitatively map heavy metal transport and immobilization in natural biofilms.
Weathering of S. Domingos (Iberian Pyritic Belt) abandoned mine slags
Authors: Rosado L. , Morais C. , Candeias A. E. , Pinto A. P. , Guimarães F. , Mirão J. 
Published: August 2008

AbstractThe S. Domingos abandoned mine is a major source of pollutant-metals contamination. Slags from the 19th-20th century contain the most hazardous material. However, the release of pollutant metals depends on the metal-retention capability of weathering products. This work shows that Zn is not effectively retained by these weathering products while As and Pb are partially stored in sulphates. Copper, on the other hand, has a different behaviour and is the most leachable of the elements studied.
Can chromite weathering be a source of Cr in soils?
Authors: Garnier J. , Quantin C. , Guimarães E. , Becquer T. 
Published: August 2008

AbstractAt Niquelândia, Cr extracted from the soil (5,000–9,300 mg.kg-1) is likely the result of the Cr-bearing Fe-oxides compared to the Cr-spinels, showing that low Cr-containing minerals present in the dunite (enstatite, olivine and clay minerals) have been completely dissolved. The chromites, accumulated inside soil profiles, have undergone chemical weathering, leading to a Cr enrichment during soil genesis. Traces of dissolution inside the soil chromites suggest that they can be slowly weathered. In this case chromites could represent a diffuse source of available Cr(III) within the soil profiles.
The impact of Eisenia veneta on As, Cu, Pb and Zn uptake by ryegrass (Lolium perenne L.)
Authors: Sizmur T. , Hodson M. E. 
Published: August 2008

AbstractEarthworms are an essential part of the soil fauna in many global soils, represent a significant proportion of the soil biomass and are regarded as a useful indicator of soil health and quality (Edwards, 2004). They are also often the subject of inoculation programmes during the restoration of degraded lands (Butt, 1999) and the inoculation of earthworms to metal-contaminated soils has been suggested(Dickinson, 2000) largely due to the role earthworms are known to play in soil formation at such sites (Frouz et al., 2007).
Speciation studies in understanding high As content in ground water
Authors: Szocs T. , I. Horváth  , Bartha A. , Bertalan É. , Ballók M. , Horváth É. 
Published: August 2008

AbstractTwo sites with five wells in the Danube-Tisza interfluvial were studied in order to help understand the genesis of the high-As content of shallow ground water. Separation of As species was carried out in the field as it proved to be the best method by which to preserve the As species. Different geochemical environments could be separated by the speciation studies which correlate with the concentrations of oxyanion-forming elementss uch asV, Se, Mo, U and W.
Mapping singularities — a technique to identify potential Cu mineral deposits using sediment geochemical data, an example for Tibet, west China
Authors: Zuo R. , Cheng Q. 
Published: August 2008

AbstractGeochemical anomalies can be used in mineral resource exploration. We demonstrate a technique for mapping anomalies. The Gangdese mineral district in Tibet, west China was chosen as a study area for identifying geochemical anomalies and predicting Cu mineral resources using sediment geochemical data. The results show that the anomalies are associated both with known deposits in the middle of the study area, but also with E—W and N——E oriented faults in the north of area. These areas should be explored for undiscovered Cu mineral deposits.
Structure and function of siderophores produced by mycorrhizal fungi
Authors: Haselwandter K. 
Published: August 2008

AbstractMost fungi synthesize siderophores as chelating agents which form soluble complexes with Fe3+ with very high stability constants, thus solubilizing ferric Fe. Ericoid mycorrhizal fungi release ferricrocin or fusigen as the main siderophores. Ferricrocin was also shown to be produced by the ectomycorrhizal fungi, Cenococcum geophilum and Hebeloma crustuliniforme. Arbuscular mycorrhizal fungi are reported to enhance Fe-uptake rates of associated host plants which can be taken as an indication that mycorrhizal siderophores of a yet unknown structure may be involved. Mycorrhizal fungi of orchids were shown to produce as the main siderophores, both well known ferrichrome-type siderophores or the novel linear trishydroxamate basidiochrome.
Geochemical investigation of weathering processes in a forested headwater catchment: mass-balance weathering fluxes
Authors: Jones B. F. , Herman J. S. 
Published: August 2008

