bluuebunny/crossref_metadata_2025 huggingface dataset:
Interdecadal Change in Properties of El Niño–Southern Oscillation in an Intermediate Coupled Model
Authors: Zhang Rong-Hua , Busalacchi Antonio J.
Published: May 2005

The role of subsurface temperature variability in modulating El Niño–Southern Oscillation (ENSO) properties is examined using an intermediate coupled model (ICM), consisting of an intermediate dynamic ocean model and a sea surface temperature (SST) anomaly model. An empirical procedure is used to parameterize the temperature of subsurface water entrained into the mixed layer (Te) from sea level (SL) anomalies via a singular value decomposition (SVD) analysis for use in simulating sea surface temperature anomalies (SSTAs). The ocean model is coupled to a statistical atmospheric model that estimates wind stress anomalies also from an SVD analysis. Using the empirical Te models constructed from two subperiods, 1963–79 (T63–79e) and 1980–96 (T80–96e), the coupled system exhibits strikingly different properties of interannual variability (the oscillation period, spatial structure, and temporal evolution). For the T63–79e model, the system features a 2-yr oscillation and westward propagation of SSTAs on the equator, while for the T80–96e model, it is characterized by a 5-yr oscillation and eastward propagation. These changes in ENSO properties are consistent with the behavior shift of El Niño observed in the late 1970s. Heat budget analyses further demonstrate a controlling role played by the vertical advection of subsurface temperature anomalies in determining the ENSO properties.
Contribution of Changes in Sea Surface Temperature and Aerosol Loading to the Decreasing Precipitation Trend in Southern China
Authors: Cheng Yanjie , Lohmann Ulrike , Zhang Junhua , Luo Yunfeng , Liu Zuoting , Lesins Glen
Published: May 2005

The effects of increasing sea surface temperature (SST) and aerosol loading in a drought region in Southern China are studied using aerosol optical depth (AOD), low-level cloud cover (LCC), visibility, and precipitation from observed surface data; wind, temperature, specific humidity, and geopotential height from the NCEP–NCAR reanalysis fields; and SST from the NOAA archive data. The results show a warming of the SST in the South China Sea and the Indian Ocean, and a strengthening of the West Pacific Subtropical High (WPSH) in the early summer during the last 40 yr, with the high pressure system extending farther westward over the continent in Southern China. Because the early summer average temperature contrast between the land and ocean decreased, the southwesterly monsoon from the ocean onto mainland China weakened and a surface horizontal wind divergence anomaly occurred over Southern China stabilizing the boundary layer. Thus, less moisture was transported to Southern China, causing a drying trend. Despite this, surface observations show that AOD and LCC have increased, while visibility has decreased. Precipitation has decreased in this region in the early summer, consistent with both the second aerosol indirect effect (reduction in precipitation efficiency caused by the more numerous and smaller cloud droplets) and dynamically induced changes from convective to more stratiform clouds. The second aerosol indirect effect and increases in SST and greenhouse gases (GHG) were simulated separately with the ECHAM4 general circulation model (GCM). The GCM results suggest that both effects contribute to the changes in LCC and precipitation in the drought region in Southern China. The flooding trend in Eastern China, however, is more likely caused by strengthened convective precipitation associated with increases in SST and GHG.
A Climatology of Midlatitude Continental Clouds from the ARM SGP Central Facility: Part I: Low-Level Cloud Macrophysical, Microphysical, and Radiative Properties
Authors: Dong Xiquan , Minnis Patrick , Xi Baike
Published: May 2005

