bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numbers, biomass and cultivable diversity of microbial populations relate to depth and borehole-specific conditions in groundwater from depths of 4–450 m in Olkiluoto, Finland
Authors: Pedersen Karsten , Arlinger Johanna , Eriksson Sara , Hallbeck Anna , Hallbeck Lotta , Johansson Jessica 
Published: April 2008

Abstract
Microbiology, chemistry and dissolved gas in groundwater from Olkiluoto, Finland, were analysed over 3 years; samples came from 16 shallow observation tubes and boreholes from depths of 3.9–16.2 m and 14 deep boreholes from depths of 35–742 m. The average total number of cells (TNC) was 3.9 × 105 cells per ml in the shallow groundwater and 5.7 × 104 cells per ml in the deep groundwater. There was a significant correlation between the amount of biomass, analysed as ATP concentration, and TNC. ATP concentration also correlated with the stacked output of anaerobic most probable number cultivations of nitrate-, iron-, manganese- and sulphate-reducing bacteria, and acetogenic bacteria and methanogens. The numbers and biomass varied at most by approximately three orders of magnitude between boreholes, and TNC and ATP were positively related to the concentration of dissolved organic carbon. Two depth zones were found where the numbers, biomass and diversity of the microbial populations peaked. Shallow groundwater down to a depth of 16.2 m on average contained more biomass and cultivable microorganisms than did deep groundwater, except in a zone at a depth of approximately 300 m where the average biomass and number of cultivable microorganisms approached those of shallow groundwater. Starting at a depth of approximately 300 m, there were steep gradients of decreasing sulphate and increasing methane concentrations with depth; together with the peaks in biomass and sulphide concentration at this depth, these suggest that anaerobic methane oxidation may be a significant process at depth in Olkiluoto.
Cigarette Smoking and Fat Distribution in 21, 828 British Men and Women: A Population‐based Study
Authors: Canoy Dexter , Wareham Nicholas , Luben Robert , Welch Ailsa , Bingham Sheila , Day Nicholas , Khaw Kay‐Tee 
Published: April 2008

AbstractObjective: To examine the relationship between cigarette smoking habits and fat distribution in a population‐based cohort of men and women.Research Methods and Procedures: We analyzed cross‐sectional data from 21, 828 men and women who were 45 to 79 years of age, residents in Norfolk, United Kingdom, and were recruited between 1993 and 1997. Cigarette smoking habits and other lifestyle factors were assessed using self‐reported questionnaires. Anthropometric measures were obtained during a health examination.Results: Waist‐hip ratio was highest among current smokers and least among never smokers after adjusting for age, BMI, alcohol intake, total energy intake, physical activity, and education. Higher waist‐hip ratio was directly associated with higher smoking pack‐years in current and former smokers and inversely with duration since quitting smoking in former smokers. Adjusting for age, BMI, and other covariates, current smokers had higher waist circumference but lower hip circumference compared with former or never smokers.Discussion: Cigarette smoking habits seem to influence fat distribution patterns. Although smokers have lower mean BMI compared with nonsmokers, they have a more metabolically adverse fat distribution profile, with higher central adiposity. The explanation for this association may help elucidate the mechanisms underlying the adverse health consequences of cigarette smoking and abdominal obesity.
Etat des maladies virales de la tomate et stratégie de lutte en Algérie*
Authors: Nechadi S. , Benddine F. , Moumen A. , Kheddam M. 
Published: April 2008

La culture de la tomate occupe une place prépondérante dans l’économie agricole algérienne. Sur une superficie globale de primeurs évaluée à plus de 292 000 ha, la culture de tomate représente 51% de la production totale en produits maraîchers. La particularitéécologique de cette culture l’expose à diverses nuisances, notamment les insectes déprédateurs et les maladies. Parmi les espèces nuisibles rencontrées, les aleurodes constituent en tant qu’agents vecteurs de maladies virales une contrainte phytosanitaire majeure. Cinq viroses ont été recensés à ce jour. Il s’agit de l’AMV, CMV, PVX, PVY et ToMV. La stratégie de lutte mise en oeuvre est orientée vers la lutte intégrée, basée particulièrement sur les moyens biologiques. En égard à l’importance de l’incidence économique des maladies virales sur la culture de tomate, les services officiels phytosanitaires lui consacrent une attention particulière grâce notamment au programme de dépistage, orienté vers les principales prohibitions.
A note on the false discovery rate and inconsistent comparisons between experiments
Authors: Higdon Roger , van Belle Gerald , Kolker Eugene 
Published: April 2008

