bluuebunny/crossref_metadata_2025 huggingface dataset:
Bat wings, bunions, and turkey wattles: body transgressions and older women's strategic clothing choices
Authors: CLARKE LAURA HURD , GRIFFIN MERIDITH , MALIHA KATHERINE
Published: May 2009

This paper examines older women's experiences and perceptions of clothing prescriptions for adults in later life. Using data from in-depth interviews with 36 women aged 71 to 93 years, we investigate the stringent, taken-for-granted social norms that older women identified with respect to appropriate fashion for the ageing female body. Specifically, the participants argued that older women should refrain from wearing bright colours and revealing or overly suggestive styles. Expressing a preference for classic or traditional styles, the women also reported that they used clothing strategically to mask or compensate for bodily transgressions that had occurred over time as a result of the physical realities of ageing, including weight gain, altered body shapes, wrinkles and sagging or ‘flabby’ arms and necks, referred to respectively as ‘bat wings’ and ‘turkey wattles’. In addition, the women contended that they consciously chose their clothing styles to compensate for age-related health issues and/or to present a competent, healthy self to others. Finally, the women talked about the ways in which their clothing choices were influenced by their changing lifestyles and constrained by a lack of desirable and affordable clothing options for the older female body. The findings are discussed in the light of Erving Goffman's concept of stigma and contemporary theorising about ageing, ageism, beauty work and the body.
The challenges of the new institutional environment: an Australian case study of older volunteers in the contemporary non-profit sector
Authors: WARBURTON JENI , McDONALD CATHERINE
Published: May 2009

Increased emphasis on efficiency and regulation is changing the nature of the non-profit sector in western countries. In this paper, we explore the impact of these contemporary changes on older, more traditional volunteers. Specifically, we use neo-institutional theory as a framework to explore the micro-effect of these processes in one large, multi-service non-profit organisation in Australia. The findings of an ethnographic study are presented using an analytical template comprising: (1) the observational space; (2) the conversational order; (3) the content of talk; and (4) areas of resistance. Findings from these categories provided evidence of two institutional orders – one a traditional way of operating consistent with a charity model, and the other, a new, dominant approach driven by market forces. It was found that older, more traditional volunteers struggled to maintain the old order as well as to make the transition to the new order. If organisations are to benefit from a pool of potential volunteers and if older people are to benefit from the social and health advantages associated with productive ageing, there are important implications in these findings. Older people are able to make a successful transition to the new order, but organisations need to be more proactive in facilitating the change. In particular, organisations need to reject ageist cultures and practices, provide training and skills development, and to work collaboratively with older people.
Intra- and interspecific variation in wood density and fine-scale spatial distribution of stand-level wood density in a northern Thai tropical montane forest
Authors: Sungpalee Witchaphart , Itoh Akira , Kanzaki Mamoru , Sri-ngernyuang Kriangsak , Noguchi Hideyuki , Mizuno Takashi , Teejuntuk Sakhan , Hara Masatoshi , Chai-udom Kwanchai , Ohkubo Tatsuhiro , Sahunalu Pongsak , Dhanmmanonda Pricha , Nanami Satoshi , Yamakura Takuo , Sorn-ngai Anan
Published: May 2009

Tropical tree wood density is often related to other species-specific functional traits, e.g. size, growth rate and mortality. We would therefore expect significant associations within tropical forests between the spatial distributions of stand-level wood density and micro-environments when interspecific variation in wood density is larger than intraspecific variation and when habitat-based species assembly is important in the forest. In this study, we used wood cores collected from 515 trees of 72 species in a 15-ha plot in northern Thailand to analyse intra- and interspecific variation in wood density and the spatial association of stand-level wood density. Intraspecific variation was lower than interspecific variation (20% vs. 80% of the total variation), indicating that species-specific differences in wood density, rather than phenotypic plasticity, are the major source of variation in wood density at the study site. Wood density of individual species was significantly negatively related to maximum diameter, growth rate of sapling diameter and mortality of saplings. Stand-level mean wood density was significantly negatively related to elevation, slope convexity, sapling growth rate and sapling mortality, and positively related to slope inclination. East-facing slopes had significantly lower stand-level mean wood densities than west-facing slopes. We hypothesized that ridges and east-facing slopes in the study forest experience strong and frequent wind disturbance, and that this severe impact may lead to faster stand turnover, creating conditions that favour fast-growing species with low wood density.
A valid two-item food security questionnaire for screening HIV-1 infected patients in a clinical setting
Authors: Young Jessica , Jeganathan Sarangapany , Houtzager Louise , Di Guilmi Aaron , Purnomo Julianita
Published: May 2009

Objective

To validate a two-item food security questionnaire (FSQ) for use in a clinical setting to screen HIV-1 infected patients for food insecurity.

Design

The present study was a questionnaire-based survey of forty-nine subjects attending an HIV clinic. Subjects completed a two-item questionnaire and a six-item validated FSQ contemporaneously.

