bluuebunny/crossref_metadata_2025_split huggingface dataset:
High diversity of ammonia‐oxidizing archaea in permanent and seasonal oxygen‐deficient waters of the eastern South Pacific
Authors: Molina Verónica , Belmar Lucy , Ulloa Osvaldo 
Published: April 2010

SummaryThe community structure of putative aerobic ammonia‐oxidizing archaea (AOA) was explored in two oxygen‐deficient ecosystems of the eastern South Pacific: the oxygen minimum zone off Peru and northern Chile (11°S–20°S), where permanent suboxic and low‐ammonium conditions are found at intermediate depths, and the continental shelf off central Chile (36°S), where seasonal oxygen‐deficient and relatively high‐ammonium conditions develop in the water column, particularly during the upwelling season. The AOA community composition based on the ammonia monooxygenase subunit A (amoA) genes changed according to the oxygen concentration in the water column and the ecosystem studied, showing a higher diversity in the seasonal low‐oxygen waters. The majority of the archaeal amoA genotypes was affiliated to the uncultured clusters A (64%) and B (35%), with Cluster A AOA being mainly associated with higher oxygen and ammonium concentrations and Cluster B AOA with permanent oxygen‐ and ammonium‐poor waters. Q‐PCR assays revealed that AOA are an abundant community (up to 105amoA copies ml−1), while bacterial amoA genes from β proteobacteria were undetected. Our results thus suggest that a diverse uncultured AOA community, for which, therefore, we do not have any physiological information, to date, is an important component of the nitrifying community in oxygen‐deficient marine ecosystems, and particularly in rich coastal upwelling ones.
Polyamines are required for the expression of key Hms proteins important for Yersinia pestis biofilm formation
Authors: Wortham Brian W. , Oliveira Marcos A. , Fetherston Jacqueline D. , Perry Robert D. 
Published: April 2010

SummaryWe previously showed that mutations in the genes encoding the two main biosynthetic enzymes responsible for polyamine production, arginine decarboxylase (SpeA) and ornithine decarboxylase (SpeC) cause a loss of biofilm formation in Yersinia pestis. In Y. pestis the development of a biofilm is dependent on 6 Hms (hemin storage) proteins (HmsH, F, R, S, T and P) grouped into 3 operons; hmsHFRS, hmsT and hmsP. In this article we show that polyamines are necessary to maintain the levels of key Hms proteins. In the absence of polyamines there is an ∼93%, ∼43% and ∼90% reduction in protein levels of HmsR, HmsS and HmsT respectively. Overexpression of hmsR and hmsT from plasmids alone can restore biofilm formation to a SpeA‐SpeC‐ mutant. Addition of exogenous putrescine also restores normal levels of HmsR, HmsS, HmsT and biofilm production. Analyses using transcriptional reporters and quantitative RT‐PCR indicate that the initiation of transcription and mRNA stability are not reduced by polyamine deficiency. Instead, translational reporters indicate that polyamines function at least in part by modulating the translation of HmsR and HmsT. Although construction of a consensus Shine–Dalgarno sequence upstream of hmsT modestly reduced the stimulation of translation by putrescine, additional mechanisms likely contribute to the polyamine‐dependent expression of HmsT. Finally, we have shown that polyamines play a role in bubonic plague.
Cultivation‐independent characterization of ‘Candidatus Magnetobacterium bavaricum’ via ultrastructural, geochemical, ecological and metagenomic methods
Authors: Jogler C. , Niebler M. , Lin W. , Kube M. , Wanner G. , Kolinko S. , Stief P. , Beck A. J. , de Beer D. , Petersen N. , Pan Y. , Amann R. , Reinhardt R. , Schüler D. 
Published: April 2010

