bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inbreeding depression and genetic load at partially linked loci in a metapopulation
Authors: ZHOU SHU-RONG , PANNELL JOHN R. 
Published: June 2010

SummaryInbreeding depression has important implications for a wide range of biological phenomena, such as inbreeding avoidance, the evolution and maintenance of sexual systems and extinction rates of small populations. Previous investigations have asked how inbreeding depression evolves in single and subdivided populations through the fixation of deleterious mutations as a result of drift, as well as through the expression of deleterious mutations segregating in a population. These studies have focused on the effects of mutation and selection at single loci, or at unlinked loci. Here, we used simulations to investigate the evolution of genetic load and inbreeding depression due to multiple partially linked loci in metapopulations. Our results indicate that the effect of linkage depends largely on the kinds of deleterious alleles involved. For weakly deleterious and partially recessive mutations, the speed of mutation accumulation at segregating loci in a random-mating subdivided population of a given structure tends to be retarded by increased recombination between adjacent loci – although the highest numbers of fixation of slightly recessive mutant alleles were for low but finite recombination rates. Although linkage had a relatively minor effect on the evolution of metapopulations unless very low values of recombination were assumed, close linkage between adjacent loci tended to enhance population structure and population turnover. Finally, within-deme inbreeding depression, between-deme inbreeding depression and heterosis generally increased with decreased recombination rates. Moreover, increased selfing reduced the effective amount of recombination, and hence the effects of tight linkage on metapopulation genetic structure were decreased with increasing selfing. In contrast, linkage had little effect on the fate of lethal and highly recessive alleles. We compare our simulation results with predictions made by models that ignore the complexities of recombination.
Augustus and ‘Syracuse’
Authors: Gowers Emily 
Published: June 2010

ABSTRACTSuetonius (Aug.72.2) records among the habits of Augustus his inclination to retreat from time to time to a place he called ‘Syracuse’ or his ‘technophuon’ (workshop). These names have been variously explained, without agreement. The paper argues that ‘Syracuse’ evokes a complex of associations beyond the obvious connection with Archimedes and his inventions. By recalling other well-known figures, such as Marcellus and Dionysius, as well as Augustus’ own experiences in Syracuse, the name of his den effectively encapsulates the courses of action available to the emperor as ruler and as private citizen.
Late Antique Ostia and a Campaign for Pious Tourism: Epitaphs for Bishop Cyriacus and Monica, Mother of Augustine
Authors: Boin Douglas Ryan 
Published: June 2010

ABSTRACTEver since Augustine narrated an account of his mother's death at Ostia, social historians have tried to adduce the identity of the person who erected Monica's tombstone, a copy of which is preserved in a ninth-century codex. Three members of thegens Anicii, all of whom were Augustine's contemporaries, have become usual suspects in the secondary literature. Throughout these debates the epitaph itself, a fragment of which was found in 1945, is frequently cited but rarely treated as a primary text. This article presents a new study of that epigraph and proposes that it was erected much later than previously suspected.
Pliny,Epistles8.14: Senate, Slavery and theAgricola
Authors: Whitton C. L. 
Published: June 2010

ABSTRACTEpistles8.14, one of Pliny's longest letters, has been widely dismissed as a clumsy combination of two ill-fitting stretches of prose. This article demonstrates a significant chain of allusions in the letter's opening to Tacitus’Agricola, as well as to Cicero, Ovid and Seneca; it shows how Pliny prompts such a reading in the surroundingEpistles8.13 and 8.15; and, through consideration of the diptych form and the theme of slavery, it demonstrates the letter's pivotal role as centrepiece to Book 8.
Risk factors for community-associatedStaphylococcus aureusinfections: results from parallel studies including methicillin-resistant and methicillin-sensitiveS. aureuscompared to uninfected controls
Authors: COMO-SABETTI K. J. , HARRIMAN K. H. , FRIDKIN S. K. , JAWAHIR S. L. , LYNFIELD R. 
Published: June 2010

SUMMARYDespite the increasing burden of community-associated methicillin-resistantStaphylococcus aureus(CA-MRSA) infections, the risk factors are not well understood. We conducted a hypothesis-generating study using three parallel case-control studies to identify risk factors for CA-MRSA and community-associated methicillin-susceptibleS. aureus(CA-MSSA) infections. In the multivariate model, antimicrobial use in the 1–6 months prior to culture was associated with CA-MRSA infection compared to CA-MSSA [adjusted odds ratio (aOR) 1·7,P=0·07] cases. Antimicrobial use 1–6 months prior to culture (aOR 1·8,P=0·04), history of boils (aOR 1·6,P=0·03), and having a household member who was a smoker (aOR 1·3,P=0·05) were associated with CA-MRSA compared to uninfected community controls. The finding of an increased risk of CA-MRSA infection associated with prior antimicrobial use highlights the importance of careful antimicrobial stewardship.
Reducing the risk of type 2 diabetes with nutrition and physical activity – efficacy and implementation of lifestyle interventions in Finland
Authors: Lindström Jaana , Absetz Pilvikki , Hemiö Katri , Peltomäki Päivi , Peltonen Markku 
Published: June 2010

