bluuebunny/crossref_metadata_2025_split huggingface dataset:
The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea
Authors: Wagner-Döbler Irene , Ballhausen Britta , Berger Martine , Brinkhoff Thorsten , Buchholz Ina , Bunk Boyke , Cypionka Heribert , Daniel Rolf , Drepper Thomas , Gerdts Gunnar , Hahnke Sarah , Han Cliff , Jahn Dieter , Kalhoefer Daniela , Kiss Hajnalka , Klenk Hans-Peter , Kyrpides Nikos , Liebl Wolfgang , Liesegang Heiko , Meincke Linda , Pati Amrita , Petersen Jörn , Piekarski Tanja , Pommerenke Claudia , Pradella Silke , Pukall Rüdiger , Rabus Ralf , Stackebrandt Erko , Thole Sebastian , Thompson Linda , Tielen Petra , Tomasch Jürgen , von Jan Mathias , Wanphrut Nittaya , Wichels Antje , Zech Hajo , Simon Meinhard 
Published: September 2009

Abstract
Dinoroseobacter shibae DFL12T, a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12T is able to synthesize the vitamins B1 and B12 for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B12 are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B12 was confirmed to be functional, and D. shibae DFL12T was shown to provide the growth-limiting vitamins B1 and B12 to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12T is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12T has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12T shows the most complex viral defense system of all Rhodobacterales sequenced to date.
Horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium Microcoleus chthonoplastes
Authors: Bolhuis Henk , Severin Ina , Confurius-Guns Veronique , Wollenzien Ute I A , Stal Lucas J 
Published: September 2009

Abstract
The filamentous, non-heterocystous cyanobacterium Microcoleus chthonoplastes is a cosmopolitan organism, known to build microbial mats in a variety of different environments. Although most of these cyanobacterial mats are known for their capacity to fix dinitrogen, M. chthonoplastes has not been assigned as a diazotrophic organism. None of the strains that were correctly identified as M. chthonoplastes has been shown to fix dinitrogen and it has repeatedly been reported that these organisms lacked the cyanobacterial nifH, the structural gene for dinitrogenase reductase. In this study, we show that a complete nif-gene cluster is present in the genome of M. chthonoplastes PCC 7420 and that the three structural nitrogenase genes, nifHDK, are present in a collection of axenic strains of M. chthonoplastes from distant locations. Phylogenetic analysis of nifHDK revealed that they cluster with the Deltaproteobacteria and that they are closely related to Desulfovibrio. The nif operon is flanked by typical cyanobacterial genes, suggesting that it is an integral part of the M. chthonoplastes genome. In this study, we provide evidence that the nif operon of M. chthonoplastes is acquired through horizontal gene transfer. Moreover, the presence of the same nif-cluster in M. chthonoplastes isolates derived from various sites around the world suggests that this horizontal gene transfer event must have occurred early in the evolution of M. chthonoplastes. We have been unable to express nitrogenase in cultures of M. chthonoplastes, but we show that these genes were expressed under natural conditions in the field.
A large-conductance calcium-activated potassium channel in potato (Solanum tuberosum) tuber mitochondria
Authors: Koszela-Piotrowska Izabela , Matkovic Karolina , Szewczyk Adam , Jarmuszkiewicz Wieslawa 
Published: September 2009