Results

A strong correlation was found between the two-item and six-item FSQ (ρ = 0·895; 95 % CI 0·821, 0·940; P < 0·0001). Cronbach's α coefficient was found to be 0·94 and 0·90 for the two-item and six-item FSQ, respectively. The two-item FSQ yielded a sensitivity of 100 % (95 % CI 75, 100) and a specificity of 78 % (95 % CI 61, 90). The negative predictive value was found to be 100 % (95 % CI 88, 100).

Conclusions

The results of the present study suggest that the two-item FSQ is a valid, reliable and sensitive screening tool of food insecurity in people living with HIV in a clinical setting.
MATRIX-BASED LOGIC FOR APPLICATION IN PHYSICS
Authors: WEINGARTNER PAUL
Published: May 2009

The paper offers a matrix-based logic (relevant matrix quantum physics) for propositions which seems suitable as an underlying logic for empirical sciences and especially for quantum physics. This logic is motivated by two criteria which serve to clean derivations of classical logic from superfluous redundancies and uninformative complexities. It distinguishes those valid derivations (inferences) of classical logic which contain superfluous redundancies and complexities and are in this sense “irrelevant” from those which are “relevant” or “nonredundant” in the sense of allowing only the most informative consequences in the derivations. The latter derivations are strictly valid inRMQ, whereas the former are only materially valid.RMQis a decidable matrix calculus which possesses a semantics and has the finite model property. It is shown in the paper howRMQby its strictly valid derivations can avoid the difficulties with commensurability, distributivity, and Bell's inequalities when it is applied to quantum physics.
NA‐SWS‐1.1: A uniform database of teleseismic shear wave splitting measurements for North America
Authors: Liu Kelly H.
Published: May 2009

This version of shear wave splitting (SWS) database (DB) for North America (NA) contains 6224 pairs of splitting parameters (fast polarization directions and splitting times) measured using all the available data recorded by digital broadband seismic stations over the period of 1980–2007 and archived at the Incorporated Research Institutions for Seismology Data Management Center. The measurements were produced using a set of robust procedures that involve automated batch processing and manual screening and were ranked quantitatively on the basis of a uniform criterion. The result is a homogeneous database of individual (rather than station‐averaged) splitting parameters that can be used by a variety of geoscientists for the understanding of the structure and dynamics of the Earth's deep interior beneath NA. This data brief describes the seismic data and techniques used to generate the SWS results, the spatial and azimuthal coverage, and the limitations of the DB. The DB will be periodically updated and enhanced by adding newly recorded data and by measuring splitting parameters using the PKS and SKKS phases in addition to SKS. The database can be accessed at http://www.mst.edu/∼liukh/SWS.
On the coupling strength between the land surface and the atmosphere: From viewpoint of surface exchange coefficients
Authors: Chen Fei , Zhang Ying
Published: May 2009

This study addresses the land‐atmospheric coupling strength by using long‐term AmeriFlux data from a wide range of land covers and climate regimes to reconstitute the surface exchange coefficient, Ch, which governs the total surface heat fluxes. For spring and summer, results show stronger coupling for tall canopy with Ch values ten times larger than for shorter vegetation. Observed Ch are then compared to values from the Noah land model. Results indicate that Noah underestimated (overestimated) Ch for forest (grass and crops), implying an insufficient (too efficient) coupling for tall canopy (short canopy). This discrepancy is attributed to the treatment of the roughness length for heat. With modest adjustments, the Noah model can reproduce the observed Ch. This study highlights the crucial role of treating the surface exchange processes in coupled land/weather/climate models and the need to use long‐term flux data for different vegetation types and climate regimes to assess and mitigate their deficiencies.
Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave
Authors: Chen Yin , Wu Liqin , Boden Rich , Hillebrand Alexandra , Kumaresan Deepak , Moussard Hélène , Baciu Mihai , Lu Yahai , Colin Murrell J
Published: May 2009

Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monooxygenase). Sulfur oxidizers from both Gammaproteobacteria and Betaproteobacteria were detected in 16S rRNA, soxB and RuBisCO gene libraries. DNA-based stable-isotope probing analyses using 13C-bicarbonate showed that Thiobacillus spp. were most active in assimilating CO2 and also implied that ammonia and nitrite oxidizers were active during incubations. Nitrosomonas spp. were detected in both 16S rRNA and amoA gene libraries from the ‘heavy’ DNA and sequences related to nitrite-oxidizing bacteria Nitrospira and Candidatus ‘Nitrotoga’ were also detected in the ‘heavy’ DNA, which suggests that ammonia/nitrite oxidation may be another major primary production process in this unique ecosystem. A significant number of sequences associated with known methylotrophs from the Betaproteobacteria were obtained, including Methylotenera, Methylophilus and Methylovorus, supporting the view that cycling of one-carbon compounds may be an important process within Movile Cave. Other sequences detected in the bacterial 16S rRNA clone library included Verrucomicrobia, Firmicutes, Bacteroidetes, alphaproteobacterial Rhodobacterales and gammaproteobacterial Xanthomonadales. Archaeal 16S rRNA sequences retrieved were restricted within two groups, namely the Deep-sea Hydrothermal Vent Euryarchaeota group and the Miscellaneous Crenarchaeotic group. No sequences related to known sulfur-oxidizing archaea, ammonia-oxidizing archaea, methanogens or anaerobic methane-oxidizing archaea were detected in this clone library. The results provided molecular biological evidence to support the hypothesis that Movile Cave is driven by chemolithoautotrophy, mainly through sulfur oxidation by sulfur-oxidizing bacteria and reveal that ammonia- and nitrite-oxidizing bacteria may also be major primary producers in Movile Cave.
Resting Energy Expenditure Changes With Weight Loss: Racial Differences
Authors: Wang Xuewen , You Tongjian , Lenchik Leon , Nicklas Barbara J.
Published: May 2009

