bluuebunny/crossref_metadata_2025 huggingface dataset:
Pattern of participation in leisure activities among older people in relation to their health conditions and contextual factors: a survey in a Swedish urban area
Authors: PAILLARD-BORG STEPHANIE , WANG HUI-XIN , WINBLAD BENGT , FRATIGLIONI LAURA
Published: May 2009

The objective of this study is to describe the pattern of participation in leisure activities in an older population in relation to contextual factors as well as to mental and physical health. A cohort of 1,623 participants aged 75 or older living in Stockholm, Sweden was asked to list all the leisure activities they were engaged in. These were successively organised into 31 major categories and further grouped into mental, social, physical, productive and recreational types. The pattern of participation was examined in relation to age, gender, contextual factors (education, social network) and health status (depressive symptoms, cognitive impairment, dementia, somatic diseases and physical limitation). In spite of their advanced age, the majority of the population was active, as 70 per cent had participated in at least one activity. Reading (19%) was the most prevalent individual activity, and mental activities (43%) the most prevalent activity type. Older age, female gender, low education status, having a poor or limited social network, mental disorders, and physical limitation, were all factors correlated with a decreased engagement in ‘at least one activity’. Contextual factors and health-related factors were related to the five activity types in different ways. The pattern of participation in leisure activities is associated with multiple factors and their recognition is essential to the facilitation of an active lifestyle in the older population.
Association of bone and joint diseases with health-related quality of life among older people: a population-based cross-sectional study in rural Bangladesh
Authors: RANA AKM MASUD , WAHLIN ÅKE , STREATFIELD PETER KIM , KABIR ZARINA NAHAR
Published: May 2009

This study examined the cross-sectional association of bone and joint diseases with health-related quality of life (HRQoL) among 850 randomly sampled people aged 60 or more years in a rural area of Bangladesh. Information about arthritis, back and joint pain was collected through self-reports and two physicians' assessments at a health centre. Health-related quality of life was measured using a multi-dimensional generic instrument designed for older people that has questions on the construct's physical, psychological, social, economic, spiritual and environmental dimensions. Bivariate analyses showed that the most negative effects of bone and joint diseases were on the physical and psychological dimensions. Hierarchical linear regression analyses revealed that joint pain, whether doctor-diagnosed or self-reported, and self-reported back pain were all associated with lower HRQoL scores and accounted for almost 20 per cent of the variation (adjusted for age, sex, education, marital status, household size, income, expenditure and occupation). The analyses further revealed that women with self-reported back pain had significantly lower psychological, environmental and overall HRQoL scores than equivalent men, while self-reported joint pain was associated with significantly lower scores only for the environmental dimension. The strong association of bone and joint diseases with HRQoL underscores the importance of regarding these illnesses as public health problems.
Does the population density of primate species decline from centre to edge of their geographic ranges?
Authors: Fuller H. L. , Harcourt A. H. , Parks S. A.
Published: May 2009

It has long been suggested that species might exhibit their highest densities at the centre of their geographic range and decline in density towards their range limits. If true, this pattern would have important implications for ecological theory and for conservation management. However, empirical support for this pattern remains equivocal. Furthermore, most research on this topic has emphasized temperate taxa, as is true of much of ecology. Therefore, we here test for a decline in population density from centre to edge of the geographic range of a tropical taxon, primates. In the literature we found data on 30 species and 27 genera from a total of 115 studies with duration of at least 3 mo. Mixed-effects linear models and Wilcoxon matched-pairs signed-rank tests indicated no centre–edge gradient in primate densities. However, densities were significantly lower in more disturbed sites, independent of position in the geographic range.
Do dragonflies migrate across the western Indian Ocean?
Authors: Anderson R. Charles
Published: May 2009

In the tropical Indian Ocean, the Maldive Islands lack surface freshwater, so are unsuitable for dragonfly reproduction. Nevertheless, millions of dragonflies (Insecta, Odonata; mostly globe skimmer, Pantala flavescens) appear suddenly every year starting in October. Arrival dates in the Maldives and India demonstrate that the dragonflies travel from southern India, a distance of some 500–1000 km. Dates of arrival and occurrence coincide with the southward passage of the Inter-tropical Convergence Zone (ITCZ). Circumstantial evidence suggests that the dragonflies fly with north-easterly tail winds, within and behind the ITCZ, at altitudes over 1000 m. It is proposed that this massive movement of dragonflies is part of an annual migration across the western Indian Ocean from India to East Africa. Arrival dates in the Seychelles support this hypothesis. Dragonflies also appear (in smaller numbers) in the Maldives in May, with the onset of the southwest monsoon, suggesting a possible return migration from Africa. These proposed migrations of dragonflies, regularly crossing 3500 km or more of open ocean, were previously unknown. It is known that these dragonflies exploit ephemeral rain pools for reproduction; the monsoons and ITCZ bring not only alternating, seasonal rains to India and Africa, but also appropriate winds for dragonflies to follow those rains. Several bird species migrate from India across the western Indian Ocean to wintering grounds in Africa. They do so at the same time as the dragonflies, presumably taking advantage of the same seasonal tail winds. Many of these birds also eat dragonflies; the possible significance of this was not previously appreciated.
Importance of nurse logs as a substrate for the regeneration of pioneer tree species on Barro Colorado Island, Panama
Authors: Sanchez Evelyn , Gallery Rachel , Dalling James W.
Published: May 2009