A record of single-layer and overcast low cloud (stratus) properties has been generated using approximately 4000 h of data collected from January 1997 to December 2002 at the Atmospheric Radiation Measurement (ARM) Southern Great Plains Central Facility (SCF). The cloud properties include liquid-phase and liquid-dominant mixed-phase low cloud macrophysical, microphysical, and radiative properties including cloud-base and -top heights and temperatures, and cloud physical thickness derived from a ground-based radar and lidar pair, and rawinsonde sounding; cloud liquid water path (LWP) and content (LWC), and cloud-droplet effective radius (re) and number concentration (N) derived from the macrophysical properties and radiometer data; and cloud optical depth (τ), effective solar transmission (γ), and cloud/top-of-atmosphere albedos (Rcldy/RTOA) derived from Eppley precision spectral pyranometer measurements. The cloud properties were analyzed in terms of their seasonal, monthly, and hourly variations. In general, more stratus clouds occur during winter and spring than in summer. Cloud-layer altitudes and physical thicknesses were higher and greater in summer than in winter with averaged physical thicknesses of 0.85 and 0.73 km for day and night, respectively. The seasonal variations of LWP, LWC, N, τ, Rcldy, and RTOA basically follow the same pattern with maxima and minima during winter and summer, respectively. There is no significant variation in mean re, however, despite a summertime peak in aerosol loading. Although a considerable degree of variability exists, the 6-yr average values of LWP, LWC, re, N, τ, γ, Rcldy, and RTOA are 151 gm−2 (138), 0.245 gm−3 (0.268), 8.7 μm (8.5), 213 cm−3 (238), 26.8 (24.8), 0.331, 0.672, and 0.563 for daytime (nighttime). A new conceptual model of midlatitude continental low clouds at the ARM SGP site has been developed from this study. The low stratus cloud amount monotonically increases from midnight to early morning (0930 LT), and remains large until around local noon, then declines until 1930 LT when it levels off for the remainder of the night. In the morning, the stratus cloud layer is low, warm, and thick with less LWC, while in the afternoon it is high, cold, and thin with more LWC. Future parts of this series will consider other cloud types and cloud radiative forcing at the ARM SCF.
Observed Trends and Teleconnections of the Siberian High: A Recently Declining Center of Action
Authors: Panagiotopoulos Fotis , Shahgedanova Maria , Hannachi Abdelwaheb , Stephenson David B.
Published: May 2005

This study investigates variability in the intensity of the wintertime Siberian high (SH) by defining a robust SH index (SHI) and correlating it with selected meteorological fields and teleconnection indices. A dramatic trend of –2.5 hPa decade−1 has been found in the SHI between 1978 and 2001 with unprecedented (since 1871) low values of the SHI. The weakening of the SH has been confirmed by analyzing different historical gridded analyses and individual station observations of sea level pressure (SLP) and excluding possible effects from the conversion of surface pressure to SLP.

SHI correlation maps with various meteorological fields show that SH impacts on circulation and temperature patterns extend far outside the SH source area extending from the Arctic to the tropical Pacific. Advection of warm air from eastern Europe has been identified as the main mechanism causing milder than normal conditions over the Kara and Laptev Seas in association with a strong SH. Despite the strong impacts of the variability in the SH on climatic variability across the Northern Hemisphere, correlations between the SHI and the main teleconnection indices of the Northern Hemisphere are weak. Regression analysis has shown that teleconnection indices are not able to reproduce the interannual variability and trends in the SH. The inclusion of regional surface temperature in the regression model provides closer agreement between the original and reconstructed SHI.
Formation, Mechanisms, and Predictability of the Aleutian–Icelandic Low Seesaw in Ensemble AGCM Simulations
Authors: Honda Meiji , Kushnir Yochanan , Nakamura Hisashi , Yamane Shozo , Zebiak Stephen E.
Published: May 2005

The potential predictability associated with the remote influence of midlatitude tropospheric anomalies over the North Pacific or the North Atlantic, via a seesawlike interannual oscillation between the surface Aleutian and Icelandic lows (AL and IL, respectively) is investigated. Data from a 24-member ensemble of 50-yr atmospheric general circulation model simulation forced with observed sea surface temperature (SST) conditions are analyzed by separating the total simulated fluctuations into the external component forced by the prescribed SST and the internal component generated by atmospheric internal dynamics. The AL–IL seesaw can be identified in both the external and internal components of the variability. In the external variability, determined through the ensemble mean, the seesaw is gradually formed from December to March through the development of a Pacific–North American (PNA) pattern–like wave train, remotely forced by the El Niño–Southern Oscillation. The amplitudes of the externally forced North Atlantic anomalies are only about half as large as the North Pacific anomalies. The potential predictability of the Atlantic anomalies, defined as the ratio of the SST-forced variance to the total variance, does not exceed the 20% level. In the internal component of the variability, determined from the deviations of each ensemble member from the ensemble mean, the negative correlation between the AL and IL anomalies is modest but persistent through winter. It is confirmed that, regardless of the polarity of the AL–IL seesaw, the IL anomalies are formed through eastward wave activity propagation of the stationary Rossby wave train emanating from the AL region in the form of what may be called a “PNAA pattern,” the extension of the PNA-like wave train into the Atlantic. Thus, the midwinter development of North Pacific anomalies is found to be a necessary, though not sufficient, condition for the seesaw formation. The persistence of the North Pacific anomalies beyond a 1-month time span appears to augment the probability of the seesaw formation by sustaining eastward wave activity propagation to the North Atlantic.
E-Democracy, E-Commerce, and E-Research
Authors: Thomas John Clayton , Streib Gregory
Published: May 2005

