bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta‐omics
Authors: Urich Tim , Lanzén Anders , Stokke Runar , Pedersen Rolf B. , Bayer Christoph , Thorseth Ingunn H. , Schleper Christa , Steen Ida H. , Øvreas Lise 
Published: October 2013

SummaryDeep‐sea hydrothermal vents are unique environments on Earth, as they host chemosynthetic ecosystems fuelled by geochemical energy with chemolithoautotrophic microorganisms at the basis of the food webs. Whereas discrete high‐temperature venting systems have been studied extensively, the microbiotas associated with low‐temperature diffuse venting are not well understood. We analysed the structure and functioning of microbial communities in two diffuse venting sediments from the Jan Mayen vent fields in the Norwegian‐Greenland Sea, applying an integrated ‘omics’ approach combining metatranscriptomics, metaproteomics and metagenomics. Polymerase chain reaction‐independent three‐domain community profiling showed that the two sediments hosted highly similar communities dominated by Epsilonproteobacteria, Deltaproteobacteria and Gammaproteobacteria, besides ciliates, nematodes and various archaeal taxa. Active metabolic pathways were identified through transcripts and peptides, with genes of sulphur and methane oxidation, and carbon fixation pathways highly expressed, in addition to genes of aerobic and anaerobic (nitrate and sulphate) respiratory chains. High expression of chemotaxis and flagella genes reflected a lifestyle in a dynamic habitat rich in physico‐chemical gradients. The major metabolic pathways could be assigned to distinct taxonomic groups, thus enabling hypotheses about the function of the different prokaryotic and eukaryotic taxa. This study advances our understanding of the functioning of microbial communities in diffuse hydrothermal venting sediments.
A three‐component signalling system fine‐tunes expression kinetics of HPPK responsible for folate synthesis by positive feedback loop during stress response of Xanthomonas campestris
Authors: Wang Fang‐Fang , Deng Chao‐Ying , Cai Zhen , Wang Ting , Wang Li , Wang Xiao‐Zheng , Chen Xiao‐Ying , Fang Rong‐Xiang , Qian Wei 
Published: October 2013

SummaryDuring adaptation to environments, bacteria employ two‐component signal transduction systems, which contain histidine kinases and response regulators, to sense and respond to exogenous and cellular stimuli in an accurate spatio‐temporal manner. Although the protein phosphorylation process between histidine kinase and response regulator has been well documented, the molecular mechanism fine‐tuning phosphorylation levels of response regulators is comparatively less studied. Here we combined genetic and biochemical approaches to reveal that a hybrid histidine kinase, SreS, is involved in the SreK‐SreR phosphotransfer process to control salt stress response in the bacterium Xanthomonas campestris. The N‐terminal receiver domain of SreS acts as a phosphate sink by competing with the response regulator SreR to accept the phosphoryl group from the latter's cognate histidine kinase SreK. This regulatory process is critical for bacterial survival because the dephosphorylated SreR protein participates in activating one of the tandem promoters (P2) at the 5′ end of the sreK‐sreR‐sreS‐hppK operon, and then modulates a transcriptional surge of the stress‐responsive gene hppK, which is required for folic acid synthesis. Therefore, our study dissects the biochemical process of a positive feedback loop in which a ‘three‐component’ signalling system fine‐tunes expression kinetics of downstream genes.
NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite‐oxidizing Nitrospira
Authors: Pester Michael , Maixner Frank , Berry David , Rattei Thomas , Koch Hanna , Lücker Sebastian , Nowka Boris , Richter Andreas , Spieck Eva , Lebedeva Elena , Loy Alexander , Wagner Michael , Daims Holger 
Published: October 2013

