bluuebunny/crossref_metadata_2025 huggingface dataset:
Prenatal diagnosis of chromosomal abnormalities in a resource‐poor setting
Authors: Geerts Lut
Published: August 2008

Objective

To compare the efficacy and efficiency of systematic, ultrasound‐based risk adjustment using a published algorithm with that of a maternal age cutoff of 37 years for the prenatal detection of chromosomal abnormalities (especially autosomal trisomies).

Methods

These approaches were compared in a retrospective study of 136 chromosomal abnormalities confirmed by karyotyping prenatally (n = 46) or postnatally (n = 90). There were 114 autosomal trisomies.

Results

Maternal age was known for 103 fetuses with confirmed abnormalities. The ultrasound‐based risk adjustment approach was more sensitive for autosomal trisomy (93.9% vs 44.1%), and karyotyping for younger women with abnormalities on ultrasound was more effective than routine karyotyping in older women (1 trisomy detected in 13.5 vs 42.8 samples, P < 0.001). A lack of screening was the main reason for the postnatal diagnosis.

Conclusion

Ultrasound‐based risk adjustment was the more effective approach.
When did Ownership Separate from Control? Corporate Governance in the Early Nineteenth Century
Authors: HILT ERIC
Published: August 2008

This article analyzes the ownership structures and governance institutions of New York's corporations in the 1820s, using a new dataset collected from the records of the state's 1823 capital tax, and from the corporate charters. In contrast to Berle and Means's account of the development of the corporation, the results indicate that many firms were dominated by large shareholders, who were represented on the firms' boards, and held sweeping power to utilize the firms' resources for their own benefit. To address this problem, many firms configured their voting rights in a way that curtailed the power of large investors.

“…we complain of directors considering themselves thecompany,when they are merely theagents.”1
The Effect of Geography and Vitamin D on African American Stature in the Nineteenth Century: Evidence from Prison Records
Authors: CARSON SCOTT ALAN
Published: August 2008

The use of height data to measure living standards is now a well-established method in economic literature. Although blacks and whites today reach similar terminal statures in the United States, nineteenth-century African American statures were consistently shorter than those of whites. Greater insolation (vitamin D production) is documented here to be associated with taller black statures. Black farmers were taller than workers in other occupations, and, ironically, black youth statures increased during the antebellum period and decreased with slavery's elimination.
Russian Living Standards under the Tsars: Anthropometric Evidence from the Volga
Authors: MIRONOV BORIS , A'HEARN BRIAN
Published: August 2008

The trend in mean height in the Russian province of Saratov is estimated for birth cohorts from 1755 to 1892 on the basis of newly gathered archival data and published sources. Heights fell in the late eighteenth century due an increasing burden of taxes and feudal dues. Stature increased slowly throughout the nineteenth century, offering no support for the hypothesis of an agrarian crisis that provoked or followed from the abolition of serfdom in 1861. Improving living conditions can be attributed to economic development, rising productivity in agriculture, and diversification of peasant economic activity into other sectors.
Role of early voice therapy in patients affected by unilateral vocal fold paralysis
Authors: D'Alatri L , Galla S , Rigante M , Antonelli O , Buldrini S , Marchese M R
Published: August 2008

Objective:

To evaluate the functional results obtained after voice therapy in patients with unilateral vocal fold paralysis caused by different aetiologies.

Design:

Prospective analysis of the outcome of unilateral vocal fold paralysis cases treated at our speech and language rehabilitation service from November 2003 to January 2006. Thirty cases underwent behavioural treatment, between two and six weeks after unilateral vocal fold paralysis onset. A multi-dimensional assessment was carried out before, immediately after and six months after treatment.

Results:

After behavioural therapy, the prevalence of complete glottal closure increased significantly (p < 0.05). Subjects' pre-therapy mean values for jitter, shimmer and noise-to-harmonic ratio were statistically significantly different from those taken both immediately and six months after treatment (p < 0.05). The mean values for voice turbulence index significantly improved only six months after therapy (0.08 vs 0.04). At both post-treatment assessments, voice range profile analysis showed a significant decrease of lowest voice frequency and a significant increase of the number of semitones (p < 0.05). Mean values for grade, instability, breathiness, asthenia and voice handicap index scores were significantly decreased both immediately and six months after treatment, compared with pre-treatment values (p < 0.05).

Conclusions:

Early voice therapy may enable significant improvement in vocal function, allowing the patient to avoid surgery.
Displacement and ethnic reintegration in Ituri, DR Congo: challenges ahead
Authors: Pottier Johan
Published: August 2008

This article examines the ethnic character of Ituri's complex emergency. It considers the local context in which the IDP predicament has unfolded, asking questions about the prospect of, and responsibilities for, post-conflict reintegration. As militia disarmament and peace are linked but not coterminous, it is argued that militant ethnic agendas at the core of the conflict must be scrutinised for their ongoing significance. Revealing the past to be a contested terrain, these agendas call for an apartheid-style solution along lines of segregation first envisaged by Belgian colonialists. To move towards ethnic reintegration, Iturians face the challenge that they must create a common history freed from the stranglehold of extremist interpretations.
Records of Oncaeidae (Copepoda) from the Gulf of Naples, with new records of three species of Triconia
Authors: Di Capua Iole , Boxshall Geoff A.
Published: August 2008