Few doubt that the Internet is changing citizen interactions with government. To assess those changes, the authors analyze data from a telephone survey on how Georgia residents connect with government via the Internet. They find that citizens visit government Web sites for many reasons, which can be divided into three categories: e-democracy, e-commerce, and e-research. E-democracy is the least common activity, and it alone resembles traditional political behavior by being more prevalent among respondents interested in politics and government. The authors discuss the implications of these findings for future citizen engagement with e-governance and for the role of government in facilitating that engagement.
The Implications of Public Opinion for Public Managers
Authors: Van Slyke David M. , Horne Christopher S. , Thomas John Clayton
Published: May 2005

In the contemporary policy-implementation process where policies in practice often reflect a compromise, public managers increasingly must consult with the relevant public to learn what that public wants. The purpose of this article is to argue that public managers might sometimes find public-opinion polls valuable as a source of information on public preferences. After explaining when and why this might be the case, the authors illustrate their argument using public-opinion data on the attitudes of Georgia residents toward the issue of Charitable Choice and provide examples of how these data might assist public managers in implementing the program.
Pragmatism, Neopragmatism, and Public Administration
Authors: Hildebrand David L.
Published: May 2005

The project of harmonizing ideals and practical realities often falls to the organs of public administration. Because this task involves the application of general and fixed concepts (policies, laws, standards) to particular and fluid practicalities (situations, circumstances, persons), those in public administration need strategies to deal with unusual or problematic cases. Pragmatism seems to offer such a strategy. But which pragmatism should be used? This article is a philosophical response to two disputes. What distinguishes classical pragmatism and neopragmatism? And which pragmatism holds greater promise for public administration agencies and why? The author discusses how public administration agents might find themselves obligated to philosophize about their agency’s fundamental mission and how the resources of pragmatism might serve that (largest scale) problematic situation. Finally, the author considers two obstacles likely to be encountered by those who employ a pragmatist approach.
Socialization in Virtual Groups
Authors: Ahuja Manju K. , Galvin John E.
Published: May 2005

Virtual groups, that communicate and coordinate their activities using information technology, continue to become prevalent as an organizational form (Ahuja & Carley, 199 9). Research in this area, however, is still in its infancy. Specifically, extant research provides little insight into how new members are socialized into virtual groups using electronic communication. This paper examines the influence of member tenure on individual communication patterns in virtual groups. A content analysis of e-mail communication among members of the group during a 3-month period showed that in virtual groups, newcomers primarily exhibit an information seeking mode in their communication and established members exhibit an information providing mode. Interestingly, and contrary to expectations, newcomers did actively engage in discussions regarding cognitive information, perhaps helped by the comfort provided by a lean and faceless electronic communication medium. However, the limited anonymity provided by the electronic media did not translate into newcomers seeking normative and regulative information in explicit ways, implying a need for organizational mechanisms aimed at virtual member socialization.
The Impact of Psychological Contract Fulfillment on the Performance of In-Role and Organizational Citizenship Behaviors
Authors: Turnley William H. , Bolino Mark C. , Lester Scott W. , Bloodgood James M.
Published: May 2005

This research examines the relationships between psychological contract fulfillment and three types of employee behavior: in-role performance, organizational citizenship behavior directed at the organization, and organizational citizenship behavior directed at individuals within the organization. Using a sample of 134 supervisor-subordinate dyads, this study suggests that the extent of psychological contract fulfillment is positively related to the performance of all three types of employee behavior. In addition, the results indicate that psychological contract fulfillment is more strongly related to citizenship behavior directed at the organization than to citizenship behavior directed at one’s colleagues. Finally, this research investigates if employees’ attributions regarding the reasons that psychological contract breach occurred also impact their work performance. However, the data provide only limited support for the idea that employees are most likely to reduce their work effort when they perceive that the organization has intentionally failed to live up to its commitments.
The Outsourcing of Training and Development: Factors Impacting Client Satisfaction
Authors: Gainey Thomas W. , Klaas Brian S.
Published: May 2005

