bluuebunny/crossref_metadata_2025 huggingface dataset:
Organ‐Specific Distributions of Lysophosphatidylcholine and Triacylglycerol in Mouse Embryo
Authors: Hayasaka Takahiro , Goto‐Inoue Naoko , Zaima Nobuhiro , Kimura Yoshishige , Setou Mitsutoshi
Published: August 2009

Imaging mass spectrometry (IMS) has been developed as a method for determining and visualizing the distribution of proteins and lipids across sections of dissected tissue. Although lipids play an important role in mammal development, their detailed distributions have not been analyzed by conventional methods. In this study, we tried to determine and visualize lysophosphatidylcholine (LysoPtdCho) and triacylglycerol (TAG) in a mouse embryo by matrix‐assisted laser desorption/ionization (MALDI) hybrid quadrupole time‐of‐flight (TOF) mass spectrometer. Many peaks were detected from a raster scan of the whole embryonic sections. The peaks at m/z 496.33, 524.36, 879.72, 881.74, and 921.74 were identified by MS/MS analyses as [LysoPtdCho (16:0) + H]+, [LysoPtdCho (18:0) + H]+, [TAG (16:0/18:2/18:1) + Na]+, [TAG (16:0/18:1/18:1) + Na]+, and [TAG (16:0/20:3/18:1) + K]+, respectively. The ion images constructed from the peaks revealed that LysoPtdCho were distributed throughout the body and TAGs were distributed around the brown adipose tissue and in the liver at embryo day 17.5. Thus, IMS system based on MALDI hybrid quadrupole TOF MS revealed the distribution of LysoPtdCho and, more importantly, the organ‐specific distribution of TAGs in the embryonic stages of mammals for the first time. We can conclude that this technique enables us to analyze the roles of various lipids during embryogenesis and gives insight for lipid research.
Evidence of a genetic bottleneck in an El Niño affected population of South American fur seals,Arctocephalus australis
Authors: de Oliveira Larissa Rosa , Meyer Diogo , Hoffman Joseph , Majluf Patricia , Morgante João S.
Published: August 2009

The South American fur seal,Arctocephalus australis, was one of the earliest otariid seals to be exploited by humans: at least 6000 years ago on the Atlantic coast and 4000 on the Pacific coast of South America. More than 750,000 fur seals were killed in Uruguay until 1991. However, a climatological phenomenon—the severe 1997–1998 El Niño Southern Oscillation (ENSO)—was responsible for the decline of 72% of the Peruvian fur seal population due to starvation as a consequence of warming of sea-surface temperatures and primary productivity reduction. Currently, there is no precise information on global population size or on the species' conservation status. The present study includes the first bottleneck test for the Pacific and Atlantic populations ofA. australisbased on the analysis of seven microsatellite loci. Genetic bottleneck compromises the evolutionary potential of a population to respond to environmental changes. The perspective becomes even more alarming due to current global warming models that predict stronger and more frequent ENSO events in the future. Our analysis found moderate support for deviation from neutrality–equilibrium for the Pacific population of fur seals and none for the Atlantic population. This difference among population reflects different demographic histories, and is consistent with a greater reduction in population size in the Pacific. Such an event could be a result of the synergic effects of recurrent ENSO events and the anthropogenic impact (sealing and prey overfishing) on this population.
Exploring older women's citizenship: understanding the impact of migration in later life
Authors: COOK JOANNE
Published: August 2009

Research on the ways in which having been an international migrant in later life shapes the welfare needs, preferences and expectations of non-native older people in rich countries is in its infancy, for both the ageing and migration fields have been slow to examine the experiences of older migrants. This paper focuses upon the welfare citizenship experiences of older women who migrated in later life to England, either as refugees or as post-retirement migrants. It reports findings from interviews and focus groups conducted with black Caribbean, Irish, Chinese and Somali older women migrants in Sheffield, Yorkshire, UK, as part of the Older Women's Lives and Voices Study. The paper explores their experiences of accessing welfare citizenship and the barriers they encountered in accessing mainstream services. In particular, it examines the unequal platform from which older migrants who do not speak English access welfare citizenship rights and services, and assesses the important constraints of discrimination and language differences. Despite the obstacles, the older women participants were actively pursuing their inclusion in welfare rights and services. The paper argues for more recognition of the important enabling role that informal systems of support provided by participation in community or cultural organisations plays in the welfare citizenship and agency of minority ethnic older women.
Selection criteria for flagship species by conservation organizations
Authors: HOME ROBERT , KELLER CLAUDIA , NAGEL PETER , BAUER NICOLE , HUNZIKER MARCEL
Published: August 2009

