bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of a pre-coded food diary used among 13-year-olds: comparison of energy intake with energy expenditure
Authors: Andersen Lene F , Pollestad Magnhild L , Jacobs David R , Løvø Arne , Hustvedt Bo-Egil
Published: December 2005

Objective

To validate energy intake (EI) estimated from pre-coded food diaries against energy expenditure (EE) measured with a validated position-and-movement monitor (ActiReg®) in groups of 13-year-old Norwegian schoolchildren.

Design

Two studies were conducted. In study 1 the monitoring period was 4 days; participants recorded their food intake for four consecutive weekdays using food diaries and wore the ActiReg® during the same period. In study 2 the monitoring period was 7 days; participants recorded their food intake for four consecutive days but wore the ActiReg® for a whole week.

Settings

Participants were recruited from grade 8 in a school in and one outside Oslo (Norway).

Subjects

Forty-one and 31 participants from study 1 and 2, respectively, completed the study.

Results

The group average EI was 34% lower than the measured EE in study 1 and 24% lower in study 2. The width of the 95% confidence limits of agreement in a Bland–Altman plot for EI and EE varied from -0.2 MJ to 8.2 MJ in study 1 and from -2.3 MJ to 6.9 MJ in study 2. The Pearson correlation coefficients between reported energy intake and expenditure were 0.47 (P = 0.002) in study 1 and 0.74 (P < 0.001) in study 2.

Conclusion

The data showed that there was substantial variability in the accuracy of the food diary at the individual level. Furthermore, the diary underestimated the average energy intake. The ability of the food diary to rank individuals according to energy intake was found to be good in one of the studies and moderate in the other.
Green tea consumption in everyday life and mental health
Authors: Shimbo Mari , Nakamura Keiko , Shi Hui Jing , Kizuki Masashi , Seino Kaoruko , Inose Tomoko , Takano Takehito
Published: December 2005

Objective

Green tea has been widely acknowledged in Japan to induce a pleasurable mental feeling. Recent laboratory studies have suggested positive psychological effects as a result of consuming green tea. The present study examined whether green tea consumption in everyday life in Japan is associated with positive mental health.

Design

A cross-sectional study was performed in February–March 2002.

Setting and subjects

The subjects of the study consisted of a general population of 600 Japanese aged 20–69 years. Responses of 380 subjects, obtained by home-visit interview, were analysed. The questionnaire inquired about consumption of brewed green tea and other beverages, perceived mental health status, lifestyle and others. The 12-item General Health Questionnaire (GHQ 12) was used for the assessment of mental ill-health (GHQ score ≥4).

Results

After adjustments for age, area, perceived mental stress, lifestyle and daily caffeine intake, the consumption of brewed green tea was not statistically associated with any decrease in risk of mental ill-health among either males or females (odds ratio (OR) = 0.78, 95% confidence interval (CI) = 0.47–1.29 for males; OR = 0.77, 95% CI = 0.51–1.14 for females). Daily caffeine intake (100 mg) inclusive of green tea, black tea, coffee and other caffeine-containing beverages was associated with a higher risk of mental ill-health among females (OR = 1.26, 95% CI = 1.01–1.56).

Conclusions

The results provide population-based evidence on the consumption of brewed green tea in everyday life and mental health, together with information on consumption patterns of various beverages and lifestyles.
A population-based case–control study of diet and melanoma risk in northern Italy
Authors: Vinceti Marco , Pellacani Giovanni , Malagoli Carlotta , Bassissi Stefania , Sieri Sabina , Bonvicini Francesca , Krogh Vittorio , Seidenari Stefania
Published: December 2005

Objective

We aimed at examining the association between dietary constituents and risk of cutaneous melanoma.

Design

In an area of northern Italy we recruited 59 newly diagnosed melanoma patients and 59 age- and sex-matched population controls, to whom we administered a validated semi-quantitative food-frequency questionnaire.

Results

We found an excess risk of melanoma in subjects with a higher energy-adjusted intake of total polyunsaturated fatty acids and, in particular, of linoleic acid (relative risk = 2.16 for intake in the highest tertile compared with the lowest tertile,Pfor linear trend = 0.061). Conversely, disease risk was inversely associated with the consumption of soluble carbohydrates (relative risk = 0.34 for intake in the upper vs. the lowest tertile adjusting for total energy intake,Pfor linear trend = 0.046). No other dietary factors, including alcohol, vitamins and trace elements, correlated with melanoma risk. The association of melanoma risk with linoleic acid and soluble carbohydrates intakes was further strengthened in multivariate analysis, and when analysis was limited to females.

Conclusions

Overall, these results indicate that an excess energy-adjusted intake of linoleic acid and a lower consumption of soluble carbohydrates may increase melanoma risk.
Taxing food: implications for public health nutrition
Authors: Caraher Martin , Cowburn Gill
Published: December 2005

Aim

To set out a policy analysis of food taxes as a way of influencing food consumption and behaviour.

Design

The study draws on examples of food taxes from the developed world imposed at national and local levels. Studies were identified from a systemised search in six databases with criteria designed to identity articles of policy relevance.