AbstractMotivation: The false discovery rate (FDR) has been widely adopted to address the multiple comparisons issue in high-throughput experiments such as microarray gene-expression studies. However, while the FDR is quite useful as an approach to limit false discoveries within a single experiment, like other multiple comparison corrections it may be an inappropriate way to compare results across experiments. This article uses several examples based on gene-expression data to demonstrate the potential misinterpretations that can arise from using FDR to compare across experiments. Researchers should be aware of these pitfalls and wary of using FDR to compare experimental results. FDR should be augmented with other measures such as p-values and expression ratios. It is worth including standard error and variance information for meta-analyses and, if possible, the raw data for re-analyses. This is especially important for high-throughput studies because data are often re-used for different objectives, including comparing common elements across many experiments. No single error rate or data summary may be appropriate for all of the different objectives.Contact: Eugene.Kolker@seattlechildrens.org
Prediction of disordered regions in proteins based on the meta approach
Authors: Ishida Takashi , Kinoshita Kengo 
Published: April 2008

Abstract
Motivation: Intrinsically disordered regions in proteins have no unique stable structures without their partner molecules, thus these regions sometimes prevent high-quality structure determination. Furthermore, proteins with disordered regions are often involved in important biological processes, and the disordered regions are considered to play important roles in molecular interactions. Therefore, identifying disordered regions is important to obtain high-resolution structural information and to understand the functional aspects of these proteins.
Results: We developed a new prediction method for disordered regions in proteins based on the meta approach and implemented a web-server for this prediction method named ‘metaPrDOS’. The method predicts the disorder tendency of each residue using support vector machines from the prediction results of the seven independent predictors. Evaluation of the meta approach was performed using the CASP7 prediction targets to avoid an overestimation due to the inclusion of proteins used in the training set of some component predictors. As a result, the meta approach achieved higher prediction accuracy than all methods participating in CASP7.
Availability: http://prdos.hgc.jp/meta/
Contact: t-ishida@hgc.jp
A global pathway crosstalk network
Authors: Li Yong , Agarwal Pankaj , Rajagopalan Dilip 
Published: April 2008

AbstractMotivation: Given the complex nature of biological systems, pathways often need to function in a coordinated fashion in order to produce appropriate physiological responses to both internal and external stimuli. Therefore, understanding the interaction and crosstalk between pathways is important for understanding the function of both cells and more complex systems.Results: We have developed a computational approach to detect crosstalk among pathways based on protein interactions between the pathway components. We built a global mammalian pathway crosstalk network that includes 580 pathways (covering 4753 genes) with 1815 edges between pathways. This crosstalk network follows a power-law distribution: P(k) ∼ k−γ, γ = 1.45, where P(k) is the number of pathways with k neighbors, thus pathway interactions may exhibit the same scale-free phenomenon that has been documented for protein interaction networks. We further used this network to understand colorectal cancer progression to metastasis based on transcriptomic data.Contact: yong.2.li@gsk.comSupplementary information: Supplementary data are available at Bioinformatics online.
Modelling combined harvest and effort regulations: the case of the Dutch beam trawl fishery for plaice and sole in the North Sea
Authors: Hoff A. , Frost H. 
Published: April 2008

Abstract
Hoff, A. and Frost, H. 2008. Modelling combined harvest and effort regulations: the case of the Dutch beam trawl fishery for plaice and sole in the North Sea. – ICES Journal of Marine Science, 65: 822–831. Currently, several European fishing fleets are regulated through a combination of harvest and effort control. The two regulation schemes are interrelated, i.e. a given quota limit will necessarily determine the effort used, and vice versa. It is important to acknowledge this causality when assessing combined effort and harvest regulation systems. A bioeconomic feedback model is presented that takes into account the causality between effort and harvest control by switching back and forth between the two, depending on which is the binding rule. The model consists of a biological and an economic operation module, the former simulating stock assessment and quota establishment, and the latter simulating the economic fleet dynamics. When harvest control is binding, catch is evaluated using the biological projection formula, whereas the economics-based Cobb–Douglas production function is used when effort is binding. The method is applied to the Dutch beam trawl fishery for plaice and sole in the North Sea.
Side-aspect target-strength measurements of bay anchovy (Anchoa mitchilli) and Gulf menhaden (Brevoortia patronus) derived from ex situ experiments
Authors: Boswell Kevin M. , Wilson Charles A. 
Published: April 2008