Flagship species are among key marketing tools used by conservation organizations to motivate public support, but are often selected in an ad hoc, rather than systematic, manner. Furthermore, it is unclear whether selected flagship species do motivate public support. This paper describes a multi-method exploratory study, carried out in Switzerland, which aimed to determine the selection criteria for flagship species and measure whether a species selected according to these criteria was able to motivate support. Fourteen representatives of international, regional and local conservation organizations were interviewed and the selection criteria for their flagship species were identified. A charismatic species (the great spotted woodpecker) that meets these criteria and an apparently less charismatic species (the clover stem weevil) were selected as treatments in a quantitative experiment with 900 respondents. Using conjoint analysis, it was found that both charismatic and uncharismatic species have the ability to positively influence public preferences for habitat variables that encourage biodiversity in urban landscapes. These results may be used by conservation organizations to assist in the selection of flagship species, and in particular for flagship species that are intended to perform a specific conservation function.
Measles outbreak linked to a minority group in Austria, 2008
Authors: SCHMID D. , HOLZMANN H. , SCHWARZ K. , KASPER S. , KUO H-W. , ABERLE S. W. , REDLBERGER-FRITZ M. , HAUTMANN W. , SANTIBANEZ S. , MANKERTZ A. , KÖNIG C. , MAGNET E. , REICHART S. , MEUSBURGER S. , LUCKNER-HORNISCHER A. , DE MARTIN A. , BECHTER E. , STIRLING J. , ALLERBERGER F.
Published: August 2009

We report on a measles outbreak originating in an anthroposophic community in Austria, 2008. A total of 394 (94·9%) cases fulfilled the outbreak case definition including 168 cases affiliated to the anthroposophic community. The source case was a school pupil from Switzerland. The Austrian outbreak strain was genotype D5, indistinguishable from the Swiss outbreak strain. A school-based retrospective cohort study in the anthroposophic school demonstrated a vaccine effectiveness of 97·3% in pupils who had received a single dose of measles-containing vaccine and 100% in those who had received two doses. The vaccination coverage of the cases in the anthroposophic community was 0·6%. Of the 226 outbreak cases not belonging to the anthroposophic community, the 10–24 years age group was the most affected. Our findings underline the epidemiological significance of suboptimal vaccination coverage in anthroposophic communities and in older age groups of the general population in facilitating measles virus circulation. The findings of this outbreak investigation suggest that the WHO European Region is unlikely to achieve its 2010 target for measles and rubella elimination.
Pharmacological characterization, localization, and regulation of ionotropic glutamate receptors in skate horizontal cells
Authors: KREITZER MATTHEW A. , BIRNBAUM ANDREA D. , QIAN HAOHUA , MALCHOW ROBERT PAUL
Published: August 2009

Glutamate is believed to be the primary excitatory neurotransmitter in the vertebrate retina, and its fast postsynaptic effects are elicited by activating NMDA-, kainate-, or AMPA-type glutamate receptors. We have characterized the ionotropic glutamate receptors present on retinal horizontal cells of the skate, which possess a unique all-rod retina simplifying synaptic circuitry within the outer plexiform layer (OPL). Isolated external horizontal cells were examined using whole-cell voltage-clamp techniques. Glutamate and its analogues kainate and AMPA, but not NMDA, elicited dose-dependent currents. The AMPA receptor antagonist GYKI 52466 at 100μmabolished glutamate-elicited currents. Desensitization of glutamate currents was removed upon coapplication of cyclothiazide, known to potentiate AMPA receptor responses, but not by concanavalin A, which potentiates kainate receptor responses. The dose–response curve to glutamate was significantly broader in the presence of the desensitization inhibitor cyclothiazide. Polyclonal antibodies directed against AMPA receptor subunits revealed prominent labeling of isolated external horizontal cells with the GluR2/3 and GluR4 antibodies. 1-Naphthylacetyl spermine, known to block calcium-permeable AMPA receptors, significantly reduced glutamate-gated currents of horizontal cells. Downregulation of glutamate responses was induced by increasing extracellular ion concentrations of Zn2+and H+. The present study suggests that Ca2+-permeable AMPA receptors likely play an important role in shaping the synaptic responses of skate horizontal cells and that alterations in extracellular concentrations of calcium, zinc, and hydrogen ions have the potential to regulate the strength of postsynaptic signals mediated by AMPA receptors within the OPL.
Double activation improves rabbit freeze–thawed oocytes developmental potential
Authors: Wang J. , Cong L. , Zhang Z.G. , Cao Y.X. , Wei Z.L. , Zhou P. , Zhao J.H. , He X.J.
Published: August 2009

Objective: To investigate the effects of various activation methods on freeze–thawed rabbit oocytes developmental potential. Methods: Rabbit oocytes were vitrified by cryoleafs and cryoprotected with ethylene glycol and propanediol. After thawing, the oocytes were fertilized by intracytoplasmic sperm injection (ICSI). Surviving oocytes after ICSI were divided into five groups at random. Group 1: Oocytes (n = 30) activated 1 h after ICSI by calcium ionomycin (I0634); Group 2: Oocytes (n = 26) activated by strontium chloride an hour after ICSI; Group 3: Oocytes (n = 33) activated by I0634 twice; Group 4: Oocytes (n = 28) were activated by strontium chloride twice; Control Group: Inactivated oocytes (n = 39). Blastocysts derived from each group were transplanted to recipient rabbits. Results: Rates of fertilization, cleavage and blastocyst formation of Group 3 were higher than those of Group 1 and Group 2 (81.8% vs 33.3% vs 53.8%, 54.5% vs 16.7% vs 26.9%, p < 0.05; 15.2% vs 3.3% vs 7.7%, p > 0.05). The rabbit transplanted with embryos derived from Group 3 became pregnant. Embryos derived from double activation could implant into endometrium. Conclusion: Double activation may increase freeze–thawed oocytes developmental potential. After activation, oocytes cleavage velocity may be faster than that of oocytes without activation.
Anaemia among pregnant Palestinian women in the Occupied Palestinian Territory
Authors: Khader A , Madi H , Riccardo F , Sabatinelli G
Published: August 2009

Objective

To assess anaemia prevalence and correlated social and biological determinants among pregnant women in the Occupied Palestinian Territory (oPt).