Results

The dominant approach identified from the literature was the imposition of food taxes on food to raise general revenue, such as Value Added Tax in the European Union. Food taxes can be applied in various ways, ranging from attempts to directly influence behaviour to those which collect taxes for identified campaigns on healthy eating through to those applied within closed settings such as schools. There is a case for combining taxes of unhealthy foods with subsidies of healthy foods. The evidence from the literature concerning the use and impact of food taxes on food behaviour is not clear and those cases identified are mainly retrospective descriptions of the process. Many food taxes have been withdrawn after short periods of time due to industry lobbying.

Conclusions for policy

Small taxes with the clear purpose of promoting the health of key groups, e.g. children, are more likely to receive public support. The focus of many tax initiatives is unclear; although they are generally aimed at consumers, another focus could be food manufacturers, using taxes and subsidies to encourage the production of healthier foods, which could have an effect at a population level. Further consideration needs to be given to this aspect of food taxes. Taxing food (and subsidies) can influence food behaviour within closed systems such as schools and the workplace.
Effects of retirement on lifestyle in relation to changes in weight and waist circumference in Dutch men: a prospective study
Authors: Nooyens Astrid CJ , Visscher Tommy LS , Schuit A Jantine , van Rossum Caroline TM , Verschuren WM Monique , van Mechelen Willem , Seidell Jacob C
Published: December 2005

Objective

To study changes in lifestyle in relation to changes in body weight and waist circumference associated with occupational retirement in men.

Design

A prospective cohort study with 5 years of follow-up. At baseline and at follow-up, questionnaires were completed and body weight and waist circumference were measured.

Setting

The Doetinchem Cohort Study, consisting of inhabitants of Doetinchem, a town in a rural area of The Netherlands.

Subjects

In total 288 healthy men aged 50–65 years at baseline, who either remained employed or retired over follow-up.

Results

The effect of retirement on changes in weight and waist circumference was dependent on type of former occupation. Increase in body weight and waist circumference was higher among men who retired from active jobs (0.42 kg year−1 and 0.77 cm year−1, respectively) than among men who retired from sedentary jobs (0.08 kg year−1 and 0.23 cm year−1, respectively). Weight gain and increase in waist circumference were associated with a decrease in fruit consumption and fibre density of the diet, with an increase in frequency of eating breakfast, and with a decrease in several physical activities, such as household activities, bicycling, walking and doing odd jobs.

Conclusion

Retirement was associated with an increase in weight and waist circumference among those with former active jobs, but not among those with former sedentary jobs. Retirement may bring opportunities for healthy changes in diet and physical activity, which could be used in health promotion programmes.
Why do adolescents eat what they eat? Personal and social environmental predictors of fruit, snack and breakfast consumption among 12– 14-year-old Dutch students
Authors: Martens MK , Assema P van , Brug J
Published: December 2005

Objective

The aim of the study was to investigate the relative importance of personal and social environmental predictors of the consumption of fruit, high-fat snacks and breakfast.

Design

A school-based cross-sectional survey. Data were collected through written questionnaires.

Setting

Students from eight schools in the southern part of The Netherlands.

Subjects

Six hundred and one students from preparatory secondary vocational education schools.

Results

About a quarter of the variation in actual behaviours and intentions to change the behaviours could be explained. Stepwise multiple regression analysis revealed that, for all three behaviours, higher intention to change was especially associated with a more positive attitude and subjective norm, and higher intentions to increase fruit intake with more positive self-efficacy expectations. With regard to actual consumption, a more positive attitude towards eating fruit was the only significant correlate of a higher consumption of fruit. A more positive attitude towards eating high-fat snacks, perceived lower intake of the mother, and higher food availability and accessibility were associated with consumption of high-fat snacks, and a more positive attitude to breakfast more frequently was associated with more frequent breakfast consumption.

Conclusion

The results indicate that adolescents’ attitudes are the most important determinants of different health-related eating behaviours and intentions to change. Interventions promoting a healthy diet for adolescents should include creative strategies to achieve positive associations with healthy dietary changes.
Is the prevalence of dehydration among community-dwelling older adults really low? Informing current debate over the fluid recommendation for adults aged 70+years
Authors: Stookey Jodi Dunmeyer , Pieper Carl F , Cohen Harvey Jay
Published: December 2005

Objective

The fluid recommendation for adults aged 70+ years has been criticised on the basis of a low prevalence of dehydration in community-dwelling older adults. This study explores whether the low prevalence might reflect limitations of individual dehydration indices.

Design

Cross-sectional data on plasma sodium, blood urea nitrogen (BUN), creatinine, glucose and potassium were used to classify 1737 participants of the 1992 Established Populations for Epidemiologic Studies of the Elderly (EPESE) (70+ years) according to multiple dehydration indices. Associations between dehydration indices, health and functional status were evaluated.

Results

Depending on the indicator used, the prevalence of dehydration ranged from 0.5% for hypotonic hypovolaemia only (plasma tonicity <285 mOsm l−1 with orthostatic hypotension) to 60% with dehydration defined as either plasma sodium ≥145 mEq l−1, BUN/creatinine ratio ≥20, tonicity ≥295 mOsm l−1, or hypotonic hypovolaemia. Elevated tonicity and BUN/creatinine ratio were respectively associated with chronic disease and functional impairment.