Summary‘Candidatus Magnetobacterium bavaricum’ is unusual among magnetotactic bacteria (MTB) in terms of cell size (8–10 µm long, 1.5–2 µm in diameter), cell architecture, magnetotactic behaviour and its distinct phylogenetic position in the deep‐branching Nitrospira phylum. In the present study, improved magnetic enrichment techniques permitted high‐resolution scanning electron microscopy and energy dispersive X‐ray analysis, which revealed the intracellular organization of the magnetosome chains. Sulfur globule accumulation in the cytoplasm point towards a sulfur‐oxidizing metabolism of ‘Candidatus M. bavaricum’. Detailed analysis of ‘Candidatus M. bavaricum’ microhabitats revealed more complex distribution patterns than previously reported, with cells predominantly found in low oxygen concentration. No correlation to other geochemical parameters could be observed. In addition, the analysis of a metagenomic fosmid library revealed a 34 kb genomic fragment, which contains 33 genes, among them the complete rRNA gene operon of ‘Candidatus M. bavaricum’ as well as a gene encoding a putative type IV RubisCO large subunit.
Aggregate formation in a freshwater bacterial strain induced by growth state and conspecific chemical cues
Authors: Blom Judith F. , Horňák Karel , Šimek Karel , Pernthaler Jakob 
Published: April 2010

SummaryWe investigated the induction of aggregate formation in the freshwater bacterium Sphingobium sp. strain Z007 by growth state and protistan grazing. Dialysis bag batch culture experiments were conducted in which these bacteria were grown spatially separated from bacteria or from co‐cultures of bacteria and predators. In pure cultures of Sphingobium sp. strain Z007, the concentrations of single cells and aggregates inside and outside the dialysis membranes developed in a similar manner over 3 days of incubation, and the proportions of aggregates were highest during the exponential growth phase. Cell production of Sphingobium sp. strain Z007 was enhanced in the presence of another isolate, Limnohabitans planktonicus, from an abundant freshwater lineage (R‐BT065) outside the bags, and even more so if that strain was additionally grazed upon by the bacterivorous flagellate Poterioochromonas sp. However, the ratios of single cells to aggregates of Sphingobium sp. strain Z007 were not affected in either case. By contrast, the feeding of flagellates on Sphingobium sp. strain Z007 outside the dialysis bags led to significantly higher proportions of aggregates inside the bags. This was not paralleled by an increase in growth rates, and all cultures were in a comparable growth state at the end of the experiment. We conclude that two mechanisms, growth state and the possible release of infochemicals by the predator, may induce aggregate formation of Sphingobium sp. strain Z007. Moreover, these infochemicals only appeared to be generated by predation on cells from the same species.
Contrast‐enhanced ultrasound vs multidetector‐computed tomography for detecting liver metastases in colorectal cancer: a prospective, blinded, patient‐by‐patient analysis
Authors: Rafaelsen S. R. , Jakobsen A. 
Published: April 2010

AbstractAim  This study compared the sensitivity and specificity of contrast‐enhanced ultrasound (CEUS) and multidetector‐computed tomography (MDCT) in the detection of liver metastases in patients with colorectal cancer.Method  Between September 2004 and December 2008, 271 consecutive patients (146 men and 125 women; median age 68 years, range: 34–91 years) with primary colorectal cancer were evaluated. All underwent combined liver ultrasound and CEUS following intravenous injection of 2.4 ml of SonoVueTM. The interval from injection to arrival time in the hepatic vein (ATHV) was noted. Contrast‐enhanced MDCT in the portal phase was performed and interpreted blindly. In all patients, intra‐operative ultrasound was used as the reference point. In addition, magnetic resonance imaging (MRI) or biopsy was performed on all suspicious lesions or if there was inconsistency in the results.Results  Liver metastases were detected in 21 (8%) patients. Both CEUS and MDCT had a sensitivity of 85.7%, with respective specificities of 97.6% and 95.6%, and positive predictive values of 75%vs 62%. The negative predictive value of both methods was 99%. In patients with and without liver metastases, ATHV was 18 and 22 s, respectively (P < 0.05).Conclusion  CEUS has potential as a diagnostic alternative to MDCT in the detection of liver metastases. ATHV was shorter in patients with liver metastases.
Vildagliptin add‐on to metformin produces similar efficacy and reduced hypoglycaemic risk compared with glimepiride, with no weight gain: results from a 2‐year study
Authors: Matthews D. R. , Dejager S. , Ahren B. , Fonseca V. , Ferrannini E. , Couturier A. , Foley J. E. , Zinman B. 
Published: April 2010