It is controversial whether weight loss reduces resting energy expenditure (REE) to a different magnitude in black and white women. This aim of this study was to determine whether changes in REE with weight loss were different between black and white postmenopausal women, and whether changes in body composition (including regional lean and fat mass) were associated with REE changes within each race. Black (n = 26) and white (n = 65) women (age = 58.2 ± 5.4 years, 25 < BMI < 40 kg/m2) completed a 20‐week weight‐loss intervention. Body weight, lean and fat mass (total body, limb, and trunk) via dual‐energy X‐ray absorptiometry, and REE via indirect calorimetry were measured before and after the intervention. We found that baseline REE positively correlated with body weight, lean and fat mass (total, limb, and trunk) in white women only (P < 0.05 for all). The intervention decreased absolute REE in both races similarly (1,279 ± 162 to 1,204 ± 169 kcal/day in blacks; 1,315 ± 200 to 1,209 ± 185 kcal/day in whites). REE remained decreased after adjusting for changes in total or limb lean mass in black (1,302–1,182 kcal/day, P = 0.043; 1,298–1,144 kcal/day, P = 0.006, respectively), but not in white, women. Changes in REE correlated with changes in body weight (partial r = 0.277) and fat mass (partial r = 0.295, 0.275, and 0.254 for total, limb, and trunk, respectively; P < 0.05) independent of baseline REE in white women. Therefore, with weight loss, REE decreased in proportion to the amount of fat and lean mass lost in white, but not black, women.
Circadian Rhythm of Clock Genes in Human Adipose Explants
Authors: Gómez‐Santos Cecilia , Gómez‐Abellán Purificación , Madrid Juan A. , Hernández‐Morante Juan J. , Lujan Juan A. , Ordovas José M. , Garaulet Marta
Published: May 2009

To analyze in severely obese women the circadian expression of the clock genes hPer2, hBmal1, and hCry1 in explants from subcutaneous (SAT) and visceral (VAT) adipose tissue (AT), in order to elucidate whether this circadian clockwork can oscillate accurately and independently of the suprachiasmatic nucleus (SCN) and if glucocorticoid metabolism‐related genes such as glucocorticoid receptor (hGr) and 11β‐hydroxysteroid dehydrogenase 1 (h11βHsd1) and the transcription factor peroxisome proliferator activated receptor γ (hPPARγ) are part of the clock controlled genes. AT biopsies were obtained from morbid obese patients (BMI ≥40 kg/m2) (n = 7). Anthropometric variables were measured and fasting plasma lipids and lipoprotein concentrations were analyzed. In order to carry out rhythmic expression analysis, AT explants were cultured during 24 h and gene expression was performed at the following times (T): 0, 6, 12, and 18 h, with quantitative real‐time PCR. Clock genes oscillated accurately and independently of the SCN in AT explants. Their intrinsic oscillatory mechanism regulated the timing of other genes such as hPPARγ and glucocorticoid‐related genes. Circadian patterns differed between VAT and SAT. Correlation analyses between the genetic circadian oscillation and components of the metabolic syndrome (MetS) revealed that subjects with a higher sagittal diameter showed an increased circadian variability in hPer2 expression (r = 0.91; P = 0.031) and hBmal1 (r = 0.90; P = 0.040). Data demonstrate the presence of peripheral circadian oscillators in human AT independently of the central circadian control mechanism. This knowledge paves the way for a better understanding of the circadian contribution to medical conditions such as obesity and MetS.
Nonlocal analysis of the excitation of the geodesic acoustic mode by drift waves
Authors: Guzdar P. N. , Kleva R. G. , Chakrabarti N. , Naulin V. , Rasmussen J. J. , Kaw P. K. , Singh R.
Published: May 2009

The geodesic acoustic modes (GAMs) are typically observed in the edge region of toroidal plasmas. Drift waves have been identified as a possible cause of excitation of GAMs by a resonant three wave parametric process. A nonlocal theory of excitation of these modes in inhomogeneous plasmas typical of the edge region of tokamaks is presented in this paper. The continuum GAM modes with coupling to the drift waves can create discrete “global” unstable eigenmodes localized in the edge “pedestal” region of the plasma. Multiple resonantly driven unstable radial eigenmodes can coexist on the edge pedestal.
Solid phases in electro- and magnetorheological systems
Authors: Brandt Philip C. , Ivlev Alexei V. , Morfill Gregor E.
Published: May 2009

