bluuebunny/crossref_metadata_2025 huggingface dataset:
G‐BLAST: a Grid‐based solution for mpiBLAST on computational Grids
Authors: Yang Chao‐Tung , Han Tsu‐Fen , Kan Heng‐Chuan
Published: December 2008

Over the past few years, research and development in bioinformatics (e.g. genomic sequence alignment) has grown with each passing day fueling continuing demands for vast computing power to support better performance. This trend usually requires solutions involving parallel computing techniques because cluster computing technology reduces execution times and increases genomic sequence alignment efficiency. One example, mpiBLAST is a parallel version of NCBI BLAST that combines NCBI BLAST with message passing interface (MPI) standards. However, as most laboratories cannot build up powerful cluster computing environments, Grid computing framework concepts have been designed to meet the need. Grid computing environments coordinate the resources of distributed virtual organizations and satisfy the various computational demands of bioinformatics applications. In this paper, we report on designing and implementing a BioGrid framework, called G‐BLAST, that performs genomic sequence alignments using Grid computing environments and accessible mpiBLAST applications. G‐BLAST is also suitable for cluster computing environments with a server node and several client nodes. G‐BLAST is able to select the most appropriate work nodes, dynamically fragment genomic databases, and self‐adjust according to performance data. To enhance G‐BLAST capability and usability, we also employ a WSRF Grid Service Portal and a Grid Service GUI desk application for general users to submit jobs and host administrators to maintain work nodes. Copyright © 2008 John Wiley & Sons, Ltd.
A review of lipidomic technologies applicable to sphingolipidomics and their relevant applications
Authors: Han Xianlin , Jiang Xuntian
Published: December 2008

Sphingolipidomics, a branch of lipidomics, focuses on the large‐scale study of the cellular sphingolipidomes. In the current review, two main approaches for the analysis of cellular sphingolipidomes (i.e. LC‐MS‐ or LC‐MS/MS‐based approach and shotgun lipidomics‐based approach) are briefly discussed. Their advantages, some considerations of these methods, and recent applications of these approaches are summarized. It is the authors' sincere hope that this review article will add to the readers understanding of the advantages and limitations of each developed method for the analysis of a cellular sphingolipidome.
Synthesis of Gabosine A and N from Ribose by the Use of Ring‐Closing Metathesis
Authors: Monrad Rune Nygaard , Fanefjord Mette , Hansen Flemming Gundorph , Jensen N. Michael E. , Madsen Robert
Published: December 2008

A concise synthetic route is described for the synthesis of gabosine A and N. The key step uses a zinc‐mediated tandem reaction where methyl 5‐deoxy‐5‐iodo‐2,3‐O‐isopropylidene‐β‐D‐ribofuranoside is fragmented to give an unsaturated aldehyde which is allylated in the same pot with 3‐benzoyloxy‐2‐methylallyl bromide. The functionalized octa‐1,7‐diene, thus obtained, is converted into the six‐membered gabosine skeleton by ring‐closing olefin metathesis. Subsequent protective group manipulations and oxidation gives rise to gabosine N in a total of 8 steps from ribose while the synthesis of gabosine A employs an additional step for inverting a secondary hydroxy group. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Tuberculosis and subsequent risk of lung cancer in Xuanwei, China
Authors: Engels Eric A. , Shen Min , Chapman Robert S. , Pfeiffer Ruth M. , Yu Ying‐Ying , He Xingzhou , Lan Qing
Published: December 2008

Tobacco and indoor air pollution from smoky coal are major causes of lung cancer in rural Xuanwei County, China. Tuberculosis has been suggested to increase lung cancer risk, but data from prior studies are limited. We conducted an analysis of data from a retrospective cohort study of 42,422 farmers in Xuanwei. In 1992, interviewers administered a standardized questionnaire that included lifetime medical history, including tuberculosis. Subjects were followed from 1976, with deaths from lung cancer ascertained through 1996. We used proportional hazards regression to assess the association between tuberculosis and subsequent lung cancer mortality. Tuberculosis was reported by 246 subjects (0.6%), and 2,459 (5.8%) died from lung cancer during follow‐up. Lung cancer mortality was substantially higher in subjects with tuberculosis than in those without (25 vs. 3.1 per 1,000 person‐years). The association was especially pronounced in the first 5 years after tuberculosis diagnosis (hazard ratios [HRs] ranging 6.7–13) but remained strong 5–9.9 years (HR 3.4, 95% CI 1.3–9.1) and 10+ years (HR 3.0, 95% CI 1.3–7.3) after tuberculosis. These associations were similar among men and women and among smoky coal users (70.5% of subjects). Adjustment for demographic characteristics, lung disease and tobacco use did not affect results. In Xuanwei, China, tuberculosis is an important risk factor for lung cancer. The increased lung cancer risk, persisting years after a tuberculosis diagnosis, could reflect the effects of chronic pulmonary inflammation and scarring arising from tuberculosis. Published 2008 Wiley‐Liss, Inc.
Components of precipitation and temperature anomalies and change associated with modes of the Southern Hemisphere
Authors: Watterson I. G.
Published: December 2008