Three species of Oncaeidae, Triconia umerus, T. hawii and T. rufa are reported for the first time in the coastal waters of the Gulf of Naples, Tyrrhenian Sea, western Mediterranean Sea. They were found in meso-zooplankton samples collected in 2004 and were absent from samples collected prior to 2004. Specimens of Triconia umerus and T. hawii were compared with material collected from the type locality (the Red Sea). In order to facilitate identification, brief differential diagnoses, supported by scanning electron micrographs, are presented for the five species of Triconia that have small body size (450 to 600 μm) and co-occur in the upper 50 m of the water column of the Gulf of Naples. Surface ornamentation on the genital double-somite of the female is reported in T. minuta and T. hawii for the first time, but it is difficult to observe using light microscopy and we infer that it has probably been overlooked in these species hitherto. Possible explanations for the new discovery of these species in such a well-studied area are discussed and it is suggested that they represent relatively recent additions to the fauna. A key to the eleven species of Oncaeidae found in the Gulf of Naples is presented.
Appetitive traits and child obesity: measurement, origins and implications for intervention
Authors: Carnell Susan , Wardle Jane
Published: August 2008

Childhood obesity has multiple causes, most of them capable of explaining only one part of the problem. The population-wide impact of sedentary lifestyles and availability of energy-dense food is undeniable, but substantial individual differences in body weight persist, suggesting that individuals respond differently to the ‘obesogenic’ environment. One plausible mechanism for this variation is the early expression of appetitive traits, including low responsiveness to internal satiety signals, high responsiveness to external food cues, high subjective reward experienced when eating liked foods and preferences for energy-dense foods. Case–control studies support the existence of abnormalities in these traits among obese children compared with normal-weight children, and correlations between psychometric measures of child appetite and child weight suggest that appetitive trait profiles may not only promote obesity but also protect against it. The origins of appetitive traits are as yet uncharted, but will include both genetic and environmental influences. Parental feeding style may affect the development of appetite but the exact nature of the relevant behaviours is unclear and many studies are cross-sectional or begin late in childhood, obscuring causal relationships. Future research should explore determinants and biological mechanisms by using prospective designs beginning early in life, measuring relevant biomarkers such as gut hormones and incorporating neuroimaging and genotyping technologies. Potential clinical applications include the identification of ‘at risk’ children early in life and interventions to modify appetitive traits or ameliorate their impact on intake and weight.
Effect of circular arc feet on a control law for a biped
Authors: Kinugasa T. , Chevallereau C. , Aoustin Y.
Published: August 2008

The purpose of our research is to study the effects of circular arc feet on the biped walk with a geometric tracking control. The biped studied is planar and is composed of five links and four actuators located at each hip and each knee thus the biped is underactuated in single support phase. A geometric evolution of the biped configuration is controlled, instead of a temporal evolution. The input-output linearization with a PD control law and a feed forward compensation is used for geometric tracking. The controller virtually constrains 4 degrees of freedom (DoF) of the biped, and 1 DoF (the absolute orientation of the biped) remained. The temporal evolution of the remained system with impact events is analyzed using Poincaré map. The map is given by an analytic expression based on the angular momentum about the contact point. The effect of the radii of the circular arc feet on the stability is studied. As a result, the speed of convergence decreases when the radii increases, if the radius is larger than the leg length the cyclic motion is not more stable. Among the stable cyclic motion, larger radius broadens the basin of attraction. Our results agree with those obtained for passive dynamic walking on stability, even if the biped is controlled through the geometric tracking.
Introduction and Comments
Authors: Johnson James
Published: August 2008

This journal is an experiment, an attempt on the part of APSA to encourage political scientists to find ways to communicate with others beyond their narrow specialty or sub-specialty, using a form other than the familiar research article. This is in may ways a difficult undertaking precisely because there are few models of how to proceed in the space between the familiar journal article and a more journalistic essay. Many of the contributions to this issue of Perspectives on Politics afford some aid in direction
Understanding the Limits to Ethnic Change: Lessons from Uganda's “Lost Counties”
Authors: Green Elliott D.
Published: August 2008

The historically constructed nature of ethnicity has become a widely accepted paradigm in the social sciences. Scholars have especially have focused on the ways modern states have been able to create and change ethnic identities, with perhaps the strongest case studies coming from colonial Africa, where the gap between strong states and weak societies has been most apparent. I suggest, however, that in order to better understand how and when ethnic change occurs it is important to examine case studies where state-directed ethnic change has failed. To rectify this oversight I examine the case of the “lost counties” of Uganda, which were transferred from the Bunyoro kingdom to the Buganda kingdom at the onset of colonial rule. I show that British attempts to assimilate the Banyoro residents in two of the lost counties were an unmitigated failure, while attempts in the other five counties were successful. I claim that the reason for these differing outcomes lies in the status of the two lost counties as part of the historic Bunyoro homeland, whereas the other five counties were both geographically and symbolically peripheral to Bunyoro. The evidence here thus suggests that varying ethnic attachments to territory can lead to differing outcomes in situations of state-directed assimilation and ethnic change.
On Race and Policy History: A Dialogue about the G.I. Bill
Authors: Katznelson Ira , Mettler Suzanne
Published: August 2008