Ensembles of particles with a spherically symmetric repulsive Yukawa interaction and additional dipole-dipole interaction induced by an external field exhibit numerous solid-solid phase transitions controlled by the magnitude of the field. Such interactions emerge most notably in electro- and magnetorheological fluids and plasmas. We propose a simple variational approach based on the Bogoliubov inequality for determining equilibrium solid phases. Phase diagrams for several regimes are calculated and compared with previously performed Monte Carlo and molecular dynamics simulations.
Sialic acid in human testis and changes with aging
Authors: Gheri G. , Vichi D. , Thyrion G. D. Zappoli , Bonaccini L. , Vannelli G. B. , Marini M. , Sgambati E.
Published: May 2009

The aim of the present study was to investigate the distribution of the glycoconjugates sialoderivatives in the human testis. Orchidectomy specimens from men aged 18–30 years (Group 1) and from men aged 70–93 years (Group 2) were obtained at autopsy. The study was performed using digoxigenin-labelled lectins, namely Maackia amurensis II lectin (MAA), Sambucus nigra agglutinin (SNA) and Arachis hypogaea lectin (PNA), in addition to enzymatic and chemical treatments (neuraminidase, KOH–neuraminidase, mild oxidation–neuraminidase, mild oxidation–KOH–neuraminidase, strong oxidation–neuraminidase, strong oxidation–KOH–neuraminidase), to characterise the different glycosidic linkages of the sialoderivatives and to obtain information regarding their structure. In all Group 2 samples, sialic acids linked α-2,3 to galactose and α-2,6 to galactose/N-acetyl-d-galactosamine (Gal/GalNAc), revealed by MAA and SNA, respectively, were observed in testicular interstitial tissue and in the lamina propria. Sialic acid linked α-2,6 to Gal/GalNAc was detected in only some samples from Group 1. After treatment, PNA showed structural changes and/or the gradual disappearance of sialic acid linked to d-galactose-β(1–3)-N-acetyl-d-galactosamine in testicular components with aging. These findings indicate that changes in the metabolism of sialoderivatives in the testis could be related to morphofunctional changes in various testicular components typical of this organ during aging. This suggests that sialoderivatives are important in the functionality of the mature testis in men, as well as its involution.
The wildland fuel cell concept: an approach to characterize fine-scale variation in fuels and fire in frequently burned longleaf pine forests
Authors: Hiers J. Kevin , O'Brien Joseph J. , Mitchell R. J. , Grego John M. , Loudermilk E. Louise
Published: May 2009

In ecosystems with frequent surface fire regimes, fire and fuel heterogeneity has been largely overlooked owing to the lack of unburned patches and the difficulty in measuring fire behavior at fine scales (0.1–10 m). The diverse vegetation in these ecosystems varies at these fine scales. This diversity could be driven by the influences of local interactions among patches of understorey vegetation and canopy-supplied fine fuels on fire behavior, yet no method we know of can capture fine-scale fuel and fire measurements such that these relationships could be rigorously tested. We present here an original method for inventorying of fine-scale fuels and in situ measures of fire intensity within longleaf pine forests of the south-eastern USA. Using ground-based LIDAR (Light Detection and Ranging) with traditional fuel inventory approaches, we characterized within-fuel bed variation into discrete patches, termed wildland fuel cells, which had distinct fuel composition, characteristics, and architecture that became spatially independent beyond 0.5 m2. Spatially explicit fire behavior was measured in situ through digital infrared thermography. We found that fire temperatures and residence times varied at similar scales to those observed for wildland fuel cells. The wildland fuels cell concept could seamlessly connect empirical studies with numerical models or cellular automata models of fire behavior, representing a promising means to better predict within-burn heterogeneity and fire effects.
Spatial fuel data products of the LANDFIRE Project
Authors: Reeves Matthew C. , Ryan Kevin C. , Rollins Matthew G. , Thompson Thomas G.
Published: May 2009

The Landscape Fire and Resource Management Planning Tools (LANDFIRE) Project is mapping wildland fuels, vegetation, and fire regime characteristics across the United States. The LANDFIRE project is unique because of its national scope, creating an integrated product suite at 30-m spatial resolution and complete spatial coverage of all lands within the 50 states. Here we describe development of the LANDFIRE wildland fuels data layers for the conterminous 48 states: surface fire behavior fuel models, canopy bulk density, canopy base height, canopy cover, and canopy height. Surface fire behavior fuel models are mapped by developing crosswalks to vegetation structure and composition created by LANDFIRE. Canopy fuels are mapped using regression trees relating field-referenced estimates of canopy base height and canopy bulk density to satellite imagery, biophysical gradients and vegetation structure and composition data. Here we focus on the methods and data used to create the fuel data products, discuss problems encountered with the data, provide an accuracy assessment, demonstrate recent use of the data during the 2007 fire season, and discuss ideas for updating, maintaining and improving LANDFIRE fuel data products.
LANDFIRE: a nationally consistent vegetation, wildland fire, and fuel assessment
Authors: Rollins Matthew G.
Published: May 2009