A long simulation of climate by the CSIRO Mark 3 coupled atmosphere—ocean model is analysed to assess the role of three modes of the Southern Hemisphere (SH) circulation on the inter‐annual variability of precipitation and surface temperature and the contribution of the modes to patterns of change under global warming. Indices of El Niño‐southern oscillation (ENSO) and the high‐ and low‐latitude modes (HLM, LLM) of zonal mean zonal wind are extracted from monthly means during the period 1871–1970. The model El Niño brings mostly drier and warmer conditions to Australia—New Zealand (NZ), South America and southern Africa in both annual and seasonal means. The HLM and LLM modes impact rainfall and temperature in banded patterns. Positive HLM [which is closely related to the southern annular mode (SAM) in pressure] moistens and cools around 20–35°S particularly near the east coast of each continent. Farther south it mostly dries and warms, especially in the austral winter. The LLM has some impacts, including increased summer rain in western Australia, and temperature anomalies in eastern South America in autumn. Mostly similar patterns are found in the ERA40 observational data. Changes in the indices in the 22nd century, following warming forced by the A1B greenhouse gas (GHG) scenario, are positive, in most cases, and similar in magnitude to their inter‐annual variability. The drying and warming of Australia associated with an El Niño‐like change are largely countered by the HLM‐like change, and similar effects are seen in parts of the other continents. The far south of NZ and South America are dried and warmed by the HLM change, but these relative changes are countered by non‐modal effects in the Southern Ocean. Overall the impact of the simulated modes is largest on Australia, with the HLM being as important as ENSO in the mid‐latitudes. Copyright © 2008 Royal Meteorological Society
The human promyelocytic leukemia protein is a tumor suppressor for murine skin carcinogenesis
Authors: Virador Victoria M. , Flores‐Obando Rafael E. , Berry Adam , Patel Rinal , Zakhari Julia , Lo Yu‐Chien , Strain Kathryn , Anders Joanna , Cataisson Christophe , Hansen Laura A. , Yuspa Stuart H.
Published: December 2008

Expression of the PMLRARα fusion dominant‐negative oncogene in the epidermis of transgenic mice resulted in spontaneous skin tumors attributed to changes in both the PML and RAR pathways [Hansen et al., Cancer Res 2003; 63:5257–5265]. To determine the contribution of PML to skin tumor susceptibility, transgenic mice were generated on an FVB/N background, that overexpressed the human PML protein in epidermis and hair follicles under the control of the bovine keratin 5 promoter. PML was highly expressed in the epidermis and hair follicles of these mice and was also increased in cultured keratinocytes where it was confined to nuclear bodies. While an overt skin phenotype was not detected in young transgenic mice, expression of keratin 10 (K10) was increased in epidermis and hair follicles and cultured keratinocytes. As mice aged, they exhibited extensive alopecia that was accentuated on the C57BL/6J background. Following skin tumor induction with 7, 12‐dimethylbenz[a]anthracene (DMBA) as initiator and 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA) as promoter, papilloma multiplicity and size were decreased in the transgenic mice by 35%, and the conversion of papillomas to carcinomas was delayed. Cultured transgenic keratinocytes underwent premature senescence and upregulated transcripts for p16 and Rb but not p19 and p53. Together, these changes suggest that PML participates in regulating the growth and differentiation of keratinocytes that likely influence its activity as a suppressor for tumor development. Published 2008 Wiley‐Liss, Inc.
High pressure Raman study of carotene‐encapsulating single‐wall carbon nanotubes
Authors: Arvanitidis J. , Christofilos D. , Souliou S. M. , Yanagi K. , Kataura H. , Kourouklis G. A. , Ves S.
Published: December 2008

The pressure response of carotene‐encapsulating single‐wall carbon nanotubes is investigated by means of Raman spectroscopy. The pressure evolution of the tangential G band frequencies of the carbon nanotubes is linear without any specific features. On the other hand, the pressure response of the carotene's ν1 mode frequency is quite distinct, having a smaller low pressure slope than that reported in the literature for the molecule. This behaviour is compatible with the pressure screening effect in the interior of carbon nanotubes. For pressure higher than 2 GPa, the pressure slope becomes even smaller, an effect which can be attributed to the theoretically predicted cross‐section deformation of the encapsulating tubes. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
CXCR2 and RET Single Nucleotide Polymorphisms in Pancreatic Cancer
Authors: Donahue Timothy R. , Hines O. Joe
Published: December 2008

Enhanced angiogenesis and perineural invasion are markers of poor prognosis in patients with pancreatic cancer. Systemic therapies for pancreatic cancer have been largely ineffective, and thus improved, targeted therapies are needed. Single nucleotide polymorphisms (SNP) are DNA sequence variations that result in vast diversity of disease susceptibility and response to disease. CXCR2 is an important mediator of CXC chemokine‐induced angiogenesis and is upregulated in pancreatic cancer. In a preclinical corneal micropocket assay, treatment of pancreatic cancer cell lines that express CXCR2 with anti‐CXCR2 antibody inhibited angiogenesis. To date, there have not been any CXCR2 SNP associated with pancreatic cancer, but CXCR2 SNP has been postulated to be associated with angiogenesis in systemic sclerosis. The receptor tyrosine kinase encoded by the RET gene and its ligand glial derived neurotrophic factor (GDNF) are upregulated in pancreatic cancer. In vitro treatment of pancreatic cancer cell lines that express RET with anti‐RET antibody or RET siRNA‐inhibited GDNF‐induced invasiveness. G691S RET SNP has been previously shown to be associated with enhanced pancreatic cancer invasiveness. We suggest that molecular profiling of each patient’s tumor for G691S RET SNP, potentially CXCR2 SNP, and also other yet‐to‐be identified SNP associated with pancreatic cancer will allow for both improved understanding of individual prognosis and allow for utilization of more personalized, targeted adjuvant therapies.
Which Method Should We Select for Pancreatic Anastomosis After Pancreaticoduodenectomy?
Authors: Kim Ji Hun , Yoo Byung Moo , Kim Jin Hong , Kim Wook Hwan
Published: December 2008

Background

This study was designed to compare surgical, morphological, and functional outcomes of pancreaticoduodenectomy (PD) according to the types of pancreaticoenterostomy performed and to suggest a proper anastomotic method after PD.