Fallen tree trunks (‘nurse logs’) are important recruitment sites for trees in temperate forest, however nurse log use is seldom reported in tropical forests. We predicted that logs should be important for the regeneration of small-seeded tropical pioneer species because surface leaf litter and competition with established vegetation reduces the establishment success of these species from soil seed banks. In a survey on Barro Colorado Island, Panama, we found that pioneer seedlings were present on logs in 40 of 95 recent treefall gaps. In gaps where seedlings were present on logs, seedling density was not significantly different from adjacent areas of soil. However, species composition was significantly different; logs were disproportionately colonized by smaller-seeded and wind-dispersed species. In growing-house experiments using 12 species, we found that wood substrate had little effect on seed germination. In contrast, seedling growth was 50% lower on decayed wood than soil. Furthermore, species growth rates on wood were not significantly correlated with growth rates in soil (df = 10, r = 0.48). If establishment on logs eventually leads to recruitment to the forest canopy, then logs may promote the maintenance of diversity by favouring a different group of species from those that recruit in soil.
Microbial activity in contrasting conditions of soil C and N availability in a tropical dry forest
Authors: Montaño Noé Manuel , Sandoval-Pérez Ana Lidia , García-Oliva Felipe , Larsen John , Gavito Mayra E.
Published: May 2009

We studied the relationships between soil nutrient availability and microbial biomass and activity of two contrasting soil conditions in a tropical deciduous forest in western Mexico. Hilltops have higher pH, water, dissolved organic C, and ammonium concentrations than hillslopes. Our main hypothesis was that soil microbial biomass, microbial activity and bacterium species richness would be higher in soils with high availability of nutrients. Fifteen soil cores, 0–5 cm depth, were taken in the dry, early rainy and rainy season, from each of the ten replicate plots in hilltop and hillslope positions located on three contiguous small watersheds. We measured moisture, C, N and P availability, potential C mineralization, net nitrification, microbial biomass and culturable heterotrophic and nitrifying bacteria in composite samples from each plot. Microbial biomass, species richness of culturable heterotrophic bacteria and C mineralization were significantly higher on hilltops than on hillslopes. Net nitrification was, in contrast, significantly higher on hillslopes than on hilltops and counts of culturable nitrifying bacteria were also significantly higher in the rainy-season samples. Hilltops and hillslopes had low similarity in composition of culturable heterotrophic bacterial species, particularly during the rainy season. The results suggested that C and N availability and seasonal changes in soil moisture are important controlling factors for some soil culturable-bacterial species, which may affect both C mineralization and nitrification in these tropical deciduous forest soils.
EXTERNALISM, INTERNALISM, AND LOGICAL TRUTH
Authors: BESSON CORINE
Published: May 2009

The aim of this paper is to show what sorts of logics are required by externalist and internalist accounts of the meanings of natural kind nouns. These logics give us a new perspective from which to evaluate the respective positions in the externalist--internalist debate about the meanings of such nouns. The two main claims of the paper are the following: first, that adequate logics for internalism and externalism about natural kind nouns are second-order logics; second, that an internalist second-order logic is a free logic—a second order logic free of existential commitments for natural kind nouns, while an externalist second-order logic is not free of existential commitments for natural kind nouns—it is existentially committed.
PLURAL QUANTIFICATION LOGIC: A CRITICAL APPRAISAL
Authors: BEN-YAMI HANOCH
Published: May 2009

I first show that most authors who developed Plural Quantification Logic (PQL) argued it could capture various features of natural language better than can other logic systems. I then show that it fails to do so: it radically departs from natural language in two of its essential features; namely, in distinguishing plural from singular quantification and in its use of an ‘is-one-of’ relation. Next, I sketch a different approach that is more adequate than PQL for capturing plural aspects of natural language semantics and logic. I conclude with a criticism of the claim that PQL should replace natural language for specific philosophical or scientific purposes.
ON THE ONTOLOGICAL COMMITMENT OF MEREOLOGY
Authors: CARRARA MASSIMILIANO , MARTINO ENRICO
Published: May 2009

In Parts of Classes (1991) and Mathematics Is Megethology (1993) David Lewis defends both the innocence of plural quantification and of mereology. However, he himself claims that the innocence of mereology is different from that of plural reference, where reference to some objects does not require the existence of a single entity picking them out as a whole. In the case of plural quantification “we have many things, in no way do we mention one thing that is the many taken together”. Instead, in the mereological case: “we have many things, we do mention one thing that is the many taken together, but this one thing is nothing different from the many” (Lewis, 1991, p. 87). The aim of the paper is to argue that—for a certain use of mereology, weaker than Lewis’ one—an innocence thesis similar to that of plural reference is defensible. To give a precise account of plural reference, we use the idea of plural choice. We then propose a virtual theory of mereology in which the role of individuals is played by plural choices of atoms.
Improved estimates of percolation and anisotropic permeability from 3‐D X‐ray microtomography using stochastic analyses and visualization
Authors: Liu Jie , Regenauer‐Lieb Klaus , Hines Chris , Liu Keyu , Gaede Oliver , Squelch Andrew
Published: May 2009