Conclusions

The true prevalence of dehydration among community-dwelling adults may be low or high, depending on the indicator(s) used to define dehydration. Before we can pinpoint a generalisable prevalence of dehydration for community-dwelling seniors and draw conclusions about fluid recommendations, validation studies of dehydration indices and longitudinal studies of dehydration, health and functional status are needed.
Development and potential of genetically engineered oilseeds
Authors: Dyer John M. , Mullen Robert T.
Published: December 2005

Oilseed crops are major sources of oils for human nutrition, and an increasing proportion is also being utilized for industrial purposes. Recent advances in our understanding of the basic biochemistry of seed oil biosynthesis, coupled with identification of genes for oilseed modification, have set the stage for the genetic engineering of oilseed crops that produce ‘designer’ plant seed oils tailored for specific applications. In this review we provide an overview of seed oil biosynthesis and highlight the enzymatic steps that have already been targeted for genetic manipulation, with the end goal of producing seed oils containing desired amounts of fatty acid components. Furthermore, we describe the identification of genes from various wild plant species that are capable of producing structurally diverse fatty acids, and how these advances open the door to the production of entirely novel oils in conventional oilseed crops. Transgenic oilseeds producing high amounts of these novel fatty acids represent renewable sources of raw materials that may compete with, and eventually replace, some petrochemicals that are derived from non-renewable crude oil.
Recent advances in understanding cotton fibre and seed development
Authors: Ruan Yong-Ling
Published: December 2005

The unique feature of the seed of tetraploid cotton (Gossypium hirsutumandGossypium barbadense) is that about 30% of the seed coat epidermal cells develop into cellulose-enriched fibres, while the embryos synthesize oils and proteins. Hence, both the maternal and filial tissues of the cotton seed are of significant economic value. After initiation from the ovule epidermis at or just before anthesis, the single-celled fibres elongate to 2.5–6.0 cm long in the tetraploid species before they switch to intensive secondary cell wall cellulose synthesis. Thus, apart from its agronomic importance, the cotton fibre represents a model single-cell system to study the control of cell differentiation and elongation, carbon partitioning to cellulose synthesis and also the interaction between maternal (fibre) and embryonic tissues in seeds. Over the past decade or so, significant effort has been made to understand the cellular and molecular basis of cotton fibre development and oil biosynthesis in the embryo. Metabolic engineering of the oil biosynthetic pathway in cotton seed has successfully produced healthier and stable oils. A number of candidate genes and cellular processes that potentially regulate various aspects of fibre development have been identified. Further elucidation of thein vivofunctions of those candidate genes could significantly deepen our understanding of fibre development and offer potential for improvement of fibre quality through genetic engineering or marker-assisted breeding approaches.
Plant hormone interactions during seed dormancy release and germination
Authors: Kucera Birgit , Cohn Marc Alan , Leubner-Metzger Gerhard
Published: December 2005

This review focuses mainly on eudicot seeds, and on the interactions between abscisic acid (ABA), gibberellins (GA), ethylene, brassinosteroids (BR), auxin and cytokinins in regulating the interconnected molecular processes that control dormancy release and germination. Signal transduction pathways, mediated by environmental and hormonal signals, regulate gene expression in seeds. Seed dormancy release and germination of species with coat dormancy is determined by the balance of forces between the growth potential of the embryo and the constraint exerted by the covering layers, e.g. testa and endosperm. Recent progress in the field of seed biology has been greatly aided by molecular approaches utilizing mutant and transgenic seeds ofArabidopsis thalianaand theSolanaceaemodel systems, tomato and tobacco, which are altered in hormone biology. ABA is a positive regulator of dormancy induction and most likely also maintenance, while it is a negative regulator of germination. GA releases dormancy, promotes germination and counteracts ABA effects. Ethylene and BR promote seed germination and also counteract ABA effects. We present an integrated view of the molecular genetics, physiology and biochemistry used to unravel how hormones control seed dormancy release and germination.
Endogenous jasmonates and octadecanoids in hypersensitive tomato mutants during germination and seedling development in response to abiotic stress
Authors: Andrade Andrea , Vigliocco Ana , Alemano Sergio , Miersch Otto , Botella Miguel A. , Abdala Guillermina
Published: December 2005