Aim: To show that vildagliptin added to metformin is non‐inferior to glimepiride in reducing HbA1c levels from baseline over 2 years. Methods: A randomized, double‐blind, active‐comparator study of patients with type 2 diabetes mellitus inadequately controlled (HbA1c 6.5–8.5%) by metformin monotherapy. Patients received vildagliptin (50 mg twice daily) or glimepiride (up to 6 mg/day) added to metformin. Results: In all, 3118 patients were randomized (vildagliptin, n = 1562; glimepiride, n = 1556). From similar baseline values (7.3%), after 2 years adjusted mean (s.e.) change in HbA1c was comparable between vildagliptin and glimepiride treatment: −0.1% (0.0%) and −0.1% (0.0%), respectively. The primary objective of non‐inferiority was met. A similar proportion of patients reached HbA1c <7% (36.9 and 38.3%, respectively), but with vildagliptin more patients reached this target without hypoglycaemia (36.0% vs. 28.8%; p = 0.004). The initial response (IR) was sustained for a mean (s.d.) of 309 (244) days with vildagliptin versus 270 (223) days for glimepiride (p < 0.001) (IR = nadir HbA1c where change from baseline ≥0.5% or HbA1c ≤6.5% within the first six months of treatment. After IR was detected, sustained response = time between nadir and an increase of >0.3% above IR). Independent of disease duration, age was a predictor of effect sustainability. Fewer patients experienced hypoglycaemia with vildagliptin (2.3% vs. 18.2% with glimepiride) with a 14‐fold difference in the number of hypoglycaemic events (59 vs. 838). Vildagliptin had a beneficial effect on body weight [mean (s.e.) change from baseline −0.3 (0.1) kg; between‐group difference −1.5 kg; p < 0.001]. Overall, both treatments were well tolerated and displayed similar safety profiles. Conclusions: Vildagliptin add‐on has similar efficacy to glimepiride after 2 years' treatment, with markedly reduced hypoglycaemia risk and no weight gain.
Application of Visual Analytics for Thermal State Management in Large Data Centres
Authors: Hao M. C. , Sharma R. K. , Keim D. A. , Dayal U. , Patel C. , Vennelakanti R. 
Published: April 2010

AbstractToday's large data centres are the computational hubs of the next generation of IT services. With the advent of dynamic smart cooling and rack level sensing, the need for visual data exploration is growing. If administrators know the rack level thermal state changes and catch problems in real time, energy consumption can be greatly reduced. In this paper, we apply a cell‐based spatio‐temporal overall view with high‐resolution time series to simultaneously analyze complex thermal state changes over time across hundreds of racks. We employ cell‐based visualization techniques for trouble shooting and abnormal state detection. These techniques are based on the detection of sensor temperature relations and events to help identify the root causes of problems. In order to optimize the data centre cooling system performance, we derive new non‐overlapped scatter plots to visualize the correlations between the temperatures and chiller utilization. All these techniques have been used successfully to monitor various time‐critical thermal states in real‐world large‐scale production data centres and to derive cooling policies. We are starting to embed these visualization techniques into a handheld device to add mobile monitoring capability.
Changing patterns in HIV‐1 non‐B clade prevalence and diversity in Italy over three decades*
Authors: Lai A , Riva C , Marconi A , Balestrieri M , Razzolini F , Meini G , Vicenti I , Rosi A , Saladini F , Caramma I , Franzetti M , Rossini V , Galli A , Galli M , Violin M , Zazzi M , Balotta C 
Published: April 2010

BackgroundHIV‐1 non‐B subtypes have recently entered Western Europe following immigration from other regions. The distribution of non‐B clades and their association with demographic factors, over the entire course of the HIV‐1 epidemic, have not been fully investigated in Italy.MethodsWe carried out a phylogenetic analysis of HIV‐1 pol sequences derived from 3670 patients followed at 50 Italian clinical centres over nearly three decades.ResultsOverall, 417 patients (11.4%) carried non‐B subtypes. The prevalence of non‐B strains increased from 2.6% in 1980–1992 to 18.9% in 1993–2008 (P<0.0001) in a subset of 2479 subjects with a known year of diagnosis. A multivariate analysis on a subset of 1364 patients for whom relevant demographic data were available indicated that African ethnicity, heterosexual route of infection and year of diagnosis were independently associated with non‐B HIV‐1 infection (P≤0.0001). All pure subtypes, except for clade K, and seven circulating recombinant forms were detected, accounting for 56.6 and 34.1% of the non‐B infections, respectively. The F1 subtype was the most prevalent non‐B clade among Europeans and was acquired heterosexually in half of this patient population. Unique recombinant forms accounted for 9.4% of the non‐B sequences and showed a B/F1 recombination pattern in one‐third of cases.ConclusionsThe circulation of non‐B clades has significantly increased in Italy in association with demographic changes. Spread of the F1 subtype and B/F recombinants appears to predominate, which may result in a redistribution of the relative proportions of the different strains, and this could lead to overlapping epidemics. Thus, the HIV‐1 landscape in Italy may in future be distinct from that of the rest of Europe.
The Experiences of Parents During Diagnosis and Forward Planning for Children with Autism Spectrum Disorder
Authors: Keenan Mickey , Dillenburger Karola , Doherty Alvin , Byrne Tony , Gallagher Stephen 
Published: April 2010