LANDFIRE is a 5-year, multipartner project producing consistent and comprehensive maps and data describing vegetation, wildland fuel, fire regimes and ecological departure from historical conditions across the United States. It is a shared project between the wildland fire management and research and development programs of the US Department of Agriculture Forest Service and US Department of the Interior. LANDFIRE meets agency and partner needs for comprehensive, integrated data to support landscape-level fire management planning and prioritization, community and firefighter protection, effective resource allocation, and collaboration between agencies and the public. The LANDFIRE data production framework is interdisciplinary, science-based and fully repeatable, and integrates many geospatial technologies including biophysical gradient analyses, remote sensing, vegetation modelling, ecological simulation, and landscape disturbance and successional modelling. LANDFIRE data products are created as 30-m raster grids and are available over the internet at www.landfire.gov, accessed 22 April 2009. The data products are produced at scales that may be useful for prioritizing and planning individual hazardous fuel reduction and ecosystem restoration projects; however, the applicability of data products varies by location and specific use, and products may need to be adjusted by local users.
Genetic evidence for shared mechanisms of epimorphic regeneration in zebrafish
Authors: Qin Zhao , Barthel Linda K. , Raymond Pamela A.
Published: May 2009

In a microarray-based gene profiling analysis of Müller glia-derived retinal stem cells in light-damaged retinas from adult zebrafish, we found that 2 genes required for regeneration of fin and heart tissues in zebrafish,
hspd1
(
heat shock 60-kDa protein 1
) and
mps1
(
monopolar spindle 1
), were up-regulated. Expression of both genes in the neurogenic Müller glia and progenitors was independently verified by quantitative reverse transcriptase PCR and in situ hybridization. Functional analysis of temperature-sensitive mutants of
hspd1
and
mps1
revealed that both are necessary for Müller glia-based cone photoreceptor regeneration in adult zebrafish retina. In the amputated fin,
hspd1
is required for the induction of mesenchymal stem cells and blastema formation, whereas
mps1
is required at a later step for rapid cell proliferation and outgrowth. This temporal sequence of
hspd1
and
mps1
function is conserved in the regenerating retina. Comparison of gene expression profiles from regenerating zebrafish retina, caudal fin, and heart muscle revealed additional candidate genes potentially implicated in injury-induced epimorphic regeneration in diverse zebrafish tissues.
Trafficking of Murine Hematopoietic Stem and Progenitor Cells in Health and Vascular Disease
Authors: SCHULZ CHRISTIAN , VON ANDRIAN ULRICH H. , MASSBERG STEFFEN
Published: May 2009

Hematopoietic stem cells (HSCs) possess the unique capacity for self‐renewal and differentiation into various hematopoietic cell lineages. Here we summarize the processes that underlie their mobilization and directed migration from bone marrow into peripheral tissues and back to the bone marrow compartment. We specifically focus on the potential role of hematopoietic stem and progenitor cell (HSPC) migration in vascular diseases and review data from recent studies on mice. A better understanding of the mechanisms that guide HSPCs to vascular tissues will be critical for the development of novel therapeutic strategies to prevent or reverse cardiovascular diseases.
“The strangers within our gates”: managing visitors at Temple Square
Authors: Olsen Daniel H.
Published: May 2009

While religious travel to religious sites has existed for millennia, only recently has this phenomenon been examined by tourism scholars. Within the research on religious site management, the empirical nature of the organizational and operational management of sacred sites has been
understudied in the tourism management literature.The purpose of this paper is to correct this deficiency by examining the management structure and practices at Temple Square, the spiritual center of The Church of Jesus Christ of Latter‐day Saints in Salt Lake City, Utah. This is
done through briefly examining both the historical development tourism at Temple Square and the theological reasoning behind its current tourism‐oriented organization and lack of commodification.
Substitution treatment and HCV/HIV‐infection in a sample of 31 German prisons for sentenced inmates
Authors: Schulte B. , Stover H. , Thane K. , Schreiter C. , Gansefort D. , Reimer J.
Published: May 2009

Injection drug use (IDU) and IDU‐related infectious diseases such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV) infections are highly prevalent among prisoners worldwide. However, little is known about the prevalence of IDUs, HCV/HIV and the availability of respective treatment options in German prisons. Data provided by prison physicians of 31 prisons, representing 14,537 inmates, were included in this analysis. The proportion of IDUs among all prisoners was
21.9%. Substitution treatment was available in three out of four prisons (74.2%). Overall, 1137 substitution treatments were provided annually with a wide range of treatment aims. The prevalence rate was 14.3% for HCV and 1.2% for HIV. Around 5.5% of all HCV‐infected prisoners were in antiviral treatment annually, 86.5% of all HIV‐positive inmates in antiretroviral HIV‐treatment. Generally, substitution treatment, and HCV and HIV testing and treatment are available. However,
due to abstinence‐orientated treatment aims, substitution treatment is rarely available as maintenance treatment, and HCV/HIV‐treatment is mainly provided for patients with an existing treatment before imprisonment. The inconsistent data quality necessitates changes in prison‐related policy to improve surveillance and to generate aggregated data in German prisons. The selection process in this analysis might lead to overestimating the provision of substitution and antiviral HCV‐treatment.
A NEW FAMILY OF MULTISTEP METHODS WITH IMPROVED PHASE-LAG CHARACTERISTICS FOR THE INTEGRATION OF ORBITAL PROBLEMS
Authors: Vlachos D. S. , Anastassi Z. A. , Simos T. E.
Published: May 2009