Design

A cross-sectional survey conducted among pregnant women attending/accessing UNRWA (United Nations Relief and Works Agency for Palestine Refugees in the Near East) health centres in the Gaza Strip and the West Bank in September and October 2006.

Setting

Fifty-five UNRWA health centres in the oPt (eighteen in the Gaza Strip and thirty-seven in the West Bank).

Subjects

A random sample of 1740 pregnant women.

Results

Overall anaemia prevalence was 38·6 % (95 % CI 36·3, 40·9 %). A substantial difference in anaemia prevalence was observed between the Gaza Strip and the West Bank (44·9 %v. 31·1 %, respectively), as well as a significant increase in anaemia prevalence in the Gaza Strip compared with an Agency-wide survey conducted in 2004 (44·9 %v. 35·7 %, respectively). Anaemia prevalence was found to increase with age, parity and trimester of gestation.

Conclusions

Anaemia still appears to be a public health problem among pregnant women in spite of UNRWA interventions. The West Bank shows prevalence rates similar to those observed in neighbouring countries, while the Gaza Strip has higher rates. Prevalence rates of anaemia among pregnant Palestinian women are more than two times higher than those observed in Europe.
An integrated analysis of controlled and passive source seismic data across an Archean‐Proterozoic suture zone in the Rocky Mountains
Authors: Rumpfhuber Eva‐Maria , Keller G. Randy
Published: August 2009

We conducted a new integrated analysis of the controlled and passive source seismic data from the Continental Dynamics of the Rocky Mountains (CD‐ROM) experiment in the western United States. A specific goal of our study was to establish a stronger tie between the CD‐ROM and Deep Probe experiments that together form a transect that extends almost 3000 km from northern New Mexico to the southern Northwest Territories of Canada. We created a new P wave velocity and interface model from the controlled source seismic (CSS) data on the basis of an advanced picking strategy that produced substantially more arrivals whose traveltimes could be picked. In addition, we were able to identify a substantial set of S wave arrivals and to establish an independent S wave model, which allowed us to estimate the Vp/Vs and Poisson's ratios in the crust. An integrated analysis of the CSS data with recently generated receiver function results and gravity data allowed us to construct a well‐constrained multiparameter structural model. This model resolves the structural framework of the crust and uppermost mantle of the transition from the Wyoming craton to the north, across the Cheyenne belt suture zone, and into the Proterozoic terranes to the south. Our tectonic interpretation that crustal‐scale crocodile structures are present provides an explanation for the south dip of the Cheyenne belt in the upper crust and the north dipping slab in the mantle revealed by earlier tomographic results. The very distinct crustal structures north and south of the suture zone are clearly shown in our model and document that the blocks that collided at ∼1.8 Ga to form the Cheyenne belt suture zone have retained their basic crustal and uppermost mantle structure since then.
Effects of topography on the cumulative mixing efficiency in exchange flows
Authors: Prastowo T. , Griffiths R. W. , Hughes G. O. , Hogg A. M.
Published: August 2009

Buoyancy‐driven, hydraulically controlled two‐layer exchange flows were established in a laboratory flume with a lateral constriction and a bottom sill placed at its midpoint. The shear flow was unstable within the constriction, and the overall amount of turbulent mixing was determined from measurements of vertical density profiles after the exchange. The potential energy changes are used to evaluate the mixing efficiency (or flux Richardson number), defined as the fraction of the available potential energy released into kinetic energy that is converted to potential energy through irreversible mixing. Mixing efficiencies asymptote at large Reynolds numbers to values of 8% for a sill with sloping sides and 11% ± 1% for both a weir with vertical sides and the same constriction with no bottom topography. The latter is identical to the value previously reported for shorter, smoothly varying lateral constrictions. Thus, all controlled exchanges examined here undergo less mixing than implied by the commonly assumed maximum turbulent mixing efficiency of 20%, and the actual efficiency is insensitive to the form of the topography. This result implies that calculations of the global energy balance of the ocean may need to be reevaluated.
Spatial and temporal variations of aerosols around Beijing in summer 2006: Model evaluation and source apportionment
Authors: Matsui H. , Koike M. , Kondo Y. , Takegawa N. , Kita K. , Miyazaki Y. , Hu M. , Chang S.‐Y. , Blake D. R. , Fast J. D. , Zaveri R. A. , Streets D. G. , Zhang Q. , Zhu T.
Published: August 2009