X‐ray microtomography (micro‐CT) with micron resolution enables new ways of characterizing microstructures and opens pathways for forward calculations of multiscale rock properties. A quantitative characterization of the microstructure is the first step in this challenge. We developed a new approach to extract scale‐dependent characteristics of porosity, percolation, and anisotropic permeability from 3‐D microstructural models of rocks. The Hoshen‐Kopelman algorithm of percolation theory is employed for a standard percolation analysis. The anisotropy of permeability is calculated by means of the star volume distribution approach. The local porosity distribution and local percolation probability are obtained by using the local porosity theory. Additionally, the local anisotropy distribution is defined and analyzed through two empirical probability density functions, the isotropy index and the elongation index. For such a high‐resolution data set, the typical data sizes of the CT images are on the order of gigabytes to tens of gigabytes; thus an extremely large number of calculations are required. To resolve this large memory problem parallelization in OpenMP was used to optimally harness the shared memory infrastructure on cache coherent Non‐Uniform Memory Access architecture machines such as the iVEC SGI Altix 3700Bx2 Supercomputer. We see adequate visualization of the results as an important element in this first pioneering study.
Variability of marine aerosol fine‐mode fraction and estimates of anthropogenic aerosol component over cloud‐free oceans from the Moderate Resolution Imaging Spectroradiometer (MODIS)
Authors: Yu Hongbin , Chin Mian , Remer Lorraine A. , Kleidman Richard G. , Bellouin Nicolas , Bian Huisheng , Diehl Thomas
Published: May 2009

In this study, we examine seasonal and geographical variability of marine aerosol fine‐mode fraction (fm) and its impacts on deriving the anthropogenic component of aerosol optical depth (τa) and direct radiative forcing from multispectral satellite measurements. A proxy of fm, empirically derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 5 data, shows large seasonal and geographical variations that are consistent with the Goddard Chemistry Aerosol Radiation Transport (GOCART) and Global Modeling Initiative (GMI) model simulations. The so‐derived seasonally and spatially varying fm is then implemented into a method of estimating τa and direct radiative forcing from the MODIS measurements. It is found that the use of a constant value for fm as in previous studies would have overestimated τa by about 20% over global ocean, with the overestimation up to ∼45% in some regions and seasons. The 7‐year (2001–2007) global ocean average τa is 0.035, with yearly average ranging from 0.031 to 0.039. Future improvement in measurements is needed to better separate anthropogenic aerosol from natural ones and to narrow down the wide range of aerosol direct radiative forcing.
Environmental factors controlling the Barents Sea spring‐summer phytoplankton blooms
Authors: Signorini Sergio R. , McClain Charles R.
Published: May 2009

We provide an analysis of the seasonal change of the physical forcing factors and their impact on the timing and intensity of phytoplankton blooms in the Barents Sea, with emphasis on the different functional groups that can be distinguished (coccolithophores and other phytoplankton groups) using satellite remote sensing algorithms. Our analyses are based on an integration of satellite derived products and historical hydrographic data. There is a significant phase shift between the peaks of the diatom bloom in May to the coccolithophore bloom in August. Light and nutrient variability, driven by the large seasonal changes of solar irradiance and mixed layer depth in the Barents Sea, are the major environmental factors controlling these phytoplankton blooms. Based on previous field campaigns that identified Emiliana huxleyi as the most predominant species of coccolithophores in the Barents Sea, we conclude that the high concentration of calcite retrieved by ocean color satellites in summer is a result of bloom‐forming coccolithophores of this species. A strong correlation between calcite concentration and wind speed squared (r2 = 0.8) was found during the peak of the bloom. We suggest that this correlation is an indication of CO2 fertilization resulting from regionally enhanced uptake of atmospheric CO2.
Finding the best proxies for the solar UV irradiance
Authors: Dudok de Wit T. , Kretzschmar M. , Lilensten J. , Woods T.
Published: May 2009

Solar UV emission has a profound impact on the upper terrestrial atmosphere. Because of instrumental constraints, however, solar proxies often need to be used as substitutes for the solar spectral variability. Finding proxies that properly reproduce specific spectral bands or lines is an ongoing problem. Using daily observations from 2003 to 2008 and a multiscale statistical approach, we test the performance of 9 proxies for the UV solar flux. Their relevance is evaluated at different time‐scales and a novel representation allows all quantities to be compared simultaneously. This representation reveals which proxies are most appropriate for different spectral bands and for different time scales.
Transient response of the MOC and climate to potential melting of the Greenland Ice Sheet in the 21st century
Authors: Hu Aixue , Meehl Gerald A. , Han Weiqing , Yin Jianjun
Published: May 2009

The potential effects of Greenland Ice Sheet (GrIS) melting on the Atlantic meridional overturning circulation (MOC) and global climate in the 21st century are assessed using the Community Climate System Model version 3 with prescribed rates of GrIS melting. Only when GrIS melting flux is strong enough to be able to produce net freshwater gain in upper subpolar North Atlantic does the MOC weaken further in the 21st century. Otherwise this additional melting flux does not alter the MOC much relative to the simulation without this added flux. The weakened MOC doesn't make the late 21st century global climate cooler than the late 20th century, but does reduce the magnitude of the warming in the northern high latitudes by a few degrees. Moreover, the additional dynamic sea level rise due to this weakened MOC could potentially aggravate the sea level problem near the northeast North America coast.
Upstream conditions at Mercury during the first MESSENGER flyby: Results from two independent solar wind models
Authors: Zieger Bertalan , Hansen Kenneth C. , Cohen Ofer , Gombosi Tamas I. , Zurbuchen Thomas H. , Anderson Brian J. , Korth Haje
Published: May 2009

