bluuebunny/crossref_metadata_2025_split huggingface dataset:
Speciation of adsorbed arsenic(V) on red mud using a sequential extraction procedure
Authors: Rubinos D. A. , Arias M. , Díaz-Fierros F. , Barral M. T. 
Published: December 2005

AbstractThe distribution of sorbed arsenic(V) among different geochemical fractions for arsenic(V)-loaded red mud, an oxide-rich residue from bauxite refining that has been proposed as an adsorbent for arsenic, was studied as a function of sorbed arsenic(V) concentration using a sequential extraction procedure. The release of previously sorbed arsenic(V) was also studied as a function of pH and arsenic(V) concentration. Most sorbed arsenic(V) (0.39–7.86 mmol kg–1) was associated with amorphous and crystalline Al and Fe oxides (24.1–43.8% and 24.7–59.0% of total sorbed arsenic, respectively). Exchangeable arsenic was the smallest fraction (0.4–5.2% of total sorbed arsenic). The distribution of sorbed arsenic(V) was related to the arsenic surface coverage. For arsenic surface coverages >∼30% the percentage of arsenic(V) associated with the amorphous Al oxide fraction increased and that associated with the crystalline oxide fraction decreased. The arsenic(V) exchangeable fraction increased from 1.4 to 756 μmol kg–1 as surface coverage increased from 388 to 7855 μmol kg–1. The release of sorbed arsenic(V) from red mud was greater at alkaline pH values (maximum release of ∼33% of previously sorbed arsenic at pH = 12), but for high arsenic(V) initial concentration (0.2 mM arsenic) considerable amounts of arsenic (6.5% of previously sorbed arsenic) were released at pH 4, in accordance with the dissolution of amorphous Al oxides in the red mud. The results obtained suggest a greater mobility of sorbed arsenic(V) as its surface concentration approaches saturation.
Ecological risk assessment of contaminated soil
Authors: Weeks J. M. , Comber S. D. W. 
Published: December 2005

AbstractThe basis for an ecological risk assessment based on meeting the needs of recent UK and EU legislation is described. The background to the framework and the legislative driver and relevant definitions of harm are provided, prior to an overview of the proposed ecological risk assessment process, which has been broken down into a Tiered approach. Tier 0 requires the establishment of a conceptual site model, where potential contaminant-pathway-receptor linkages are sought and, assuming they are identified, lead on to higher Tier assessments. Tier 1 relies largely on chemical analysis of soil contaminant levels and comparison with soil quality guideline values to assess the likelihood of harm. In some cases biological screening assays may also be undertaken within this Tier. Based on a weight of evidence approach, should data from Tier 1 indicate harm or leave uncertainty, then Tier 2 biological testing is undertaken using assays relevant to the site of interest. In situations where harm is identified under Tier 2 then Tier 3 is reserved for establishing the extent of harm within the ecosystem. Finally the use of the 'weight-of-evidence' approach to generate scientifically robust conclusions regarding the harm (or potential for harm) within the ecosystem is briefly outlined. The framework discussed is currently being adopted by the UK Environment Agency, with implementation expected in 2005. The UK scheme compares favourably with comparative schemes operating in other countries possessing the merits of being iterative, tiered, flexible with agreed exit points subject to satisfying defined criteria and so speeding the decision-making process.
A preliminary study of the release of platinum and palladium from metallic particles in the surface environment by organic acids: relevance to weathering of particles from vehicle exhaust catalysts
Authors: Bowles J. F. W. , Gize A. P. 
Published: December 2005

AbstractStudies of the weathering of platinum-group minerals in natural deposits have indicated that the platinum-group elements (PGE) can be mobilized under appropriate conditions and have sufficient solubility to move into solution. Although inorganic chemistry provides feasible mechanisms under the extreme conditions encountered in laterites it appears likely that PGE-organic complexes offer a more convincing explanation of the apparent solubility. Experimental work undertaken to illustrate the organic processes and the reaction timescale examined various reactions including those between Pt and Pd foils and humic and fulvic acid solutions. These reactions appear pertinent to those that may occur between the PGE particles ejected by vehicle exhaust catalysts and the natural environment.The experimental work produced up to 195 μ/l Pt and 102 μ/l Pd in humic acid solutions exposed to the metal foils for about a year at room temperature. The experimental conditions can be compared to those encountered in roadside drainage supplied with PGE particles and decaying vegetation.Consideration of the possible health effects of the PGE from the particles ejected by vehicle exhaust catalysts has centred on inhalation of the particles or absorption through the skin. Intake from drinking water or from food produced using PGE-bearing water should now also be investigated. Due to the variety of organic compounds produced by decaying vegetation the identity of the PGE-organic products is not yet known so their toxicity cannot be estimated.
The leaching behaviour of lead metallurgical slag in high-molecular-weight (HMW) organic solutions
Authors: Ettler V. , Jehlička J. , Mašek V. , J. Hruška  
Published: December 2005