In the present study, we describe the existence of a novel potassium channel in the plant [potato (Solanum tuberosum) tuber] mitochondrial inner membrane. We found that substances known to modulate large-conductance calcium-activated potassium channel activity influenced the bioenergetics of potato tuber mitochondria. In isolated mitochondria, Ca2+ and NS1619 {1,3-dihydro-1-[2-hydroxy-5-(trifluoromethyl)phenyl]-5-(trifluoromethyl)-2H-ben-zimidazole-2-one; a potassium channel opener} were found to depolarize the mitochondrial membrane potential and to stimulate resting respiration. These effects were blocked by iberiotoxin (a potassium channel inhibitor) in a potassium-dependent manner. Additionally, the electrophysiological properties of the large-conductance potassium channel present in the potato tuber inner mitochondrial membrane are described in a reconstituted system, using planar lipid bilayers. After incorporation in 50/450 mM KCl gradient solutions, we recorded large-conductance potassium channel activity with conductance from 502±15 to 615±12 pS. The probability of channel opening was increased by Ca2+ and reduced by iberiotoxin. Immunological analysis with antibodies raised against the mammalian plasma-membrane large-conductance Ca2+-dependent K+ channel identified a pore-forming α subunit and an auxiliary β2 subunit of the channel in potato tuber mitochondrial inner membrane. These results suggest that a large-conductance calcium-activated potassium channel similar to that of mammalian mitochondria is present in potato tuber mitochondria.
Statins have beneficial effects on platelet free radical activity and intracellular distribution of GTPases in hyperlipidaemia
Authors: Hamilton Paul K. , Hughes Sinead M.T. , Plumb Richard D. , Devine Adrian , Leahey William , Lyons Kristopher S. , Johnston Dennis , McVeigh Gary E. 
Published: September 2009

In addition to lowering cholesterol, statins may alter endothelial release of the vasodilator NO and harmful superoxide free radicals. Statins also reduce cholesterol intermediates including isoprenoids. These are important for post-translational modification of substances including the GTPases Rho and Rac. By altering the membrane association of these molecules, statins affect intracellular positioning and hence activity of a multitude of substances. These include eNOS (endothelial NO synthase), which produces NO (inhibited by Rho), and NADPH oxidase, which produces superoxide (dependent on Rac). Statins may improve endothelial function by enhancing production of NO while decreasing superoxide production. A total of 40 hypercholesterolaemic patients were randomized to treatment with either atorvastatin or placebo; 20 normolipidaemic patients were also studied. Platelet nitrite, NO and superoxide were examined as was the cellular distribution of the GTPases Rho and Rac at baseline and after 8 weeks of treatment. Following atorvastatin therapy, platelet NO was increased (3.2 pmol/108 platelets) and superoxide output was attenuated [−3.4 pmol·min−1·(108 platelets)−1] when compared with placebo. The detection of both Rho and Rac was significantly reduced in the membranes of platelets, implying reduced activity. In conclusion, the results of the present study show altered NO/superoxide production following statin therapy. A potential mechanism for this is the change in the distribution of intracellular GTPases, which was considered to be secondary to decreases in isoprenoid intermediates, suggesting that the activity of the former had been affected by atorvastatin.
Assessing enquiry‐based learning: developing objective criteria from personal knowledge
Authors: Small Tim 
Published: September 2009

What gives personal knowledge its objectivity, Polanyi maintains, is the free and responsible submission to the claims laid upon the inquirer by the truth he is seeking to discover. (Fitzpatrick 1982, 185)
This article takes as its starting point the idea that policies of ‘personalising learning’ and promoting ‘creativity’ raise issues for assessment which the present framework for assessment and testing in schools in England and Wales does little to address. It explores the notion, also touched on elsewhere in this issue, of a dichotomy that needs resolving between subjective (or ‘personal’) and objective (or ‘public’) concerns in the assessment of learning. Drawing on previous research using Rosenblatt's transactional theory of response to literature, the article proposes a resolution based on the unifying concepts of a continuum between two poles and movement of the selective attention between them. Tracing this movement offers a ‘vantage point’ from which the ‘hidden’ or ‘inner’ values of a creative process can be glimpsed, which is likened to the dynamic self‐assessment of learning power. Relating closely to Polanyi's philosophy of personal or ‘tacit’ knowledge, the article argues that enquiry‐based learning is essentially as creative an activity as composing or responding aesthetically to poetry. After constructing five principles from theoretical observations on the evaluation of creativity, the article goes on to develop a set of criteria and objectives, related to the values already discussed, which are offered as a framework to support self‐assessment and joint assessment of enquiry‐based learning.
Epidemiology of Methicillin-Resistant Staphylococcus aureus in a University Medical Center Day Care Facility
Authors: Hewlett Angela L. , Falk Pamela S. , Hughes Katrina S. , Mayhall C. Glen 
Published: September 2009