Firms increasingly use outside vendors to provide their training and development needs. However, the strategic importance of many training programs often introduces unique challenges for organizations outsourcing this function. To better understand the effects of outsourcing in this key area, we use transaction cost economics, social exchange theory, and the resource-based view to identify factors thought to impact client satisfaction with external training vendors. Using data obtained from 157 organizations, structural equation modeling results suggest that socially-oriented trust and contractual specificity mediate the relationship between client satisfaction and a number of vendor, relationship, training, and firm characteristics.
The Construct-Related Validity of Assessment Center Ratings: A Review and Meta-Analysis of the Role of Methodological Factors
Authors: Woehr David J. , Arthur Winfred
Published: May 2005

In the present study, we provide a systematic review of the assessment center literature with respect to specific design and methodological characteristics that potentially moderate the construct-related validity of assessment center ratings. We also conducted a meta-analysis of the relationship between these characteristics and construct-related validity outcomes. Results for rating approach, assessor occupation, assessor training, and length of assessor training were in the predicted direction such that a higher level of convergent, and lower level of discriminant validity were obtained for the across-exercise compared to the within-exercise rating method; psychologists compared to managers/supervisors as assessors; assessor training compared no assessor training; and longer compared to shorter assessor training. Partial support was also obtained for the effects of the number of dimensions and assessment center purpose. Our review also indicated that relatively few studies have examined both construct-related and criterion-related validity simultaneously. Furthermore, these studies provided little, if any support for the view that assessment center ratings lack construct-related validity while at the same time demonstrating criterion-related validity. The implications of these findings for assessment center construct-related validity are discussed.
Toward a Dynamic Process Model of Staffing Composition and Subsidiary Outcomes in Multinational Enterprises
Authors: Gong Yaping
Published: May 2005

Subsidiary staffing composition is defined as the distribution of parent country nationals (PCNs), host country nationals (HCNs), and third country nationals (TCNs) in subsidiaries of multinational enterprises (MNEs). Subsidiary staffing composition varies along the dimension of nationality heterogeneity. The MNE staffing literature has mainly focused on expatriate PCNs and individual-level outcomes. This article develops a dynamic process model in which heterogeneity of staffing composition influences affective, behavioral, cognitive, and strategic outcomes, which in turn affect subsidiary financial performance. Drawing upon organizational learning and social identification theories, this article offers testable propositions regarding relationships between staffing composition and subsidiary outcomes, and changes in these relationships over time. Finally, it proposes a preliminary research program to test the model.
Suspect Technologies: Scrutinizing the Intersection of Science, Technology, and Policy
Authors: Campbell Nancy D.
Published: May 2005

Drug testing is widely deployed in the United States throughout the public and private sectors. This case study uses two emergent drug-testing technologies—hair analysis and the sweat patch—as examples of techniques of governance that should be subjected to the political equivalent of strict scrutiny. The article contributes to conceptual debates in science and technology studies, arguing that the study of social structure and subject formation should be integral rather than epiphenomenal to analysis in the transdisciplinary field of science and technology studies (STS). The article contextualizes the development and deployment of drug-testing technologies within the structural and epistemological categories of racial and ethnic difference, gender, sexuality, and class formation. Conflicts between proponents of the technologies and critical advocates who seek to constrain their use mark sites of productive theoretical engagement with structural sociology, racial formation theory, critical race theory, and feminist critique.1 Finally, the article demonstrates how STS analyses can contribute to the struggles of strategic counterpublics as they advocate for changing the meaning and material consequences of suspect technologies.
Studying Obduracy in the City: Toward a Productive Fusion between Technology Studies and Urban Studies
Authors: Hommels Anique
Published: May 2005

This article draws the city into the limelight of social studies of technology. Considering that cities consist of a wide range of technologies, it is remarkable that cities as an object of research have so far have been relatively neglected in the field of technology studies. This article focuses on the role of obduracy in urban sociotechnical change, an issue that, it is argued, has considerable importance for both students of the cities and the daily practice of town planners and architects, and, at the same time, forms an important theoretical debate in science, technology, and society (STS) studies. The article provides an overview of theoretical conceptions of obduracy in both technology studies and urban studies and proposes a heuristic model for the analysis of this phenomenon. In this way, this article aims to contribute to the establishment of a common interdisciplinary playground for these disciplines.
New Civic Epistemologies of Quantification: Making Sense of Indicators of Local and Global Sustainability
Authors: Miller Clark A.
Published: May 2005