Although jasmonates (JAs) are involved in germination and seedling development, the regulatory mechanism of JAs, and their relation with endogenous level modifications in these processes, is not well understood. We report here the detection of 12-oxo-phytodienoic acid (OPDA), jasmonic acid (JA), 11-hydroxyjasmonate (11-OH-JA), 12-hydroxyjasmonate (12-OH-JA) and methyljasmonate (JAME) in unimbibed seeds and seedlings of tomatoLycopersicon esculentumMill cv. Moneymaker (wild type) andtss1,tss2,tos1mutants. The main compounds in wild-type andtss1,tss2,tos1seeds were the hydroxylate-JAs; 12-OH-JA was the major component in dry seeds of the wild type and intss2andtos1. The amounts of these derivatives were higher in seeds than in seedlings. Changes in JAs during wild-type andtss1imbibition were analysed in seeds and the imbibition water. In wild-type imbibed seeds, 11-OH-JA content was higher than intss1. 12-OH-JA showed a different tendency with respect to 11-OH-JA, with high levels in the wild type at early imbibition. Intss1, levels of 12-OH-JA rose from 24 to 48 h of imbibition. At 72 h of imbibition, when radicles had emerged, the amounts of both hydroxylates in wild-type andtss1seeds were minimal. An important release of the hydroxylate forms was observed in the imbibition water. 11-OH-JA decreased in the imbibition water of wild-type seeds at 48 h. On the contrary, a high and sustained liberation of this compound was observed intss1after 24 h. 12-OH-JA increased in wild-type as well intss1until 24 h. Thereafter, a substantial reduction in the content of this compound was registered. NaCl-treated wild-type seedlings increased their 12-OH-JA, buttss1seedlings increased their JA in response to salt treatment. Intss2seedlings, NaCl caused a slight decrease in 11-OH-JA and JAME, whereastos1seedlings showed a dramatic OPDA and 12-OH-JA decrease in response to salt treatment. Under salt stress the mutant seedlings showed different patterns of JAs according to their differential hypersensitivity to abiotic stress. The JA-hydroxylate forms found, and the differential accumulation of JAs during germination, imbibition and seedling development, as well as their response to NaCl stress, provide new evidence about the control of many developmental processes by JA.
Simple purification of small RNAs from seeds and efficient detection of multiple microRNAs expressed in Arabidopsis thaliana and tomato (Lycopersicon esculentum) seeds
Authors: Martin Ruth C. , Liu Po-Pu , Nonogaki Hiroyuki
Published: December 2005

MicroRNAs (miRNAs) play critical roles in the development of animals and plants. Characterizing the stage- and tissue-specific expression of miRNAs that potentially regulate target transcription factor expression is becoming more important for understanding the regulatory mechanisms of critical events during plant development. A simple method for purifying small RNAs from seeds is described, as well as an efficient non-radioactive labelling system for making miRNA probes. In Arabidopsis thaliana seed extracts, low molecular-weight (LMW) RNAs (e.g. 5S rRNA, tRNA and miRNA) were separated from high molecular-weight (HMW) nucleic acids (e.g. 28S and 18S rRNA, mRNA and genomic DNA) by fractionation using isopropanol. HMW RNAs precipitated in 20% isopropanol, while most LMW RNAs remained in the supernatant. The purified LMW RNAs were used successfully for RNA gel blotting to detect miRNAs expressed in Arabidopsis and tomato (Lycopersicon esculentum) seeds. To increase the detection sensitivity of the microRNA probes, additional digoxigenin-labelled uridine triphosphates (UTPs) were incorporated into the miRNA probes by designing template oligo DNAs with three extra adenines (A) at each end of their sequence. These DNA oligomers were used to make double-stranded DNA templates for miRNA probe synthesis. This probe (termed AAAPLUS) exhibited stronger signals than normal probes. A technique was also developed to quickly screen expressed miRNAs in seeds using a miniblot system, which enabled simultaneous examination with multiple miRNA probes. This method provides a simple alternative to microRNA microarrays to identify the major miRNAs expressed in seeds.
Dormancy release in Australian fire ephemeral seeds during burial increases germination response to smoke water or heat
Authors: Baker Katherine S. , Steadman Kathryn J. , Plummer Julie A. , Merritt David J. , Dixon Kingsley W.
Published: December 2005

Fire ephemerals are short-lived plants that primarily germinate after fire. Fresh and laboratory-stored seeds are difficult to germinateex situ, even in response to fire-related cues such as heat and smoke. Seeds of eight Australian fire ephemeral species were buried in unburnt and recently burnt sites of natural bushland during autumn. Seeds were exhumed after 6 and 12 months and incubated in water and smoke water, either with or without a heat treatment at 70°C for 1 h. Generally, germination did not increase after 6 months of burial, but after 12 months of burial germination was enhanced in seven of the eight species.Actinotus leucocephalusproduced higher germination following 12 months of burial without any further treatment, and smoke water and heat further improved germination. The fourGyrostemonaceaespecies,Codonocarpus cotinifolius,Gyrostemon racemiger,Gyrostemon ramulosusandTersonia cyathiflora, only germinated in the presence of smoke water, and their germination was enhanced by burial. Burial improved germination in response to a heat treatment inGrevillea scapigeraandAlyogyne huegeliiseeds, but did not enhanceAlyogyne hakeifoliagermination. During concurrent dry laboratory storage of seeds at 15°C, onlyActinotus leucocephalusproduced increased germination in response to smoke water and heat over time. In summary, soil burial can alter the dormancy status of a number of Australian fire ephemeral seeds, rendering them more responsive to germination cues such as smoke water and heat. The requirement for a period of burial before seeds become responsive to smoke and/or heat would ensure that seeds persist in the soil until a subsequent fire, when there is an increase in nutrients available for growth and reduced competition from other plants.
Underdeveloped embryos in dwarf seeds and implications for assignment to dormancy class
Authors: Baskin Carol C. , Baskin Jerry M.
Published: December 2005