AbstractGeochemical research on natural weathering has often been directed towards explanations of the chemical composition of surface water and ground water resulting from subsurface water-rock interactions. These interactions are often defined as the incongruent dissolution of primary silicates, such as feldspar, producing secondary weathering products, such as clay minerals and oxyhydroxides, and solute fluxes (Meunier and Velde, 1979). The chemical composition of the clay-mineral product is often ignored. However, in earlier investigations, the saprolitic weathering profile at the South Fork Brokenback Run (SFBR) watershed, Shenandoah National Park, Virginia, was characterized extensively in terms of its mineralogical and chemical composition (Piccoli, 1987; Pochatila et al., 2006; Jones et al., 2007) and its basichydrology. O’Brien et al. (1997) attempted to determine the contribution of primary mineral weathering to observed stream chemistry at SFBR. Mass-balance model results, however, could provide only a rough estimate of the weathering reactions because idealized mineral compositions were utilized in the calculations. Making use of detailed information on the mineral occurrence in the regolith, the objective of the present study was to evaluate the effects of compositional variation on mineral-solute mass-balance modelling and to generate plausible quantitative weathering reactions that support both the chemical evolution of the surface water and ground water in the catchment, as well as the mineralogical evolution of the weathering profile.
Effect of cyanobacterial growth on biotite surfaces under laboratory nutrient-limited conditions
Authors: Kapitulčinova D. , Cockell C. S. , Hallam K. R. , Ragnarsdottir K. V. 
Published: August 2008

AbstractLaboratory experiments with two cyanobacterial strains grown on low-nutrient agar media in the presence of biotite flakes were performed in order to reveal possible mechanisms and rates of cyanobacterial bioweathering. Both cyanobacteria colonized the biotite flakes. Leptolyngbya grew mostly in the biotite interlayers, whereas Hassallia colonized the sides and the topmost surface of the biotite flakes. After a 3-month incubation, rounded features including cyanobacterium-shaped pits were observed on the biotite surface cleared of the organic material. No such features were observed on flakes incubated for 1 month.
Pseudomorphic replacement of single calcium carbonate crystals by polycrystalline apatite
Authors: Kasioptas A. , Perdikouri C. , Putnis C. V. , Putnis A. 
Published: August 2008

AbstractDuring chemical weathering and natural hydrothermal reactions, apatite can form by replacing calcium carbonates. In hydrothermal experiments in which aragonite and calcite single crystals have been reacted with phosphate solutions, the carbonates are replaced by polycrystalline hydroxylapatite (HAP). In both cases the crystals have retained their overall morphology while their compositions have changed significantly. The HAP appears to have a crystallographic relationship to the parent carbonate crystals. The textural relationships are consistent with an interface-coupled dissolution-precipitation mechanism. Structural relationships and relative molar volumes and solubilities appear to be factors that greatly affect replacement reactions.
Incongruent weathering of Cd and Zn from mine tailings
Authors: Kossoff D. , Hudson-Edwards K. A. , Dubbin W. E. , Alfredsson M. 
Published: August 2008

AbstractWeathering ofdischarged mine tailings contaminates streams, rivers and floodplains with toxic metals on a vast scale. The magnitude of the problem depends on input tailings mineralogy, storage and dispersal, and climatic conditions. To better understand the mechanisms of long-term tailings weathering, a leaching column study was established, incorporating tailings and soil from Potosí, Bolivia, with the aim of modelling a 25 year field period. The Zn/Cd molar ratio ofthe tailings leachate water, initially 738 for the unaltered tailings, is highly variable over 15 model years of leaching, particularly in the mixed tailings-soil columns. Columns with soil have ratios as high as 2563, while pure tailings columns reach ratios of <376. We employ complementary techniques, involving atomistic computational modelling, leachate analysis and mineralogical characterization, to elucidate the mechanisms governing these incongruent Cd and Zn weathering dynamics.
Influence of surface-area estimation on rates of plagioclase weathering determined from naturally weathered 3400 y old Hawaiian basalt
Authors: Velbel M. A. , Losiak A. I. 
Published: August 2008