The primary goal of this paper is to provide estimates of upstream solar wind plasma conditions at Mercury during the January 2008 MESSENGER flyby, based on two completely independent solar wind models. The first is a steady‐state three‐dimensional (3‐D) magnetohydrodynamic (MHD) model of the solar corona and inner heliosphere, which simulates the solar wind propagation from the source surface outward to Mercury, using synoptic charts of the photospheric magnetic field as input. The second model is a time‐dependent 1‐D MHD model of solar wind propagation that employs actual solar wind data at 1 AU as boundary conditions and propagates the solar wind backward in time to Mercury. We compare and validate the two models with each other as well as with actual magnetic field data from the MESSENGER Magnetometer instrument. Our combined method can produce the most accurate results for the solar wind speed and the sector structure of the interplanetary magnetic field.
The Role of Obesity‐associated Loci Identified in Genome‐wide Association Studies in the Determination of Pediatric BMI
Authors: Zhao Jianhua , Bradfield Jonathan P. , Li Mingyao , Wang Kai , Zhang Haitao , Kim Cecilia E. , Annaiah Kiran , Glessner Joseph T. , Thomas Kelly , Garris Maria , Frackelton Edward C. , Otieno F. George , Shaner Julie L. , Smith Ryan M. , Chiavacci Rosetta M. , Berkowitz Robert I. , Hakonarson Hakon , Grant Struan F.A.
Published: May 2009

The prevalence of obesity in children and adults in the United States has increased dramatically over the past decade. Besides environmental factors, genetic factors are known to play an important role in the pathogenesis of obesity. A number of genetic determinants of adult BMI have already been established through genome‐wide association (GWA) studies. In this study, we examined 25 single‐nucleotide polymorphisms (SNPs) corresponding to 13 previously reported genomic loci in 6,078 children with measures of BMI. Fifteen of these SNPs yielded at least nominally significant association to BMI, representing nine different loci including INSIG2, FTO, MC4R, TMEM18, GNPDA2, NEGR1, BDNF, KCTD15, and 1q25. Other loci revealed no evidence for association, namely at MTCH2, SH2B1, 12q13, and 3q27. For the 15 associated variants, the genotype score explained 1.12% of the total variation for BMI z‐score. We conclude that among 13 loci that have been reported to associate with adult BMI, at least nine also contribute to the determination of BMI in childhood as demonstrated by their associations in our pediatric cohort.
Relationship Between Basal Metabolic Rate, Gender, Age, and Body Composition in 8,780 White Obese Subjects
Authors: Lazzer Stefano , Bedogni Giorgio , Lafortuna Claudio L. , Marazzi Nicoletta , Busti Carlo , Galli Raffaela , de Col Alessandra , Agosti Fiorenza , Sartorio Alessandro
Published: May 2009

The objective of the present study was to explore the relationship between basal metabolic rate (BMR), gender, age, anthropometric characteristics, and body composition in severely obese white subjects. In total, 1,412 obese white children and adolescents (BMI > 97° percentile for gender and age) and 7,368 obese adults (BMI > 30 kg/m2) from 7 to 74 years were enrolled in this study. BMR was measured using an indirect calorimeter equipped with a canopy and fat free mass (FFM) were obtained using tetrapolar bioelectrical impedance analysis (BIA). Using analysis of covariance, we tested the effect of gender on the relationship between BMR, age, anthropometry, and body composition. In children and adolescents, the predictor × gender interaction was significant in all cases except for FFM × gender. In adults, all predictor × gender interactions were significant. A prediction equation based on body weight (BW), age, and gender had virtually the same accuracy of the one based on FFM, age, and gender to predict BMR in both children and adults (R2adj = 0.59 and 0.60, respectively). In conclusion, gender was a significant determinant of BMR in children and adolescents but not in adults. Our results support the hypothesis that the age‐related decline in BMR is due to a reduction in FFM. Finally, anthropometric predictors of BMR are as accurate as body composition estimated by BIA.
Multipotential ability of primitive germ cells from neonatal pig testis cultured in vitro
Authors: Goel Sandeep , Fujihara Mayako , Tsuchiya Kazuo , Takagi Yuji , Minami Naojiro , Yamada Masayasu , Imai Hiroshi
Published: May 2009