Methods

From January 2001 to December 2006, 147 PDs were performed at Ajou University Medical Center. Surgical, morphological, functional, and nutritional outcomes after PD were retrospectively compared according to the types of management of pancreatic remnant and whether pancreaticogastrostomy (PG) or pancreaticojejunostomy (PJ), including duct‐to‐mucosa or invagination method, was performed.

Results

For the reconstruction method, 43 PG (30 duct‐to‐mucosa and 13 invagination) and 100 PJ (33 duct‐to‐mucosa and 67 invagination) were performed. Pancreatic leak rate in PG group (7%) was less than that in PJ group (13%); however, it was not significant (P > 0.05). On the other hand, there was a significant difference in pancreatic leak between duct‐to‐mucosa and invagination (3.2 vs. 17.5%, P < 0.05). Surprisingly, there was no pancreatic leak in PG duct‐to‐mucosa anastomosis after PD. There were no significant differences in the change of remnant pancreatic duct size, pancreatic thickness, presence of steatorrhea, and new‐onset diabetes mellitus (DM) between PG and PJ. In the invagination group, the main pancreatic duct diameter was increased and pancreatic thickness was progressively reduced.

Conclusion

The duct‐to‐mucosa method is safer and has a good duct patency and low pancreas atrophy compared with the invagination method. In addition, PG duct‐to‐mucosa is safer than PG invagination, but not in the PJ group. Therefore, we recommend PG duct‐to‐mucosa for reconstruction after PD because of safety and good duct patency, especially for inexperienced surgeons.
OR Construction Project: From Planning to Execution
Authors: Worley Dorothea J. , Hohler Sharon E.
Published: December 2008

OPERATING ROOM RENOVATION PROJECTS require planning and collaboration among physicians, hospital staff members, and vendors.

RENOVATION INVOLVES many details, from how many electrical plugs to install in each OR to integration of the latest technologies.

DETAILS OF A MULTIPHASE OR renovation project undertaken at Saint Francis Medical Center in Cape Girardeau, MO, provide information and tools that any facility planning a renovation can use. AORN J 88 (December 2008) 917–941. © AORN, Inc, 2008.
A Revolutionary Modernity: The Cultural Policy of the Cuban Revolution
Authors: MILLER NICOLA
Published: December 2008

This article seeks to explain why such a wide range of Cuban cultural producers have opted to remain on the island and work ‘within the revolution’, despite all the notorious problems caused by state censorship, political persecution and material shortages. It accounts for the importance of culture to the legitimacy of the revolutionary government; suggests that the regime has drawn effectively on the long-established significance of culture in Cuba's radical tradition; and illustrates the extent to which the government has backed up its rhetoric of commitment to culture for all with a sustained policy of support for institutions, organisations and events across the island. The main argument is that culture has been a key element – perhaps the only successful element – in the revolution's attempt to implement an alternative model of modernity that was distinctive not only from the Western capitalist version but also from that promoted by the Soviet Union.
Feminists, Queers and Critics: Debating the Cuban Sex Trade
Authors: STOUT NOELLE M.
Published: December 2008

Cuban scholars and women's advocates have criticised the widespread emergence of sex tourism in post-Soviet Cuba and attributed prostitution to a crisis in socialist values. In response, feminist scholars in the United States and Europe have argued that Cuban analysts promote government agendas and demonise sex workers. Drawing on nineteen months of field research in Havana, I challenge this conclusion to demonstrate how queer Cubans condemn sex tourism while denouncing an unconditional allegiance to Cuban nationalism. By introducing gay Cuban critiques into the debate, I highlight the interventionist undertones of feminist scholarship on the Cuban sex trade.
En Casa: Women and Households in Post-Soviet Cuba
Authors: PERTIERRA ANNA CRISTINA
Published: December 2008

This paper argues that the household has become a renewed space of significance for Cuban women in the post-Soviet period. It draws from existing scholarship and ethnographic fieldwork conducted with women in the city of Santiago de Cuba to discuss the effect of post-Soviet crisis and reform upon women's domestic practices, the management of domestic economies, and longstanding gender ideals that link women to the domestic sphere. Physical, economic and social factors leading to post-Soviet Cuban women's increased concentration upon the household are argued to be both the result of pre-existing social orientations towards households as a womanly space and a response to specific politico-economic shifts since the collapse of the Soviet Union.
Analysis of common‐mode effects in a dual‐polarized planar connected‐array antenna
Authors: Hay S. G. , O'Sullivan J. D.
Published: December 2008