AbstractThe reactivity of primary Pb metallurgical slags in high-molecular-weight (HMW) organic solutions has been studied in order to determine the processes of release and attenuation of metal and metalloid contaminants (Pb, Zn, Cu, As) in 'soil-like' environments. Slag was submitted to a 112-day batch leaching experiment in Suwannee River fulvic acid solution and peat water (∼50 mg DOC l–1). The leaching was coupled with investigation of the secondary phases (SEM/EDS, Raman microspectrometry) and thermodynamic speciation-solubility modelling using MINTEQA2. Metals and As are released in large amounts during the early stage of the experiment, followed by a decrease in the concentrations in the leachate as a result of adsorption on secondary (hydrous) ferric oxides (HFO/FO), predicted by MINTEQA2 calculations and confirmed on the leached slag surface by SEM and Raman spectrometry. Compared to other contaminants, Zn exhibits more pronounced mobility and is adsorbed on HFO/FO only at pH >7. Such a scavenging process may be predominant during the long-term interaction of slag with an HMW organic solution of real soil. As a result, the soil cover and subsequent re-vegetation of slag dumps may be considered as a possible scenario for slag management.
Gamma-emitting radionuclides and metallic elements in urban dusts and sediments, Coventry, UK: implications of dosages for dispersal and disposal
Authors: Charlesworth S. M. , Foster I. D. L. 
Published: December 2005

AbstractGully pot sediments and pavement and road gutter dusts have been collected from the city of Coventry in the West Midlands, UK. These samples have been subjected to metallic element analysis and the activity of a number of gamma-emitting radionuclides have been measured in order to assess whether they exceed published trigger or action levels, and whether their disposal or dispersal may have implications for receiving landfills and/or water courses. Results indicate above-background levels of metallic elements in dusts and sediments with Cu and Zn exceeding ICRCL action levels in some cases. The highest activities of some radionuclides are found in road gutter and street dusts and the lowest activities are found in gully pot sediments. Road dusts are more likely to be recirculated into the ambient air by passing traffic and could potentially pose a risk to pedestrians. The effective dose rates calculated for these dusts and sediments indicate that some samples approach and even exceed the 1 mSv y—1 limit to members of the public recommended by ICRP (1991). Some individual nuclides exceed their clearance levels laid down in the revised basic safety standards of the 1993b Radioactive Substances Act, 1993 (DoETR, 1999), by as much as 2.5 times. This is especially true of 210Pbun and 7Be, two fallout nuclides, and also of 40K.
In situ analysis of thioarsenite complexes in neutral to alkaline arsenic sulphide solutions
Authors: Bostick B. C. , Fendorf S. , Brown G. E. 
Published: December 2005

