bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shallow groundwater in the northeast arid zone of Nigeria
Authors: Carter R. C. , Alkali A. G. 
Published: November 2007

Abstract
The natural resources of the northeast arid zone of Nigeria have been the subject of a recent five-year, European Union-funded research programme, carried out in support of rural development initiatives in the area. The shallow groundwater resources of the extensive river floodplain alluvial aquifers, and of the interfluves of uplands, have been an important focus of the research. The main issue in relation to sustainable development of these resources is the estimation of their recharge.
Recharge to the alluvial aquifer of the Yobe river downstream of Gashua is showmn to be limited by an extensive clay cove overlying the aquifer. As a consequence of this the main mechanism of recharge is channel seepage, vertical infiltration being severely restricted. if, as is though by most consultants, this is the only source of recharge to the area as a whole, then it is shown that recharge to the area amounts to less than 1 mm/a. This is probably less than the present abstraction from the shallow aquifers.
The paper challenges the current presumption that rainfed recharge to the shallow aquifers beneath the upland is nil. Observations from ther parts of the Sahel are used to show the typical magnitudes of water table decline which have coincided with the Sahel drought (early 1960s to date). These rates of decline cannot be explained by increases in abstraction. They can however be explained by significant reductions in recharge (of several mm/a) over the period in which rainfall has reduced, and this in turn implies recharge values significantly greater than zero in the very recent past, or to date. Detailed studies by the first author in the Manga Grasslands of north east Nigeria, in which recharge of 30–60 mm/a was estimated, are used to exemplify the likely situation in at least some parts of the upland.
Ignorance or uncertainty of both the natural replenishment processes, and of the impact of climatic and anthropogenic changes, is no basis for sound water resource management policy. Because of the importance of establishing a more sound understanding of the recharge processes in the northeast arid zone, an outline programme of further research is presented.
Slope stability of Tehri Dam Reservoir Area, India, using landslide hazard zonation (LHZ) mapping
Authors: Gupta Pankaj , Anbalagan R. 
Published: November 2007

Abstract

A 260 m high dam is under construction across the Bhagirathi River in the Garhwal Himalaya (India) to impound 3.6 x 10
9
m
3
of water at the maximum reservoir level. The reservoir will over a distance of about 44 km in the Bhagirathi Valley and about 25 km in the Bhillangna Valley. A landslide hazard zonation map of the reservoir area has been prepared. The relative influences of six major causative factors have been calculated to identify the important controlling factors in high hazard slope facets.
Modelling river-aquifer interactions at the Spey Abstraction Scheme, Scotland: implications for aquifer protection
Authors: Chen M. , Soulsby C. , Willetts B. 
Published: November 2007

Abstract

Groundwater resources in Scotland are receiving increasing attention because of the high costs of surface water treatment and the stringent water quality requirements of the EC Drinking Water Directive. On the River Spey, a unique abstraction scheme has been developed, involving a wellfield comprising 36 production boreholes in the river gravels of the lower catchment. The scheme aims to provide a maximum of 27 000 m
3
/d to meet increasing water demands in northeast Scotland by 2011. This yield is equivalent to one-third of the current total public groundwater abstraction in Scotland.

This paper describes a steady-state quasi-three-dimensional numerical model of the Spey river-aquifer system which was used in conjunction with a particle tracking program to delineate travel time related capture zones of the Spey abstraction wellfield. Three scenarios were simulated: pre-development, current pumping rate (16 000 m
3
/d) and projected maximum pumping rate. The pre-development water budget indicates that 940f total groundwater inflow is discharged into the river, whereas the budgets for stressed conditions give the percentage of water abstracted from the river as 69% and 74 0.000000or current and maximum pumping rates respectively.

Capture zones of 50-day (Zone 1) and 400-day (Zone 2) travel time to the wellfield are defined for the projected maximum pumping rate. These indicate that the river itself is the primary potential polluting source. However, extensive areas of the river floodplain also contribute significantly to the abstraction, thus certain restrictions on potentially polluting activities are needed. It is concluded that rigorous programmes for monitoring water quality both in the river upstream, and within the modelled catchment are required to protect the Spey Abstraction Scheme.
An unusual coexistence of sulphate-reducing bacteria and algae in a confined groundwater production system
Authors: Walton N. R. G. 
Published: November 2007

Abstract
An unusual occurrence of the coexistence of algae, oxygen and hydrogen sulphide from sulphate-reducing bacteria (SRB) in an overseas groundwater production system is described that had an interesting origin and some important implications both for groundwater professionals and for the water industry in general.

A deep, confined anaerobic groundwater source containing SRBs was being pumped to a new municipal water treatment works by underground pipeline from a wellfield some 3 km distant. Pumping continued at a steady rate of around 70 000 m
3
/d for a period of three months from start-up without significant problems. However, in the fourth month of operation, progressively serious fouling problems appeared in the sand filters that nearly caused a plant shutdown, with the consequent near loss of supply of a major drinking water source for a nearby city.