Abstract
Boswell, K. M., and Wilson, C. A. 2008. Side-aspect target strength measurements of bay anchovy (Anchoa mitchilli) and Gulf menhaden (Brevoortia patronus) derived from ex situ experiments. – ICES Journal of Marine Science, 65: 1012–1020. Acoustic target strengths (TSs) of bay anchovy [Anchoa mitchilli, 4.7–6.1 cm TL (total length)] and Gulf menhaden (Brevoortia patronus, 5.1–7.7 cm TL) were measured at 420 kHz during side-aspect, ex situ experiments. TS–TL relationships were derived at aspect for tethered individuals, and TS distributions were compared with those of free-swimming fish. Linear models relating TS and TL were fitted to data at two levels of pulse duration (0.1 and 0.4 ms) for both side aspect and all horizontal aspects of each species, and for pooled data from both species. At a pulse duration of 0.4 ms, the side-aspect TS–TL relationships were anchovy: TSlateral = 19.5 log10 TLcm − 62.4; menhaden: TSlateral = 26.1 log10 Lcm − 65.6; pooled: TSlateral = 32 log10 TLcm − 70.9. For all horizontal-aspect orientations (0–180° in the horizontal) the best-fit TS–TL relationships were anchovy: TSall = 20 log10 TLcm− 65.4; menhaden: TSall = 20 log10 TLcm − 64.8; pooled: TSall = 20 log10 TLcm− 65. However, the “fit” for all angles was consistently low. Predicted TS comparisons with side-aspect models presented by earlier authors suggested biases in the estimated TL. Additionally, relationships between TS and wet weight (W) were derived for each species. Variation in TS by pulse-duration level suggests the potential for the use of this factor as a time-dependent variable by which to separate echoes from bay anchovy and Gulf menhaden.
Reduction of Plastid-Localized Carbonic Anhydrase Activity Results in Reduced Arabidopsis Seedling Survivorship
Authors: Ferreira Fernando J. , Guo Cathy , Coleman John R. 
Published: April 2008

Abstract
Carbonic anhydrase (CA; EC 4.2.1.1) catalyzes the interconversion of CO2 and HCO3 − and is a major protein constituent of the C3 higher plant chloroplast where it is presumed to play a role in photosynthetic carbon assimilation. In this study, we have used both RNA antisense and gene knockout lines to specifically reduce the activity of the chloroplast βCA1 polypeptide (At3g01500) in the model plant Arabidopsis (Arabidopsis thaliana). Although able to germinate, seedling establishment of transgenic plants is significantly reduced relative to wild-type plants when grown at ambient levels of CO2. Growth at elevated (1,500 μL L−1) CO2 or on plates supplemented with sucrose restores seedling establishment rates to wild-type levels. Seed from wild-type and transgenic plants exhibited no significant differences in seed protein, lipid content, or reserve mobilization during seedling growth. βCA1-deficient seedlings do, however, exhibit reduced capacity for light-dependent 14CO2 assimilation prior to the development of true leaves. The small number of surviving seedlings able to grow and develop are phenotypically similar to wild-type plants, even when subsequently grown at subambient levels of CO2. Microarray analysis of mature leaves of βCA1-deficient plants shows some differences in transcript abundance, particularly with genes involved in ethylene signaling and response. The data suggest that reduced levels of seedling establishment by βCA1-deficient plants could be the result of poor cotyledon photosynthetic performance at the onset of phototrophic growth and prior to the development of true leaves.
Stable interactions between the transmembrane domains of the adenosine A2Areceptor
Authors: Thévenin Damien , Lazarova Tzvetana 
Published: April 2008