An analysis is presented of the efficiency of a dual‐polarized planar connected‐array antenna, with particular reference to possible use in wideband focal‐plane‐array applications. The modeling approach is described, and the results of different numerical techniques are compared. The analysis includes the effects of transmission lines used to load the array at a groundplane. Different types of loading are compared including optimum single‐ended loading and optimum differential‐mode loading with short‐circuit and open‐circuit common‐mode terminations. The results indicate that high efficiency over useful bandwidths should be possible. In the case of differential‐mode loading, the efficiency may be reduced at certain frequencies due to resonances of common‐mode currents on the transmission lines. The current distributions on the array are analysed, and observations are made which may be useful for modified designs.
Spatial delineation of groundwater salinity using deep time domain electromagnetic geophysical measurements: A feasibility study
Authors: Levi Eldad , Goldman Mark , Hadad Avichay , Gvirtzman Haim
Published: December 2008

The objective of this study was to delineate the spatial distribution of fresh, brackish, and saline groundwater bodies, as well as brine, beneath the Judea Desert, Israel. We used the deep time domain electromagnetic (TDEM) geophysical system, Cycle‐5M, which provides the maximum exploration capability, to depths ∼1.5–2 km below land surface. The study was conducted at 21 locations at the desert plateau, where fresh groundwater flows through the upper aquifers from the replenishment area at the Judea Mountains toward the Dead Sea springs. In deeper aquifers, brackish and saline groundwater bodies exist, which originated from lakes and lagoons that existed at the Dead Sea Rift valley during the Pleistocene and Pliocene, respectively. It was found that within carbonate formations, fresh groundwater (C < 103 ppm total dissolved solids (TDS)) is characterized by a resistivity of more than 15 Ω m, brackish groundwater (103 < C < 104 ppm TDS) is characterized by 5–15 Ω m, saline groundwater (104 < C < 105 ppm TDS) is characterized by 0.5–5 Ω m, and brine (105 < C ppm TDS) is characterized by less than 0.5 Ω m.
Informatics and the 2007–2008 Electronic Geophysical Year
Authors: Baker Daniel N. , Barton C. E. , Peterson W. K. , Fox P.
Published: December 2008

Humanity is poised to take the next major steps toward an interdisciplinary, worldwide revolution in the way we store, access, and analyze information. For the geosciences, our ability to gather data about the Earth and its space environment is unprecedented. We can obtain data and services via the Internet and grid systems from anywhere in the world, we can store and serve data with true interoperability, and we can deal with real‐time data applications, assimilate data into models, build virtual observatories, and more.

The challenges of organizing and using data effectively expand as data volumes, data complexity, the need for interoperability, and our ability to access data and information increase. In particular, there remains great reluctance among research scientists and others to invest time in good data management practices and thereby ensure that publicly funded data are openly available for use and reuse. The reason is simple: Research scientists are rewarded only for doing research. The science community lacks any recognized system for publishing and citing data sets and for rewarding efforts to make data sets freely available and interoperable.
Observing Oceanic Submesoscale Processes From Space
Authors: Fu Lee‐Lueng , Ferrari Raffaele
Published: December 2008

Observations made by satellite altimeters since the 1980s have provided progressively improved views of the global ocean mesoscale eddy field, which contains most of the kinetic energy of the ocean circulation. Along with these improved views, ocean models have progressed from coarseresolution, highly dissipative mesh grids to higher resolutions where mesoscale eddies dominate the model simulations. We are now able to produce simulations of the present state of the ocean that compare increasingly well with observations. However, the skill of these models in making long‐range predictions of the ocean is still very limited, because the models lack a physically based representation of the submesoscales, i.e., scales of 1100 kilometers, that are important for turbulent transport and energy dissipation. Ocean models running at sufficient resolutions to address submesoscale dynamics have just recently begun to emerge [e.g., Capet et al., 2008], but we need global observations at these scales to guide the model development.
Dynamical prediction of terrestrial ecosystems and the global carbon cycle: A 25‐year hindcast experiment
Authors: Zeng Ning , Yoon Jin‐Ho , Vintzileos Augustin , Collatz G. James , Kalnay Eugenia , Mariotti Annarita , Kumar Arun , Busalacchi Antonio , Lord Stephen
Published: December 2008

Using a 25‐year hindcast experiment, we explore the possibility of seasonal‐interannual prediction of terrestrial ecosystems and the global carbon cycle. This has been achieved using a prototype forecasting system in which the dynamic vegetation and terrestrial carbon cycle model VEGAS was forced with 15‐member ensemble climate predictions generated by the NOAA/NCEP coupled climate forecasting system (CFS) for the period 1981–2005, with lead times up to 9 months. The results show that the predictability is dominated by the ENSO signal with its major influence on the tropical and subtropical regions, including South America, Indonesia, southern Africa, eastern Australia, western United States, and central Asia. There is also important non‐ENSO related predictability such as that associated with midlatitude drought. Comparison of the dynamical prediction results with benchmark statistical prediction methods such as anomaly persistence and damping show that the dynamical method performs significantly better. The hindcasted ecosystem variables and carbon flux show significantly slower decrease in skill at longer lead time compared to the climate forcing variables, partly because of the memories in land and vegetation processes that filter out the higher‐frequency noise and sustain the signal.
Axial high topography and partial melt in the crust and mantle beneath the western Galápagos Spreading Center
Authors: Blacic Tanya M. , Ito Garrett , Shah Anjana K. , Canales Juan Pablo , Lin Jian
Published: December 2008