Studies were conducted to determine if small embryos (i.e. low embryo length:seed length ratio) in mature dwarf seeds (0.2–2 mm) are underdeveloped. In this case, they would grow (inside the seed) prior to germination, and seeds would have morphological or morphophysiological dormancy. Prior to radicle emergence, embryo length in seeds ofDrosera anglica(Droseraceae),Campanula americana,Lobelia appendiculata,L. spicata(Campanulaceae) andSabatia angularis(Gentianaceae) increased 0, 103, 182, 83 and 57%, respectively. Since embryo growth did not occur in seeds ofD. anglicaprior to germination, embryos, although small, are fully developed; seeds have only physiological dormancy. The underdeveloped embryo in seeds ofC. americanahas little or no physiological dormancy; thus, seeds have morphological dormancy. On the other hand, underdeveloped embryos in seeds ofL. appendiculata,L. spicataandS. angularisare physiologically dormant, and seeds have morphophysiological dormancy. Therefore, since small embryos in dwarf seeds may or may not be underdeveloped, assignment of seeds to a dormancy class requires that studies be done to determine if embryos grow inside the seed before germination can occur. Such information is important in understanding the evolutionary relationship of the different kinds of seed dormancy.
Targeting and processing of membrane-anchored YFP fusion proteins to protein storage vacuoles in transgenic tobacco seeds
Authors: Fung Ka Leung , Yim Yin Fun , Tse Yu Chung , Miao Yansong , Sun Samuel S.M. , Jiang Liwen
Published: December 2005

Seeds that store proteins in protein storage vacuoles are attractive bioreactors for producing and storing large amounts of pharmaceutical proteins. However, foreign proteins expressed in transgenic plants are subjected to the delivery and modification processes present within plant cells. Here, it is demonstrated that unique membrane sequences deliver a yellow fluorescent protein (YFP) to the seed protein storage vacuoles in transgenic tobacco (Nicotiana tabacum L.) plants, where the YFP is then separated from its membrane anchors. This precise targeting and separation is required for the successful delivery of useful proteins to seed protein storage vacuoles for their stable accumulation in transgenic crops.
NO news is no new news
Authors: Fotheringham C.J. , Keeley Jon E.
Published: December 2005

In the paper ‘NO News’, Prestonet al.(2004) make a number of erroneous assumptions regarding nitrogen oxide chemistry. These authors also present some very significant misinterpretations of previous research into the effects of various nitrogen oxides on germination of post-fire followers. Methodological differences between the study by Prestonet al.(2004) and previous work are also problematic, such as using NO-donors in solution versus the use of direct application of various nitrogen oxides in the gaseous phase. A closer review of these studies, with the proper understanding of nitrogen oxide chemistry, and interpretations of the available literature, would lead to the conclusion that, contrary to the authors' assertions, the Prestonet al.(2004) study supports, rather than refutes, earlier findings by Keeley and Fotheringham (1997, 1998a, b, 2000).
Smoke and mirrors: reply to Fotheringham and Keeley
Authors: Baldwin Ian T. , Preston Catherine A. , Krock Bernd
Published: December 2005

In their rebuttal, Fotheringham and Keeley (2005) (F&K, hereafter) assert that misinterpretations of previous research, errors in the presentation of the chemistry of nitrogen oxides and devious presentation of experimental results led to the conclusion of Prestonet al.(2004). [These conclusions refute those of Keeley and Fotheringham's publication inScience(Keeley and Fotheringham, 1997).] We disagree and argue that the experimental evidence is consistent with the hypothesis that the ecologically relevant germination signals for the two post-fire annuals,Emmenanthe pendulifloraandNicotiana attenuata, are the specific pyrolysis products of cellulose rather than chemical scarification by nitrogen oxides (Keeley and Fotheringham, 1997).
MAP kinase phosphatase 1 controls innate immune responses and suppresses endotoxic shock
Authors: Zhao Qun , Wang Xianxi , Nelin Leif D. , Yao Yongxue , Matta Ranyia , Manson Mary E. , Baliga Reshma S. , Meng Xiaomei , Smith Charles V. , Bauer John A. , Chang Cheong-Hee , Liu Yusen
Published: December 2005

Septic shock is a leading cause of morbidity and mortality. However, genetic factors predisposing to septic shock are not fully understood. Excessive production of proinflammatory cytokines, particularly tumor necrosis factor (TNF)-α, and the resultant severe hypotension play a central role in the pathophysiological process. Mitogen-activated protein (MAP) kinase cascades are crucial in the biosynthesis of proinflammatory cytokines. MAP kinase phosphatase (MKP)-1 is an archetypal member of the dual specificity protein phosphatase family that dephosphorylates MAP kinase. Thus, we hypothesize that knockout of the Mkp-1 gene results in prolonged MAP kinase activation, augmented cytokine production, and increased susceptibility to endotoxic shock. Here, we show that knockout of Mkp-1 substantially sensitizes mice to endotoxic shock induced by lipopolysaccharide (LPS) challenge. We demonstrate that upon LPS challenge, Mkp-1−/− cells exhibit prolonged p38 and c-Jun NH2-terminal kinase activation as well as enhanced TNF-α and interleukin (IL)-6 production compared with wild-type cells. After LPS challenge, Mkp-1 knockout mice produce dramatically more TNF-α, IL-6, and IL-10 than do wild-type mice. Consequently, Mkp-1 knockout mice develop severe hypotension and multiple organ failure, and exhibit a remarkable increase in mortality. Our studies demonstrate that MKP-1 is a pivotal feedback control regulator of the innate immune responses and plays a critical role in suppressing endotoxin shock.
KEL-8 Is a Substrate Receptor for CUL3-dependent Ubiquitin Ligase That Regulates Synaptic Glutamate Receptor Turnover
Authors: Schaefer Henry , Rongo Christopher
Published: January 2006