Processes of globalization and decentralization are changing the relationship among statistical knowledge production, nation, and state. This article explores these changes through a comparison of five projects to design and implement indicators of sustainable development to replace conventional measures of economic welfare and social demographics—community sustainability indicators, Metropatterns, greening the gross domestic product, the Living Planet Index, and standardized accounting rules for inventorying greenhouse gas emissions. Drawing on a coproductionist idiom, the article argues that these projects constitute experiments in modifying the civic epistemologies of democratic societies, transforming not only knowledge production but also political identities, relationships, and institutions.
Reading Digital Denmark: IT Reports as Material-Semiotic Actors
Authors: Jensen Casper Bruun , Lauritsen Peter
Published: May 2005

During the past decade, several governmental reports have discussed how information technology can transform Danish society. Most important among these reports is Digital Denmark from 1999.In this article, the authors examine how to analyze Digital Denmark by considering two strategies for engaging reports. The first aims at uncovering and making explicit hidden assumptions or ideologies in the text. This approach is called “reading against the text.” The second approach—inspired by science, technology, and society studies—considers where a text goes and what it does rather than how to critically interpret it. Texts may be read as material-semiotic actors, having effects on their environment that exceed or bypass discussions of content or motivation. This approach is called “reading with the text,” and the authors argue that traveling with Digital Denmark makes visible the limitations of critical analyses, while adding agency to the report as it moves in between practices.
Psychosocial Correlates of Smoking Trajectories Among Urban African American Adolescents
Authors: Fergus Stevenson , Zimmerman Marc A. , Caldwell Cleopatra H.
Published: May 2005

Little is known of smoking trajectories or of the correlates of smoking trajectories among African American youth. Ninth-grade African American adolescents (n = 566) were interviewed in Year 1 and then were subsequently interviewed annually for 3 additional years. Five trajectories of cigarette smokers were identified: abstainers, experimenters/consistent light smokers, consistent regular smokers, accelerators, and quitters. Psychological well-being at Year 1 was lower among consistent regular smokers and accelerators as compared to abstainers. Variance in other problem behaviors mirrored the smoker trajectories. At Year 4,the abstainers and experimenters/consistent light smokers reported greater participation in sports activities as compared to the quitters, whereas the abstainers reported greater participation in other school activities as compared to the consistent regular smokers.
From Ally McBeal to Sábado Gigante
Authors: Rivadeneyra Rocío , Ward L. Monique
Published: May 2005

Although previous findings indicate that frequent television viewing is associated with holdingmore stereo typical attitudes aboutgender, no studies have examinedthis connection among Latino youth, who are frequent viewers of both English- and Spanish-language programming. The present study attempted to rectify this situation by examining connections between exposure to this content, viewer involvement, and the gender role beliefs of Latino adolescents. Surveying 186 Latino high school students, we found that girls who watched more television andwho perceived it to be realistic exhibitedmore traditional gender role attitudes. Similar contributions were seen from the viewing of specific genres of English- and Spanish-language programming, underscoring the importance of investigating associations by language, sex, and genre.
Looking Back on September 11, 2001:
Authors: Levine Linda J. , Whalen Carol K. , Henker Barbara , Jamner Larry D.
Published: May 2005

This study investigated changes over time in adolescents’and parents’memories for how they felt when they learned of the terrorist attacks on September 11, 2001. Adolescents recalled having felt less negative emotion than parents did both 3 months and 8 months after the attacks. Moreover, the intensity of negative emotion recalled decreased over time for adolescents but increased for parents. Parental anxiety and stress at 3 months predicted adolescent reactions at 8 months, and there was no evidence of bidirectional effects. Adolescents (but not parents) appraised the attacks as having less impact on themselves than on others. Appraising the attacks as having less impact predicted lower recalled negative emotion and fewer posttraumatic stress symptoms. The results suggest that adolescents’tendency to view themselves as less vulnerable than others, which can lead to risky behaviors, may also serve a protective function when adolescents confront distant traumatic events.
Physical Intimacy and Sexual Coercion Among Adolescent Intimate Partners in the Philippines
Authors: Serquina-Ramiro Laurie
Published: May 2005