The hot spot‐influenced western Galápagos Spreading Center (GSC) has an axial topographic high that reaches heights of ∼700 m relative to seafloor depth ∼25 km from the axis. We investigate the cause of the unusual size of the axial high using a model that determines the flexural response to loads resulting from the thermal and magmatic structure of the lithosphere. The thermal structure simulated is appropriate for large amounts of cooling by hydrothermal circulation, which tends to minimize the amount of partial melt needed to explain the axial topography. Nonetheless, results reveal that the large axial high near 92°W requires that either the crust below the magma lens contains >35% partial melt or that 20% melt is present in the lower crust and at least 3% in the mantle within a narrow column (<∼10 km wide) extending to depths of 45–65 km. Because melt fractions >35% in the crust are considered unreasonable, it is likely that much of the axial high region of the GSC is underlain by a narrow region of partially molten mantle of widths approaching those imaged seismically beneath the East Pacific Rise. A narrow zone of mantle upwelling and melting, driven largely by melt buoyancy, is a plausible explanation.
Lava lake surface characterization by thermal imaging: Erta 'Ale volcano (Ethiopia)
Authors: Spampinato L. , Oppenheimer C. , Calvari S. , Cannata A. , Montalto P.
Published: December 2008

Active lava lakes represent the exposed, uppermost part of convecting magma systems and provide windows into the dynamics of magma transport and degassing. Erta 'Ale volcano located within the Danakil Depression in Ethiopia hosts one of the few permanent convecting lava lakes, probably active for a century or more. We report here on the main features of the lava lake surface based on observations from an infrared thermal camera made on 11 November 2006. Efficient magma circulation was reflected in the sustained transport of the surface, which was composed of pronounced incandescent cracks that separated wide plates of cooler crust. These crossed the lake from the upwelling to the downwelling margin with mean speeds ranging between 0.01 and 0.15 m s−1. Hot spots eventually opened in the middle of crust plates and/or along cracks. These produced mild explosive activity lasting commonly between ∼10 and ∼200 s. Apparent temperatures of cracks ranged between ∼700 and 1070°C, and of crust between ∼300 and 500°C. Radiant power output of the lake varied between ∼45 and 76 MW according to the superficial activity and continuous resurfacing of the lake. Time series analysis of the radiant power output data reveals cyclicity with a period of ∼10 min. The combination of visual and thermal observations with apparent mean temperatures and convection rates allows us to interpret these signals as the periodic release of hot overpressured gas bubbles at the lake surface.
Main features of rain drop size distributions observed in Benin, West Africa, with optical disdrometers
Authors: Moumouni Sounmaila , Gosset Marielle , Houngninou Etienne
Published: December 2008

As part of the African Monsoon Multidisciplinary Analysis (AMMA) field campaign, rain Drop Size Distribution (DSD) measurements were carried out in Benin, in the Sudanese climatic zone, with optical disdrometers, over 3 rainy seasons. The observed DSDs are well modelled by a gamma distribution, with the value of the shape parameter (μ) close to 5. The average normalized intercept parameter (N0*) is close to 103 mm−1m−3. After classification of the convective and stratiform spectra, it is shown that for a given rain rate the proportion of the bigger drops is higher in the stratiform spectra, consistent with the observed occurrences of ‘N0 jumps’ within the squall lines. Specific reflectivity‐rain rate (Z‐R) relationships were derived for the whole data set, for the squall lines and for the convective and stratiform regions.
The statistical distribution of meteorological outliers
Authors: van den Brink H. W. , Können G. P.
Published: December 2008

A general expression for the statistical distribution of the probability of the highest event occurring in a record is presented. This result can be empirically applied to situations where records are available for multiple geographical locations. The empirical estimation of the probability of the highest events provides a means to assess whether the assumed (extreme value) distribution is appropriate for extrapolation or not. The approach allows for combining the highest events from different records and to validate estimated return periods in the order of the length of the combined records. The method is illustrated with an analysis of the annual extreme wind speeds over the North Atlantic area according to the ERA40 dataset, showing that the Gumbel distribution is in favor of the GEV distribution to estimate the (appropriately transformed) extreme wind speeds up to return periods of 104 years.
Real refractive index: Dependence on relative humidity and solute composition with relevancy to atmospheric aerosol particles
Authors: Wang Wei , Rood Mark J.
Published: December 2008

A closure evaluation of the hygroscopic response in refractive index (n) was completed with measurements and a semi‐empirical model using aqueous solutions containing inorganic salts, dicarboxylic acids, and their mixtures. Measurements of n were made for subsaturated aqueous solutions at select mass fractions of solute with an ellipsometer and a refractometer. The semi‐empirical model was based on the Zdanovskii‐Stokes‐Robinson (ZSR) mixing rule, the partial molar refraction (PMR) method and previously published thermodynamic data. Closure was obtained within 0.75%, as represented by the average absolute error, for n values obtained from the ellipsometry/refractometry measurements and the ZSR‐PMR model for aqueous solutions. It was observed that the hygroscopic response of n on relative humidity could be described by a linear equation. Sensitivity of the top of the atmosphere aerosol radiative forcing to changes in n is also discussed. Finally, strengths and limitations for the ellipsometer, the refractometer, and the ZSR‐PMR method, are discussed.
Atmospheric impact of the Carrington event solar protons
Authors: Rodger Craig J. , Verronen Pekka T. , Clilverd Mark A. , Seppälä Annika , Turunen Esa
Published: December 2008