The regulated localization of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type glutamate receptors (AMPARs) to synapses is an important component of synaptic signaling and plasticity. Regulated ubiquitination and endocytosis determine the synaptic levels of AMPARs, but it is unclear which factors conduct these processes. To identify genes that regulate AMPAR synaptic abundance, we screened for mutants that accumulate high synaptic levels of the AMPAR subunit GLR-1 in Caenorhabditis elegans. GLR-1 is localized to postsynaptic clusters, and mutants for the BTB-Kelch protein KEL-8 have increased GLR-1 levels at clusters, whereas the levels and localization of other synaptic proteins seem normal. KEL-8 is a neuronal protein and is localized to sites adjacent to GLR-1 postsynaptic clusters along the ventral cord neurites. KEL-8 is required for the ubiquitin-mediated turnover of GLR-1 subunits, and kel-8 mutants show an increased frequency of spontaneous reversals in locomotion, suggesting increased levels of GLR-1 are present at synapses. KEL-8 binds to CUL-3, a Cullin 3 ubiquitin ligase subunit that we also find mediates GLR-1 turnover. Our findings indicate that KEL-8 is a substrate receptor for Cullin 3 ubiquitin ligases that is required for the proteolysis of GLR-1 receptors and suggest a novel postmitotic role in neurons for Kelch/CUL3 ubiquitin ligases.
Improving missing value estimation in microarray data with gene ontology
Authors: Tuikkala Johannes , Elo Laura , Nevalainen Olli S. , Aittokallio Tero
Published: December 2005

Motivation: Gene expression microarray experiments produce datasets with frequent missing expression values. Accurate estimation of missing values is an important prerequisite for efficient data analysis as many statistical and machine learning techniques either require a complete dataset or their results are significantly dependent on the quality of such estimates. A limitation of the existing estimation methods for microarray data is that they use no external information but the estimation is based solely on the expression data. We hypothesized that utilizing a priori information on functional similarities available from public databases facilitates the missing value estimation.

Results: We investigated whether semantic similarity originating from gene ontology (GO) annotations could improve the selection of relevant genes for missing value estimation. The relative contribution of each information source was automatically estimated from the data using an adaptive weight selection procedure. Our experimental results in yeast cDNA microarray datasets indicated that by considering GO information in the k-nearest neighbor algorithm we can enhance its performance considerably, especially when the number of experimental conditions is small and the percentage of missing values is high. The increase of performance was less evident with a more sophisticated estimation method. We conclude that even a small proportion of annotated genes can provide improvements in data quality significant for the eventual interpretation of the microarray experiments.

Availability: Java and Matlab codes are available on request from the authors.

Supplementary material: Available online at

Contact:  jotatu@utu.fi
GenomeDiagram: a python package for the visualization of large-scale genomic data
Authors: Pritchard Leighton , White Jennifer A. , Birch Paul R.J. , Toth Ian K.
Published: December 2005

Summary: We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems.

Availability: GenomeDiagram is freely available as source code (under GNU Public License) at , and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages.

Contact:  lpritc@scri.ac.uk

Supplementary Information A user manual, example code and images are available at
ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression
Authors: Blake Jonathon , Schwager Christian , Kapushesky Misha , Brazma Alvis
Published: December 2005

With the production of whole genome microarray chips the ability arises to investigate whether the regulation of particular groups of genes may be influenced by their chromosomal localization. Chromosome Co-Localization probability calculator (ChroCoLoc) is a publicly available web-based tool for the analysis of co-localization of co-expressed genes identified by microarray experiments.

Availability:  

Contact:  blake@ebi.ac.uk
Effects of Lidocaine and Prednisolone on Endoscopic Rigid Laryngoscopy
Authors: Kocamanoglu Ismail Serhat , Sener Elif Bengi , Ustun Emre , Tur Ayla
Published: January 2006

Objective/Hypothesis: The aim of this study is to compare the effects of lidocaine and methylprednisolone on postoperative respiratory complications caused by short‐term laryngeal surgery by way of rigid laryngoscope under general anesthesia. The effects of these drugs on recovery from anesthesia are also compared.

Study Design: One hundred American Society of Anesthesiologists physical status I to II patients over 20 years of age admitted for laryngeal mass, nodule, or polyp were included in this prospective, placebo‐controlled, randomized, and double‐blinded study.

Methods: Patients were randomly allocated to four groups; methylprednisolone 3 mg.kg−1 (group 1), 0.9% saline physiologic 5 mL (group 2), lidocaine 1.5 mg.kg−1 (group 3) intravenously, seven puffs of lidocaine aerosol 10% to oropharyngolaryngeal structures topically (group 4) sprayed. Anesthesia recovery time was calculated. Respiratory system was evaluated using a scoring table during early postoperative period.

Results: Ninety‐two cases were suitable for analysis. Recovery time was longer in group 1 (9.8 3± 3.79 minutes) than in groups 3 and 4 (7.22 ± 2.38, 7.50 ± 2.30 minutes, respectively) (P < .05). Postoperative respiratory complications were lower in groups 3 and 4 than group 2 (P < .05).