In this paper, we introduce a new family of 10-step linear multistep methods for the integration of orbital problems. The new methods are constructed by adopting a new methodology which improves the phase-lag characteristics by vanishing both the phase-lag function and its first derivatives at a specific frequency. The efficiency of the new family of methods is proved via error analysis and numerical applications.
Simulations of ITER with combined effects of internal and edge transport barriers
Authors: Onjun T. , Pianroj Y.
Published: May 2009

Predictive simulations of ITER with the presence of both an edge transport barrier (ETB) and an internal transport barrier (ITB) are carried out using the BALDUR integrated predictive modelling code. In these simulations, the boundary is taken at the top of the pedestal, where the pedestal values are described using theory-based pedestal models. These pedestal temperature models are based on three different pedestal width scalings: magnetic and flow shear stabilization (Δ ∝ ρi
s
2), flow shear stabilization (
) and normalized poloidal pressure (
). The pedestal width scalings are combined with a pedestal pressure gradient scaling based on the ballooning mode limit to predict the pedestal temperature. A version of the semi-empirical Mixed Bohm/gyroBohm (Mixed B/gB) core transport model that includes ITB effects is used to compute the evolution of plasma profiles. In this model, the anomalous transport in the core is stabilized by the influence of E

r
× B flow shear and magnetic shear, which results in the formation of ITB. The combination of the Mixed B/gB core transport model with ITB effects, together with the pedestal model, is used to simulate the time evolution of plasma current, temperature, and density profiles for ITER standard type I ELMy H-mode discharges. It is found that ITER fusion performance using the BALDUR code with Mixed B/gB transport model without the presence of ITB is quite pessimistic (Fusion Q ∼ 3). The presence of ITB is crucial and can result in a significant improvement, which is needed for achieving a target Fusion Q of 10. The improvement due to the presence of ITB is almost the same for all simulations with those three pedestal temperature models. This is caused by the predicted pedestal temperature from each pedestal temperature model varying just slightly. The presence of ITB has a strong impact on both temperature profiles, especially near the centre of the plasma, but has a small impact on electron, deuterium, tritium and carbon density profiles, except the helium density profile. The formation of ITB does not impact on the pedestal. It is also found that during a sawtooth crash, the temperature profiles drop significantly, but there is a small change in the density profiles. However, the sawtooth oscillation has no impact on the pedestal. When the auxiliary heating power is turned off, it is found that significant fusion power is sustained.
Transcriptional Analysis of the Candida albicans Cell Cycle
Authors: Côte Pierre , Hogues Hervé , Whiteway Malcolm
Published: May 2009

We have examined the periodic expression of genes through the cell cycle in cultures of the human pathogenic fungus Candida albicans synchronized by mating pheromone treatment. Close to 500 genes show increased expression during the G1, S, G2, or M transitions of the C. albicans cell cycle. Comparisons of these C. albicans periodic genes with those already found in the budding and fission yeasts and in human cells reveal that of 2200 groups of homologous genes, close to 600 show periodicity in at least one organism, but only 11 are periodic in all four species. Overall, the C. albicans regulatory circuit most closely resembles that of Saccharomyces cerevisiae but contains a simplified structure. Although the majority of the C. albicans periodically regulated genes have homologues in the budding yeast, 20% (100 genes), most of which peak during the G1/S or M/G1 transitions, are unique to the pathogenic yeast.
Toward a gold standard for promoter prediction evaluation
Authors: Abeel Thomas , Van de Peer Yves , Saeys Yvan
Published: May 2009

Motivation: Promoter prediction is an important task in genome annotation projects, and during the past years many new promoter prediction programs (PPPs) have emerged. However, many of these programs are compared inadequately to other programs. In most cases, only a small portion of the genome is used to evaluate the program, which is not a realistic setting for whole genome annotation projects. In addition, a common evaluation design to properly compare PPPs is still lacking.

Results: We present a large-scale benchmarking study of 17 state-of-the-art PPPs. A multi-faceted evaluation strategy is proposed that can be used as a gold standard for promoter prediction evaluation, allowing authors of promoter prediction software to compare their method to existing methods in a proper way. This evaluation strategy is subsequently used to compare the chosen promoter predictors, and an in-depth analysis on predictive performance, promoter class specificity, overlap between predictors and positional bias of the predictions is conducted.

Availability: We provide the implementations of the four protocols, as well as the datasets required to perform the benchmarks to the academic community free of charge on request.

Contact:  yves.vandepeer@psb.ugent.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
KELLER: estimating time-varying interactions between genes
Authors: Song Le , Kolar Mladen , Xing Eric P.
Published: May 2009

Motivation: Gene regulatory networks underlying temporal processes, such as the cell cycle or the life cycle of an organism, can exhibit significant topological changes to facilitate the underlying dynamic regulatory functions. Thus, it is essential to develop methods that capture the temporal evolution of the regulatory networks. These methods will be an enabling first step for studying the driving forces underlying the dynamic gene regulation circuitry and predicting the future network structures in response to internal and external stimuli.