This paper describes the cause of those problems and highlights both the complex chain of events and the biochemical interactions involved, with particular emphasis on the unusual coexistence of SRBs and algae in a groundwater system. This apparent paradox is explained in terms of an unfolding sequence of seemingly unconnected events with a rather surprising origin.
Aspects of the occurrence and behaviour of iron bacteria in boreholes and aquifers
Authors: Tyrrel Sean F. , Howsam Peter 
Published: November 2007

Abstract
Iron bacteria are well known to borehole operators as the cause of iron biofouling—the build-up of orange-coloured slimes and encrustations on casing, pump and pipe surfaces. In addition to biofouling, these nuisance organisms play a part in: enhancing the corrosion of borehole, pump and pipe components; influencing the chemistry of polluting acidic mine drainage waters; and promoting the accumulation of soluble iron in groundwaters. This paper highlights the diversity of organisms which may be classed as iron bacteria, briefly describes the behaviour of iron bacteria in boreholes and aquifers and outlines the deleterious effects that their activity can have on the efficient functioning of groundwater abstraction systems. However, it would be wrong to classify iron bacteria only as a nuisance. There is potential for harnessing the activities of these organisms in a positive way and particular reference is made here to the benefits of biological removal of iron and arsenic from groundwaters.
Bacteria in the Castleton Karst, Derbyshire, England
Authors: Tranter J. , Gunn J. , Hunter C. , Perkins J. 
Published: November 2007

Abstract
The Castleton area contains an extensive and complex karst drainage system. Recharge is provided by allogenic stream sinks and by infiltration into a soil covered autogenic catchment. Concentrations of the sanitary indicator bacteria faecal coliform (FC) were measured weekly over a 84-week period at three stream-sinks (P6, P7 and P8) and at two contrasting springs (Russet Well and Peak Cavern Rising). Russet Well drains the allogenic catchment, but also receives some autogenic recharge whereas Peak Cavern Rising receives only autogenic recharge except at high stage when it functions as an overflow spring for the Russet Well system. Over the year as a whole and during each three-month season, median FC concentrations at P6 were significantly higher than at Russet Well. The difference was greatest during summer/autumn and was lowest in winter/spring and it appears that FC concentrations at the rising are a complex function of faecal inputs and flow through time. The relationship between FC concentrations at Russet Well and at Peak Cavern Rising proved to be complex. Over the sampling period as a whole and during the spring and autumn there was no significant difference between median FC concentrations at the two risings; during the winter, when discharge was highest, median FC concentrations at Russet Well were significantly higher than at Peak Cavern Rising; and during the summer FC concentrations at Peak Cavern Rising were significantly higher than at Russet Well. The high FC concentrations in the sinking streams and at the risings suggest that there could be a health risk to cavers, especially during storm events and the summer. Furthermore, the fact that the waters from both springs contain significant concentrations of FC bacteria indicates that even soil covered karst systems are unable to filter out potentially harmful micro-organisms.
Neural Correlates of Multisensory Integration of Ecologically Valid Audiovisual Events
Authors: Stekelenburg Jeroen J. , Vroomen Jean 
Published: November 2007

Abstract
A question that has emerged over recent years is whether audiovisual (AV) speech perception is a special case of multi-sensory perception. Electrophysiological (ERP) studies have found that auditory neural activity (N1 component of the ERP) induced by speech is suppressed and speeded up when a speech sound is accompanied by concordant lip movements. In Experiment 1, we show that this AV interaction is not speech-specific. Ecologically valid nonspeech AV events (actions performed by an actor such as handclapping) were associated with a similar speeding-up and suppression of auditory N1 amplitude as AV speech (syllables). Experiment 2 demonstrated that these AV interactions were not influenced by whether A and V were congruent or incongruent. In Experiment 3 we show that the AV interaction on N1 was absent when there was no anticipatory visual motion, indicating that the AV interaction only occurred when visual anticipatory motion preceded the sound. These results demonstrate that the visually induced speeding-up and suppression of auditory N1 amplitude reflect multisensory integrative mechanisms of AV events that crucially depend on whether vision predicts when the sound occurs.
The Neuronal Correlate of Bidirectional Synesthesia: A Combined Event-related Potential and Functional Magnetic Resonance Imaging Study
Authors: Cohen Kadosh Roi , Cohen Kadosh Kathrin , Henik Avishai 
Published: November 2007