AbstractThe solubility of arsenic in anoxic soil and sediment pore waters is strongly influenced by complexation with dissolved sulphide. Despite their importance in arsenic chemistry, thioarsenite complexes have not been well characterized, and considerable questions remain regarding their structure, protonation state, and relative stabilities. Here we use X-ray absorption spectroscopy to examine the type and structure of aqueous arsenic-sulphur complexes in sulphidic solutions under neutral to alkaline pH. Arsenic formed a variety of thioarsenites, including AsS(SH)(OH)—, As(SH)S22—, AsS33—and As(SH)4— complexes. The relative fraction of each species varied strongly with the S:As ratio — with the fraction of AsS(SH)(OH)— greatest at low S:As and trithioarsenites dominating As speciation when S:As ratios exceeded 3 in solution. As much as 40% of the total As also was present as AsS3S3+x(SH)3—x—x in solutions at S:As ratios of 3 or greater. Sulphide complexation was somewhat dependent on pH, with sulphide complexation generally increasing with pH. The speciation observed in these experiments is similar to, though distinct from, speciation predicted based on As2S3 solubility (inferred to contain AsS2— and AsS3S3+x(SH)—x3—x) and chromatographic separation of arsenic species (which does not identify polymeric species). Thus, these data indicate that stability constants for arsenic sulphide complexes must be reappraised.
Arsenic hazard in shallow Cambodian groundwaters
Authors: Polya D. A. , A. G. Gault  , Diebe N. , Feldman P. , Rosenboom J. W. , Gilligan E. , Fredericks D. , Milton A. H. , Sampson M. , Rowland H. A. L. , Lythgoe P. R. , Jones J. C. , Middleton C. , Cooke D. A. 
Published: December 2005

AbstractOur recent discovery of hazardous concentrations of arsenic in shallow sedimentary aquifers in Cambodia raises the spectre of future deleterious health impacts on a population that, particularly in non-urban areas, extensively use untreated groundwater as a source of drinking water and, in some instances, as irrigation water. We present here small-scale hazard maps for arsenic in shallow Cambodian groundwaters based on >1000 groundwater samples analysed in the Manchester Analytical Geochemistry Unit and elsewhere. Key indicators for hazardous concentrations of arsenic in Cambodian groundwaters include: (1) well depths greater than 16 m; (2) Holocene host sediments; and (3) proximity to major modern channels of the Mekong (and its distributary the Bassac). However, high-arsenic well waters are also commonly found in wells not exhibiting these key characteristics, notably in some shallower Holocene wells, and in wells drilled into older Quaternary and Neogene sediments.It is emphasized that the maps and tables presented are most useful for identifying current regional trends in groundwater arsenic hazard and that their use for predicting arsenic concentrations in individual wells, for example for the purposes of well switching, is not recommended, particularly because of the lack of sufficient data (especially at depths >80 m) and because, as in Bangladesh and West Bengal, there is considerable heterogeneity of groundwater arsenic concentrations on a scale of metres to hundreds of metres. We have insufficient data at this time to determine unequivocally whether or not arsenic concentrations are increasing in shallow Cambodian groundwaters as a result of groundwater-abstraction activities.
Characterization of aquifers conducting groundwaters with low and high arsenic concentrations: a comparative case study from West Bengal, India
Authors: Nath B. , Berner Z. , Basu Mallik S. , Chatterjee D. , Charlet L. , Stueben D. 
Published: December 2005

AbstractPossible relationships between groundwater arsenic concentration and alluvial sediment characteristics in a ∼19 km2 area in West Bengal have been investigated using a combination of hydrogeochemical, lithogeochemical and geophysical techniques. Arsenic hotspots, typically associated with elevated groundwater Fe and Mn, were found to be correlated to some extent with old river channels (abandoned meanders, oxbow lakes), where sandy aquifers included intercalated fine-grained overbank deposits, rich in As, Fe, Mn and Corg. Otherwise no demonstrably significant overall differences in any of lithology, grain-size distribution, mineral composition or Fe, Mn and organic C content of the sediments were found between two representative sites with contrastingly low (<50 μg 1—1) and high (>200 μg 1—1) As groundwater contents.Our results are consistent with microbially mediated redox reactions controlled by the presence of natural organic matter within the aquifer and the occurrence of As-bearing redox traps, primarily formed by Fe and Mn oxides/hydroxides, being the most important factors which control the release of As into shallow groundwaters at the study site.
Microcosm depth profiles of arsenic release in a shallow aquifer, West Bengal
Authors: Gault A. G. , Islam F. S. , Polya D. A. , Charnock J. M. , Boothman C. , Chatterjee D. , Lloyd J. R. 
Published: December 2005