Regional aerosol model calculations were made using the Weather Research and Forecasting (WRF)‐Community Multiscale Air Quality (CMAQ) and WRF‐chem models to study spatial and temporal variations of aerosols around Beijing, China, in the summer of 2006, when the Campaigns of Air Quality Research in Beijing and Surrounding Region 2006 (CAREBeijing) intensive campaign was conducted. Model calculations captured temporal variations of primary (such as elemental carbon (EC)) and secondary (such as sulfate) aerosols observed in and around Beijing. The spatial distributions of aerosol optical depth observed by the MODIS satellite sensors were also reproduced over northeast China. Model calculations showed distinct differences in spatial distributions between primary and secondary aerosols in association with synoptic‐scale meteorology. Secondary aerosols increased in air around Beijing on a scale of about 1000 × 1000 km2 under an anticyclonic pressure system. This air mass was transported northward from the high anthropogenic emission area extending south of Beijing with continuous photochemical production. Subsequent cold front passage brought clean air from the north, and polluted air around Beijing was swept to the south of Beijing. This cycle was repeated about once a week and was found to be responsible for observed enhancements/reductions of aerosols at the intensive measurement sites. In contrast to secondary aerosols, the spatial distributions of primary aerosols (EC) reflected those of emissions, resulting in only slight variability despite the changes in synoptic‐scale meteorology. In accordance with these results, source apportionment simulations revealed that primary aerosols around Beijing were controlled by emissions within 100 km around Beijing within the preceding 24 h, while emissions as far as 500 km and within the preceding 3 days were found to affect secondary aerosols.
Seeing the forest through the trees: Recovering large‐scale carbon flux biases in the midst of small‐scale variability
Authors: Schuh A. E. , Denning A. S. , Uliasz M. , Corbin K. D.
Published: August 2009

This paper investigates the effect of fine‐scale spatial variability in carbon fluxes upon regional carbon flux inversion estimates in North America using simulated data from 1 May through 31 August 2004 and a hypothetical sparse network of eight towers in North America. A suite of random smooth regional carbon flux patterns are created and then obscured with random fine‐scale spatial flux “noise” to mimic the effect of fine‐scale heterogeneity in carbon fluxes found in nature. Five hundred and forty grid‐scale atmospheric inversions are run using the synthetic data. We find that, regardless of the particular fine spatial scale carbon fluxes used (noise), the inversions can improve a priori carbon flux estimates significantly by capturing the large‐scale regional flux patterns. We also find significant improvement in the root‐mean‐square error of the model are possible across a wide range of spatial decorrelation length scales. Errors associated with the inversion decrease as estimates are sought for larger and larger areas. Results show dramatic differences between postaggregated fine‐scale inversion results and preaggregated coarse‐scale inversion results confirming recent warnings about the “preaggregation” of inversion regions.
Representation of landscape hydrological connectivity using a topographically driven surface flow index
Authors: Lane S. N. , Reaney S. M. , Heathwaite A. L.
Published: August 2009

This paper assesses the extent to which a topographically defined description of the spatial arrangement of catchment wetness can be used to represent landscape hydrological connectivity in temperate river catchments. A physically based distributed hydrological model is used to characterize the space‐time patterns of surface overland flow connection to the drainage network. These characterizations are compared with a static descriptor of the spatial structure of topographically controlled local wetness, called here the Network Index. Theoretically, if topography is the primary control upon hydrological response, the level of catchment wetness required to maintain connectivity along a flow path should be greater for flow paths that have a lower value of the topographically controlled local wetness. We find that our static descriptor can be used to generalize a significant proportion of the time‐averaged spatial variability in connectivity, in terms of both the propensity to and duration of connection. Although the extent to which this finding holds will vary with the extent of topographic control of hydrological response, in catchments with relatively shallow soils and impervious geology our index could improve significantly the estimation of the transfer of sediment and dissolved materials to the drainage network and so assist with both diffuse pollution and climate change impact studies. The work also provides a second reason for the concept that there are Critical Source Areas in river catchments: these arise from the extent to which that material can be delivered to the drainage network, as well as the generation of risky material itself.
Broadband calibration of the R/V Marcus G. Langseth four‐string seismic sources
Authors: Tolstoy M. , Diebold J. , Doermann L. , Nooner S. , Webb S. C. , Bohnenstiehl D. R. , Crone T. J. , Holmes R. C.
Published: August 2009

The R/V Marcus G. Langseth is the first 3‐D seismic vessel operated by the U.S. academic community. With up to a four‐string, 36‐element source and four 6‐km‐long solid state hydrophone arrays, this vessel promises significant new insights into Earth science processes. The potential impact of anthropogenic sound sources on marine life is an important topic to the marine seismic community. To ensure that operations fully comply with existing and future marine mammal permitting requirements, a calibration experiment was conducted in the Gulf of Mexico in 2007–2008. Results are presented from deep (∼1.6 km) and shallow (∼50 m) water sites, obtained using the full 36‐element (6600 cubic inches) seismic source. This array configuration will require the largest safety radii, and the deep and shallow sites provide two contrasting operational environments. Results show that safety radii and the offset between root‐mean‐square and sound exposure level measurements were highly dependent on water depth.
A large‐aperture sodium fluorescence lidar with very high resolution for mesopause dynamics and adaptive optics studies
Authors: Pfrommer Thomas , Hickson Paul , She Chiao‐Yao
Published: August 2009