Gonocytes are progenitor-type germ cells that arise from primordial germ cells and differentiate further into spermatogonia, thereby initiating spermatogenesis. In the present study, freshly isolated gonocytes were found to have either weak or no expression of pluripotency determining transcription factors, such as POU5F1, SOX2 and C-MYC. Interestingly, the expression of these transcription factors, as well as other vital transcription factors, such as NANOG, KLF4 and DAZL, were markedly upregulated in cultured cells. Cells in primary cultures expressed specific germ cell and pluripotency markers, such as lectin Dolichos biflorus agglutinin (DBA), KIT, ZBTB16, stage-specific embryonic antigen (SSEA-1), NANOG and POU5F1. Using a monoclonal antibody to specifically identify porcine germ cells, the stem cell potential of fresh and cultured cells was determined with a testis xenotransplantation assay. Colonised porcine germ cells were detected only in mouse testes that were either transplanted with fresh testicular cells or with cells from primary cultures. Interestingly, testes transplanted with cells from primary cultures showed colonisation of germ cells in the interstitial space, reflecting their tumourigenic nature. The formation of teratomas with tissues originating from the three germinal layers following the subcutaneous injection of cells into nude mice from primary cultures confirmed their multipotency. The results of the present study may provide useful information for the establishment of multipotent germ stem cell lines from neonatal pig testis.
Expression of vascular endothelial growth factor (VEGF) receptor in goat ovaries and improvement of in vitro caprine preantral follicle survival and growth with VEGF
Authors: Bruno J. B. , Celestino J. J. H. , Lima-Verde I. B. , Lima L. F. , Matos M. H. T. , Araújo V. R. , Saraiva M. V. A. , Martins F. S. , Name K. P. O. , Campello C. C. , Báo S. N. , Silva J. R. V. , Figueiredo J. R.
Published: May 2009

The aim of the present study was to evaluate the effect of vascular endothelial growth factor (VEGF) on the survival and growth of goat preantral follicles after in vitro culture and to verify the expression of VEGF receptor (VEGFR)-2 in goat ovaries. Ovarian fragments were cultured for 1 or 7 days in minimal essential medium (MEM) with different concentrations of VEGF (1, 10, 50, 100 or 200 ng mL–1). Non-cultured (fresh control) and cultured tissues were processed for histological and ultrastructural studies. The results showed that 200 ng mL–1 VEGF resulted in a similar percentage of normal preantral follicles after 1 and 7 days of culture compared with control. Compared with basic culture medium alone, an increase in follicular and oocyte diameters was observed in the presence of 10 ng mL–1 VEGF after 7 days culture. Ultrastructural analysis confirmed follicular integrity after 7 days culture in the presence of 200 ng mL–1 VEGF. Immunohistochemical studies demonstrated the expression of VEGFR-2 in oocytes and granulosa cells of all follicular stages, except in granulosa cells of primordial follicles. In conclusion, the present study has shown that VEGF maintains follicular ultrastructural integrity and promotes follicular growth. In addition, VEGFR-2 is expressed in oocytes of caprine ovarian follicles at all developmental stages and in granulosa cells of developing follicles.
Semen parameters, fertility and testosterone levels in male rats exposed prenatally to betamethasone
Authors: Piffer Renata C. , Garcia Patrícia C. , Gerardin Daniela C. C. , Kempinas Wilma G. , Pereira Oduvaldo C. M.
Published: May 2009

The present study investigated the long-term effects of prenatal betamethasone exposure on sperm quality and count, fertility and plasma testosterone levels in adult male rats. Pregnant rats received 0.1 mg kg–1 betamethasone on Days 12, 13, 18 and 19 of pregnancy. This treatment impaired sperm quality, sperm production, fertility and plasma testosterone levels in adult male offspring compared to the control group. Thus, the results of the present study indicate that the long-term effects of prenatal betamethasone exposure may be deleterious to offspring. The consequent decrease in testosterone production during adulthood, in association with damaged semen parameters, may explain for the observed decrease in the capacity of adult male offspring to themselves generate viable descendants.
Formation of 5α-reduced androgens in the testes and urogenital tract of the grey short-tailed opossum, Monodelphis domestica
Authors: Wilson Jean D. , Renfree Marilyn B. , Auchus Richard J. , Pask Andrew J. , Shaw Geoffrey
Published: May 2009

Testicular 5α-reduced androgens, largely 5α-androstane-3α,17β-diol (androstanediol), are responsible for virilisation of pouch young in one marsupial (the tammar wallaby), but are not formed until later in development in another marsupial (the brushtail possum) and in rodents. Because the mechanism of virilisation of the urogenital tract in the grey short-tailed opossum Monodelphis domestica has never been defined, androgen formation and metabolism were investigated in this species. Testis fragments from grey short-tailed opossums of a wide range of ages were incubated with [3H]-progesterone and the metabolites were separated by high-performance liquid chromatography (HPLC). The only 19-carbon metabolites identified in the youngest ages (5–26 days) and the major metabolites in adult testes were testosterone and androstenedione. At 30, 42 and 49 days of age, dihydrotestosterone and small amounts of androstanediol were present. Time-sequence studies indicated that dihydrotestosterone and androstanediol were formed from the 5α-reduction (and 3-keto reduction) of testosterone. In a second series of experiments, tissue fragments of a variety of urogenital tract tissues were incubated with [3H]-testosterone and the metabolites separated by HPLC. During the interval in which male urogenital tract differentiation takes place in this species (between Days 15 and 28), the major metabolite identified was dihydrotestosterone. We conclude that the timing of 5α-reductase expression in the testes of the grey short-tailed possum resembles that of rodents and the brushtail possum rather than that of the tammar wallaby and that dihydrotestosterone is probably the intracellular androgen responsible for virilisation of the urogenital tract in this species.
Reorganisation of human sperm nuclear architecture during formation of pronuclei in a model system
Authors: Mudrak Olga , Chandra Rajeev , Jones Estella , Godfrey Earl , Zalensky Andrei
Published: May 2009