We have independently analyzed the effects of the G.I. Bill's widely-utilized education and training benefits, and reached different conclusions. One of us argues that the implementation of these benefits, especially in the South, helped widen the income and wealth gaps between whites and blacks and further marginalized many African Americans; the other considers them to have been a rare example of a relatively inclusive policy, one that fostered equal citizenship. Because we are both historical institutionalists and we both share interests in matters of social policy, equality, and race, these dissimilar accounts require explanation. This dialogue first considers methodological issues, explaining our decisions about which forms of data to use and to emphasize, and how we made sense of contradictory findings. It next discusses interpretive matters, examining the processes through which we sometimes reached different conclusions even when we confronted the same evidence. Finally, the exchange considers some implications of our findings, probing the lessons they convey both about policy research and practice.
Small‐scale sea ice deformation in the Beaufort Sea seasonal ice zone
Authors: Hutchings J. K. , Hibler W. D.
Published: August 2008

During spring 2003, the deformation of a single lead in the Beaufort Sea was investigated using four Global Positioning System recording stations. The lead was situated in first‐year ice, in the transition zone between multiyear, and seasonal ice packs. We discuss the opening rate and shear of this lead in the context of weather system forcing of the Beaufort Sea sea ice. It is found that in an opening mode, the lead displays semidiurnal fluctuations in divergence. It was also observed that the lead predominately ridged first‐year ice in closing. The volume of ice ridged was the same order of magnitude as ice growth within the study region during the time period studied. Further work is required to fully understand the implications of the subdiurnal forcing of the ice pack on deformation in the shear zone at the edge of the perennial ice pack in the Beaufort Sea. This study provides information about the temporal and spatial scales that must be resolved in these future investigations.
Coseismic sediment deformation during the 1989 Loma Prieta earthquake
Authors: Borja Ronaldo I. , Sun WaiChing
Published: August 2008

Inelastic horizontal sediment deformation from the MS 7.1, 17 October 1989 Loma Prieta earthquake has been estimated to be on the order of 20 cm at a site in Gilroy, California, about 32 km east of the epicenter. This estimate was based on combined deterministic‐stochastic simulations using ground motion data and sediment properties measured from in situ seismic tests and laboratory tests on cored sediment samples of up to 170 m deep. The calculated deformation is comparable to measured horizontal coseismic displacements at various stations in the Santa Cruz network, suggesting that previously back‐figured fault rupture mechanisms may have been influenced by the coseismic sediment deformation.
Water contrast between Precambrian and Phanerozoic continental lower crust in eastern China
Authors: Yang Xiao‐Zhi , Deloule Etienne , Xia Qun‐Ke , Fan Qi‐Cheng , Feng Min
Published: August 2008

The presence of water, even in small amounts, in the continental lower crust may play a critical role in its physical and chemical properties and behavior. However, the environment and evolution of water in the deep crust remain poorly constrained. Investigation of water, dissolved as H‐related point defects in minerals of lower crustal granulites, may provide clues to clarify this issue. The analyzed and compiled water data of nominally anhydrous clinopyroxene (cpx), orthopyroxene (opx), and plagioclase (plag) in lower crustal granulites from Hannuoba, Nushan, and Daoxian in eastern China reveal significant contrast in water contents (ppm H2O by weight) between Precambrian and Phanerozoic samples, e.g., 200–2330 versus 275–720 ppm for cpx, 140–1875 versus 60–185 ppm for opx, 145–900 versus 65–345 ppm for plag, and 155–1120 versus 165–360 ppm for the bulk concentrations. Our data show consistently higher water contents in the Precambrian granulites, implying a more hydrous lower crust in the Precambrian than in the Phanerozoic. Such a difference may reflect variable water contents in the original melts, indicating higher water contents in the Precambrian upper mantle or a plume source for that part of the Precambrian lower crust.
Assimilation of high‐frequency radar currents in a nested model of the West Florida Shelf
Authors: Barth A. , Alvera‐Azcárate A. , Weisberg R. H.
Published: August 2008

High‐frequency radar currents are assimilated in a West Florida Shelf (WFS) model based on the Regional Ocean Model System (ROMS), which is nested in the Atlantic Hybrid Coordinate Ocean Model (HYCOM) for the purpose of including both local and deep‐ocean forcing, particularly the Gulf of Mexico Loop Current. Tides are not included in this model. An ensemble simulation of the WFS model is carried out under different wind‐forcings in order to estimate the error covariance of the model state vector and the covariance between ocean currents and winds. Radial currents measured by high‐frequency radar antennas near Saint Petersburg and Venice, Florida, USA, are assimilated using this ensemble‐based error covariance. Different assimilation techniques using a time‐average ensemble, a filter to reduce surface‐gravity waves and an extended state vector including wind stress were tested. Results of the WFS model assimilating surface currents show an improvement of the model currents not only at the surface but also at depth.
Size distribution of organic and inorganic species in Hong Kong aerosols during the wet and dry seasons
Authors: Zheng Mei , Kester Dana R. , Wang Fu , Shi Xinmei , Guo Zhigang
Published: August 2008