AbstractDimensions of plagioclase (An65) crystals in a polished thin section of naturally weathered 3400 y old Hawaiian basalt were measured by scanning electron microscopy (in backscattered electron imaging mode). The three-dimensional shape, size, volume and surface area of the plagioclase crystals were then estimated using the method of Morgan and Jerram (2006). The weathering rate of plagioclase (mass loss divided by initial geometric surface area during 3400 y) is –12.116 log10 mol m–2 s–1. This weathering rate represents a time span (3.4 ka) intermediate between laboratory experimental timescales and the ages of regoliths in field studies of natural weathering rates. Weathering rates of the same plagioclase are recalculated using different assumptions concerning the method of estimating surface area, including simple geometric surface area and geometric surface area adjusted for surface roughness. Varying assumptions about surface area result in variations of up to two orders of magnitude in rates estimated from the same basic crystal geometry. The slowest rate estimated here approaches but does not fall within the range of previously determined field rates of plagioclase weathering.
Polystage apatite recrystallization and svanbergite formation during weathering in an acid karstic environment
Authors: Mordberg L. E. , Stanley C. J. , Antonov A. V. 
Published: August 2008

AbstractA Devonian weathering profile was developed near the contact of Riphean dolostone containing disseminated carbonate-fluorapatite and intensively pyritized black shales. Samples from the profile were investigated by XRF, SEM, electron microprobe and ion microprobe. Rock-forming minerals are apatite, diaspore, chlorite and kaolinite, while accessory minerals are svanbergite, anatase, pyrite and zircon.Primary marine carbonate-fluorapatite is represented by extremely weathered crystals concentrated near the footwall. Dissolution of apatite and pyrite provided an acidic environment that is expressed in the formation of S-rich apatite and svanbergite. The environment allowed Ti migration which formed anatase in weathered apatite grains. Coupled substitution Na+ + S6+ = Ca2+ + P5+ is suggested in S-rich apatite. A large volume of dissolved carbonate rocks was a source of Sr necessary for svanbergite formation. Apatite of the third generation formed at the final stage of weathering is represented by small (10—30 μm) very well shaped crystals.
Clinical features and treatment outcome of nasal-type NK/T-cell lymphoma of Waldeyer ring
Authors: Li Ye-Xiong , Fang Hui , Liu Qing-Feng , Lu Jiade , Qi Shu-Nan , Wang Hua , Jin Jing , Wang Wei-Hu , Liu Yue-Ping , Song Yong-Wen , Wang Shu-Lian , Liu Xin-Fan , Feng Xiao-Li , Yu Zi-Hao 
Published: August 2008

AbstractThe clinical characteristics and prognosis remain unclear for nasal-type NK/T-cell lymphoma of Waldeyer ring (WR-NKTL). The aim of this study is to determine the clinical features and outcome. Ninety-one patients with WR-NKTL were reviewed. According to the Ann Arbor system, 15, 56, 12, and 8 patients had stage I, II, III, and IV. Of patients with stage I and II, 54 received combined chemotherapy and radiotherapy (CMT), 13 received radiotherapy alone, and 4 patients received chemotherapy alone. All 20 patients with stage III/IV received primary chemotherapy. The disease is characterized by predominance in young males, good performance, a propensity for nodal involvement, frequent stage II through IV diseases, low frequency of elevated LDH, low-risk international prognostic index (IPI), high sensitivity to radiotherapy, and intermediate sensitivity to chemotherapy. The 5-year overall survival and progression-free survival for all patients were 65% and 51%, respectively. The age, B symptoms, stage, and IPI were important prognostic factors. CMT tended to improve the survival compared with radiotherapy alone for patients with stage I and II diseases. Both nodal involvement and distant extranodal dissemination were the primary failure patterns. WR-NKTL appears to have distinct clinical characteristics and favorable outcomes.
A genetic polymorphism of the osteoprotegerin gene is associated with an increased risk of advanced prostate cancer
Authors: Narita Naofumi , Yuasa Takeshi , Tsuchiya Norihiko , Kumazawa Teruaki , Narita Shintaro , Inoue Takamitsu , Ma Zhiyong , Saito Mitsuru , Horikawa Yohei , Satoh Shigeru , Ogawa Osamu , Habuchi Tomonori 
Published: August 2008

Abstract

Background
The purpose of this study was to evaluate the role of osteoprotegerin gene (OPG) polymorphisms as genetic modifiers in the etiology of prostate cancer (PCa) and disease progression.