Objective.Few data are available on methicillin-resistant Staphylococcus aureus (MRSA) colonization in day care. We performed a study in a medical university child care center to study the epidemiology of MRSA in this population.Design.Survey.Setting.A child care center on the campus of a university medical center.Methods.One hundred four children who attended the child care center and 32 employees gave samples that were cultured for MRSA. Seventeen household members of the children and employee found to be colonized with MRSA also gave samples that were cultured. Parents and employees completed questionnaires about demographic characteristics, medical conditions and treatments, and possible exposure risks outside the child care center. In addition, 195 environmental samples were taken from sites at the childcare center. Isolates were analyzed for relatedness by use of molecular typing, and statistical analysis was performed.Results.The prevalence of MRSA in the children was 6.7%. One employee (3.1%) was colonized with MRSA. Cultures of samples given by 6 of 17 (35.3%) family members of these children and the employee yielded MRSA. MRSA was recovered from 4 of 195 environmental samples. Molecular typing revealed that many of the MRSA isolates were indistinguishable, and 18 of the 21 isolates were community-associated MRSA. Multivariable analysis revealed that receipt of macrolide antibiotics (P = .002; odds ratio, 39.6 [95% confidence interval, 3.4—651.4]) and receipt of asthma medications (P = .024; odds ratio, 26.9 [95% confidence interval, 1.5-500.7]) were related to MRSA colonization.Conclusions.There was a low prevalence of MRSA colonization in children and employees in the child care center but a higher prevalence of colonization in their families. Molecular typing showed that transmission of MRSA likely occurred in the child care center. The use of macrolide antibiotics and asthma medications may increase the risk of MRSA colonization in this population.
Effectiveness of Oral Rinse with Chlorhexidine in Preventing Nosocomial Respiratory Tract Infections among Intensive Care Unit Patients
Authors: Bellissimo-Rodrigues Fernando , Bellissimo-Rodrigues Wanessa Teixeira , Viana Jaciara Machado , Teixeira Gil Cezar Alkmim , Nicolini Edson , Auxiliadora-Martins Maria , Passos Afonso Dinis Costa , Martinez Edson Zangiacomi , Basile-Filho Anibal , Martinez Roberto 
Published: September 2009

Objective.To evaluate the effectiveness of the oral application of a 0.12% solution of Chlorhexidine for prevention of respiratory tract infections among intensive care unit (ICU) patients.Design.The study design was a double-blind, randomized, placebo-controlled trial.Setting.The study was performed in an ICU in a tertiary care hospital at a public university.Patients.Study participants comprised 194 patients admitted to the ICU with a prospective length of stay greater than 48 hours, randomized into 2 groups: those who received Chlorhexidine (n = 98) and those who received a placebo (n = 96).Intervention.Oral rinses with Chlorhexidine or a placebo were performed 3 times a day throughout the duration of the patient's stay in the ICU. Clinical data were collected prospectively.Results.Both groups displayed similar baseline clinical features. The overall incidence of respiratory tract infections (RR, 1.0 [95% confidence interval [CI], 0.63-1.60]) and the rates of ventilator-associated pneumonia per 1,000 ventilator-days were similar in both experimental and control groups (22.6 vs 22.3; P = .95). Respiratory tract infection-free survival time (7.8 vs 6.9 days; P = .61), duration of mechanical ventilation (11.1 vs 11.0 days; P = .61), and length of stay (9.7 vs 10.4 days; P = .67) did not differ between the Chlorhexidine and placebo groups. However, patients in the Chlorhexidine group exhibited a larger interval between ICU admission and onset of the first respiratory tract infection (11.3 vs 7.6 days; P = .05). The chances of surviving the ICU stay were similar (RR, 1.08 [95% CI, 0.72-1.63]).Conclusion.Oral application of a 0.12% solution of Chlorhexidine does not prevent respiratory tract infections among ICU patients, although it may retard their onset.
3. Sampling, study size, and power
Authors: Cole Tim J. 
Published: September 2009