High‐resolution observations of the density structure of atomic sodium in the Earth's mesosphere and lower thermosphere, using a large‐aperture lidar system, reveal features of this dynamic region in greater detail. The sodium is highly structured, showing multiple layers that vary in density and altitude on timescales ranging from minutes to hours. Large‐scale instabilities and Kelvin‐Helmholtz billows are observed along with an overall downward propagation of the layers. Coherent short‐period gravity wave oscillations are sometimes seen extending over the entire sodium region. Individual meteor ablation trails produce transient density spikes that last at most a few seconds. The mean sodium altitude is found to have a temporal power spectrum proportional to the –1.9 power of the frequency, close to that expected for Kolmogorov turbulence.
A Madden–Julian Oscillation‐triggered record ozone minimum over the Tibetan Plateau in December 2003 and its association with stratospheric “low‐ozone pockets”
Authors: Liu Chuanxi , Liu Yi , Cai Zhaonan , Gao Shouting , Lü Daren , Kyrölä Erkki
Published: August 2009

A record minimum in total column ozone over the Tibetan Plateau in December 2003 is analyzed using both satellite observations and a chemical transport model (MOZART‐3). Ozone profiles observed by the MIPAS and GOMOS over the ozone minimum region (25°–35°N, 85°–110°E) show pronounced ozone reduction in both the upper troposphere and lower stratosphere (UTLS) and the middle stratosphere regions. MOZART‐3 simulation indicates that ozone reduction in the UTLS region is generally caused by uplift of the local tropopause and northward transport of tropical ozone‐poor air associated with an anomalous anticyclone in the upper troposphere. MIPAS observation suggests that the displacement of “low‐ozone pockets” is responsible for ozone decline in the middle‐stratospheric region and contributes to 29–46% of the total column ozone reduction. Further analysis shows that the upper‐tropospheric anticyclonic anomaly is closely associated with the Rossby‐wave triggered by the eastward propagating Madden–Julian Oscillation convective heating.
Impact of sea‐surface dust radiative forcing on the oceanic primary production: A 1D modeling approach applied to the West African coastal waters
Authors: Mallet Marc , Chami Malik , Gentili Bernard , Sempéré Richard , Dubuisson P.
Published: August 2009

The impact of the dust sea‐surface forcing (DSSF) on the oceanic Primary Production (PP) is investigated here by using 1D modelling approach coupling an atmospheric radiative transfer model and a simple PP model. Simulations reveal that dust are able to induce a significant decrease of PP due to the attenuation of light by about 15–25% for dust optical depth (DOD) larger than 0.6–0.7 (at 550 nm). For DOD lower than ∼0.2–0.3, the influence of dust on PP is weak (∼5%). In addition to DOD, the important role played by dust single scattering albedo (DSSA) is also shown. Realistic applications over the Senegal coast are studied using SeaWiFS and AERONET observations. The analysis showed that PP could be reduced by about 15–20% during the spring period. This study highlights that dust/light interactions need to be parameterized in coupled ocean‐atmosphere models used to estimate PP at regional scales.
Ionospheric effects of solar flares at Mars
Authors: Mahajan K. K. , Lodhi Neelesh K. , Singh Sachchidanand
Published: August 2009

From an analysis of electron density profiles recorded aboard Mars Global Surveyor, we report observations of some new and aeronomically important solar flare effects in the ionosphere of Mars. We find that all flares result in the formation of a well defined E layer peak, not always seen on other days. Further, while majority of flares result in elevated electron densities in the E region alone, some flares affect both the E and F1 layers. These altitude ‐ related effects can provide vital information on the relative enhancement of photon fluxes in the various wavelength bands during solar flares. By using the unit optical depth values at Mars from Fox (2004) and the XUV irradiance model of Meier et al. (2002) for the Bastille Day solar flare, we infer that the well defined E peaks could result from enhancement of photon fluxes in the 10–13 nm spectral band. The extension of effect to the F1 layer is due to hardening of the 26–91 nm spectral band, as supported by Solar EUV Monitor measurements on Solar Heliospheric Observatory.
The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA
Authors: Yang Xiao , Molimau Seeseei , Doherty Geoff P , Johnston Elecia B , Marles‐Wright Jon , Rothnagel Rosalba , Hankamer Ben , Lewis Richard J , Lewis Peter J
Published: August 2009

There are three stages of transcribing DNA into RNA. These stages are initiation, elongation and termination, and they are well‐understood biochemically. However, despite the plethora of structural information made available on RNA polymerase in the last decade, little is available for RNA polymerase in complex with transcription elongation factors. To understand the mechanisms of transcriptional regulation, we describe the first structure, to our knowledge, for a bacterial RNA polymerase in complex with an essential transcription elongation factor. The resulting structure formed between the RNA polymerase and NusA from Bacillus subtilis provides important insights into the transition from an initiation complex to an elongation complex, and how NusA is able to modulate transcription elongation and termination.
Uberon: towards a comprehensive multi-species anatomy ontology
Authors: Haendel Melissa , Gkoutos Georgios , Lewis Suzanna , Mungall Chris
Published: August 2009

The lack of a single unified species-neutral ontology covering the anatomy of a variety of metazoans is a hindrance to translating model organism research to human health. We have developed an Uber-anatomy ontology to fill this need, filling the gap between the CARO upper-level ontology and species-specific anatomical ontologies.
Translating Environmental Science into Policy and Action
Authors: Talbot Lee
Published: August 2009