By fertilisation, two terminally differentiated cells, namely the egg and spermatozoon, are combined to create a totipotent zygote. During this process, the inactive sperm nucleus is transformed into a functional male pronucleus. Recent studies demonstrate that human sperm chromatin has an elaborate multilevel organisation, but almost nothing is known about how sperm chromosomes are transformed during fertilisation. Because of ethical reasons and technical complications, experimentation with human embryos is generally unworkable and adequate model systems are necessary to study the formation of male pronuclei. Here, we analyse remodelling of human sperm chromatin and chromosome architecture in Xenopus egg extracts using immunofluorescent localisation of protamines and centromere protein A, as well as fluorescence in situ hybridisation localisation of major α-satellite DNA and whole chromosome territory (CT). We demonstrate noticeable relocalisation of centromeres and remodelling of CT during the decondensation–recondensation cycle, mimicking cellular events that occur in the paternal genome in vivo during fertilisation.
Soil moisture dynamics and smoldering combustion limits of pocosin soils in North Carolina, USA
Authors: Reardon James , Curcio Gary , Bartlette Roberta
Published: May 2009

Smoldering combustion of wetland organic soils in the south-eastern USA is a serious management concern. Previous studies have reported smoldering was sensitive to a wide range of moisture contents, but studies of soil moisture dynamics and changing smoldering combustion potential in wetland communities are limited. Linking soil moisture measurements with estimates of the sustained smoldering limits of organic soils will improve our understanding of changes in ground fire potential over time. Seasonal soil moisture trends were monitored in six North Carolina coastal plain pocosin sites from January 2005 to November 2007. Measurements of the root-mat upper soil horizons were sampled at 2-week intervals while measurements of lower horizon muck (sapric) soil moisture contents and watertable depths were made with automated data logging equipment. The watertable and soil moisture responses were influenced by seasonal and yearly differences in precipitation and hydrologic factors. The maximum estimated probabilities of sustained smoldering were highest in the fall of 2007 and lowest in 2006. Watertable depth was not a consistent predictor of the smoldering combustion potential in the upper organic soil horizons. Maximum Keetch–Byram Drought Index values on all sites were between 500 and 662 during 2005 and 2007 and these values were not consistent with measured soil moistures.
A simple model for wind effects of burning structures and topography on wildland–urban interface surface-fire propagation
Authors: Rehm Ronald G. , Mell William (Ruddy)
Published: May 2009

The present paper presents a simple model to demonstrate the effect on grass-fire propagation of the winds induced by structural fires in a wildland–urban interface setting. The model combines an empirical formula for wind-driven grass-fire spread and a physics-based analytical solution to the Euler equations to determine the ground-level wind produced by the burning structure. The scaling of the wind is based on the heat release rate of the structural fire as well as other parameters. Also considered are an ambient wind and a topographical wind, assumed to be proportional to the ground slope. Data on grass and structure fires required by the model are discussed. Fire front propagation predicted by this model is illustrated by three examples: a front passing a single burning structure on flat terrain, a front passing a burning structure on a hill, and a front passing several burning structures. The model predicts that a fire front will be accelerated toward the burning structure upon approach and decelerated after passing the structure. Several burning structures multiply the effects of an individual burning structure.
Refining the polytypic species concept of mangrove monitors (Squamata: Varanus indicus group): a new cryptic species from the Talaud Islands, Indonesia, reveals the underestimated diversity of Indo-Australian monitor lizards
Authors: Koch André , Arida Evy , Schmitz Andreas , Böhme Wolfgang , Ziegler Thomas
Published: May 2009

The description of a new cryptic member of the mangrove monitor (Varanus indicus) (Daudin, 1802) group from Indonesia presents a refinement of the systematic concept for a polytypic complex of closely related species. The new species is recognised on the basis of morphological and molecular evidence. It is so far known only from the type locality, the remote Talaud Islands, located between Sulawesi, Halmahera and Mindanao at the outer boundary of the Wallacea transition zone between the Oriental and Australian faunal regions. While the descriptions of several sibling and mostly sympatric species within the last 15 years have not affected the range of V. indicus, here, we demonstrate that morphologically distinct island populations represent independent evolutionary lineages and warrant specific recognition as distinct species within an evolving superspecies complex. In addition, some basic natural history information is provided for the new species based on observations at the type locality. These systematic and zoogeographic investigations reveal shortcomings in the current knowledge concerning the diversity and endemism of Indo-Australian monitor lizards, particularly within the Wallacean region.
ELECTRIC CHARGING OF DUST AGGREGATES AND ITS EFFECT ON DUST COAGULATION IN PROTOPLANETARY DISKS
Authors: Okuzumi Satoshi
Published: May 2009