Organic compounds including alkanes, fatty acids, and polycyclic aromatic hydrocarbons (PAHs) and trace and major elements in four size fractions (<0.49 μm, 0.49–0.95 μm, 0.95–2.5 μm, and 2.5–10 μm) collected from June 1998 to January 1999 in Hong Kong were physically and chemically characterized by scanning electron microscope (SEM), gas chromatography/mass spectrometry (GC‐MS), and inductively coupled plasma/mass spectrometry (ICP‐MS) to study their size distributions, seasonal variations, and sources. SEM micrographs show that abundances and shapes of particles in each size fraction exhibit distinct difference between wet and dry seasons. Solvent extractable organic compounds (SEOC) investigated in this study were significantly enriched in fine particulate matter (PM2.5) since 97% of PAH, 88% of alkane, and 69% of fatty acids in PM10 were actually from PM2.5. The pollution elements and SEOC showed a change from a maxima in the finest fraction (<0.49 μm) in the wet season, to an obvious increase in the 0.49–2.5 μm fraction in September and October, and to a maxima in the finest fraction again in November and December. This corresponds to a change from a strong local emission from pollution sources, to possibly aged materials in the transition period of Asian monsoon, and to the pollution emissions dominated by those transported from the continent. The distinct difference of particle size distributions between wet and dry seasons suggests that the health effects of particles in Hong Kong may be different in those seasons.
Strong spectral variation of biomass smoke light absorption and single scattering albedo observed with a novel dual‐wavelength photoacoustic instrument
Authors: Lewis Kristin , Arnott William P. , Moosmüller Hans , Wold Cyle E.
Published: August 2008

A dual‐wavelength photoacoustic instrument operating at 405 and 870 nm was used during the 2006 Fire Lab at Missoula Experiment to measure light scattering and absorption by smoke from the combustion of a variety of biomass fuels. Simultaneous measurements of aerosol light scattering by reciprocal nephelometry within the instrument's acoustic resonator accompany photoacoustic aerosol light absorption measurements. Single scattering albedo values at 405 nm ranging from 0.37 to 0.95 were measured for different fuel types, and the spectral dependence of absorption was quantified using the Ångström exponent of absorption. An absorption Ångström exponent near unity is commonly observed for motor vehicle emission‐generated black carbon aerosol. For biomass smoke, Ångström exponents as high as 3.5 were found in association with smoke having single scattering albedo near unity. The measurements strongly suggest that light‐absorbing organic material is present in wood smoke. A second single‐wavelength photoacoustic instrument with reciprocal nephelometry was used to quantify aerosol scattering and absorption at 532 nm. Absorption Ångström exponents calculated using 532 and 870 nm data were as large as 2.5 for smoke with single scattering albedos near unity. The spectral variation in optical properties provides insight into the differentiation of aerosols from mobile or industrial sources versus those from biomass burning. Optical properties of biomass smokes could be classified by general fuel type such as flowering shrubs versus pine needle litter.
Effective saturated hydraulic conductivity of two‐dimensional random multifractal fields
Authors: Koirala S. R. , Perfect E. , Gentry R. W. , Kim J. W.
Published: August 2008

A means of upscaling the effective saturated hydraulic conductivity, 〈K〉, based on spatial variation in the saturated hydraulic conductivity (K) field is essential for the application of flow and transport models to practical problems. Multifractals are inherently scaling and thus may offer solutions to this dilemma. Random two‐dimensional geometrical multifractal fields (multifractal Sierpinski carpets with a scale factor b = 3) were constructed for iterations i = 1 through 5 using different generator probability values (p). The resulting average mass fractions were normalized and assumed to be directly proportional to K. The objectives were to explore how the frequency distribution of K changes as a function of p and i, how 〈K〉 varies with i for different p values, and how 〈K〉 is related to the generalized dimensions of the multifractal field. Numerical simulations of flow were performed in the multifractal fields, with 〈K〉 computed using Darcy's law. The results showed that 〈K〉 increases with increasing i level and increasing p value. The scaling of 〈K〉 with resolution, 1/bi, followed a power law relationship, similar to that observed for a variety of natural porous media. At the highest resolution (i = 5), ln 〈K〉 was best predicted by the correlation dimension (D2); ln 〈K〉 increased as D2 increased (R2 = 0.991, p < 0.0001). This relationship indicates that 〈K〉 decreases with increasing long‐range spatial correlation among the K values in the field. Furthermore, as 〈K〉 decreases it becomes increasingly dominated by flow channeling. This is because high values of K become more and more clustered as p decreases. This approach may prove useful for the prediction of 〈K〉 from generalized dimensions estimated by multifractal analysis of field measurements of K. The results may also be applicable to the design of sampling strategies for multiple small‐scale slug tests at a given resolution.
Dust iron dissolution in seawater: Results from a one‐year time‐series in the Mediterranean Sea
Authors: Wagener Thibaut , Pulido‐Villena Elvira , Guieu Cécile
Published: August 2008