Methods
Three hundred and sixty one patients with PCa and 195 normal controls were enrolled in the study, and two genetic polymorphisms, 149 T/C and 950 T/C in the putative promoter region of OPG, were genotyped.

Results
There was no significant difference in the genotype frequencies between PCa patients and controls (P = 0.939 and 0.294 for 149 T/C and 950 T/C polymorphisms, respectively). However, those patients with TC and TT genotypes in the 950 T/C polymorphism had a significantly increased risk of extraprostatic (age-adjusted odds ratio; aOR = 1.74 and 2.03 for TC and TT genotypes compared with the CC genotype, P = 0.028) and metastatic disease (aOR = 1.72 and 2.76 for TC and TT genotypes compared with the CC genotype, P = 0.009) compared with those with the CC genotype. In addition, analysis of the metastatic PCa patients (Stage D) showed that the presence of the T allele of the OPG 950 T/C polymorphism was an independent risk factor predicting survival by Cox proportional hazard regression analyses (P = 0.031).

Conclusion
Progression of PCa may be influenced by an intrinsic genetic factor of the host's bone metabolism. The variant C allele of 950 T/C in the OPG promoter may play a major role as a genetic safe guard against progression in patients with PCa.
Malaria morbidity in Papua Indonesia, an area with multidrug resistant Plasmodium vivax and Plasmodium falciparum
Authors: Karyana Muhammad , Burdarm Lenny , Yeung Shunmay , Kenangalem Enny , Wariker Noah , Maristela Rilia , Umana Ketut Gde , Vemuri Ram , Okoseray Maurits J , Penttinen Pasi M , Ebsworth Peter , Sugiarto Paulus , Anstey Nicholas M , Tjitra Emiliana , Price Richard N 
Published: August 2008

Abstract

Background
Multidrug resistance has emerged to both Plasmodium vivax and Plasmodium falciparum and yet the comparative epidemiology of these infections is poorly defined.

Methods
All laboratory-confirmed episodes of malaria in Timika, Papua, Indonesia, presenting to community primary care clinics and an inpatient facility were reviewed over a two-year period. In addition information was gathered from a house-to-house survey to quantify the prevalence of malaria and treatment-seeking behaviour of people with fever.

Results
Between January 2004 and December 2005, 99,158 laboratory-confirmed episodes of malaria were reported, of which 58% (57,938) were attributable to P. falciparum and 37% (36,471) to P. vivax. Malaria was most likely to be attributable to pure P. vivax in children under one year of age (55% 2,684/4,889). In the household survey, the prevalence of asexual parasitaemia was 7.5% (290/3,890) for P. falciparum and 6.4% (248/3,890) for P. vivax. The prevalence of P. falciparum infection peaked in young adults aged 15–25 years (9.8% 69/707), compared to P. vivax infection which peaked in children aged 1 to 4 years (9.5% 61/642). Overall 35% (1,813/5,255) of people questioned reported a febrile episode in the preceding month. Of the 60% of people who were estimated to have had malaria, only 39% would have been detected by the surveillance network. The overall incidence of malaria was therefore estimated as 876 per 1,000 per year (Range: 711–906).

Conclusion
In this region of multidrug-resistant P. vivax and P. falciparum, both species are associated with substantial morbidity, but with significant differences in the age-related risk of infection.
The relationship between the haemoglobin concentration and the haematocrit in Plasmodium falciparum malaria
Authors: Lee Sue J , Stepniewska Kasia , Anstey Nicholas , Ashley Elizabeth , Barnes Karen , Binh Tran Quang , D'Alessandro Umberto , Day Nicholas PJ , de Vries Peter J , Dorsey Grant , Guthmann Jean-Paul , Mayxay Mayfong , Newton Paul , Nosten Francois , Olliaro Piero , Osario Lyda , Pinoges Loretxu , Price Ric , Rowland Mark , Smithuis Frank , Taylor Robert , White Nicholas J 
Published: August 2008

Abstract

Background
Malaria is a very important cause of anaemia in tropical countries. Anaemia is assessed either by measurement of the haematocrit or the haemoglobin concentration. For comparisons across studies, it is often necessary to derive one measure from the other.