Background  For families of children diagnosed with autism spectrum disorder (ASD) getting a diagnosis is a traumatic experience on which future care and education plans for the child depend. In this paper parental experiences of diagnosis and forward planning for children with ASD are reported.Method  This paper is part of a large cross‐sectional study conducted in Northern Ireland and the Republic of Ireland that assessed the needs and experiences of parents of children diagnosed with ASD. Questionnaires were designed and completed by 95 parents, reporting on 100 children, as well as 67 multi‐disciplinary professionals.Results  Findings confirm that diagnostic and planning processes are extremely stressful for parents, that statutory diagnosis takes a long time, that care and education plans do not include full parental participation, and that reviews of plans do not consistently include intervention data.Conclusion  Policy and practice implications of these findings are important for future revisions of diagnostic tools and manuals.
Thermodynamic model for mineral solubility in aqueous fluids: theory, calibration and application to model fluid‐flow systems
Authors: DOLEJŠ D. , MANNING C. E. 
Published: April 2010

Geofluids(2010)10, 20–40AbstractWe present a thermodynamic model for mineral dissolution in aqueous fluids at elevated temperatures and pressures, based on intrinsic thermal properties and variations of volumetric properties of the aqueous solvent. The standard thermodynamic properties of mineral dissolution into aqueous fluid consist of two contributions: one from the energy of transformation from the solid to the hydrated‐species state and the other from the compression of solvent molecules during the formation of a hydration shell. The latter contribution has the dimension of the generalized Krichevskii parameter. This approach describes the energetics of solvation more accurately than does the Born electrostatic theory and can be extended beyond the limits of experimental measurements of the dielectric constant of H2O. The new model has been calibrated by experimental solubilities of quartz, corundum, rutile, calcite, apatite, fluorite and portlandite in pure H2O at temperatures up to 1100°C and pressures up to 20 kbar. All minerals show a steady increase in solubility along constant geothermal gradients or water isochores. By contrast, isobaric solubilities initially increase with rising temperature but then decline above 200–400°C. This retrograde behavior is caused by variations in the isobaric expansivity of the aqueous solvent, which approaches infinity at its critical point. Oxide minerals predominantly dissolve to neutral species; so, their dissolution energetics involve a relatively small contribution from the solvent volumetric properties and their retrograde solubilities are restricted to a relatively narrow window of temperature and pressure near the critical point of water. By contrast, Ca‐bearing minerals dissolve to a variety of charged species; so, the energetics of their dissolution reactions involve a comparatively large contribution from volume changes of the aqueous solvent and their isobaric retrograde solubility spans nearly all metamorphic and magmatic conditions. These features correlate with and can be predicted from the standard partial molar volumes of aqueous species.The thermodynamic model can be used over much wider range of settings for terrestrial fluid–rock interaction than has previously been possible. To illustrate, it is integrated with transport theory to show quantitatively that integrated fluid fluxes characteristic of crustal shear zones are capable of precipitating quartz or calcite veins from low‐ and medium‐grade metamorphic conditions, at a geothermal gradient of 20°C km−1. For subduction zones, modeled by a geotherm of 7°C km−1, the required fluid fluxes are one to two orders of magnitude lower and predict enhanced efficiency of mass transfer and metasomatic precipitation in comparison with orogenic settings. The new model thus can be applied to shallow hydrothermal, metamorphic, magmatic and subduction fluids, and for retrieval of dependent thermodynamic properties for mass transfer or geodynamic modeling.
Fluid flows and metal deposition near basement /cover unconformity: lessons and analogies from Pb–Zn–F–Ba systems for the understanding of Proterozoic U deposits
Authors: BOIRON M.‐C. , CATHELINEAU M. , RICHARD A. 
Published: April 2010