AbstractArsenic mobilization and Fe(III) reduction in acetate-amended sediments collected from a range of depths from an aquifer with elevated groundwater arsenic concentrations in West Bengal were monitored over a 1 month period. Significant arsenic release was noted in sediment collected from 24 m and 45 m depth, with some Fe(III) reduction also observed in the 24 m sample. The structure of the microbial communities present in the sediments prior to incubation showed marked differences down the sediment column. Profiling of the microbial community in the 24 m and 45 m samples revealed a relatively complex make-up, with Acinetobacter species comprising the bulk of the 24 m sedimentary bacterial population, but no previously characterized As(V)-reducers were detected in either sample.
Potential role of the Fe(III)-reducing bacteria Geobacter and Geothrix in controlling arsenic solubility in Bengal delta sediments
Authors: Islam F. S. , Boothman C. , Gault A. G. , Polya D. A. , Lloyd J. R. 
Published: December 2005

AbstractPrevious studies from our laboratory have suggested a role for indigenous metal-reducing bacteria in the reduction of sediment-bound As(V), and have also shown that a stable enrichment culture of Fe(III)-reducing bacteria was able to mobilize arsenic (as As(III)) from sediments collected from West Bengal (Islam et al., 2004). To identify the Fe(III)-reducing bacteria that may play a role in the reduction of As(V) and mobilization of As(III), we made a detailed molecular analysis of this enrichment culture. It was dominated by a close relative of Geothrix fermentans, but the type strain of this organism was unable to conserve energy for growth via the dissimilatory reduction of As(V), or reduce As(V) present in a defined medium containing fumarate as the electron acceptor. Furthermore, when the cells were grown using soluble Fe(III)-citrate as an electron acceptor in the presence of As(V), bacterial Fe(III) reduction resulted in the precipitation of the Fe(II)-bearing mineral vivianite in 2 weeks. This was accompanied by the efficient removal of As from solution. These results demonstrate that Geothrix fermentans, in common with other key Fe(III)-reducing bacteria such as Geobacter sulfurreducens, does not reduce As(V) enzymatically, but can capture arsenic in Fe(II) minerals formed during respiration using Fe(III) as an electron acceptor. Thus, the reduction of arsenic-bearing Fe(III) oxide minerals is not sufficient to mobilize arsenic, but may result in the formation of Fe(II) biominerals that could potentially act as sinks for arsenic in sediments. Additional mechanisms, including dissimilatory As(V) reduction by other specialist anaerobic bacteria, are implicated in the mobilization of arsenic from sediments.
Core erythropoietin receptor signals for late erythroblast development
Authors: Menon Madhu P. , Fang Jing , Wojchowski Don M. 
Published: December 2005

AbstractCritical signals for erythroblast formation are transduced by activated, tyrosine-phosphorylated erythropoietin receptor (EpoR) complexes. Nonetheless, steady-state erythropoiesis is supported effectively by EpoR alleles that are deficient in cytoplasmic phosphotyrosine sites. To better define core EpoR action mechanisms, signaling capacities of minimal PY-null (EpoR-HM) and PY343-retaining (EpoR-H) alleles were analyzed for the first time in bone marrow–derived erythroblasts. Jak2 activation via each allele was comparable. Stat5 (and several Stat5-response genes) were induced via EpoR-H but not via EpoR-HM. Stat1 and Stat3 activation was nominal for all EpoR forms. For both EpoR-HM and EpoR-H, Akt and p70S6-kinase activation was decreased multifold, and JNK activation was minimal. ERKs, however, were hyperactivated uniquely via EpoR-HM. In vivo, Epo expression in EpoR-HM mice was elevated, while Epo-induced reticulocyte production was diminished. In vitro, EpoR-HM erythroblast maturation also was attenuated (based on DNA content, forward-angle light scatter, and hemoglobinization). These EpoR-HM–specific defects were corrected not only upon PY343 site restoration in EpoR-H, but also upon MEK1,2 inhibition. Core EpoR PY site-independent signals for erythroblast formation therefore appear to be Stat5, Stat1, Stat3, p70S6-kinase, and JNK independent, but ERK dependent. Wild-type signaling capacities, however, depend further upon signals provided via an EpoR/PY343/Stat5 axis.
Efficient analysis and extraction of MS/MS result data from Mascot™ result files
Authors: Grosse-Coosmann Florian , Boehm Andreas M , Sickmann Albert 
Published: December 2005

Abstract
Background
Mascot™ is a commonly used protein identification program for MS as well as for tandem MS data. When analyzing huge shotgun proteomics datasets with Mascot™'s native tools, limits of computing resources are easily reached. Up to now no application has been available as open source that is capable of converting the full content of Mascot™ result files from the original MIME format into a database-compatible tabular format, allowing direct import into database management systems and efficient handling of huge datasets analyzed by Mascot™.