Methods
Data on patients with slide-confirmed uncomplicated falciparum malaria were pooled from 85 antimalarial drug trials conducted in 25 different countries, to assess the haemoglobin/haematocrit relationship at different time points in malaria. Using a linear random effects model, a conversion equation for haematocrit was derived based on 3,254 measurements from various time points (ranging from day 0 to day 63) from 1,810 patients with simultaneous measurements of both parameters. Haemoglobin was also estimated from haematocrit with the commonly used threefold conversion.

Results
A good fit was obtained using Haematocrit = 5.62 + 2.60 * Haemoglobin. On average, haematocrit/3 levels were slightly higher than haemoglobin measurements with a mean difference (± SD) of -0.69 (± 1.3) for children under the age of 5 (n = 1,440 measurements from 449 patients).

Conclusion
Based on this large data set, an accurate and robust conversion factor both in acute malaria and in convalescence was obtained. The commonly used threefold conversion is also valid.
Targeting focal adhesions:Helicobacter pylori-host communication in cell migration
Authors: Schneider Sabine , Weydig Christiane , Wessler Silja 
Published: August 2008

Abstract
Highly dynamic integrin-based focal adhesions provide an important structural basis for anchoring the cellular actin cytoskeleton to the surrounding extracellular matrix. The human pathogen Helicobacter pylori (H. pylori) directly targets integrins with drastic consequences on the epithelial cell morphology and migration, which might contribute to the disruption of the gastric epithelium in vivo. In this review, we summarize the recent findings concerning the complex mechanism through which H. pylori interferes with host integrin signaling thereby deregulating focal adhesions and the actin cytoskeleton of motile epithelial cells.
Intracerebroventricular Administration of N-Acetylaspartylglutamate (NAAG) Peptidase Inhibitors is Analgesic in Inflammatory Pain
Authors: Yamamoto Tatsuo , Kozikowski Alan , Zhou Jia , Neale Joseph H 
Published: August 2008

Background: The peptide neurotransmitter N-Acetylaspartylglutamate (NAAG) is the third most prevalent transmitter in the mammalian central nervous system. Local, intrathecal and systemic administration of inhibitors of enzymes that inactivate NAAG decrease responses to inflammatory pain in rat models. Consistent with NAAG's activation of group II metabotropic glutamate receptors, this analgesia is blocked by a group II antagonist. Results: This research aimed at determining if analgesia obtained following systemic administration of NAAG peptidase inhibitors is due to NAAG activation of group II mGluRs in brain circuits that mediate perception of inflammatory pain. NAAG and NAAG peptidase inhibitors, ZJ43 and 2-PMPA, were microinjected into a lateral ventricle prior to injection of formalin in the rat footpad. Each treatment reduced the early and late phases of the formalin-induced inflammatory pain response in a dose-dependent manner. The group II mGluR antagonist reversed these analgesic effects consistent with the conclusion that analgesia was mediated by increasing NAAG levels and the peptide's activation of group II receptors. Conclusion: These data contribute to proof of the concept that NAAG peptidase inhibition is a novel therapeutic approach to inflammatory pain and that these inhibitors achieve analgesia by elevating synaptic levels of NAAG within pain processing circuits in brain.
A highly conserved family of inactivated archaeal B family DNA polymerases
Authors: Rogozin Igor B , Makarova Kira S , Pavlov Youri I , Koonin Eugene V 
Published: August 2008

Abstract
A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly separated from each other and from a small group of bacterial homologs. These findings are compatible with an ancient duplication of the DNA polymerase gene followed by inactivation and parallel loss in some of the lineages although contribution of horizontal gene transfer cannot be ruled out. The inactivated derivative of the archaeal DNA polymerase could form a complex with the active paralog and play a structural role in DNA replication.

Reviewers

This article was reviewed by Purificacion Lopez-Garcia and Chris Ponting. For the full reviews, please go to the Reviewers' Reports section.