The Carrington event of August/September 1859 was the most significant solar proton event (SPE) of the last 450 years, about four times larger than the solar proton fluence of the largest event from the “spacecraft era” (August 1972). Recently, much attention has focused upon increasing our understanding of the Carrington event, in order to better quantify the impact of extreme space weather events. In this study the Sodankylä Ion and Neutral Chemistry (SIC) model is used to estimate the impact of the Carrington event to the neutral atmosphere and the ionosphere, and the disruption to HF communication. We adopt a reported intensity‐time profile for the solar proton flux and examine the relative atmospheric response to different SPE‐energy spectra, and in particular, the comparatively soft energy spectrum of the August 1972 or March 1991 SPE which is believed to provide the best representation of the Carrington event. Our calculations indicate that large changes in electron density and atmospheric constituents occur during the period of SPE forcing, depending upon the nature of the spectrum and also on the hemisphere considered. However, the most important SPE‐driven atmospheric response is an unusually strong and long‐lived Ox decrease in the upper stratosphere (Ox levels drop by ∼40%) primarily caused by the very large fluxes of >30 MeV protons. This depletion is an indication of the extreme changes possible for the largest SPE. We find that there are comparatively small long‐term differences in the atmospheric and ionospheric response between the 3 suggested SPE spectra.
Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea
Authors: Carlson Craig A , Morris Robert , Parsons Rachel , Treusch Alexander H , Giovannoni Stephen J , Vergin Kevin
Published: December 2008

Bacterioplankton belonging to the SAR11 clade of a-proteobacteria were counted by fluorescence in situ hybridization (FISH) over eight depths in the surface 300 m at the Bermuda Atlantic Time-series Study (BATS) site from 2003 to 2005. SAR11 are dominant heterotrophs in oligotrophic systems; thus, resolving their temporal dynamics can provide important insights to the cycling of organic and inorganic nutrients. This quantitative time-series data revealed distinct annual distribution patterns of SAR11 abundance in the euphotic (0–120) and upper mesopelagic (160–300 m) zones that were reproducibly correlated with seasonal mixing and stratification of the water column. Terminal restriction fragment length polymorphism (T-RFLP) data generated from a decade of samples collected at BATS were combined with the FISH data to model the annual dynamics of SAR11 subclade populations. 16S rRNA gene clone libraries were constructed to verify the correlation of the T-RFLP data with SAR11 clade structure. Clear vertical and temporal transitions were observed in the dominance of three SAR11 ecotypes. The mechanisms that lead to shifts between the different SAR11 populations are not well understood, but are probably a consequence of finely tuned physiological adaptations that partition the populations along physical and chemical gradients in the ecosystem. The correlation between evolutionary descent and temporal/spatial patterns we describe, confirmed that a minimum of three SAR11 ecotypes occupy the Sargasso Sea surface layer, and revealed new details of their population dynamics.
β‐Cell Function and Insulin Sensitivity in Adolescents From an OGTT
Authors: Sunehag Agneta L. , Dalla Man Chiara , Toffolo Gianna , Haymond Morey W. , Bier Dennis M. , Cobelli Claudio
Published: December 2008

Given the increase in the incidence of insulin resistance, obesity, and type 2 diabetes in children and adolescents, it would be of paramount importance to assess quantitative indices of insulin secretion and action during a physiological perturbation, such as a meal or an oral glucose‐tolerance test (OGTT). A minimal model method is proposed to measure quantitative indices of insulin secretion and action in adolescents from an oral test. A 7 h, 21‐sample OGTT was performed in 11 adolescents. The C‐peptide minimal model was identified on C‐peptide and glucose data to quantify indices of β‐cell function: static φs and dynamic φd responsivity to glucose from which total responsivity φ was also measured. The glucose minimal model was identified on glucose and insulin data to estimate insulin sensitivity, SI, which was compared to a reference measure, SIref, provided by a tracer method. Disposition indices, which adjust insulin secretion for insulin action, were then calculated. Indices of β‐cell function were φs = 51.35 ± 8.89 × 10−9min−1, φd = 1,392 ± 258 × 10−9, and φ = 82.09 ± 17.70 × 10−9min−1. Insulin sensitivity was SI = 14.19 ± 2.73 × 10−4, not significantly different from SIref = 14.96 ± 3.04 × 10−4 dl/kg·min per µU/ml, and well correlated: r = 0.98, P < 0.0001, thus indicating that SI can be accurately measured from an oral test. Disposition indices were DIs = 1,040 ± 201 × 10−14 dl/kg/min2 per pmol/l, DId = 33,178 ± 10,720 × 10−14 dl/kg/min per pmol/l, DI = 1,844 ± 522 × 10−14 dl/kg/min2 per pmol/l. Virtually the same minimal model assessment was obtained with a reduced 3 h, 9‐sample protocol. OGTT interpreted with C‐peptide and glucose minimal model has the potential to provide novel insight regarding the regulation of glucose metabolism in adolescents, and to evaluate the effect of obesity and interventions such as diet and exercise.
Characteristics Associated With Fasting Appetite Hormones (Obestatin, Ghrelin, and Leptin)
Authors: Beasley Jeannette M. , Ange Brett A. , Anderson Cheryl A.M. , Miller Edgar R. , Holbrook Janet T. , Appel Lawrence J.
Published: December 2008