Abstract
The neuronal correlate of a rare explicit bidirectional synesthesia was investigated with numerical and physical size comparison tasks using both functional magnetic resonance imaging and event-related potentials. Interestingly, although participant I.S. exhibited similar congruity effects for both tasks at the behavioral level, subsequent analyses of the imaging data revealed that different brain areas were recruited for each task, and in different time windows. The results support: (1) the genuineness of bidirectional synesthesia at the neuronal level, (2) the possibility that discrepancy in the neuronal correlates of synesthesia between previous studies might be task-related, and (3) the possibility that synesthesia might not be a unitary phenomenon.
A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays
Authors: Lamy Philippe , Andersen Claus L , Dyrskjot Lars , Torring Niels , Wiuf Carsten 
Published: November 2007

AbstractBackgroundAffymetrix SNP arrays can interrogate thousands of SNPs at the same time. This allows us to look at the genomic content of cancer cells and to investigate the underlying events leading to cancer. Genomic copy-numbers are today routinely derived from SNP array data, but the proposed algorithms for this task most often disregard the genotype information available from germline cells in paired germline-tumour samples. Including this information may deepen our understanding of the "true" biological situation e.g. by enabling analysis of allele specific copy-numbers. Here we rely on matched germline-tumour samples and have developed a Hidden Markov Model (HMM) to estimate allelic copy-number changes in tumour cells. Further with this approach we are able to estimate the proportion of normal cells in the tumour (mixture proportion).ResultsWe show that our method is able to recover the underlying copy-number changes in simulated data sets with high accuracy (above 97.71%). Moreover, although the known copy-numbers could be well recovered in simulated cancer samples with more than 70% cancer cells (and less than 30% normal cells), we demonstrate that including the mixture proportion in the HMM increases the accuracy of the method. Finally, the method is tested on HapMap samples and on bladder and prostate cancer samples.ConclusionThe HMM method developed here uses the genotype calls of germline DNA and the allelic SNP intensities from the tumour DNA to estimate allelic copy-numbers (including changes) in the tumour. It differentiates between different events like uniparental disomy and allelic imbalances. Moreover, the HMM can estimate the mixture proportion, and thus inform about the purity of the tumour sample.
Functional evolution of the vitamin D and pregnane X receptors
Authors: Reschly Erica J , Bainy Afonso Celso Dias , Mattos Jaco Joaquim , Hagey Lee R , Bahary Nathan , Mada Sripal R , Ou Junhai , Venkataramanan Raman , Krasowski Matthew D 
Published: November 2007

AbstractBackgroundThe vitamin D receptor (VDR) and pregnane X receptor (PXR) are nuclear hormone receptors of the NR1I subfamily that show contrasting patterns of cross-species variation. VDR and PXR are thought to have arisen from duplication of an ancestral gene, evident now as a single gene in the genome of the chordate invertebrateCiona intestinalis(sea squirt). VDR genes have been detected in a wide range of vertebrates including jawless fish. To date, PXR genes have not been found in cartilaginous fish. In this study, the ligand selectivities of VDRs were compared in detail across a range of vertebrate species and compared with those of theCionaVDR/PXR. In addition, several assays were used to search for evidence of PXR-mediated hepatic effects in three model non-mammalian species: sea lamprey (Petromyzon marinus), zebrafish (Danio rerio), and African clawed frog (Xenopus laevis).ResultsHuman, mouse, frog, zebrafish, and lamprey VDRs were found to have similar ligand selectivities for vitamin D derivatives. In contrast, using cultured primary hepatocytes, only zebrafish showed evidence of PXR-mediated induction of enzyme expression, with increases in testosterone 6β-hydroxylation activity (a measure of cytochrome P450 3A activity in other species) and flurbiprofen 4-hydroxylation activity (measure of cytochrome P450 2C activity) following exposure to known PXR activators. A separate assay in vivo using zebrafish demonstrated increased hepatic transcription of another PXR target, multidrug resistance gene (ABCB5), following injection of the major zebrafish bile salt, 5α-cyprinol 27-sulfate. The PXR target function, testosterone hydroxylation, was detected in frog and sea lamprey primary hepatocytes, but was not inducible in these two species by a wide range of PXR activators in other animals. Analysis of the sea lamprey draft genome also did not show evidence of a PXR gene.ConclusionOur results show tight conservation of ligand selectivity of VDRs across vertebrate species from Agnatha to mammals. Using a functional approach, we demonstrate classic PXR-mediated effects in zebrafish, but not in sea lamprey or African clawed frog liver cells. Using a genomic approach, we failed to find evidence of a PXR gene in lamprey, suggesting that VDR may be the original NR1I gene.
In silico genetic robustness analysis of microRNA secondary structures: potential evidence of congruent evolution in microRNA
Authors: Shu Wenjie , Bo Xiaochen , Ni Ming , Zheng Zhiqiang , Wang Shengqi 
Published: November 2007