AbstractBackgroundThe prevalence of type 2 diabetes has been increasing in Finland, in parallel with a gradual increase in overweight and obesity during the past decades. The expanding prevalence of type 2 diabetes brings along complications, most importantly CVD. Therefore, it is extremely important to implement activities to prevent type 2 diabetes.ObjectiveIn the present paper, the clinical evidence for the prevention of type 2 diabetes is presented with the Finnish diabetes prevention study. In addition, the paper discusses the practical implementation of prevention of type 2 diabetes using three different types of prevention programmes as examples: FIN-D2D, including risk-screening and repeated consultation in primary health-care; FINNAIR, a workplace-targeted intervention project involving airline employees; and the good ageing in Lahti region (GOAL) programme, a community-based prevention programme.ConclusionsFIN-D2D, the FINNAIR project and the GOAL programme have shown that screening for type 2 diabetes risk and implementing large-scale lifestyle intervention in primary health-care are feasible. However, the crucial questions still are whether it is possible to replicate the results concerning effectiveness of lifestyle intervention in primary and occupational health-care systems. Furthermore, it remains to be shown whether it is possible to achieve the same results in different health-care settings, cultures, regions and age groups, especially in adolescents and young adults among whom the increase in the incidence has been the highest. In addition, the importance of co-operation among all sections of society, citizens’ awareness of healthy lifestyles and the social inequalities in health must be emphasised because the diabetes epidemic cannot be solved only by concentrating on preventive actions carried out by health-care systems.
Monitoring diet and diet-related chronic disease risk factors in Finland
Authors: Männistö Satu , Laatikainen Tiina , Helakorpi Satu , Valsta Liisa M 
Published: June 2010

AbstractHealth and dietary monitoring has a long history in Finland. The aim of this review is to summarise the main sources of Finnish dietary information including food balance sheets, household budget survey data, questionnaires related to dietary behaviour and risk factors of main chronic diseases as well as dietary surveys. According to these sources, dietary behaviour and food choices have changed considerably during the last decades. For example, the total fat intake (E %) has decreased remarkably from nearly 40 % in the late 1960s to close to 30 % in 2007. Furthermore, the type of fat consumed has changed noticeably due to the increased popularity of oil used in cooking and the large variety of softer spreads available. There has also been a notable decrease in intake of salt, and a multiple increase in the consumption of fruits and vegetables since the 1970s. The future challenges of dietary monitoring include keeping the participation rates in dietary surveys at acceptable levels, controlling under/over-reporting of diet, developing a national monitoring system for children and adapting to international changes and requirements to harmonise dietary monitoring in Europe.
FINDIET 2007 Survey: energy and nutrient intakes
Authors: Pietinen Pirjo , Paturi Merja , Reinivuo Heli , Tapanainen Heli , Valsta Liisa M 
Published: June 2010

AbstractObjectiveThe National FINDIET surveys are carried out every 5 years to monitor dietary habits and nutrient intake of the adult Finnish population. The latest survey was carried out in 2007.DesignCross-sectional population-based study. Dietary assessment was carried out using 48 h recall interviews. A picture book of food portions was used to estimate portion sizes and the national Food Composition Database Fineli® to calculate nutrient intakes.SettingA representative sample taken in five regions in Finland.SubjectsA total of 730 men and 846 women aged 24–64 years.ResultsThe percentage contribution of fat to the total energy intake was 33 % in men and 31 % in women. The respective percentages for SFA in men and women were 13 % and 12 %, respectively, and 0·4 % for trans fatty acids in both genders. The average intakes of folate, vitamin D and fibre fell below the recommended levels, whereas the average salt intake was somewhat higher than the recommendations. Women’s diet was higher in protein, dietary fibre and sucrose compared to that of men.ConclusionsAccording to the FINDIET 2007 Survey, the dietary habits of the adult Finnish population have headed in a positive direction overall. However, although the quality of the fats consumed has continued to improve, and the intake of salt has decreased, they still do not meet the recommended levels of intake. Similarly, the average intakes of folate and vitamin D continue to fall below the recommendations. There is also a need to increase fibre intake and to cut down the intake of sucrose.
Food consumption and nutrient intake in Finnish 1–6-year-old children
Authors: Kyttälä Pipsa , Erkkola Maijaliisa , Kronberg-Kippilä Carina , Tapanainen Heli , Veijola Riitta , Simell Olli , Knip Mikael , Virtanen Suvi M 
Published: June 2010