A better comprehension of atmospheric iron dissolution in seawater would be a key advance in understanding the atmospheric supply of iron to the ocean and its role on marine biogeochemistry. So far, different studies have demonstrated that dissolution of atmospheric iron depends on physical and chemical properties of the particles, which can be modified during their transport from the source. Here, based on a one‐year time‐series in the Western Mediterranean Sea, we show that dissolution of iron from a Saharan desert dust sample in seawater follows the seasonal trend of the dissolved organic carbon (DOC) variability in the surface layer. As part of the DOC pool, the role of iron binding ligands, probably derived from bacteria activity, has also been investigated. The dust iron dissolution rates are found to be linearly dependent on iron binding ligands and dissolved organic carbon concentrations (r2 > 0.65, p < 0.01, n = 9).
A multi‐temporal InSAR method incorporating both persistent scatterer and small baseline approaches
Authors: Hooper Andrew
Published: August 2008

Synthetic aperture radar (SAR) interferometry is a technique that provides high‐resolution measurements of the ground displacement associated with many geophysical processes. Advanced techniques involving the simultaneous processing of multiple SAR acquisitions in time increase the number of locations where a deformation signal can be extracted and reduce associated error. Currently there are two broad categories of algorithms for processing multiple acquisitions, persistent scatterer and small baseline methods, which are optimized for different models of scattering. However, the scattering characteristics of real terrains usually lay between these two end‐member models. I present here a new method that combines both approaches, to extract the deformation signal at more points and with higher overall signal‐to‐noise ratio than can either approach alone. I apply the combined method to data acquired over Eyjafjallajökull volcano in Iceland, and detect time‐varying ground displacements associated with two intrusion events.
Supercells and mesocyclones in outer rainbands of Hurricane Katrina (2005)
Authors: Lee Wen‐Chau , Bell Michael M. , Goodman Keith E.
Published: August 2008

This study documents and describes supercells embedded within the outer rainbands of Hurricane Katrina (2005). Radar reflectivity and velocity data collected on 29 August 2005 by Weather Surveillance Radar 1988 Doppler radars were used to track the supercells. Radar analysis indicates that the supercells were characterized by heavy precipitation collocated with band‐relative mesocylonic circulations containing strong vorticity and a wind speed enhancement to their northeast. Atmospheric soundings and dual‐Doppler derived shear suggest that environmental conditions were comparable to those in previous hurricane‐spawned supercell studies. Twenty‐three storms from 0300–0900 UTC were tracked, and single‐ and dual‐Doppler radar analyses were used to examine characteristics such as shear and rotational velocity. Remarkably, the majority of the supercells formed over the Gulf of Mexico rather than over land, which contrasts with previous studies. Furthermore, the ground‐relative wind speeds of these potentially tornadic mesocyclones in the outer rainbands could have been Category 4 intensity despite sustained winds in Katrina's eyewall only reaching Category 3 at landfall.
Stimulation-Induced Increases of Astrocytic Oxidative Metabolism in Rats and Humans Investigated with 1-11C-Acetate
Authors: Wyss Matthias T , Weber Bruno , Treyer Valerie , Heer Stefan , Pellerin Luc , Magistretti Pierre J , Buck Alfred
Published: August 2008

The purpose of this study was to investigate astrocytic oxidative metabolism using 1-11C-acetate. 1-11C-acetate kinetics were evaluated in the rat somatosensory cortex using a β(−scintillator during different manipulations (test-retest, infraorbital nerve stimulation, and administration of acetazolamide or dichloroacetate). In humans a visual activation paradigm was used and kinetics were measured with positron emission tomography. Data were analyzed using a one-tissue compartment model. The following features supported the hypothesis that washout of radiolabel ( k2) is because of 11C-CO2 and therefore related to oxygen consumption (CMRO2): (1) the onset of 11C washout was delayed; (2) k2 was not affected by acetazolamide-induced blood flow increase; (3) k2 demonstrated a significant increase during stimulation in rats (from 0.014 ± 0.007 to 0.027 ± 0.006 per minute) and humans (from 0.016 ±0.010 to 0.026 ± 0.006 per minute); and (4) dichloroacetate led to a substantial decrease of k2. In the test-retest experiments K1 and k2 were very stable. In summary, 1-11C-acetate seems a promising tracer to investigate astrocytic oxidative metabolism in vivo. If the washout rate indeed represents the production of 11C-CO2, then its increase during stimulation would point to a substantially higher astrocytic oxidative metabolism during brain activation. However, the quantitative relationship between k2 and CMRO2 needs to be determined in future experiments.
Motor Nucleus of the Trigeminal Nerve
Authors:   Allen Institute for Brain Science, Kostakis Nicholas , Ng Lydia , Guillozet-Bongaarts Angela
Published: August 2008