Geofluids (2010) 10, 270–292AbstractFluid circulation at basement/cover unconformities is of first importance for metal transfer and especially the formation of Pb–Zn, F, Ba and U‐deposits. This is typically the case for world‐class Proterozoic U deposits (Canada, Australia, Gabon) in basins, which show many similarities with younger Pb–Zn–F–Ba systems (Irish Paleozoic Pb–Zn deposits, F–Pb–Zn–Ba deposits related to extensional tectonics from Spain, western France and Silesia and fluid movements related to continental rifting in the Rhine graben). As fluid mixing near the basement/cover unconformity is one of the key factors for ore formation, a series of parameters have been considered for both systems: the time gap between basin formation and metal deposit, the origin and nature of the ore fluids, the temperature of fluid end members and the style of migration. Results show great similarities in all fluid systems: (i) a wide range of fluid salinity indicating the lack of homogeneity of fluid chemistry at the scale of the reservoirs, (ii) the deep penetration of brines through faults and dense networks of microfractures within the basement below the unconformity, (iii) local fluid–rock interaction leading to porosity increase and significant fluid changes in fluid chemistry, (iv) a pulsatory fluid regime during fluid trapping, (v) anisothermal fluid mixing revealed by a systematic temperature gap between brines and recharge fluids, (vi) stages of fluid movements facilitated by discontinuous opening related to later tectonic/telogenetic stages linked to major geodynamic events, typically without related sedimentation and burial (exception in a few cases characterized by the synchronous production and penetration of surface brines and ore genesis). By analogy with younger systems, the conditions of burial and penetration of brines in the Archean basement suggest that thermal convection drove the brine movements, and was possibly linked to extensional tectonics in a part of the giant mid‐Proterozoic U‐deposits.
Improved survival in pregnancy and pulmonary hypertension using a multiprofessional approach
Authors: Kiely DG , Condliffe R , Webster V , Mills GH , Wrench I , Gandhi SV , Selby K , Armstrong IJ , Martin L , Howarth ES , Bu’Lock FA , Stewart P , Elliot CA 
Published: April 2010

Please cite this paper as: Kiely D, Condliffe R, Webster V, Mills G, Wrench I, Gandhi S, Selby K, Armstrong I, Martin L, Howarth E, Bu’Lock F, Stewart P, Elliot C. Improved survival in pregnancy and pulmonary hypertension using a multiprofessional approach. BJOG 2010;117:565–574.Objective  Pregnancy in women with pulmonary hypertension (PH) is reported to carry a maternal mortality rate of 30–56%. We report our experience of the management of pregnancies using a strategy of early introduction of targeted pulmonary vascular therapy and early planned delivery under regional anaesthesia.Design  Retrospective observational study.Setting  Specialist quaternary referral pulmonary vascular unit.Population  Nine women with PH who chose to proceed with ten pregnancies.Methods  A retrospective review of the management of all women who chose to continue with their pregnancy in our unit during 2002–2009.Main outcome measures  Maternal and fetal survival.Results  All women commenced nebulised targeted therapy at 8–34 weeks of gestation. Four women required additional treatment or conversion to intravenous prostanoid therapy. All women were delivered between 26 and 37 weeks of gestation. Delivery was by planned caesarean section in nine cases. All women received regional anaesthesia and were monitored during the peripartum period in a critical care setting. There was no maternal mortality during pregnancy and all infants were free from congenital abnormalities. One woman died 4 weeks after delivery following patient‐initiated discontinuation of therapy. All remaining women and infants were alive after a median of 3.2 years (range, 0.8–6.5 years) of follow‐up.Conclusion  Although the risk of mortality in pregnant women with PH remains significant, we describe improved outcomes in fully counselled women who chose to continue with pregnancy and were managed with a tailored multiprofessional approach involving early introduction of targeted therapy, early planned delivery and regional anaesthetic techniques.