Mutual sticking of dust aggregates is the first step toward planetesimal formation in protoplanetary disks. In spite that the electric charging of dust particles is well recognized in some contexts, it has been largely ignored in the current modeling of dust coagulation. In this study, we present a general analysis of the dust charge state in protoplanetary disks, and then demonstrate how the electric charging could dramatically change the currently accepted scenario of dust coagulation. First, we describe a new semianalytical method to calculate the dust charge state and gas ionization state self-consistently. This method is far more efficient than previous numerical methods, and provides a general and clear description of the charge state of a gas–dust mixture. Second, we apply this analysis to compute the collisional cross section of growing aggregates taking their charging into account. As an illustrative example, we focus on early evolutionary stages where the dust has been thought to grow into fractal (D ∼ 2) aggregates with a quasi-monodisperse (i.e., narrow) size distribution. We find that, for a wide range of model parameters, the fractal growth is strongly inhibited by the electric repulsion between colliding aggregates and eventually “freezes out” on its way to the subsequent growth stage involving collisional compression. Strong disk turbulence would help the aggregates to overcome this growth barrier, but then it would cause catastrophic collisional fragmentation in later growth stages. These facts suggest that the combination of electric repulsion and collisional fragmentation would impose a serious limitation on dust growth in protoplanetary disks. We propose a possible scenario of dust evolution after the freezeout. Finally, we point out that the fractal growth of dust aggregates tends to maintain a low ionization degree and, as a result, a large magnetorotationally stable region in the disk.
A lower hybrid current drive system for ITER
Authors: Hoang G.T. , Bécoulet A. , Jacquinot J. , Artaud J.F. , Bae Y.S. , Beaumont B. , Belo J.H. , Berger-By G. , Bizarro João P.S. , Bonoli P. , Cho M.H. , Decker J. , Delpech L. , Ekedahl A. , Garcia J. , Giruzzi G. , Goniche M. , Gormezano C. , Guilhem D. , Hillairet J. , Imbeaux F. , Kazarian F. , Kessel C. , Kim S.H. , Kwak J.G. , Jeong J.H. , Lister J.B. , Litaudon X. , Magne R. , Milora S. , Mirizzi F. , Namkung W. , Noterdaeme J.M. , Park S.I. , Parker R. , Peysson Y. , Rasmussen D. , Sharma P.K. , Schneider M. , Synakowski E. , Tanga A. , Tuccillo A. , Wan Y.X.
Published: May 2009

A 20 MW/5 GHz lower hybrid current drive (LHCD) system was initially due to be commissioned and used for the second mission of ITER, i.e. the Q = 5 steady state target. Though not part of the currently planned procurement phase, it is now under consideration for an earlier delivery. In this paper, both physics and technology conceptual designs are reviewed. Furthermore, an appropriate work plan is also developed. This work plan for design, R&D, procurement and installation of a 20 MW LHCD system on ITER follows the ITER Scientific and Technical Advisory Committee (STAC) T13-05 task instructions. It gives more details on the various scientific and technical implications of the system, without presuming on any work or procurement sharing amongst the possible ITER partnersb The LHCD system of ITER is not part of the initial cost sharing.. This document does not commit the Institutions or Domestic Agencies of the various authors in that respect.
On the merits of heating and current drive for tearing mode stabilization
Authors: De Lazzari D. , Westerhof E.
Published: May 2009

Neoclassical tearing modes (NTMs) are magnetohydrodynamic modes that can limit the performance of high β discharges in a tokamak, leading eventually to a plasma disruption. A NTM is sustained by the perturbation of the ‘bootstrap’ current, which is a consequence of the pressure flattening across a magnetic island. Control and suppression of this mode can be achieved by means of electron cyclotron waves (ECWs) which allow the deposition of highly localized power at the island location. The ECW power replenishes the missing bootstrap current by generating a current perturbation either inductively, through a temperature perturbation (electron cyclotron resonance heating), or non-inductively by direct current drive (electron cyclotron current drive). Although both methods have been applied successfully to experiments showing a predominance of ECRH for medium-sized limiter tokamaks (TEXTOR, T-10) and of ECCD for mid-to-large-sized divertor tokamaks (AUG, DIII-D, JT-60), conditions determining their relative importance are still unclear. We address this problem with a numerical study focused on the contributions of heating and current drive to the temporal evolution of NTMs as described by the modified Rutherford equation. For the effects of both heating as well as current drive, simple analytical expressions have been found in terms of an efficiency fore-factor times a ‘geometrical’ term depending on the power deposition width w
dep, location and modulation. When the magnetic island width w equals the width of the deposition profile, w ≈ w
dep, both geometric terms are practically identical. Whereas for current drive the geometric term approaches a constant for small island widths and is inversely proportional to (w/w
dep)2 for large island widths, the heating term approaches a constant for large island widths and is proportional to (w/w
dep) for small island widths. For medium-sized tokamaks (TEXTOR, AUG) the heating and current drive efficiencies are of the same order of magnitude, whereas in a future, large reactor like ITER the current drive efficiency is expected to be significantly larger.
Estrogen Inhibits ATR Signaling to Cell Cycle Checkpoints and DNA Repair
Authors: Pedram Ali , Razandi Mahnaz , Evinger Albert J. , Lee Eva , Levin Ellis R.
Published: May 2009