AbstractG‐protein‐coupled receptors (GPCRs) must properly insert and fold in the membrane to adopt a stable native structure and become biologically active. The interactions between transmembrane (TM) helices are believed to play a major role in these processes. Previous studies in our group showed that specific interactions between TM helices occur, leading to an increase in helical content, especially in weakly helical TM domains, suggesting that helix–helix interactions in addition to helix–lipid interactions facilitate helix formation. They also demonstrated that TM peptides interact in a similar fashion in micelles and lipid vesicles, as they exhibit relatively similar thermal stability and α‐helicity inserted in SDS micelles to that observed in liposomes. In this study, we perform an analysis of pairwise interactions between peptides corresponding to the seven TM domains of the human A2Areceptor (A2AR). We used a combination of Förster resonance energy transfer (FRET) measurement and circular dichroism (CD) spectroscopy to detect and analyze these interactions in detergent micelles. We found that strong and specific interactions occur in only seven of the 28 possible peptide pairs. Furthermore, not all interactions, identified by FRET, lead to a change in helicity. Our results identify stabilizing contacts that are likely related to the stability of the receptor and that are consistent with what is known about the three‐dimensional structure and stability of rhodopsin and the β2adrenergic receptor.
Structural effects of Parkinson's disease linked DJ‐1 mutations
Authors: Malgieri Gaetano , Eliezer David 
Published: April 2008

AbstractMutations in the protein DJ‐1 are associated with familial forms of Parkinson's disease, indicating that DJ‐1 may be involved in pathways related to the etiology of this disorder. Here we have used solution state NMR and circular dichroism spectroscopies to evaluate the extent of structural perturbations associated with five different Parkinson's disease linked DJ‐1mutations: L166P, E64D, M26I, A104T, and D149A. Comparison of the data with those obtained for the wild‐type protein shows that the L166P mutation leads to severe and global destabilization and unfolding of the protein structure, while the structure of the E64D mutation, as expected, is nearly unperturbed. Interestingly, the remaining three mutants all show different degrees of structural perturbation, which are accompanied by a reduction in the thermodynamic stability of the protein. The observed structural and thermodynamic differences are likely to underlie any functional variations between these mutants and the wild type, which in turn are likely responsible for the pathogenicity of these mutations.
Human homolog of NOTUM, overexpressed in hepatocellular carcinoma, is regulated transcriptionally by β‐catenin/TCF
Authors: Torisu Yuichi , Watanabe Akira , Nonaka Aya , Midorikawa Yutaka , Makuuchi Masatoshi , Shimamura Takahiro , Sugimura Haruhiko , Niida Atsushi , Akiyama Tetsu , Iwanari Hiroko , Kodama Tatsuhiko , Zeniya Mikio , Aburatani Hiroyuki 
Published: April 2008

The Drosophila Notum gene, which is regulated by the Wingless pathway, encodes a secreted hydrolase that modifies heparan sulfate proteoglycans. In comparative analysis of the gene expression profiles in primary human hepatocellular carcinomas (HCC) and normal organs, we observed that the human ortholog of Drosophila Notum was overexpressed markedly in a subset of HCC, but expressed rarely in adult normal tissues. Immunoblotting confirmed the overexpression of NOTUM protein in 12 of 40 primary HCC cases (30%). High levels of NOTUM protein were significantly associated with intracellular (nuclear or cytoplasmic) accumulation of β‐catenin protein: all 10 HCC with high intracellular β‐catenin also had high NOTUM expression, whereas only 2 of 30 cases (6.7%) without intracellular β‐catenin had high NOTUM expression (P < 0.00001). NOTUM expression in HepG2 cells was downregulated significantly by induction of a dominant‐negative mutant of TCF4, a β‐catenin partner. In vivo binding of the β‐catenin/TCF complex to the NOTUM promoter was demonstrated by chromatin immunoprecipitation in HepG2 and SW480 cells, where canonical Wnt signaling is activated constitutively. These findings provide evidence that NOTUM is a novel target of β‐catenin/TCF4 and is upregulated in Wnt/β‐catenin signaling‐activated HCC. (Cancer Sci 2008; 99: 1139–1146)
HrpN of Erwinia amylovora functions in the translocation of DspA/E into plant cells
Authors: BOCSANCZY ANA M. , NISSINEN RIITTA M. , OH CHANG‐SIK , BEER STEVEN V. 
Published: April 2008