Abstract
Precise definitions of study populations and samples are key to the interpretation and generalizability of findings. This chapter describes types of sampling, how to deal with non-response, and validity of measures (including problems relating to bias and variance). Details are then given of how sample size relates to the testing of the null hypothesis, and the meaning and definition of significance level and power. This is followed by detailed techniques for the determination of sample size for different types of epidemiological studies (ecological, cross-sectional, case-control studies, cohort studies, and experimental studies). It defines sample size and power in relation to measures of difference between matched and unmatched samples, correlation, odds ratio, and relative risk.
4. Covariate measurement errors in nutritional epidemiology: effects and remedies
Authors: Clayton David , Gill Caroline 
Published: September 2009

Abstract
The key problem in epidemiological studies is the identification of relevant exposures and outcomes, and the relationship (and error modelling) between observed and relevant measures, and between relevant measures and relevant outcomes. Measurement errors and bias undermine the ability to detect diet-disease relationships, and the problem is particularly acute in nutritional epidemiological studies because of the difficulties of measuring relevant dietary exposures accurately, and the particular problem of differential misclassification (i.e., the differences in bias in the measurements between individuals, or between one subset of a sample and another). Correcting for measurement error is a controversial topic, but the chapter provides illustrations of the extent of attenuation or misrepresentation of diet-disease associations.
9. Socio-demographic and psycho-social variables
Authors: Macintyre Sally , Anderson Annie 
Published: September 2009

Abstract
This chapter describes and defines socio-demographic and psycho-social variables, and highlights the importance of attaining accurate measures of socio-demographic and psycho-social variables in the context of nutritional epidemiological studies. The scales of measurement and their determination are set out in detail. Criteria for developing sound and comparable measures are given.
10. Anthropometric measures
Authors: Ulijaszek Stanley J. 
Published: September 2009

Abstract
Anthropometric measures play a dual role in nutritional epidemiology, as measures of exposure and measures of outcome. General problems associated with anthropometric measurement are discussed, including the training of field workers and use of equipment. Anthropometric indices are defined. The treatment of data prior to analysis is described. Appropriate measurements and indices for the assessment of under- and over-nutrition in children and adults are considered. The relative merits of the use of reference data from different sources are reviewed.
11. Gene–nutrient interactions in nutritional epidemiology
Authors: Kohlmeier Lenore , DeMarini David , Piegorsch Walter 
Published: September 2009

Abstract
There is increasing evidence that the ways in which nutrients are handled metabolically is, to a greater or lesser extent, under genetic control. Equally, nutrient (and non-nutrient) intakes affect the expression of genetic predispositions. These complex interactions (nutrient regulation of gene transcription, food-induced DNA damage, phytochemical enhancement or protection of DNA integrity, genetic susceptibility to nutrition-related diseases) increasingly shed light on epidemiological relationships between diet and health and disease. This chapter considers design and analytical implications for understanding gene-nutrient interactions, including specific statistical models. It concludes with a discussion of ethical issues, and an appendix for sample size determination in relation to the determination of genetic characteristics in nutritional epidemiological studies.
12. Ecological studies
Authors: Hiller Janet E. , McMichael Anthony J. 
Published: September 2009

Abstract
Ecological studies examine characteristics of population groups rather than individuals. This chapter provides useful examples of how to develop hypotheses using ecological data (based on the collection of relevant indices of diet and health status), assess geographic differences and time trends, and understand the value of ecological studies especially in international comparisons of diet and disease. The need to collect non-nutritional population data and the limitations of the ecological approach are illustrated, including a discussion of calibration. Sampling is discussed in detail, as are the issues of time-lagging, cohort analysis, and adjusting for confounders. The chapter concludes with a discussion of the criteria for ‘proof’ in ecological studies, their limitations, and a consideration of when ecological studies are the method of choice.
13. Cross-sectional studies
Authors: Cade Janet E. 
Published: September 2009