SummaryNitrospira are the most widespread and diverse known nitrite‐oxidizing bacteria and key nitrifiers in natural and engineered ecosystems. Nevertheless, their ecophysiology and environmental distribution are understudied because of the recalcitrance of Nitrospira to cultivation and the lack of a molecular functional marker, which would allow the detection of Nitrospira in the environment. Here we introduce nxrB, the gene encoding subunit beta of nitrite oxidoreductase, as a functional and phylogenetic marker for Nitrospira. Phylogenetic trees based on nxrB of Nitrospira were largely congruent to 16S ribosomal RNA‐based phylogenies. By using new nxrB‐selective polymerase chain reaction primers, we obtained almost full‐length nxrB sequences from Nitrospira cultures, two activated sludge samples, and several geographically and climatically distinct soils. Amplicon pyrosequencing of nxrB fragments from 16 soils revealed a previously unrecognized diversity of terrestrial Nitrospira with 1801 detected species‐level operational taxonomic units (OTUs) (using an inferred species threshold of 95% nxrB identity). Richness estimates ranged from 10 to 946 coexisting Nitrospira species per soil. Comparison with an archaeal amoA dataset obtained from the same soils [Environ. Microbiol. 14: 525–539 (2012)] uncovered that ammonia‐oxidizing archaea and Nitrospira communities were highly correlated across the soil samples, possibly indicating shared habitat preferences or specific biological interactions among members of these nitrifier groups.
Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
Authors: Eiler Alexander , Zaremba‐Niedzwiedzka Katarzyna , Martínez‐García Manuel , McMahon Katherine D. , Stepanauskas Ramunas , Andersson Siv G. E. , Bertilsson Stefan 
Published: October 2013

SummaryLittle is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta‐diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic‐ compared with freshwater‐dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.
Songbirds as general transmitters but selective amplifiers of Borrelia burgdorferi sensu lato genotypes in Ixodes rinicus ticks
Authors: Heylen Dieter , Matthysen Erik , Fonville Manoj , Sprong Hein 
Published: October 2013

SummaryWe investigated to what extent a European songbird (Parus major) selectively transmits and amplifies Borrelia burgdorferi s.l. bacteria. Borrelia‐naïve birds were recurrently exposed to Ixodes ricinus nymphs carrying a community of more than 34 5S–23S genotypes belonging to five genospecies (Borrelia garinii, Borrelia valaisiana, Borrelia afzelii, B. burgdorferi s.s. and Borrelia spielmanii). Fed ticks were screened for Borrelia after moulting. We found evidence for co‐feeding transmission of avian and possibly also mammalian genotypes. Throughout the course of infestations, the infection rate of B. garinii and B. valaisiana increased, indicating successful amplification and transmission, while the infection rate for B. afzelii, B. burgdorferi s.s and B. spielmanii tended to decrease. Within the B. garinii and B. valaisiana genotype communities, certain genotypes were transmitted more than others. Moreover, birds were able to host mixed infections of B. garinii and B. valaisiana, as well as mixed infections of genotypes of the same genospecies. We experimentally show that resident songbirds transmit a broad range of Borrelia genotypes, but selectively amplify certain genotypes, and that one bird can transmit simultaneously several genotypes. Our results highlight the need to explicitly consider the association between genotypes and hosts, which may offer opportunities to point out which hosts are most responsible for the Borrelia presence in questing ticks.
Contesting theIndian City: Global Visions and the Politics of the Local
Authors: Shatkin Gavin 
Published: October 2013

AbstractThis symposium brings together three empirical studies and one conceptual overview examining the politics of redevelopment in contemporaryIndian cities. Collectively these articles seek to redress the relative dearth of concerted attention to the institutional, economic and socio‐spatial changes that are shifting the terrain of urban politics in post‐liberalization India.
Use of prescription contraceptive methods in the UK general population: a primary care study
Authors: Cea‐Soriano L , García Rodríguez LA , Machlitt A , Wallander M‐A 
Published: October 2013