Conclusions: Lidocaine intravenous or topical administration was effective in reducing postoperative respiratory complications after short‐term laryngeal surgery by way of rigid laryngoscope. Methylprednisolone prolonged recovery time from anesthesia.
Up‐Regulation of Peroxidase Proliferator‐Activated Receptorγ in Cholesteatoma
Authors: Hwang Soon Jae , Kang Hee Joon , Song Jae‐Jun , Kang Jae Seong , Woo Jeong Soo , Chae Sung Won , Lee Heung‐Man
Published: January 2006

Objective: To evaluate the localization and expression of peroxidase proliferator‐activated receptor (PPAR)γ in cholesteatoma epithelium.

Study Design: Experimental study.

Methods: Reverse‐transcription polymerase chain reaction was performed on cholesteatoma tissues from 10 adult patients undergoing tympanomastoid surgery for middle ear cholesteatoma and on 10 samples of normal external auditory canal skin tissue. The expression levels of PPARγ to glyceraldehyde‐3‐phosphate dehydrogenase transcripts were semiquantified by densitometry. We also characterized the cellular localization of the PPARγ protein immunohistochemically. Ki‐67 was also localized to compare the proliferative activity of cells in cholesteatoma epithelium and in normal external auditory canal skin.

Results: PPARγ mRNA and protein were detected in normal external auditory canal skin and in cholesteatoma epithelium. The expression level of PPARγ mRNA in cholesteatoma was significantly increased compared with that in normal external auditory canal skin. PPARγ protein was expressed in cells mainly in the granular and prickle cell layers. However, the intensity of its expression was generally decreased in the parabasal layer of the cholesteatoma epithelium. Ki‐67 was expressed in the nuclei of cells in the basal and parabasal layers, and a greater number of cells were Ki‐67 immunopositive in cholesteatoma epithelium.

Conclusion: PPARγ is up‐regulated in the cholesteatoma epithelium compared with normal external auditory canal skin. These results suggest that PPARγ may play an important role in the pathogenesis of cholesteatoma.
Continuous Laryngoscopy Exercise Test: A Method for Visualizing Laryngeal Dysfunction during Exercise
Authors: Heimdal John‐Helge , Roksund Ola D. , Halvorsen Thomas , Skadberg Britt T. , Olofsson Jan
Published: January 2006

Objectives/Hypothesis: To assess the diagnostic feasibility and patient acceptance of a new developed diagnostic test for exercise induced upper airway flow limitation.

Study Design: Clinical case control study including evaluation of contemporary ergo‐spirometry and laryngoscopy continuously performed during exercise.

Methods: Twelve nonsymptomatic controls and four young females with documented dyspnea and noisy breathing during exercise were studied. All subjects exercised to exhaustion on a treadmill while attached to a fully equipped ergo‐spirometry unit and a fiberoptic laryngoscope linked to a video camera and a sound recorder.

Results: The test situation was well tolerated. Two control subjects had a minor inspiratory synchronous medial motion of the aryepiglottic folds without limitation of laryngeal airflow. In the four symptomatic subjects, exercise induced inspiratory synchronous medial motion of the dorsal part of the aryepiglottic folds as well as vocal cord adduction and inspiratory stridor was demonstrated.

Conclusion: The continuous laryngoscopy exercise test was easy to perform, well tolerated, and can be implemented in future diagnostic work‐up programs of laryngeal dysfunction.
Effects of Nonabsorbable Packing in Middle Meatus after Sinus Surgery
Authors: Bugten Vegard , Nordgård Ståle , Skogvoll Eirik , Steinsvåg Sverre
Published: January 2006

Objectives/Hypothesis: The aim of this study was to evaluate the effects of a nonabsorbable packing (NAP) in the middle meatus (MM) for 5 days after sinus surgery.

Study Design: A randomized, partly blinded, controlled clinical trial.

Methods: Sixty‐one patients (M/F = 30/31, mean age 42, range 18–72) with chronic or acute recurrent rhinosinusitis were included. Fifty‐nine underwent surgery. Thirty‐one had NAP in the MM for 5 days, and 28 served as controls with daily saline irrigations postoperatively. Primary outcome variables were nasal congestion, nasal pain, and headache the first 2 weeks rated on visual analogue scales (VAS; 0–100) and the amount of postoperative bleeding recorded on an ordinal scale (1–4). Secondary outcome variable was the extent of adhesions in MM 10 to 14 weeks after surgery judged by blinded evaluation of endoscopic video recordings.

Results: Fifty‐eight patients completed a diary. No significant differences in primary outcome variables between the groups were found. Nasal congestion decreased most the first 5 to 7 days postoperatively. Removal of the NAP caused little pain (mean 23 on VAS). Temporary bleeding occurred in three patients. Bilateral adhesions were observed in 10 control patients but in none with NAP. Unilateral adhesions were found in nine control patients and in seven with NAP (exact P < .001).

Conclusions: NAP in the MM for 5 days significantly reduced the extent of adhesions in MM compared with saline irrigation alone. NAP did not cause additional discomfort.
Should Ossicular Reconstruction Be Staged Following Tympanomastoidectomy
Authors: Kim Harold H. , Battista Robert A. , Kumar Arvind , Wiet Richard J.
Published: January 2006

Objectives: To determine whether ossicular reconstruction (OCR) performed concurrent with tympanomastoidectomy for cholesteatoma results in significantly different hearing results when compared to OCR performed in a separate, staged procedure.