Background/Question/Methods:

Many ecologists are skilled at identifying environmental problems and defining solutions, but not at achieving concrete action to implement those insights. The question, then, is how to help ecologists translate environmental science into policy and action. Most ecologists' education and training do not prepare them to be effective in the policy arena, much less in ways to achieve action. Ecologists find disincentives in the form of the academic attitude that somehow the application of science is inferior to so-called "pure science." This ivory tower holdover has been largely discredited in the context of environmental issues, and the discipline of conservation biology exists explicitly to foster applications of science, but the attitude remains a potent obstacle, especially for younger ecologists seeking academic acceptance and tenure. Even when ecologists ignore or overcome this obstacle there are few resources available to provide guidance for achieving action. For example, most textbooks that describe the policy process present an academic picture that bears little relationship to the messy real world process. One approach to providing such guidance has been developed in the Department of Environmental Science and Policy at George Mason University, Fairfax, Virginia. This is a course developed specifically to identify and analyze the basic principles, skills and strategies involved in turning scientific knowledge and information, and the policies derived from them, into action. The course uses a series of actual case histories drawn from experience with local and national U.S. and foreign governments, UN organizations, NGOs and other relevant situations. The approach is to give a case hissory, analyze it and derive from it the principles, strategies and skills that work. The professor describes the setting, background, objective, procedure followed and the result. This is followed by class discussion to analyze the case and identify what lessons can be learned and what specific principles, skills and strategies were responsible for or contributed to the results.

Results/Conclusions:

While there are some basic principles that hold true in many situations, no single formula for achieving action can be applied in every case. Each situation is somewhat different and to succeed one has to be able to select from an array of principles and skills to fit them to the special needs. This course is a proven way to provide students with a "tool kit" of principles, skills and strategies to guide them effectively to translate environmental science into policy and action.
Demographic vital rates and population growth: rethinking the relationship in a harvested elk population
Authors: Conard Jonathan , Gipson Philip
Published: August 2009

Understanding the nature of the relationship between demographic vital rates and the rate of population change (λ) is important for determining effective strategies for population management and conservation. We examined the relative impacts of various demographic vital rates on λ within the range of temporal vital rate variability observed in a harvested population to test the hypotheses that adult survival rates in ungulates are relatively invariant when compared to other vital rates and that variability in calf survival has a greater influence on rates of population change than adult survival. Vital rates were estimated for an elk (Cervus elaphus) population at Fort Riley, Kansas from October 2003 – February 2007. The magnitude of adult survival rates were similar to other harvested populations and models including a negative relationship between survival and age received the highest levels of support. Prime-age adult survival had the highest stage-specific elasticity values, indicating a high contribution of these matrix elements to λ. Life-stage simulation analysis indicated that variation in calf survival had the highest correlation with variation in λ (r^2^ = 0.61). Our results suggest that adult survival rates in harvested populations may experience increased levels of variability, but that calf survival rates have the greatest relative influence on λ due to the wider range of variability observed for this vital rate.
Signalling pathways in prostate carcinogenesis: potentials for molecular-targeted therapy
Authors: Ramsay Alison K. , LEUNG Hing Y.
Published: August 2009

Prostate cancer represents a major health issue and its incidence is rising globally. In developed countries, prostate cancer is the most frequently diagnosed cancer and the second most common cause of death from cancer in men. Androgen deprivation reduces tumour activity in approx. 80% of patients with advanced disease, but most tumours relapse within 2 years to an incurable hormone-resistant state. Even for patients with early disease at the time of diagnosis, a proportion of patients will unfortunately develop relapsed disease following radical therapy. Treatment options for patients with hormone-resistant prostate cancer are very limited and, even with toxic therapy, such as docetaxel, the life expectancy is only improved by a median of 2 months. Advances in molecular oncology have identified key signalling pathways that are considered to be driving events in prostate carcinogenesis. The activation of multiple signalling pathways increases further the possibility of cross-talk among ‘linear’ signalling cascades. Hence signalling networks that may incorporate distinct pathways in prostate cancer, particularly in hormone-resistant disease, are increasingly appreciated in drug development programmes. With the development of potent small-molecule inhibitors capable of specifically suppressing the activities of individual ‘linear’ cascades, it may be that, by combining these agents as guided by the molecular signature of prostate cancer, a more efficient therapeutic regime may be developed. Therefore the present review focuses on evidence of abnormal signalling in prostate cancer and the potential of these targets in drug development, and incorporates key findings of relevant clinical trials to date.
Corrigendum to: Synthesis of Epoxides Catalyzed by a Halide-Free Reaction-Controlled Phase-Transfer Catalytic System: [(CH3(CH2)17)2N(CH3)2]3[PW4O32]/H2O2/Dioxan/Olefin
Authors: Ding Yong , Ma Baochun , Tong Dejie , Hua Hui , Zhao Wei
Published: August 2009