ObjectiveTo determine prescription contraceptive use in the UK.DesignObservational study using a primary care database.SettingThe Health Improvement Network (THIN).PopulationWomen in THIN aged 12–49 years in 2008, registered with their primary care doctor for at least 5 years, and with a prescription history of at least 1 year were included.MethodsTHIN was searched using the Read and MULTILEX codes for the following methods: combined oral contraceptives (COCs), progestogen‐only pills (POPs), copper intrauterine devices (Cu‐IUDs), the levonorgestrel‐releasing intrauterine system (LNG‐IUS), progestogen‐only implants, progestogen‐only injections, and contraceptive patches.Main outcome measuresPrevalence, switching, and duration of prescriptions.ResultsA cohort of 194 054 women was identified. The prevalence of contraceptive use was: COCs, 16.2% (95% confidence interval, 95% CI 16.1–16.3%); POPs, 5.6% (95% CI 5.5–5.6%); Cu‐IUD, 4.5% (95% CI 4.4–4.5%); LNG‐IUS, 4.2% (95% CI 4.1–4.2%); progestogen‐only implants, 1.5% (95% CI 1.5–1.6%); progestogen‐only injections, 2.4% (95% CI 2.3–2.4%); and contraceptive patches, 0.1% (95% CI 0.1–0.2%). Within 1 year, 9.8% of new COC users switched to alternative COCs, and 9.0% changed to a different method. Among new COC users who did not switch method, 34.8% did not continue use beyond 3 months, and were no longer using a prescription contraceptive.ConclusionsAmong users of oral contraceptives who did not switch method, over one‐third did not continue use beyond 3 months. This supports current UK guidelines recommending a follow‐up consultation with a healthcare professional 3 months after the first prescription of COCs.
Holding governments accountable? Individual heterogeneity in performance voting
Authors: de Vries Catherine E. , Giger Nathalie 
Published: October 2013

AbstractThis study suggests that performance voting is characterised by extensive individual heterogeneity. Most economic voting studies to date treat voters as rather homogeneous in their reactions to economic performance of incumbents. Yet, a large and well‐established line of research from the American context demonstrates the conditional impact of political sophistication and salience on voters' political attitudes and behaviour. Building on this work, this article explores individual‐level variation in performance voting due to political sophistication and salience. Utilising cross‐national data from the Comparative Study of Electoral Systems (CSES) including 25 democracies, performance voting is examined across an array of policy areas including the economy, social welfare, immigration and national security, and it is shown that political sophistication and salience are key moderators of performance voting. The findings suggest that holding governments to account for past performance is mainly the prerogative of the highly sophisticated and thus may be more laborious than previously assumed. At the same time, the results indicate that the sophistication gap in performance voting narrows when voters attach a higher degree of salience to a policy area. As long as voters care enough about government activities in a particular policy area, incumbents can expect credit or blame for policy outcomes. This should provide at least some impetus for responsive policy making.
Mental Health and High‐Cost Health Care Utilization: New Evidence from Axis II Disorders
Authors: Maclean Johanna Catherine , Xu Haiyong , French Michael T. , Ettner Susan L. 
Published: October 2013

ObjectiveTo analyze the associations between Axis II (A2) disorders and two measures of health care utilization with relatively high cost: emergency department (ED) episodes and hospital admissions.Data Source/Study SettingWave I (2001/2002) and Wave II (2004/2005) of the National Longitudinal Survey on Alcohol and Related Conditions (NESARC).Study DesignA national probability sample of adults. Gender‐stratified regression analysis adjusted for a range of covariates associated with health care utilization.Data CollectionThe target population of the NESARC is the civilian noninstitutionalized population aged 18 years and older residing in the United States. The cumulative survey response rate is 70.2 percent with a response rate of 81 percent (N = 43,093) in Wave I and 86.7 percent (N = 34,653) in Wave II.Principal FindingsBoth men and women with A2 disorders are at elevated risk for ED episodes and hospital admissions. Associations are robust after adjusting for a rich set of confounding factors, including Axis I (clinical) psychiatric disorders. We find evidence of a dose–response relationship, while antisocial and borderline disorders exhibit the strongest associations with both measures of health care utilization.ConclusionsThis study provides the first published estimates of the associations between A2 disorders and high‐cost health care utilization in a large, nationally representative survey. The findings underscore the potential implications of these disorders on health care expenditures.
Characterization of Digital Cameras for Reflected Ultraviolet Photography; Implications for Qualitative and Quantitative Image Analysis During Forensic Examination
Authors: Garcia Jair E. , Wilksch Philip A. , Spring Gale , Philp Peta , Dyer Adrian 
Published: October 2013