Obestatin, derived from the same gene as the hunger hormone ghrelin, may reduce food intake in animals. The role of obestatin in human physiology is unclear. We evaluated cross‐sectional associations between participant characteristics and fasting levels of obestatin as well two other hormones associated with energy balance, ghrelin and leptin. Data are from the baseline visit of the Optimal Macronutrient Intake Trial to Prevent Heart Disease (OMNI‐Heart) Trial that enrolled adults with elevated blood pressure (systolic 120–159 mm Hg or a diastolic of 80–99 mm Hg) but who were otherwise healthy. Partial Spearman's correlations and linear regression models estimated the association between age, gender, BMI, physical activity, and smoking with fasting hormones. Obestatin was directly associated with ghrelin (r = 0.45, P < 0.05). On average, overweight (BMI 25–30) and obese (BMI > 30) individuals had obestatin concentrations that were 12.6 (s.d. 8.8) and 25.4 (s.d. 8.4) pg/ml lower compared to normal weight (BMI < 25) individuals, respectively (P for trend = 0.002). Overweight (BMI 25–30) and obese (BMI > 30) individuals had ghrelin concentrations that were 161.7 (s.d. 69.6) and 284.7 (s.d. 66.5) pg/ml lower compared to normal weight (BMI < 25) individuals, respectively (P for trend <0.0001). A 5 unit increase in BMI was associated with 41.3% (s.d. 4.3%) (P < 0.0001) higher leptin. Obestatin and ghrelin are directly correlated and share the same patterns of association with participant characteristics. Modifiable risk factors for chronic diseases, such as BMI, are associated with fasting levels of leptin, obestatin, and ghrelin.
Production and analysis of organic acids in hairy‐root cultures of Isatis indigotica Fort. (indigo woad)
Authors: Xu Tiefeng , Zhang Lei , Sun Xiaofen , Zhang Hanming , Tang Kexuan
Published: December 2008

Hairy roots were induced from both cotyledon and hypocotyl explants of Isatis indigotica Fort. (indigo woad) through transformation with Agrobaterium rhizogenes strain A4, R1601 and ATCC15834. The results showed that the cotyledons were the preferred explants to hypocotyls and A4 was the most suitable A. rhizogenes strain for the transformation and induction of hairy roots of I. indigotica. High‐voltage paper electrophoresis (HVPE) analysis demonstrated the production of mannopine in hairy roots and confirmed the successful transfer of Ri T‐DNA (root‐inducing transferred DNA) of A. rhizogenes into the I. indigotica genome. Five organic acids, namely CPQ [3‐(2‐carboxyphenol)‐4(3H)‐quinazolinone], syringic acid, salicylic acid, benzoic acid and 2‐aminobenzoic acid, which were considered as main antiviral components of I. indigotica, were detected in natural roots, hairy roots and liquid media with high‐performance capillary electrophoresis. The results showed CPQ production in hairy roots was significantly higher than that in natural roots. Our results also revealed that all the five organic acids could be excreted from hairy roots into liquid media, and the concentrations of organic acids in the liquid media paralleled those in hairy roots. The hairy roots of I. indigotica grew fast and showed an S‐shaped growth curve that reached its apex on the day 24 of culture with a 20‐fold increase in fresh weight compared with the starting inoculums. The accumulation of the two organic acids CPQ and syringic acid in liquid media paralleled the growth of hairy roots. MS [Murashige, T. and Skoog, F. (1962) Physiol. Plant. 15, 473–497] medium or half‐strength MS medium supplemented with 30 g/l maltose was found to be best for hairy‐root culture and accumulation of CPQ.
Insulin resistance in polycystic ovary syndrome is associated with defective regulation of ERK1/2 by insulin in skeletal muscle in vivo
Authors: Rajkhowa Madhurima , Brett Sandra , Cuthbertson Daniel J. , Lipina Christopher , Ruiz-Alcaraz Antonio J. , Thomas Giles E. , Logie Lisa , Petrie John R. , Sutherland Calum
Published: December 2008

Insulin resistance is a recognized feature of PCOS (polycystic ovary syndrome). However, the molecular reason(s) underlying this reduced cellular insulin sensitivity is not clear. The present study compares the major insulin signalling pathways in skeletal muscle isolated from PCOS and controls. We measured whole-body insulin sensitivity and insulin signalling in skeletal muscle biopsies taken before and after acute exposure to hyperinsulinaemia in nine women diagnosed with PCOS and seven controls. We examined the expression, basal activity and response to in vivo insulin stimulation of three signalling molecules within these human muscle samples, namely IRS-1 (insulin receptor substrate-1), PKB (protein kinase B) and ERK (extracellular-signal-regulated kinase) 1/2. There was no significant difference in the expression, basal activity or activation of IRS-1 or PKB between PCOS and control subjects. However, there was a severe attenuation of insulin stimulation of the ERK pathway in muscle from all but two of the women with PCOS (the two most obese), and an accompanying trend towards higher basal phosphorylation of ERK1/2 in PCOS. These results are striking in that the metabolic actions of insulin are widely believed to require the IRS-1/PKB pathway rather than ERK, and the former has been reported as defective in some previous PCOS studies. Most importantly, the molecular defect identified was independent of adiposity. The altered response of ERK to insulin in PCOS was the most obvious signalling defect associated with insulin resistance in muscle from these patients.
Acceptance of Noise With Intelligible, Reversed, and Unfamiliar Primary Discourse
Authors: Gordon-Hickey Susan , Moore Robert E.
Published: December 2008

Purpose

The purpose of this study was to investigate the effects of intelligible and unintelligible primary discourse on acceptance of noise. Of particular interest was the effect of intelligibility on the most comfortable loudness (MCL) component of acceptable noise level (ANL).

Method

ANLs were measured for 30 participants using an intelligible discourse, a reversed discourse, and an unfamiliar primary discourse. For each discourse, MCL and background noise level (BNL) were found. The ANL was then computed by subtracting the mean BNL from the MCL.