This report contains a summary of expression patterns for genes that are enriched in the motor nucleus of the trigeminal nerve (V) of the pons. All data is derived from the Allen Brain Atlas (ABA) in situ hybridization mouse project. The structure's location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the motor nucleus of the trigeminal nerve were compared to the values of its larger parent structure, in this case the pons, for the purpose of extracting regionally selective gene expression data. The highest ranking genes were manually curated and verified. 50 genes were then selected and compiled for expression analysis. The experimental data for each gene may be accessed via the links provided; additional data in the sagittal plane may also be accessed using the ABA. Correlations between gene expression in the motor nucleus of the trigeminal nerve and the rest of the brain, across all genes in the coronal dataset (~4300 genes), were derived computationally. A gene ontology table (derived from DAVID Bioinformatics Resources 2007) is also included, highlighting possible functions of the 50 genes selected for this report.
Transgenesis procedures in Xenopus
Authors: Chesneau Albert , Sachs Laurent M. , Chai Norin , Chen Yonglong , Du Pasquier Louis , Loeber Jana , Pollet Nicolas , Reilly Michael , Weeks Daniel L. , Bronchain Odile J.
Published: August 2008

Stable integration of foreign DNA into the frog genome has been the purpose of several studies aimed at generating transgenic animals or producing mutations of endogenous genes. Inserting DNA into a host genome can be achieved in a number of ways. In Xenopus, different strategies have been developed which exhibit specific molecular and technical features. Although several of these technologies were also applied in various model organizms, the attributes of each method have rarely been experimentally compared. Investigators are thus confronted with a difficult choice to discriminate which method would be best suited for their applications. To gain better understanding, a transgenesis workshop was organized by the X‐omics consortium. Three procedures were assessed side‐by‐side, and the results obtained are used to illustrate this review. In addition, a number of reagents and tools have been set up for the purpose of gene expression and functional gene analyses. This not only improves the status of Xenopus as a powerful model for developmental studies, but also renders it suitable for sophisticated genetic approaches. Twenty years after the first reported transgenic Xenopus, we review the state of the art of transgenic research, focusing on the new perspectives in performing genetic studies in this species.
Molecular pathogenesis of sialic acid storage diseases: insight gained from four missense mutations and a putative polymorphism of human sialin
Authors: Ruivo Raquel , Sharifi Azita , Boubekeur Samira , Morin Pierre , Anne Christine , Debacker Cécile , Graziano Jean‐Charles , Sagné Corinne , Gasnier Bruno
Published: August 2008

Background information. Free sialic acid storage diseases are caused by mutations of a lysosomal sialic acid transporter called sialin. We showed recently that the milder clinical form, Salla disease, and a related non‐Finish case, are characterized by residual transport, whereas sialin mutants found in lethal infantile cases are inactive. In the present study, we have characterized the molecular effects of a putative polymorphism (M316I) and of four pathogenic mutations associated with either infantile (G127E and R57C) or Salla‐like (G409E) phenotypes, or both (G328E). The transport activity of human sialin was analysed using a novel assay that was based on a construct without the functional lysosomal sorting motif, which is expressed at the plasma membrane.

Results. The lysosomal localization of human sialin was not (M316I and G328E) or only partially (R57C, G127E and G409E) affected by the missense mutations. In contrast, all pathogenic mutations abolished transport, whereas the putative M316I polymorphism induced an approx. 5‐fold decrease of sialic acid transport.

Conclusions. The molecular effects of the R57C and G127E mutations strengthen the conclusion that the infantile phenotype is caused by loss‐of‐function mutations. On the other hand, the milder severity of the heterozygous G409E patient may reflect an incomplete expression of the splicing mutation present on the second allele. In the case of the G328E mutation, found in the homozygous state in a clinically heterogeneous family, the apparent severity of the transport phenotype suggests that the genetic or environmental factors underlying this clinical heterogeneity might be protective.
A SURVEY OF THE WHITE-CLAWED CRAYFISH,AUSTROPOTAMOBIUS PALLIPES (LEREBOULLET), AND OF WATERQUALITY IN TWO CATCHMENTS OF EASTERN IRELAND.
Authors: DEMERS A. , REYNOLDS J. D.
Published: August 2008

The white-clawed crayfish, Austropotamobius pallipes (Lereboullet), is the only crayfish species found in Ireland. Because of the prohibition on importation of exotic species of crayfish onto the island and of its relatively clean rivers up to now, Ireland has kept an abundant population of crayfish. A survey was conducted in the catchments of the Liffey and Boyne rivers, in eastern Ireland to assess water quality and to sample crayfish populations. The aim of the study was to evaluate the water quality requirements of the white-clawed crayfish in Ireland. Baited traps and nets were used to sample crayfish while water quality was measured with biological indices calculated from samples of macroinvertebrates. Distribution of this crayfish species is patchy in the Liffey catchment and seems to be related to factors such as soil types and water quality. They were not found in the downstream part of the river Liffey possibly due to poor water quality. In the Boyne catchment, no crayfish were found in most of the catchment. They were only present in the Kells Blackwater subcatchment. This may be due to an earlier outbreak of the fungal plague caused by Aphanomyces astaci. The disease was discovered in lakes at the top of some of the tributaries of the Boyne in 1987 and it probably spread from there through the whole catchment.
A REVIEW OF INTERNATIONAL BIOSECURITY POLICY DEVELOPMENT IN RELATION TO MOVEMENTS OF FRESHWATER CRAYFISH
Authors: EDGERTON B. F.
Published: August 2008