AbstractReflected ultraviolet imaging techniques allow for the visualization of evidence normally outside the human visible spectrum. Specialized digital cameras possessing extended sensitivity can be used for recording reflected ultraviolet radiation. Currently, there is a lack of standardized methods for ultraviolet image recording and processing using digital cameras, potentially limiting the implementation and interpretation. A methodology is presented for processing ultraviolet images based on linear responses and the sensitivity of the respective color channels. The methodology is applied to a FujiS3UVIRcamera, and a modified Nikon D70s camera, to reconstruct their respective spectral sensitivity curves between 320 and 400 nm. This method results in images with low noise and high contrast, suitable for qualitative and/or quantitative analysis. The application of this methodology is demonstrated in the recording of latent fingerprints.
Screening Biological Stains with qPCR versus Lateral Flow Immunochromatographic Test Strips: A Quantitative Comparison using Analytical Figures of Merit
Authors: Simson Oechsle Crystal , Haddad Sandra , Sgueglia Joanne B. , Grgicak Catherine M. 
Published: October 2013

AbstractBiological fluid identification is an important facet of evidence examination in forensic laboratories worldwide. While identifying bodily fluids may provide insight into which downstream DNA methods to employ, these screening techniques consume a vital portion of the available evidence, are usually qualitative, and rely on visual interpretation. In contrast, qPCR yields information regarding the amount and proportion of amplifiable genetic material. In this study, dilution series of either semen or male saliva were prepared in either buffer or female blood. The samples were subjected to both lateral flow immunochromatographic test strips and qPCR analysis. Analytical figures of merit—including sensitivity, minimum distinguishable signal (MDS) and limit of detection (LOD)—were calculated and compared between methods. By applying the theory of the propagation of random errors, LODs were determined to be 0.05 μL of saliva for the RSID™ Saliva cards, 0.03 μL of saliva for Quantifiler® Duo, and 0.001 μL of semen for Quantifiler® Duo. In conclusion, quantitative PCR was deemed a viable and effective screening method for subsequent DNA profiling due to its stability in different matrices, sensitivity, and low limits of detection.
Alcohol‐related violence presenting to the emergency department: Is ‘glassing’ the big issue?
Authors: Laing Anthony J , Sendall Marguerite C , Barker Ruth 
Published: October 2013

AbstractObjectiveThe study aims to describe the characteristics of patients presenting to EDs within Queensland, Australia with injuries because of assault with a glass implement (‘glassing’) and to set this within the broader context of presentations because of alcohol‐related violence.MethodsThis is an analysis of prospectively collected ED injury surveillance data collated by the Queensland Injury Surveillance Unit between 1999 and 2011. Cases of injury because of alcohol‐related violence were identified and analysed using coded fields supplemented with qualitative data contained within the injury description text. Descriptive statistics were used to assess the characteristics of injury presentations because of alcohol‐related violence. Violence included interpersonal violence and aggression (verbal aggression and object violence).ResultsA total of 4629 cases were studied. The study population was predominantly men (72%) and aged 18 to 24 (36%), with men in this age group comprising more than a quarter of the study population (28%). Nine per cent of alcohol‐related assault injuries were a consequence of ‘glassing’. The home was the most common location for alcohol‐related violence (31%) and alcohol‐related ‘glassings’ (33%). Overall, the most common glass object involved was a bottle (75%); however, within licensed venues an even mix of a drinking glass (44%) and glass bottle (45%) was identified.ConclusionsContrary to public perception generated by media, ‘glassing’ incidents, particularly at licensed venues, constitute a relatively small proportion of all alcohol‐related violence. The current study highlights the predominance of young men injured following alcohol‐related violence, demonstrating a key focus area within the population for aiming prevention strategies.
Coexisting with Fire? A Commentary on the Scale Politics of Adaptation
Authors: HOWITT RICHARD 
Published: October 2013