The epoxidation of alkenes was successfully catalyzed by a recyclable catalytic system: [(CH3(CH2)17)2N(CH3)2]3[PW4O32]/H2O2/dioxan/olefin. This new catalytic system is not only capable of catalyzing homogeneous epoxidation of alkenes with a unique reaction-controlled phase-transfer character, but also avoids the use of chlorinated solvents. The reactions were conducted in a biphasic mixture of aqueous H2O2/dioxan, and many kinds of alkenes could be efficiently converted to the corresponding epoxides in high yields. Both new and used [(CH3(CH2)17)2N(CH3)2]3[PW4O32] catalyst was characterized by 31P magic angle spin NMR, and IR.
RAFT Polymer End-Group Modification and Chain Coupling/Conjugation Via Disulfide Bonds
Authors: Boyer Cyrille , Liu Jingquan , Bulmus Volga , Davis Thomas P.
Published: August 2009

End-group modification of polymers prepared by reversible addition–fragmentation chain transfer (RAFT) polymerization was accomplished by the conversion of trithiocarbonate or dithioester end-groups into a pyridyl disulfide (PDS) functionality. Several different polymers, such as poly(methyl methacrylate), polystyrene, poly(oligoethylene glycol-acrylate), poly(hydroxypropylacrylamide), and poly(N-isopropylacrylamide) were prepared by RAFT polymerization, and subjected to aminolysis in the presence of 2,2′-dithiodipyridine to yield thiol-terminated polymers with yields in the range 65–90% dependent on the polymer structure. Furthermore, this PDS end-group was utilized to generate higher-order architectures, such as diblock copolymers with high yields and selectively. In addition, the PDS end-groups were used for the bioconjugation of different biomolecules, such as oligonucleotides, carbohydrates, and peptides. The successful modification of well-defined polymers was confirmed by a combination of UV-vis, NMR spectroscopy, and gel permeation chromatography.
Anhydrous Poly(2,5-benzimidazole)–Poly(vinylphosphonic Acid) Acid–Base Polymer Blends: a Detailed Solid-State NMR Investigation
Authors: Akbey Ümit , Graf Robert , Chu Peter P. , Spiess Hans Wolfgang
Published: August 2009

The present study aims at understanding the molecular structure and dynamics of the acidic polymer poly(vinylphosphonic acid) (PVPA) blended with the basic polymer poly(2,5-benzimidazole) (ABPBI) under anhydrous conditions. The extent of the acid–base complexation is probed at different mixing ratios. Advanced 1H, 13C, and 31P solid-state NMR methods are used to investigate the structural features in these systems. In addition, molecular dynamics is studied by variable-temperature 1H magic angle spinning and one-dimensional double-quantum NMR methods. Many different types of hydrogen-bonding are identified in the acid–base complexes. Addition of the acidic PVPA to the basic ABPBI changes the molecular packing arrangements of the ABPBI moieties with hydrogen-bond formation as the driving force. The complex with a 1:1 mixing ratio has the lowest activation energy for proton mobility, and at the same time contains the most structured hydrogen-bonded protons. The results show that molecular-level mixing is achieved for the complexes.
A Novel One-Pot Procedure for the Fast and Efficient Conversion of RAFT Polymers into Hydroxy-Functional Polymers
Authors: Gruendling Till , Dietrich Mathias , Barner-Kowollik Christopher
Published: August 2009

We report on the successful quantitative transformation of methacrylate and acrylate-type polymers prepared by reversible addition–fragmentation chain transfer (RAFT) polymerization carrying a dithioester-end-group into hydroxy-functional polymers. The simple reaction procedure involves stirring a solution of the dithioester-capped polymer and an azo-initiator in tetrahydrofuran at elevated temperatures (T = 60°C) in the presence of air. This reaction quantitatively yields hydroperoxide functionalities that can be efficiently reduced to hydroxy groups in a one-pot procedure using triphenylphosphine. Size exclusion chromatography–electrospray mass spectrometry was employed to monitor the progress of the reaction. The new backbone-linked hydroxy group provides a versatile anchor for chemical end-group conversions and conjugation reactions with prepared RAFT polymers, which alleviates problems with the rather limited ability of the dithioester-end-group to undergo non-radical transformations.
Controlled Dispersion Polymerization in Supercritical Carbon Dioxide
Authors: Thurecht Kristofer J. , Howdle Steven M.
Published: August 2009

Recent advances in controlled polymerization have led to increased activity in controlled free radical polymerization in unconventional solvents. This short report focuses on the renewed interest in dispersion polymerization in supercritical CO2 brought about by the application of controlled free radical polymerization techniques. The emergence of novel and industrially-applicable materials is discussed, as well as the dependence of material properties and morphology upon factors such as surfactant type and how it is employed during the polymerization.
Thermally Responsive Elastomeric Supramolecular Polymers Featuring Flexible Aliphatic Hydrogen-Bonding End-Groups
Authors: Woodward Philip , Merino Daniel Hermida , Hamley Ian W. , Slark Andrew T. , Hayes Wayne
Published: August 2009