Results

The intelligibility of the primary discourse did not affect MCL. The ANL was significantly different for the intelligible versus reversed condition and the intelligible versus unfamiliar (Chinese) condition.

Conclusion

Results indicate that ANL may change as speech intelligibility changes and/or speech recognition ability decreases in adults with normal hearing.
Identifying Tinnitus Subgroups With Cluster Analysis
Authors: Tyler Richard , Coelho Claudia , Tao Pan , Ji Haihong , Noble William , Gehringer Anne , Gogel Stephanie
Published: December 2008

Purpose

We believe it is important to uncover tinnitus subgroups to identify subsets of patients most likely to benefit from different treatments. We review strategies for subgrouping based on etiology, subjective reports, the audiogram, psychoacoustics, imaging, and cluster analysis.

Method

Preliminary results of a 2-step cluster analysis based on 246 participants from whom we had 26 categorical and 25 continuous variables were determined.

Results

A 4-cluster solution suggested the following subgroups: (a) constant distressing tinnitus, (b) varying tinnitus that is worse in noise, (c) tinnitus patients who are copers and whose tinnitus is not influenced by touch (somatic modulation), and (d) tinnitus patients who are copers but whose tinnitus is worse in quiet environments.

Conclusions

Subgroups of tinnitus patients can be identified by using statistical approaches. The subgroups we identify here represent a preliminary attempt at identifying such patients. One next step would be to explore clinical trials of tinnitus treatments based on subgroup analyses or on using subgroups in the selection criteria.
Automated Pure-Tone Audiometry: An Analysis of Capacity, Need, and Benefit
Authors: Margolis Robert H. , Morgan Donald E.
Published: December 2008

Purpose

The rationale for automating pure-tone audiometry based on the need for hearing tests and the capacity of audiologists to provide testing is presented. The personnel time savings from automated testing are analyzed. Some possible effects of automated testing on the profession are explored.

Method

Need for testing was based on prevalence of hearing impairment, number of normal hearing patients seen for testing, and an assumption of the frequency of testing. Capacity is based on the number of audiologists and the number of audiograms performed in a typical workday. Time savings were estimated from the average duration of an audiogram and an assumption that 80% can be automated.

Results

A large gap exists between the need and the capacity of audiologists to provide testing. Automating 80% of audiograms would only partially close the gap. A significant time savings could accrue, permitting reallocation of time for doctoral level services.

Conclusion

Although certain jobs could be affected, the gap between capacity and need is so great that automated audiometry will not significantly affect employment. Automation could increase the number of hearing impaired patients that could be served. The reallocation of personnel time would be a positive change for our patients and our profession.
Photoconductivity of Hf-based binary metal oxide systems
Authors: Shamuilia S. , Afanas’ev V. V. , Stesmans A. , McCarthy I. , Campbell S. A. , Boutchich M. , Roeckerath M. , Heeg T. , Lopes J. M. J. , Schubert J.
Published: December 2008

To explore the possibility of bandgap engineering in binary systems of oxide insulators we studied photoconductivity of nanometer-thin Hf oxide layers containing different concentrations of cations of different sorts (Si, Al, Sr, or Ce) deposited on (100)Si. The lowest bandgap of the Hf:Al oxide is close to the value 6–6.2 eV of elemental amorphous Al2O3 and insensitive to the Al content for concentrations of Al exceeding 36%. This result suggests that the Al oxide subnetwork with the largest bandgap preserves this energy width while development of a narrower gap of HfO2 is prevented possibly by dilution of the second cation subnetwork. When Ce is admixed to HfO2 an intermediate bandgap value (between the CeO2 and HfO2 bandgap widths) of 5.3+0.1 eV is observed for all concentrations of Ce, suggesting that the electronic structure of both elemental oxide subnetworks which form the binary metal oxide system, is affected. In Hf:Si oxide samples photoconductivity thresholds of 5.6–5.9 eV corresponding to the bandgap of HfO2 are observed for all studied Si concentrations, suggesting phase separation to occur. The photoconductivity of SrHfO3 exhibits two thresholds at 4.4 and 5.7 eV, which are close to the bandgaps of elemental SrO and HfO2, respectively, indicating, again, phase separation. Through this work we have illustrated photoconductivity as a feasible method to trace phase separation in nanometer-thin layers of binary systems of metal oxides.
Relaxation during spin-lock spin-echo pulse sequence in N14 nuclear quadrupole resonance
Authors: Gregorovič Alan , Apih Tomaž
Published: December 2008

In this work, we investigate off-resonance effect on the N14 nuclear quadrupole resonance magnetization decay during the spin-lock spin-echo pulse sequence (SLSE). The compound chosen for this study is paranitrotoluene with a single N14 site, which represents a suitable simplified model for the explosive trinitrotoluene with six nonequivalent N14 sites. We find that the quasi-steady state magnetization exhibits dips at particular frequency offsets and more interestingly that its decay rate T2 eff−1 exhibits similar dips (slower decay) at the same frequency offsets. The coexistence of dips is very important for applications where the primary use of the SLSE sequence is to increase the signal-to-noise ratio, as longer sampling times compensate for small magnetization values. A theory explaining both observations is presented which includes homonuclear dipolar interactions and spin coupling to the lattice. We show that the homonuclear dipolar interaction contributes only 20% to the total magnetization decay rate, while spin-lattice coupling is the dominant mechanism.