Freshwater crayfish are frequently traded, both alive (for human consumption or for fisheries/aquaculture stocking) and as processed products (e.g. fresh or frozen, cooked or uncooked). As the experience in Europe with crayfish plague has shown, there can be significant risks of translocating pathogens with such trade. Such risks can be assessed in an import risk analysis process. This paper will concentrate on describing the principles of import risk analysis (IRA) with particular reference to freshwater crayfish.
Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs
Authors: Coughlin Daniel J. , Pleiss Jeffrey A. , Walker Scott C. , Whitworth Gregg B. , Engelke David R.
Published: August 2008

Ribonuclease P (RNase P) is an essential endonuclease responsible for the 5′-end maturation of precursor tRNAs. Bacterial RNase P also processes precursor 4.5S RNA, tmRNA, 30S preribosomal RNA, and several reported protein-coding RNAs. Eukaryotic nuclear RNase P is far more complex than in the bacterial form, employing multiple essential protein subunits in addition to the catalytic RNA subunit. RNomic studies have shown that RNase P binds other RNAs in addition to tRNAs, but no non-tRNA substrates have previously been identified. Additional substrates were identified by using a multipronged approach in the budding yeast
Saccharomyces cerevisiae
. First, RNase P-dependant changes in RNA abundance were examined on whole-genome microarrays by using strains containing temperature sensitive (TS) mutations in two of the essential RNase P subunits, Pop1p and Rpr1r. Second, RNase P was rapidly affinity-purified, and copurified RNAs were identified by using a genome-wide microarray. Third, to identify RNAs that do not change abundance when RNase P is depleted but accumulate as larger precursors, >80 potential small RNA substrates were probed directly by Northern blot analysis with RNA from the RNase P TS mutants. Numerous potential substrates were identified, of which we characterized the box C/D intron-encoded small nucleolar RNAs (snoRNAs), because these both copurify with RNase P and accumulate larger forms in the RNase P temperature-sensitive mutants. It was previously known that two pathways existed for excising these snoRNAs, one using the pre-mRNA splicing path and the other that was independent of splicing. RNase P appears to participate in the splicing-independent path for the box C/D intron-encoded snoRNAs.
The dual-basin landscape in GFP folding
Authors: Andrews Benjamin T. , Gosavi Shachi , Finke John M. , Onuchic José N. , Jennings Patricia A.
Published: August 2008

Recent experimental studies suggest that the mature GFP has an unconventional landscape composed of an early folding event with a typical funneled landscape, followed by a very slow search and rearrangement step into the locked, active chromophore-containing structure. As we have shown previously, the substantial difference in time scales is what generates the observed hysteresis in thermodynamic folding. The interconversion between locked and the soft folding structures at intermediate denaturant concentrations is so slow that it is not observed under the typical experimental observation time. Simulations of a coarse-grained model were used to describe the fast folding event as well as identify native-like intermediates on energy landscapes enroute to the fluorescent native fold. Interestingly, these simulations reveal structural features of the slow dynamic transition to chromophore activation. Experimental evidence presented here shows that the trapped, native-like intermediate has structural heterogeneity in residues previously linked to chromophore formation. We propose that the final step of GFP folding is a “locking” mechanism leading to chromophore formation and high stability. The combination of previous experimental work and current simulation work is explained in the context of a dual-basin folding mechanism described above.
Overcoming multidrug resistance of small-molecule therapeutics through conjugation with releasable octaarginine transporters
Authors: Dubikovskaya Elena A. , Thorne Steve H. , Pillow Thomas H. , Contag Christopher H. , Wender Paul A.
Published: August 2008

Many cancer therapeutic agents elicit resistance that renders them ineffective and often produces cross-resistance to other drugs. One of the most common mechanisms of resistance involves P-glycoprotein (Pgp)-mediated drug efflux. To address this problem, new agents have been sought that are less prone to inducing resistance and less likely to serve as substrates for Pgp efflux. An alternative to this approach is to deliver established agents as molecular transporter conjugates into cells through a mechanism that circumvents Pgp-mediated efflux and allows for release of free drug only after cell entry. Here we report that the widely used chemotherapeutic agent Taxol, ineffective against Taxol-resistant human ovarian cancer cell lines, can be incorporated into a releasable octaarginine conjugate that is effective against the same Taxol-resistant cell lines. It is significant that the ability of the Taxol conjugates to overcome Taxol resistance is observed both in cell culture and in animal models of ovarian cancer. The generality and mechanistic basis for this effect were also explored with coelenterazine, a Pgp substrate. Although coelenterazine itself does not enter cells because of Pgp efflux, its octaarginine conjugate does so readily. This approach shows generality for overcoming the multidrug resistance elicited by small-molecule cancer chemotherapeutics and could improve the prognosis for many patients with cancer and fundamentally alter search strategies for novel therapeutic agents that are effective against resistant disease.
Selenoprotein N is required for ryanodine receptor calcium release channel activity in human and zebrafish muscle
Authors: Jurynec Michael J. , Xia Ruohong , Mackrill John J. , Gunther Derrick , Crawford Thomas , Flanigan Kevin M. , Abramson Jonathan J. , Howard Michael T. , Grunwald David Jonah
Published: August 2008