Abstract
Cross-sectional studies involve identifying a defined population at a given point in time and measuring a range of variables on an individual basis which can include current and past dietary exposures and well as health outcomes and disease status. They are also known as prevalence surveys. They include a type of migrant study. This chapter considers the use and limitations of cross-sectional studies and their value in generating hypotheses. It provides details of their design (including a flow chart and a consideration of the choice of variables) and discusses the approaches to analysis.
14. Cohort studies
Authors: Burr Michael L. 
Published: September 2009

Abstract
Cohort studies follow a group of individuals over time to identify changes in status (such as disease or mortality) and relate these to observations made at baseline. They can also be carried out where observations on a group of individuals have been collected in the past and can be related to their current status. This chapter summarizes the strengths and weaknesses of cohort studies, and looks in detail at some of the practical issues in their implementation. Their implementation is illustrated using studies in both infancy and childhood and in middle-aged adults and the elderly. The issue of confounding is discussed. Details of study design are summarized in a checklist for planning a cohort study, and their statistical analysis considered in detail.
Tests using single markers
Authors: Cuckle Howard S. , Wald Nicholas 
Published: September 2009

AbstractThis chapter describes screening based on the measurement of a single variable. Before considering the screening test in detail, it is necessary to consider the disorder for which screening is being carried out, its definition, its prevalence, its natural history, and the efficacy of its treatment or prevention. Information on the overlap of test values from affected and unaffected individuals is necessary to determine detection rates and false-positive rates, which, together with data on prevalence, permit the estimation of the risk of being affected. This information is also needed for subsequent screening or diagnostic tests.
Neural tube defects
Authors: Wald Nicholas 
Published: September 2009

AbstractAntenatal screening and diagnosis for neural tube defects involves the application of two methods — maternal serum alphafetoprotein (AFP) followed by amniotic fluid AFP measurement, and ultrasound examination of the fetus. The present challenge in screening is to integrate the two methods into a coherent screening strategy. This chapter quantifies the screening and diagnostic performance of the different methods, and offers a view on how they could be integrated.
Acquired haematological disorders
Authors: Letsky Elizabeth A. , Weatherall Sir David 
Published: September 2009

AbstractThis chapter discusses screening for maternal anaemia and thrombocytopaenia and fetal allo-immune thrombocytopaenia (FAIT) during pregnancy. The use of haemoglobin measurement to detect maternal anaemia is held to be justified, but screening for maternal thrombocytopaenia by measuring platelet count seems to be of no value. The possibility of screening for FAIT by typing pregnant women's platelet antigens is raised.
Genetic haematological disorders
Authors: Weatherall Sir David , Letsky Elizabeth A. 
Published: September 2009

AbstractThis main focus of this chapter is on genetic disorders of the structure or synthesis of haemoglobin — especially sickle cell disease and the thalassaemias, which are common enough in many populations to justify antenatal and neonatal screening. Glucose-6-phosphate dehydrogenase deficiency also merits screening in certain populations where it commonly causes neonatal jaundice and kernicterus; and screening for hereditary bleeding diseases is indicated if there is a history of a previously affected child.
Rhesus and other haemolytic diseases
Authors: Letsky Elizabeth A. , Leck Ian , Bowman John M. , Leek Ian 
Published: September 2009

AbstractThis chapter describes antenatal and neonatal screening for rhesus and other blood group incompatibilities. These incompatibilities can cause maternal antibodies to fetal blood cell antigens to enter the fetal circulation, leading to fetal and neonatal haemolytic disease (generally referred to as haemolytic disease of the newborn, HDN). Without screening and appropriate treatment, HDN would be an important cause of perinatal death and brain damage. With screening and treatment these complications are almost completely prevented.
Cystic fibrosis
Authors: Brock David J. H. 
Published: September 2009

AbstractThis chapter describes screening and diagnosis for cystic fibrosis (CF). CF is the most common life-shortening Mendelian disorder found in children and in young adults of Caucasian descent. It is concluded that antenatal screening for CF is highly effective and justified, but that the case for neonatal screening has not been made.