Results: We introduce a kernel-reweighted logistic regression method (KELLER) for reverse engineering the dynamic interactions between genes based on their time series of expression values. We apply the proposed method to estimate the latent sequence of temporal rewiring networks of 588 genes involved in the developmental process during the life cycle of Drosophila melanogaster. Our results offer the first glimpse into the temporal evolution of gene networks in a living organism during its full developmental course. Our results also show that many genes exhibit distinctive functions at different stages along the developmental cycle.

Availability: Source codes and relevant data will be made available at http://www.sailing.cs.cmu.edu/keller

Contact:  epxing@cs.cmu.edu
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
Authors: Du Pan , Feng Gang , Flatow Jared , Song Jie , Holko Michelle , Kibbe Warren A. , Lin Simon M.
Published: May 2009

Subjective methods have been reported to adapt a general-purpose ontology for a specific application. For example, Gene Ontology (GO) Slim was created from GO to generate a highly aggregated report of the human-genome annotation. We propose statistical methods to adapt the general purpose, OBO Foundry Disease Ontology (DO) for the identification of gene-disease associations. Thus, we need a simplified definition of disease categories derived from implicated genes. On the basis of the assumption that the DO terms having similar associated genes are closely related, we group the DO terms based on the similarity of gene-to-DO mapping profiles. Two types of binary distance metrics are defined to measure the overall and subset similarity between DO terms. A compactness-scalable fuzzy clustering method is then applied to group similar DO terms. To reduce false clustering, the semantic similarities between DO terms are also used to constrain clustering results. As such, the DO terms are aggregated and the redundant DO terms are largely removed. Using these methods, we constructed a simplified vocabulary list from the DO called Disease Ontology Lite (DOLite). We demonstrated that DOLite results in more interpretable results than DO for gene-disease association tests. The resultant DOLite has been used in the Functional Disease Ontology (FunDO) Web application at http://www.projects.bioinformatics.northwestern.edu/fundo.

Contact:  s-lin2@northwestern.edu
Global alignment of protein–protein interaction networks by graph matching methods
Authors: Zaslavskiy Mikhail , Bach Francis , Vert Jean-Philippe
Published: May 2009

Motivation: Aligning protein–protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help in the identification of functional orthologs through the detection of conserved interactions. It is, however, a difficult combinatorial problem, for which only heuristic methods have been proposed so far.

Results: We reformulate the PPI alignment as a graph matching problem, and investigate how state-of-the-art graph matching algorithms can be used for that purpose. We differentiate between two alignment problems, depending on whether strict constraints on protein matches are given, based on sequence similarity, or whether the goal is instead to find an optimal compromise between sequence similarity and interaction conservation in the alignment. We propose new methods for both cases, and assess their performance on the alignment of the yeast and fly PPI networks. The new methods consistently outperform state-of-the-art algorithms, retrieving in particular 78% more conserved interactions than IsoRank for a given level of sequence similarity.

Availability: All data and codes are freely and publicly available upon request.

Contact:  jean-philippe.vert@mines-paristech.fr
A general computational method for robustness analysis with applications to synthetic gene networks
Authors: Rizk Aurélien , Batt Gregory , Fages François , Soliman Sylvain
Published: May 2009

Motivation: Robustness is the capacity of a system to maintain a function in the face of perturbations. It is essential for the correct functioning of natural and engineered biological systems. Robustness is generally defined in an ad hoc, problem-dependent manner, thus hampering the fruitful development of a theory of biological robustness, recently advocated by Kitano.

Results: In this article, we propose a general definition of robustness that applies to any biological function expressible in temporal logic LTL (linear temporal logic), and to broad model classes and perturbation types. Moreover, we propose a computational approach and an implementation in BIOCHAM 2.8 for the automated estimation of the robustness of a given behavior with respect to a given set of perturbations. The applicability and biological relevance of our approach is demonstrated by testing and improving the robustness of the timed behavior of a synthetic transcriptional cascade that could be used as a biological timer for synthetic biology applications.

Availability: Version 2.8 of BIOCHAM and the transcriptional cascade model are available at http://contraintes.inria.fr/BIOCHAM/

Contact:  gregory.batt@inria.fr
Model-based clustering of array CGH data
Authors: Shah Sohrab P. , Cheung K-John , Johnson Nathalie A. , Alain Guillaume , Gascoyne Randy D. , Horsman Douglas E. , Ng Raymond T. , Murphy Kevin P.
Published: May 2009

Motivation: Analysis of array comparative genomic hybridization (aCGH) data for recurrent DNA copy number alterations from a cohort of patients can yield distinct sets of molecular signatures or profiles. This can be due to the presence of heterogeneous cancer subtypes within a supposedly homogeneous population.