Study Design: Retrospective.

Materials and Methods: Study subjects were patients undergoing OCR within a 2‐year period. Intervention was OCR concurrent with tympanomastoidectomy for cholesteatoma (group 1) or staged following tympanomastoidectomy for cholesteatoma (group 2). Main outcome measures were mean postoperative air‐bone gap (ABG), proportion achieving ABG closure to <20 dB and <30 dB for group 1 and group 2 overall and when controlling for type of mastoid cavity created (open or closed) and the status of the stapes suprastructure (TORP vs. PORP OCR).

Results: Eighty‐three patients were identified. Forty underwent OCR concurrent with tympanomastoidectomy and 43 underwent a staged OCR after tympanomastoidectomy. Overall, similar hearing results were seen in the two groups. When considering the status of the stapes and mastoid cavity, concurrent OCR resulted in improved mean postoperative ABG in a closed mastoid cavity with an intact stapes suprastructure (P = .024). Furthermore, a greater proportion of patients who had concurrent OCR within this group achieved ABG <20 dB and ABG <30 dB, although this difference did not reach statistical significance (P = .092 and P = .078, respectively). By contrast, staged OCR resulted in improved mean postoperative ABG and ABG <30 dB in open mastoid cavities with an absent stapes suprastructure (P = .040, and P = .019, respectively). Similarly, a greater proportion achieved ABG <20 dB, approaching statistical significance (P = .055).

Conclusions: Staged OCR is advantageous in those with most severe disease, whereas those with least severe disease may benefit from a concurrent OCR.
Limited male incubation ability and the evolution of egg size in shorebirds
Authors: Lislevand Terje , Thomas Gavin H
Published: January 2006

In bird species where males incubate but are smaller than females, egg size may be constrained by male body size, and hence ability to incubate the eggs. Using data from 71 such shorebird species, we show that egg size decreases as the degree of female-biased sexual size dimorphism increases, after controlling for female body mass. Relative egg size was not related to mean clutch size. However, when controlling for mating system, the relationship between female-biased sexual size dimorphism and relative egg size was only significant in polyandrous species. The relatively small eggs of socially polyandrous shorebirds have previously been explained as an energy-saving strategy associated with the production of multiple clutches. Our findings suggest that egg size evolution is better explained by male incubation limitation in these birds.
Electrochemical properties of 316L stainless steel with culturing L929 fibroblasts
Authors: Hiromoto Sachiko , Hanawa Takao
Published: January 2006

Potentiodynamic polarization and impedance tests were carried out on 316L stainless steel with culturing murine fibroblast L929 cells to elucidate the corrosion behaviour of 316L steel with L929 cells and to understand the electrochemical interface between 316L steel and cells, respectively. Potential step test was carried out on 316L steel with type I collagen coating and culturing L929 cells to compare the effects of collagen and L929 cells. The open-circuit potential of 316L steel slightly shifted in a negative manner and passive current density increased with cells, indicating a decrease in the protective ability of passive oxide film. The pitting potential decreased with cells, indicating a decrease in the pitting corrosion resistance. In addition, a decrease in diffusivity at the interface was indicated from the decrease in the cathodic current density and the increase in the diffusion resistance parameter in the impedance test. The anodic peak current in the potential step test decreased with cells and collagen. Consequently, the corrosion resistance of 316L steel decreases with L929 cells. In addition, collagen coating would provide an environment for anodic reaction similar to that with culturing cells.
Patterns of Sequence Loss and Cytosine Methylation within a Population of Newly Resynthesized Brassica napus Allopolyploids
Authors: Lukens Lewis N. , Pires J. Chris , Leon Enrique , Vogelzang Robert , Oslach Lynne , Osborn Thomas
Published: December 2005

Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm, which may involve programmed genetic and epigenetic changes during the initial generations following genome fusion. To study the dynamics of genome change, we synthesized 49 isogenic Brassica napus allopolyploids and surveyed them with 76 restriction fragment length polymorphism (RFLP) probes and 30 simple sequence repeat (SSR) primer pairs. Here, we report on the types and distribution of genetic and epigenetic changes within the S1 genotypes. We found that insertion/deletion (indel) events were rare, but not random. Of the 57,710 (54,383 RFLP and 3,327 SSR) parental fragments expected among the amphidiploids, we observed 56,676 or 99.9%. Three loci derived from Brassica rapa had indels, and one indel occurred repeatedly across 29% (14/49) of the lines. Loss of one parental fragment was due to the 400-bp reduction of a guanine-adenine dinucleotide repeat-rich sequence. In contrast to the 4% (3/76) RFLP probes that detected indels, 48% (35/73) detected changes in the CpG methylation status between parental genomes and the S1 lines. Some loci were far more likely than others to undergo epigenetic change, but the number of methylation changes within each synthetic polyploid was remarkably similar to others. Clear de novo methylation occurred at a much higher frequency than de novo demethylation within allopolyploid sequences derived from B. rapa. Our results suggest that there is little genetic change in the S0 generation of resynthesized B. napus polyploids. In contrast, DNA methylation was altered extensively in a pattern that indicates tight regulation of epigenetic changes.