AbstractAustralia's experience of bushfire in changing environmental, economic and social circumstances raises the need for learning to live with fire risk more effectively. But just what might it mean to coexist with fire? Rather than addressing the particular risk contexts created on fire grounds during fire events, this brief commentary considers the need to rescale questions of coexistence with fire and to reconsider just what coexistence with and adaptations to fire risk in Australian landscapes might mean.
Dietary patterns of adolescent girls attending schools in low‐income communities highlight low consumption of core foods
Authors: Schumacher Tracy L. , Dewar Deborah L. , Lubans David R. , Morgan Philip J. , Watson Jane , Guest Maya , Burrows Tracy L. , Callister Robin , Collins Clare E. 
Published: October 2013

AbstractAimOverweight and obesity prevalence is high among adolescent girls of low socioeconomic position and this increases their risk of cardiovascular disease and metabolic disorders in adulthood. The aim of this present study was to describe the dietary patterns of adolescent girls in terms of the relative contribution of core food groups to overall diet and by weight status category.MethodsYear 8 female students were recruited from schools in low‐income communities. Weight status (i.e. underweight, healthy weight, overweight, obese) was determined using age‐ and sex‐adjusted body mass index (BMI; z score). Dietary intakes were assessed using a validated semi‐quantitative food frequency questionnaire. Individual foods were collated into core food group or energy‐dense, nutrient‐poor categories in line with the Australian Guide to Healthy Eating (AGHE) and the percentage contribution to total energy intake calculated.ResultsParticipants (n = 332) were (mean ± SD) 13.7 ± 0.4 years old with BMI z score 0.63 ± 1.22. Few girls met AGHE core food group recommendations for daily serves; meat and substitutes 69.3%, vegetables 28.6%, fruit 23.8%, dairy 15.7% and breads/cereals 5.7%. Total percentage energy derived from energy‐dense, nutrient‐poor foods was 46.6% (37.2–54.6%) (median (interquartile range)), with takeaways 9.8% (7.0–13.6%), confectionery 7.0% (4.1–10.9%) and packaged snacks 6.8% (4.0–10.7%), with no significant differences by weight status.ConclusionsCore food intakes are poor with excessive consumption of energy‐dense, nutrient‐poor foods in these adolescent girls. Nutrition education programs targeting this population are needed to address this imbalance. Strategies could include substitution of unhealthy snacks for core food items and greater inclusion of core foods within main meals.
Sequentially aerated membrane biofilm reactors for autotrophic nitrogen removal: microbial community composition and dynamics
Authors: Pellicer‐Nàcher Carles , Franck Stéphanie , Gülay Arda , Ruscalleda Maël , Terada Akihiko , Al‐Soud Waleed Abu , Hansen Martin Asser , Sørensen Søren J. , Smets Barth F. 
Published: October 2013

SummaryMembrane‐aerated biofilm reactors performing autotrophic nitrogen removal can be successfully applied to treat concentrated nitrogen streams. However, their process performance is seriously hampered by the growth of nitrite oxidizing bacteria (NOB). In this work we document how sequential aeration can bring the rapid and long‐term suppression of NOB and the onset of the activity of anaerobic ammonium oxidizing bacteria (AnAOB). Real‐time quantitative polymerase chain reaction analyses confirmed that such shift in performance was mirrored by a change in population densities, with a very drastic reduction of the NOB Nitrospira and Nitrobacter and a 10‐fold increase in AnAOB numbers. The study of biofilm sections with relevant 16S rRNA fluorescent probes revealed strongly stratified biofilm structures fostering aerobic ammonium oxidizing bacteria (AOB) in biofilm areas close to the membrane surface (rich in oxygen) and AnAOB in regions neighbouring the liquid phase. Both communities were separated by a transition region potentially populated by denitrifying heterotrophic bacteria. AOB and AnAOB bacterial groups were more abundant and diverse than NOB, and dominated by the r‐strategists Nitrosomonas europaea and Ca. Brocadia anammoxidans, respectively. Taken together, the present work presents tools to better engineer, monitor and control the microbial communities that support robust, sustainable and efficient nitrogen removal.