AbstractBackgroundRobustness is a fundamental property of biological systems and is defined as the ability to maintain stable functioning in the face of various perturbations. Understanding how robustness has evolved has become one of the most attractive areas of research for evolutionary biologists, as it is still unclear whether genetic robustness evolved as a direct consequence of natural selection, as an intrinsic property of adaptations, or as congruent correlate of environment robustness. Recent studies have demonstrated that the stem-loop structures of microRNA (miRNA) are tolerant to some structural changes and show thermodynamic stability. We therefore hypothesize that genetic robustness may evolve as a correlated side effect of the evolution for environmental robustness.ResultsWe examine the robustness of 1,082 miRNA genes covering six species. Our data suggest the stem-loop structures of miRNA precursors exhibit a significantly higher level of genetic robustness, which goes beyond the intrinsic robustness of the stem-loop structure and is not a byproduct of the base composition bias. Furthermore, we demonstrate that the phenotype of miRNA buffers against genetic perturbations, and at the same time is also insensitive to environmental perturbations.ConclusionThe results suggest that the increased robustness of miRNA stem-loops may result from congruent evolution for environment robustness. Potential applications of our findings are also discussed.
Co-inherited mutations of Fas and caspase-10 in development of the autoimmune lymphoproliferative syndrome
Authors: Cerutti Elisa , Campagnoli Maria F , Ferretti Massimo , Garelli Emanuela , Crescenzio Nicoletta , Rosolen Angelo , Chiocchetti Annalisa , Lenardo Michael J , Ramenghi Ugo , Dianzani Umberto 
Published: November 2007

Abstract

Background
Autoimmune lymphoproliferative syndrome (ALPS) is a rare inherited disorder characterized by defective function of Fas, autoimmune manifestations that predominantly involve blood cells, polyclonal accumulation of lymphocytes in the spleen and lymph nodes with lymphoadenomegaly and/or splenomegaly, and expansion of TCRαβ+ CD4/CD8 double-negative (DN) T cells in the peripheral blood. Most frequently, it is due to Fas gene mutations, causing ALPS type Ia (ALPS-Ia). However, other mutations, namely of the FasL gene (ALPS-Ib) and the caspase-10 gene (ALPS-II) are occasionally detected, whereas some patients do not present any known mutations (ALPS-III). Recently, mutations of the NRAS gene have been suggested to cause ALPS-IV.

Results
This work reports two patients that are combined heterozygous for single nucleotide substitutions in the Fas and caspase-10 genes. The first patient carried a splice site defect suppressing allele expression in the Fas gene and the P501L substitution in caspase-10. The second had a mutation causing a premature stop codon (Q47X) in the Fas gene and the Y446C substitution in caspase-10. Fas expression was reduced and caspase-10 activity was decreased in both patients. In both patients, the mutations were inherited from distinct healthy parents.

Conclusion
These data strongly suggest that co-transmission of these mutation was responsible for ALPS.
A unique population of effector memory lymphocytes identified by CD146 having a distinct immunophenotypic and genomic profile
Authors: Elshal Mohamed F , Khan Sameena S , Raghavachari Nalini , Takahashi Yoshiyuki , Barb Jennifer , Bailey James J , Munson Peter J , Solomon Michael A , Danner Robert L , McCoy J Philip 
Published: November 2007

AbstractBackgroundCD146 is a well described homotypic adhesion molecule found on endothelial cells and a limited number of other cell types. In cells from the peripheral circulation, CD146 has also been reported to be on activated lymphocytesin vitroandin vivo. The function associated with CD146 expression on lymphoid cells is unknown and very little information is available concerning the nature of CD146+ lymphocytes. In the current study, lymphocytes from healthy donors were characterized based upon the presence or absence of CD146 expression.ResultsCD146 was expressed on a low percentage of circulating T lymphocytes, B lymphocytes, and NK cells in healthy individuals. CD146 expression can be induced and upregulatedin vitroon both B cells and T cells, but does not correlate with the expression of other markers of T cell activation. CD146 positive T cells do not represent clonal expansions as determined with the use of anti Vβ reagents. Data suggest that CD146 positive cells have enhanced adherence to endothelial monolayers in vitro. Gene profiling and immunophenotyping studies between CD146+ and CD146- T cells revealed several striking genotypic distinctions such as the upregulation of IL-8 and phenotypic differences including the paucity of CCR7 and CD45RA among CD146 positive T cells, consistent with effector memory function. A number of genes involved in cell adhesion, signal transduction, and cell communication are dramatically upregulated in CD146+ T cells compared to CD146- T cells.ConclusionCD146 appears to identify small, unique populations of T as well as B lymphocytes in the circulation. The T cells have immunophenotypic characteristics of effector memory lymphocytes. The characteristics of these CD146+ lymphocytes in the circulation, together with the known functions in cell adhesion of CD146 on endothelial cells, suggests that these lymphocytes may represent a small subpopulation of cells primed to adhere to the endothelium and possibly extravasate to sites of inflammation.