Mutations affecting the seemingly unrelated gene products, SepN1, a selenoprotein of unknown function, and RyR1, the major component of the ryanodine receptor intracellular calcium release channel, result in an overlapping spectrum of congenital myopathies. To identify the immediate developmental and molecular roles of SepN and RyRin vivo, loss-of-function effects were analyzed in the zebrafish embryo. These studies demonstrate the two proteins are required for the same cellular differentiation events and are needed for normal calcium fluxes in the embryo. SepN is physically associated with RyRs and functions as a modifier of the RyR channel. In the absence of SepN, ryanodine receptors from zebrafish embryos or human diseased muscle have altered biochemical properties and have lost their normal sensitivity to redox conditions, which likely accounts for why mutations affecting either factor lead to similar diseases.
Preventing Ventilator-Associated Pneumonia in the United States: A Multicenter Mixed-Methods Study
Authors: Krein Sarah L. , Kowalski Christine P. , Damschroder Laura , Forman Jane , Kaufman Samuel R. , Saint Sanjay
Published: August 2008

Objective.

To determine what practices are used by hospitals to prevent ventilator-associated pneumonia (VAP) and, through qualitative methods, to understand more fully why hospitals use certain practices and not others.

Design.

Mixed-methods, sequential explanatory study.

Methods.

We mailed a survey to the lead infection control professionals at 719 US hospitals (119 Department of Veterans Affairs [VA] hospitals and 600 non-VA hospitals), to determine what practices are used to prevent VAP. We then selected 14 hospitals for an in-depth qualitative investigation, to ascertain why certain infection control practices are used and others not, interviewing 86 staff members and visiting 6 hospitals.

Results.

The survey response rate was 72%; 83% of hospitals reported using semirecumbent positioning, and only 21% reported using subglottic secretion drainage. Multivariable analyses indicated collaborative initiatives were associated with the use of semirecumbent positioning but provided little guidance regarding the use of subglottic secretion drainage. Qualitative analysis, however, revealed 3 themes: (1) collaboratives strongly influence the use of semirecumbent positioning but have little effect on the use of subglottic secretion drainage; (2) nurses play a major role in the use of semirecumbent positioning, but they are only minimally involved with the use of subglottic secretion drainage; and (3) there is considerable debate about the evidence supporting subglottic secretion drainage, despite a meta-analysis of 5 randomized trials of subglottic secretion drainage that generally supported this preventive practice, compared with only 2 published randomized trials of semirecumbent positioning, one of which concluded that it was ineffective at preventing the development of VAP.

Conclusion.

Semirecumbent positioning is commonly used to prevent VAP, whereas subglottic secretion drainage is used far less often. We need to understand better how evidence related to prevention practices is identified, interpreted, and used to ensure that research findings are reliably translated into clinical practice.
Skp2 Regulates G2/M Progression in a p53-dependent Manner
Authors: Hu Rong , Aplin Andrew E.
Published: August 2008

Targeted proteasomal degradation mediated by E3 ubiquitin ligases controls cell cycle progression, and alterations in their activities likely contribute to malignant cell proliferation. S phase kinase-associated protein 2 (Skp2) is the F-box component of an E3 ubiquitin ligase complex that targets p27Kip1 and cyclin E1 to the proteasome. In human melanoma, Skp2 is highly expressed, regulated by mutant B-RAF, and required for cell growth. We show that Skp2 depletion in melanoma cells resulted in a tetraploid cell cycle arrest. Surprisingly, co-knockdown of p27Kip1 or cyclin E1 failed to prevent the tetraploid arrest induced by Skp2 knockdown. Enhanced Aurora A phosphorylation and repression of G2/M regulators cyclin B1, cyclin-dependent kinase 1, and cyclin A indicated a G2/early M phase arrest in Skp2-depleted cells. Furthermore, expression of nuclear localized cyclin B1 prevented tetraploid accumulation after Skp2 knockdown. The p53 status is most frequently wild type in melanoma, and the tetraploid arrest and down-regulation of G2/M regulatory genes were strongly dependent on wild-type p53 expression. In mutant p53 melanoma lines, Skp2 depletion did not induce cell cycle arrest despite up-regulation of p27Kip1. These data indicate that elevated Skp2 expression may overcome p53-dependent cell cycle checkpoints in melanoma cells and highlight Skp2 actions that are independent of p27Kip1 degradation.
A toolkit for analysing large-scale plant small RNA datasets
Authors: Moxon Simon , Schwach Frank , Dalmay Tamas , MacLean Dan , Studholme David J. , Moulton Vincent
Published: August 2008

Summary: Recent developments in high-throughput sequencing technologies have generated considerable demand for tools to analyse large datasets of small RNA sequences. Here, we describe a suite of web-based tools for processing plant small RNA datasets. Our tools can be used to identify micro RNAs and their targets, compare expression levels in sRNA loci, and find putative trans-acting siRNA loci.

Availability: The tools are freely available for use at http://srna-tools.cmp.uea.ac.uk

Contact:  vincent.moulton@cmp.uea.ac.uk