DNA damage activates the ataxia telangiectasia–mutated and Rad3-related (ATR) kinase signal cascade. How this system is restrained is not understood. We find that in estrogen receptor (ER)-positive breast cancer cells, UV or ionizing radiation and hydroxyurea rapidly activate ATR-dependent phosphorylation of endogenous p53 and Chk1. 17-β-estradiol (E2) substantially blocks ATR activity via plasma membrane-localized ERα. E2/ER reduces the enhanced association of ATR andTopBP1 proteins that follows DNA damage and strongly correlates to ATR activity. E2 inhibits ATR activation through rapid PI3K/AKT signaling: AKT phosphorylates TopBP1 at Serine 1159, thereby preventing the enhanced association of ATR with TopBP1 after DNA damage. E2 also inhibits Claspin:Chk1 protein association via AKT phosphorylation of Chk1, preventing Chk1 signaling to the G2/M checkpoint. ATR-phosphorylation of p53 induces p21 transcription, prevented by E2/ER. E2 delays the assembly and prolongs the resolution of γH2AX and Rad51 nuclear foci and delays DNA repair. E2/ER also increases the chromosomal damage seen from cell exposure to IR. Therefore, the restraint of ATR cascade activation may be a novel estrogen action relevant to breast cancer.
The Stress-activated Protein Kinase Hog1 Mediates S Phase Delay in Response to Osmostress
Authors: Yaakov Gilad , Duch Alba , García-Rubio María , Clotet Josep , Jimenez Javier , Aguilera Andrés , Posas Francesc
Published: May 2009

Control of cell cycle progression by stress-activated protein kinases (SAPKs) is essential for cell adaptation to extracellular stimuli. Exposure of yeast to osmostress activates the Hog1 SAPK, which modulates cell cycle progression at G1 and G2 by the phosphorylation of elements of the cell cycle machinery, such as Sic1 and Hsl1, and by down-regulation of G1 and G2 cyclins. Here, we show that upon stress, Hog1 also modulates S phase progression. The control of S phase is independent of the S phase DNA damage checkpoint and of the previously characterized Hog1 cell cycle targets Sic1 and Hsl1. Hog1 uses at least two distinct mechanisms in its control over S phase progression. At early S phase, the SAPK prevents firing of replication origins by delaying the accumulation of the S phase cyclins Clb5 and Clb6. In addition, Hog1 prevents S phase progression when activated later in S phase or cells containing a genetic bypass for cyclin-dependent kinase activity. Hog1 interacts with components of the replication complex and delays phosphorylation of the Dpb2 subunit of the DNA polymerase. The two mechanisms of Hog1 action lead to delayed firing of origins and prolonged replication, respectively. The Hog1-dependent delay of replication could be important to allow Hog1 to induce gene expression before replication.
Alignment of the UMLS semantic network with BioTop: methodology and assessment
Authors: Schulz Stefan , Beisswanger Elena , van den Hoek László , Bodenreider Olivier , van Mulligen Erik M.
Published: May 2009

Motivation: For many years, the Unified Medical Language System (UMLS) semantic network (SN) has been used as an upper-level semantic framework for the categorization of terms from terminological resources in biomedicine. BioTop has recently been developed as an upper-level ontology for the biomedical domain. In contrast to the SN, it is founded upon strict ontological principles, using OWL DL as a formal representation language, which has become standard in the semantic Web. In order to make logic-based reasoning available for the resources annotated or categorized with the SN, a mapping ontology was developed aligning the SN with BioTop.

Methods: The theoretical foundations and the practical realization of the alignment are being described, with a focus on the design decisions taken, the problems encountered and the adaptations of BioTop that became necessary. For evaluation purposes, UMLS concept pairs obtained from MEDLINE abstracts by a named entity recognition system were tested for possible semantic relationships. Furthermore, all semantic-type combinations that occur in the UMLS Metathesaurus were checked for satisfiability.

Results: The effort-intensive alignment process required major design changes and enhancements of BioTop and brought up several design errors that could be fixed. A comparison between a human curator and the ontology yielded only a low agreement. Ontology reasoning was also used to successfully identify 133 inconsistent semantic-type combinations.

Availability: BioTop, the OWL DL representation of the UMLS SN, and the mapping ontology are available at http://www.purl.org/biotop/.

Contact:  stschulz@uni-freiburg.de
Pokefind: a novel topological filter for use with protein structure prediction
Authors: Khatib Firas , Rohl Carol A. , Karplus Kevin
Published: May 2009

Motivation: Our focus has been on detecting topological properties that are rare in real proteins, but occur more frequently in models generated by protein structure prediction methods such as Rosetta. We previously created the Knotfind algorithm, successfully decreasing the frequency of knotted Rosetta models during CASP6. We observed an additional class of knot-like loops that appeared to be equally un-protein-like and yet do not contain a mathematical knot. These topological features are commonly referred to as slip-knots and are caused by the same mechanisms that result in knotted models. Slip-knots are undetectable by the original Knotfind algorithm. We have generalized our algorithm to detect them, and analyzed CASP6 models built using the Rosetta loop modeling method.

Results: After analyzing known protein structures in the PDB, we found that slip-knots do occur in certain proteins, but are rare and fall into a small number of specific classes. Our group used this new Pokefind algorithm to distinguish between these rare real slip-knots and the numerous classes of slip-knots that we discovered in Rosetta models and models submitted by the various CASP7 servers. The goal of this work is to improve future models created by protein structure prediction methods. Both algorithms are able to detect un-protein-like features that current metrics such as GDT are unable to identify, so these topological filters can also be used as additional assessment tools.

Contact:  firas@u.washington.edu