Results
A program called mres2x is presented, which reads Mascot™ result files, analyzes them and extracts either selected or all information in order to store it in a single file or multiple files in formats which are easier to handle downstream of Mascot™. It generates different output formats. The output of mres2x in tab format is especially designed for direct high-performance import into relational database management systems using native tools of these systems. Having the data available in database management systems allows complex queries and extensive analysis. In addition, the original peak lists can be extracted in DTA format suitable for protein identification using the Sequest™ program, and the Mascot™ files can be split, preserving the original data format. During conversion, several consistency checks are performed. mres2x is designed to provide high throughput processing combined with the possibility to be driven by other computer programs. The source code including supplement material and precompiled binaries is available via http://www.protein-ms.de and http://sourceforge.net/projects/protms/.

Conclusion
The database upload allows regrouping of the MS/MS results using a database management system and complex analyzing queries using SQL without the need to run new Mascot™ searches when changing grouping parameters.
The angiotensin-converting enzyme (ACE) gene family of Anopheles gambiae
Authors: Burnham Susan , Smith Judith A , Lee Alison J , Isaac R Elwyn , Shirras Alan D 
Published: December 2005

Abstract

Background
Members of the M2 family of peptidases, related to mammalian angiotensin converting enzyme (ACE), play important roles in regulating a number of physiological processes. As more invertebrate genomes are sequenced, there is increasing evidence of a variety of M2 peptidase genes, even within a single species. The function of these ACE-like proteins is largely unknown. Sequencing of the A. gambiae genome has revealed a number of ACE-like genes but probable errors in the Ensembl annotation have left the number of ACE-like genes, and their structure, unclear.

Results
TBLASTN and sequence analysis of cDNAs revealed that the A. gambiae genome contains nine genes (AnoACE genes) which code for proteins with similarity to mammalian ACE. Eight of these genes code for putative single domain enzymes similar to other insect ACEs described so far. AnoACE9, however, has several features in common with mammalian somatic ACE such as a two domain structure and a hydrophobic C terminus. Four of the AnoACE genes (2, 3, 7 and 9) were shown to be expressed at a variety of developmental stages. Expression of AnoACE3, AnoACE7 and AnoACE9 is induced by a blood meal, with AnoACE7 showing the largest (approximately 10-fold) induction.

Conclusion
Genes coding for two-domain ACEs have arisen several times during the course of evolution suggesting a common selective advantage to having an ACE with two active-sites in tandem in a single protein. AnoACE7 belongs to a sub-group of insect ACEs which are likely to be membrane-bound and which have an unusual, conserved gene structure.
Bacterial genome adaptation to niches: Divergence of the potential virulence genes in three Burkholderia species of different survival strategies
Authors: Kim H Stanley , Schell Mark A , Yu Yan , Ulrich Ricky L , Sarria Saul H , Nierman William C , DeShazer David 
Published: December 2005

Abstract

Background
Two closely related species Burkholderia mallei (Bm) and Burkholderia pseudomallei (Bp) are serious human health hazards and are potential bio-warfare agents, whereas another closely related species Burkholderia thailandensis (Bt) is a non-pathogenic saprophyte. To investigate the genomic factors resulting in such a dramatic difference, we first identified the Bm genes responsive to the mouse environment, and then examined the divergence of these genes in Bp and Bt.

Results
The genes down-expressed, which largely encode cell growth-related proteins, are conserved well in all three species, whereas those up-expressed, which include potential virulence genes, are less well conserved or absent notably in Bt. However, a substantial number of up-expressed genes is still conserved in Bt. Bm and Bp further diverged from each other in a small number of genes resulting from unit number changes in simple sequence repeats (ssr) in the homologs.

Conclusion
Our data suggest that divergent evolution of a small set of genes, rather than acquisition or loss of pathogenic islands, is associated with the development of different life styles in these bacteria of similar genomic contents. Further divergence between Bm and Bp mediated by ssr changes may reflect different adaptive processes of Bm and Bp fine-tuning into their host environments.