AbstractObjectiveTo study food consumption and nutrient intake in Finnish children aged 1–6 years and to assess the effect of age and sex on food consumption and nutrient intake.DesignCross-sectional samples of children participating in the Type 1 Diabetes Prediction and Prevention (DIPP) birth cohort study in Finland.SubjectsThe study population comprised healthy children recruited in the nutrition study within the DIPP study in 1998–2003. Three-day food records (2535 in total) from 1-, 2-, 3-, 4- and 6-year-old children were kept between the years 2003 and 2005.ResultsThe energy-adjusted consumption of fruits and berries, cereal products, infant formulas and meat dishes was higher and the consumption of vegetables, salads, breads, dairy products, fat spreads, drinks, sweets and sugar was lower among 1-year-old children than older age groups (Pfor all <0·05). The mean daily energy intake increased with age and was higher among boys than girls in all age groups, except among the 2-year-olds (Pfor all <0·05). The diet of the 2–6-year-old children contained too much saturated fat and sucrose, and too little PUFA compared with the current Nordic Nutrition Recommendations. The intakes of most vitamins and minerals met the recommendations. However, the intakes of vitamin D, E and iron fell below the recommended levels. The nutrient density of the diet decreased after the age of 1 year at the time that the children adapted to the regular family diet.ConclusionsIn order to improve the diet of young children, it is essential to evaluate the diet of the whole family.
Food consumption and nutrient intake in day care and at home in 3-year-old Finnish children
Authors: Lehtisalo Jenni , Erkkola Maijaliisa , Tapanainen Heli , Kronberg-Kippilä Carina , Veijola Riitta , Knip Mikael , Virtanen Suvi M 
Published: June 2010

AbstractObjectiveTo assess and compare the food consumption and nutrient intake between 3-year-old children cared for at home full-time and those attending day care outside the home. Nutrient intake on weekdays and weekends was also studied.DesignCross-sectional sample of children invited to the nutrition study within the Type 1 Diabetes Prediction and Prevention (DIPP) birth cohort born in 2001. Families returned 3-d food record completed close to the child’s third birthday.SubjectsA total of 471 pre-school children aged 3 years of whom 285 had only been cared for at home during the recording time and 186 had attended day care outside the home.ResultsAmong the children cared for outside the home, there were more consumers of recommendable foods as fresh vegetables, fruits, berries, rye bread, fish, skimmed milk and vegetable margarines, than among those cared for at home. The day-care group had higher intake of protein, dietary fibre, thiamine, potassium and magnesium, and lower intake of sucrose compared with the group cared for at home. Adjustment for sociodemographic factors did not change the results. In all children, food consumption was more varied on weekdays compared with weekends. On weekdays, children had higher intake of dietary fibre and protein and lower intake of sucrose compared to weekends.ConclusionsThe type of day care was associated with food consumption and nutrient intake among pre-school children and hence might have an impact on their nutrition and health. The diet of the children attending day care outside the home was more balanced and closer to the national recommendations.
Quality of diet and food choices of Finnish young men: a sociodemographic and health behaviour approach
Authors: Bingham Clarissa ML , Jallinoja Piia , Lahti-Koski Marjaana , Absetz Pilvikki , Paturi Merja , Pihlajamäki Harri , Sahi Timo , Uutela Antti 
Published: June 2010

AbstractObjectiveEating habits of Finns have improved dramatically in 40 years. The proportion of fat in the diet has decreased and vegetable and fruit consumption increased. Knowledge of Finnish young men’s dietary habits is limited. The aim was to assess food choices and quality of diet among young men and to analyse how background and health behaviour factors explain it.DesignIn 2007, data on eating habits, sociodemographic background factors and health behaviours of 17–21-year-old men (n 2905) entering military service were collected by self-administrated questionnaire. Two indexes – core food index (CFI) and extra food index (EFI) – were formed to describe daily and redundant snacking-type eating, respectively. Associations of background factors and health behaviours on the indexes were analysed by general linear modelling.ResultsIn all, 13 % consumed fruits and berries daily and 8 % consumed vegetables, whereas 24 % consumed pizza and 19 % consumed hamburgers more than once a week. CFI increased with educational level (P < 0·001) and was explained by background and health behaviour (smoking, physical activity and eating breakfast). EFI was inversely associated with BMI (P < 0·001) and explained by health behaviour: (smoking, physical activity, drinking beer and eating breakfast).ConclusionsThese results indicate that in early adulthood, eating habits cluster with other health behaviours among men. In this age group, education is associated with core food but not with extra food eating habits. Furthermore, seasonal variation is seen in both types of eating. When promoting healthy eating, a distinction between core foods and extra foods by using feasible indexes will be helpful in targeting the efforts.
School and workplace meals promote healthy food habits
Authors: Raulio Susanna , Roos Eva , Prättälä Ritva 
Published: June 2010