SUMMARYThe type III secretion system (T3SS) is required by plant pathogenic bacteria for the translocation of certain bacterial proteins to the cytoplasm of plant cells or secretion of some proteins to the apoplast. The T3SS of Erwinia amylovora, which causes fire blight of pear, apple and other rosaceous plants, secretes DspA/E, which is an indispensable pathogenicity factor. Several other proteins, including HrpN, a critical virulence factor, are also secreted by the T3SS. Using a CyaA reporter system, we demonstrated that DspA/E is translocated into the cells of Nicotiana tabacum‘Xanthi’. To determine if other T3‐secreted proteins are needed for translocation of DspA/E, we examined its translocation in several mutants of E. amylovora strain Ea321. DspA/E was translocated by both hrpW and hrpK mutants, although with some delay, indicating that these two proteins are dispensable in the translocation of DspA/E. Remarkably, translocation of DspA/E was essentially abolished in both hrpN and hrpJ mutants; however, secretion of DspA/E into medium was not affected in any of the mentioned mutants. In contrast to the more virulent strain Ea273, secretion of HrpN was abolished in a hrpJ mutant of strain Ea321. In addition, HrpN was weakly translocated into plant cytoplasm. These results suggest that HrpN plays a significant role in the translocation of DspA/E, and HrpJ affects the translocation of DspA/E by affecting secretion or stability of HrpN. Taken together, these results explain the critical importance of HrpN and HrpJ to the development of fire blight.
Indirect carrier detection of canine haemophilia A using factor VIII microsatellite markers
Authors: Brooks M. B. , MacNguyen R. , Hall R. , Gupta R. , Booth J. G. 
Published: April 2008

SummaryA panel of factor VIII microsatellite markers was developed for indirect carrier detection of canine haemophilia A (factor VIII deficiency). A total of 78 dogs, representing 14 different breed variants of haemophilia A, were genotyped at six intragenic factor VIII marker loci. The markers spanned approximately 110 kb and were located in the 5′ UTR of the factor VIII (F8) gene and within introns 6, 10, 12, 14 and 21. The observed heterozygosity (n = 39 females) for these markers was 0.675, 0.82, 0.868, 0.692, 0.473 and 0.775 respectively. The affected males of each breed variant had unique marker haplotypes. In addition, the marker haplotypes varied for two unrelated haemophilic Jack Russell terriers, compatible with independent mutation events causing haemophilia in different breeds and different families. A three‐marker panel (markers within introns 6, 10 and 21) was informative for 37 of the 39 females. The haemophilia‐associated haplotype was defined for six breed variants based on the genotypes of an affected male and a clear male sibling, with successful carrier detection of female siblings in each pedigree. Our results demonstrate an apparent allelic heterogeneity in canine haemophilia A; however, an indirect method based on a three‐marker panel is feasible to facilitate carrier detection and genetic counselling.
Role of pore pressure generation in sediment transport within half‐grabens
Authors: You Yao , Person Mark 
Published: April 2008

ABSTRACTSediment transport and overpressure generation are coupled primary through the impact of effective stress on subsidence and compaction. Here, we use mathematical modeling to explore the interactions between groundwater flow and diffusion‐controlled sediment transport within alluvial basins. Because of lateral variation in permeability, proximal basin facies will have pore pressure close to hydrostatic levels while distal fine‐grained facies can reach near lithostatic levels. Lateral variation in pore pressure leads to differential compaction, which deforms basins in several ways. Differential compaction reduces basin size, bends isochron surfaces across the sand–clay interface, restricts basinward progradation of sand facies, and reduces the amplitude of oscillation in the lateral position of the sand–clay interface especially in the deepest part of the section even when temporal sediment supply are held constant. Overpressure generation was found to be sensitive to change in sediment supply in permeable basins (at least 10−17 m2 in our model). We found that during basin evolution, temporal variations in overpressure and sediment supply fluctuations are not necessarily in phase with each other, especially in tight (low permeability) basins (<10−17 m2 in our model).