Results: We propose a novel statistical method for automatically detecting such subtypes or clusters. Our approach is model based: each cluster is defined in terms of a sparse profile, which contains the locations of unusually frequent alterations. The profile is represented as a hidden Markov model. Samples are assigned to clusters based on their similarity to the cluster's profile. We simultaneously infer the cluster assignments and the cluster profiles using an expectation maximization-like algorithm. We show, using a realistic simulation study, that our method is significantly more accurate than standard clustering techniques. We then apply our method to two clinical datasets. In particular, we examine previously reported aCGH data from a cohort of 106 follicular lymphoma patients, and discover clusters that are known to correspond to clinically relevant subgroups. In addition, we examine a cohort of 92 diffuse large B-cell lymphoma patients, and discover previously unreported clusters of biological interest which have inspired followup clinical research on an independent cohort.

Availability: Software and synthetic datasets are available at http://www.cs.ubc.ca/∼sshah/acgh as part of the CNA-HMMer package.

Contact:  sshah@bccrc.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
A geometric approach for classification and comparison of structural variants
Authors: Sindi Suzanne , Helman Elena , Bashir Ali , Raphael Benjamin J.
Published: May 2009

Motivation: Structural variants, including duplications, insertions, deletions and inversions of large blocks of DNA sequence, are an important contributor to human genome variation. Measuring structural variants in a genome sequence is typically more challenging than measuring single nucleotide changes. Current approaches for structural variant identification, including paired-end DNA sequencing/mapping and array comparative genomic hybridization (aCGH), do not identify the boundaries of variants precisely. Consequently, most reported human structural variants are poorly defined and not readily compared across different studies and measurement techniques.

Results: We introduce Geometric Analysis of Structural Variants (GASV), a geometric approach for identification, classification and comparison of structural variants. This approach represents the uncertainty in measurement of a structural variant as a polygon in the plane, and identifies measurements supporting the same variant by computing intersections of polygons. We derive a computational geometry algorithm to efficiently identify all such intersections. We apply GASV to sequencing data from nine individual human genomes and several cancer genomes. We obtain better localization of the boundaries of structural variants, distinguish genetic from putative somatic structural variants in cancer genomes, and integrate aCGH and paired-end sequencing measurements of structural variants. This work presents the first general framework for comparing structural variants across multiple samples and measurement techniques, and will be useful for studies of both genetic structural variants and somatic rearrangements in cancer.

Availability:  http://cs.brown.edu/people/braphael/software.html

Contact:  braphael@brown.edu
Network-based prediction of metabolic enzymes' subcellular localization
Authors: Mintz-Oron Shira , Aharoni Asaph , Ruppin Eytan , Shlomi Tomer
Published: May 2009

Motivation: Revealing the subcellular localization of proteins within membrane-bound compartments is of a major importance for inferring protein function. Though current high-throughput localization experiments provide valuable data, they are costly and time-consuming, and due to technical difficulties not readily applicable for many Eukaryotes. Physical characteristics of proteins, such as sequence targeting signals and amino acid composition are commonly used to predict subcellular localizations using computational approaches. Recently it was shown that protein–protein interaction (PPI) networks can be used to significantly improve the prediction accuracy of protein subcellular localization. However, as high-throughput PPI data depend on costly high-throughput experiments and are currently available for only a few organisms, the scope of such methods is yet limited.

Results: This study presents a novel constraint-based method for predicting subcellular localization of enzymes based on their embedding metabolic network, relying on a parsimony principle of a minimal number of cross-membrane metabolite transporters. In a cross-validation test of predicting known subcellular localization of yeast enzymes, the method is shown to be markedly robust, providing accurate localization predictions even when only 20% of the known enzyme localizations are given as input. It is shown to outperform pathway enrichment-based methods both in terms of prediction accuracy and in its ability to predict the subcellular localization of entire metabolic pathways when no a-priori pathway-specific localization data is available (and hence enrichment methods are bound to fail). With the number of available metabolic networks already reaching more than 600 and growing fast, the new method may significantly contribute to the identification of enzyme localizations in many different organisms.

Contact:  shira.mintz@weizmann.ac.il; tomersh@cs.technion.ac.il
Predicting and understanding the stability of G-quadruplexes
Authors: Stegle Oliver , Payet Linda , Mergny Jean-Louis , MacKay David J. C. , Huppert Julian Leon
Published: May 2009

Motivation: G-quadruplexes are stable four-stranded guanine-rich structures that can form in DNA and RNA. They are an important component of human telomeres and play a role in the regulation of transcription and translation. The biological significance of a G-quadruplex is crucially linked with its thermodynamic stability. Hence the prediction of G-quadruplex stability is of vital interest.

Results: In this article, we present a novel Bayesian prediction framework based on Gaussian process regression to determine the thermodynamic stability of previously unmeasured G-quadruplexes from the sequence information alone. We benchmark our approach on a large G-quadruplex dataset and compare our method to alternative approaches. Furthermore, we propose an active learning procedure which can be used to iteratively acquire data in an optimal fashion. Lastly, we demonstrate the usefulness of our procedure on a genome-wide study of quadruplexes in the human genome.

Availability: A data table with the training sequences is available as supplementary material. Source code is available online at http://www.inference.phy.cam.ac.uk/os252/projects/quadruplexes

Contact:  os252@cam.ac.uk; jlh29@cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.