AbstractObjectiveThe present study is to describe, on the basis of recent Finnish population surveys, (i) the frequencies of school and worksite canteen use, (ii) the determinants of having a hot lunch during school or working hours and (iii) the associations of lunch eating patterns with food habits.SettingThe study summarises mainly basic reports and studies concerning catering services conducted in Finland based on nationally representative population surveys.Design and subjectsCross-sectional study. The most important surveys cited in this paper are the School Health Promotion Study, the Work and the Working Conditions survey, the National FINDIET 2002 Study, and the Health Behavior and Health among Finnish Adult Population survey.ResultsSchool lunch is eaten by on average 70–90 % of children aged 9–18 years. Of all employees, 30 % eat at a worksite canteen daily, whereas 30 % of men and 45 % of women eat packed lunches. Nationally representative cross-sectional population surveys show that the use of catering services is associated with more healthy food habits; schoolchildren eating school meals and employees eating lunch at a worksite canteen tend to make food choices closer to nutritional recommendations as compared to those not using catering services to the same degree.ConclusionsSome evidence exists that catering services in schools and worksites contribute to healthy eating habits in the population. In order to verify the positive role of catering services more scientific research with prospective and intervention design studies will be needed.
(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Authors: Koch Steven , Maloney Andy , Herskowitz Lawrence 
Published: June 2010

AbstractThe osmotic pressure and kinetic properties of water play important roles in biomolecular interactions. As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1]. In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules. To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin. We're currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes. We will describe our open-source, automated analysis platform for extracting microtubule gliding speeds from image series. We will also show our preliminary analyses of the changes seen in gliding assays when done in heavy water (either heavy-hydrogen or heavy-oxygen) or osmolytes (betaine). We will discuss whether osmotic stress and isotopes, particularly heavy-oxygen water, might be an important tool for probing effects of water on binding interactions between kinesin and microtubules. We will also discuss potential applications of deuterium water for stabilizing microtubules and kinesin for lab or device applications.[1] Parsegian, V. A., Rand, R. P., & Rau, D. C. (1995). Macromolecules and water: probing with osmotic stress. Methods in Enzymology, 259.This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008 in collaboration with Dr. Susan Atlas lab (UNM).CORRECTIONS: At the workshop, Erik Schaffer pointed out to us that some of our speed differences (casein data) were surely due to microscope increasing in temperature. I’ve edited the poster to correct for this. Thanks, Erik!
Grofit: Fitting biological growth curves
Authors: Kahm Matthias , Hasenbrink Guido , Lichtenberg-Frate Hella , Ludwig Jost , Kschischo Maik 
Published: June 2010

AbstractGrowth experiments are routinely used to analyze basic properties of a given organism or cellular model. Similarly, within the TRANSLUCENT project the characterization of cellular growth and particularly under conditions of high extra cellular potassium or sodium is an important task. Any growth analysis should ideally reveal a relationship between the concentration of a compound/substrate and its effect on a particular growth parameter. In view of the quite labor intensive analysis of hundreds of growth curves - sometimes not revealing ideal relationships - the Grofit-software was developed to support biologists and such approaches. Within the software package, specifically tailored regression and bootstrapping techniques are utilized to statistically estimate the effect of different growth conditions. Grofit was implemented in R, an open source statistical software environment. A complete description of the Grofit software and information about the implemented methods is given in a manuscript published by the Journal of Statistical Software. In addition the software is available from CRAN repositories or the developers homepage http://www.rheinahrcampus.de/Research-Group-of-Maik-Kschisc.2452.0.html
Gap5—editing the billion fragment sequence assembly
Authors: Bonfield James K. , Whitwham Andrew 
Published: June 2010

AbstractMotivation: Existing sequence assembly editors struggle with the volumes of data now readily available from the latest generation of DNA sequencing instruments.Results: We describe the Gap5 software along with the data structures and algorithms used that allow it to be scalable. We demonstrate this with an assembly of 1.1 billion sequence fragments and compare the performance with several other programs. We analyse the memory, CPU, I/O usage and file sizes used by Gap5.Availability and Implementation: Gap5 is part of the Staden Package and is available under an Open Source licence from http://staden.sourceforge.net. It is implemented in C and Tcl/Tk. Currently it works on Unix systems only.Contact: jkb@sanger.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
SLIMS—a user-friendly sample operations and inventory management system for genotyping labs
Authors: Van Rossum Thea , Tripp Ben , Daley Denise 
Published: June 2010

Abstract
Summary: We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers.
Availability: Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1.
Contact: denise.daley@hli.ubc.ca