The present paper details the synthesis, characterization, and preliminary physical analyses of a series of polyisobutylene derivatives featuring urethane and urea end-groups that enable supramolecular network formation to occur via hydrogen bonding. These polymers are readily accessible from relatively inexpensive and commercially available starting materials using a simple two-step synthetic approach. In the bulk, these supramolecular networks were found to possess thermoreversible and elastomeric characteristics as determined by temperature-dependent rheological analysis. These thermoreversible and elastomeric properties make these supramolecular materials potentially very useful in applications such as adhesives and healable surface coatings.
New Insights into the Control of Self-Assembly of Block Copolymer Membranes
Authors: Fierro Daniel , Buhr Kristian , Abetz Clarissa , Boschetti-de-Fierro Adriana , Abetz Volker
Published: August 2009

The preparation and morphological characterization of a so-called composite membrane based on a 3-miktoarm star terpolymer on a support layer is reported. It is demonstrated that different levels of order and different morphological orientations can be obtained by directly casting the star terpolymer solution on the support, depending on the prior treatment of the support layer and the casting conditions.
Characterization of the Assaying Methods in Polymerization-Based Amplification of Surface Biomarkers
Authors: Johnson Leah M. , Avens Heather J. , Hansen Ryan R. , Sewell Holly L. , Bowman Christopher N.
Published: August 2009

Polymerization-based amplification (PBA), which combines bio-recognition events with polymerization reactions on surfaces, provides visual, sensitive, and cost-effective detection of biological interactions, particularly at extremely low levels of the targeted biological moiety. This study characterizes assay parameters that enhance the utility of PBA to detect nucleic acid and protein biomarkers. Here, we successfully employ PBA on surfaces that contain uniform, high density, immobilized capture molecules, including three-dimensional nitrocellulose-coated substrates. Optimized assay and polymerization conditions are used to characterize the dynamic polymer film heights on glass substrates that result from solutions of KRAS proto-oncogene biomarker targets at concentrations between 5 nM and 500 pM. Differing aqueous monomer formulations are utilized to produce 20 nm films at the 500 pM DNA detection limit.
Synthesis and Photophysical Properties of a Photoelectrochromic Polymer Containing the bis(2-(4-Pyridiniumyl)thiazole) Chromophore
Authors: Nagamura Toshihiko , Sota Yasuhiro
Published: August 2009

A new polymer and small molecules containing the chromophore bis(2-(4-pyridiniumyl)thiazole) were synthesized. Their tetraphenylborate salts showed absorption spectral changes in the visible to near-infrared region accompanying a colour change from yellow to green on steady photoirradiation. From electron spin resonance measurements and comparison with Molecular Orbital PACkage (MOPAC) calculations, this was assigned to the formation of bis(2-(4-pyridiniumyl)thiazole) radicals due to a photoinduced electron-transfer reaction from tetraphenylborate and decomposition of its oxidized form. Transient absorption spectra corresponding to those of tetraphenylborate salts were observed for bromide salts on femtosecond laser excitation of the polymer in solid films and solutions. The fastest decay of transient absorption due to back electron transfer was less than 1 picosecond.
PMMA Star-Like Polymers via One-Pot Conventional Free-Radical Copolymerization
Authors: Goh Tor Kit , Blencowe Anton , Tan Jing Fung , Coventry Kristopher D. , Qian Feng , Tachasirinugune Tatchkul , Qiao Greg G.
Published: August 2009

Poly(methyl methacrylate)-based star-like polymers (SLPs) were synthesized by a one-pot conventional free-radical copolymerization. Two aryl ester-based cross-linkers, bisphenol A dimethacrylate and 1,4-bis(methacryloxy)benzene, were found to induce SLP formation by reactivity control when copolymerized with methyl methacrylate. The formulation domain diagrams for these systems were established and high monomer concentrations (up to 70 wt-%) were achievable without the occurrence of macrogelation. Kinetic experiments confirmed that the SLP formation occurs via a pseudo two-step mechanism. Parallel plate rheological analysis of the SLP solutions demonstrated that these polymers had low viscosities, typically several orders of magnitude lower than the analogous linear polymer solution.
Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals
Authors: Salse Jérôme , Abrouk Michael , Bolot Stéphanie , Guilhot Nicolas , Courcelle Emmanuel , Faraut Thomas , Waugh Robbie , Close Timothy J. , Messing Joachim , Feuillet Catherine
Published: August 2009

Paleogenomics seeks to reconstruct ancestral genomes from the genes of today's species. The characterization of paleo-duplications represented by 11,737 orthologs and 4,382 paralogs identified in five species belonging to three of the agronomically most important subfamilies of grasses, that is, Ehrhartoideae (rice)
Panicoideae
(sorghum, maize), and
Pooideae
(wheat, barley), permitted us to propose a model for an ancestral genome with a minimal size of 33.6 Mb structured in five proto-chromosomes containing at least 9,138 predicted proto-genes. It appears that only four major evolutionary shuffling events (α, β, γ, and δ) explain the divergence of these five cereal genomes during their evolution from a common paleo-ancestor. Comparative analysis of ancestral gene function with rice as a reference indicated that five categories of genes were preferentially modified during evolution. Furthermore, alignments between the five grass proto-chromosomes and the recently identified seven eudicot proto-chromosomes indicated that additional very active episodes of genome rearrangements and gene mobility occurred during angiosperm evolution. If one compares the pace of primate evolution of 90 million years (233 species) to 60 million years of the Poaceae (10,000 species), change in chromosome structure through speciation has accelerated significantly in plants.