This study explores perceptions about intimate relationships including perspectives of pressure and sexual coercion as experienced by unmarried Filipino adolescent males and females aged 15 to 19 years. The study design included an initial qualitative phase containing focus group discussions with adults and adolescents and key informant interviews with professionals, a community survey of 600 female and male adolescents, and in-depth interviews with selected survey respondents. The results indicated that sexual coercion was regarded as common in adolescent intimate relationships. Viewed from a broader perspective, it canoccurat any stage of the intimate process using a combination of methods. Of the 600 adolescent survey respondents, 64% reported whether they have ever practiced or experienced any form of pressure and coercion in their intimate relationships. Of this number, 321 were targets of coercion, whereas 65 admitted that they had perpetrated the coercive act. Among the victims, 42.3% were males and 64.6% were females (p < .0001). The use of verbal pressure to pursue coercive sex was commonly reported. Recommendations were made to facilitate a healthy sexual development among male and female adolescents.
The Use of Ultrasound in Central Venous Access in Children
Authors: Barnacle Alex M. , Kleidon Tricia M , Roebuck Derek J.
Published: May 2005

Image-guided central venous access is forming an increasingly large proportion of the workload in interventional radiology following recognition that such techniques are less invasive and often quicker than traditional surgical techniques, with clear benefit in subjects with multiple previous attempts at venous access. Venous access sites are generally superficial in children, allowing excellent quality images during ultrasound-guided puncture and providing a greater number of options when considering the approach to catheter placement. Methods of ultrasound-guided puncture are described and the varieties of catheter devices available are discussed. Other advantages of ultrasound, such as in the assessment of thrombosed vessels and collateral veins, as well as the localization of catheter cuffs within the subcutaneous tissues, are also discussed.
A User Guide to Compound Imaging
Authors: Elliott S. T.
Published: May 2005

Compound imaging is now available on several high-end ultrasound scanners. It takes different forms and refers to different methods of creating the ultrasound image. The aim of this article is to familiarize the reader with simple background information about how it works, and to provide a clinician's view of how, why and when to use it.
Ultrasound of Haemodialysis Radiocephalic Fistula: A Pictorial Essay
Authors: Lapham R.C.
Published: May 2005

Regular vascular access for haemodialysis requires a good calibre vein with high flow. This is typically achieved by anastomosing the radial artery to the cephalic vein at the wrist, the classic Brescia–Cimino arteriovenous fistula (AVF). Alternatives include brachial artery to cephalic/basilic vein and bridge graft fistulas. Ultrasound provides an inexpensive and non-invasive method of monitoring fistula effectiveness, confirming clinical suspicion of stenosis/occlusions and steal. It informs the vascular radiologist regarding the optimal approach to angioplasty and provides rapid assessment of anomalies of the AVF, including diagnosis of aneurysms, thrombus and post-operative fluid collections. This article is intended as an illustrative guide to performing a duplex examination and to clarify some of the problems which may arise.
Ultrasound in Haemodialysis Access
Authors: Greedman Benjamin , Deane Colin
Published: May 2005

Good quality vascular access is essential to ensure successful haemodialysis. Ultrasound is effective in selecting vessels suitable for formation of permanent haemodialysis access. Post-operatively ultrasound is useful in identifying causes of access failure or poor performance. This review includes anatomic and haemodynamic parameters for pre-operative assessment and discusses the use of volume flow and conventional B-mode and Doppler ultrasound in the investigation of dialysis access. Protocols for these investigations are suggested.
Use of a Microbubble Contrast Agent in the Evaluation of Cirrhotic Patients for Hepatopulmonary Syndrome: Preliminary Assessment of a Novel Technique
Authors: Pilcher J. M. , Eckersley R. J. , Lim A. K. P. , Patel N. , Shovlin C. L. , Cosgrove D. O. , Blomley M. J. K. , Taylor-Robinson S. D.
Published: May 2005

Hepatopulmonary syndrome (HPS) may cause profound symptomatic hypoxia in patients with chronic liver disease and can be an indication for liver transplantation. The diagnosis relies on the demonstration of intrapulmonary vascular dilatation (IVD) using either contrast-enhanced echocardiography or macro-aggregated lung perfusion scans. We sought to evaluate whether a novel technique using the microbubble agent, Echovist® (Schering AG) with Doppler intensitometry of the carotid artery would be able to identify patients who fulfilled the criteria for HPS. Contrast studies were performed in 18 patients with cirrhosis, examined in the supine and upright positions. Following injection of Echovist, continuous scanning of the common carotid was performed using grey-scale and spectral Doppler for 60 s. Positive studies were determined by online signal analysis of the Doppler signal (crackle-count). Supine and upright pulse oximetry was recorded on all patients, and formal lung function tests where clinically indicated. Two patients met the criteria for HPS. They had positive results on supine and upright scans, with an increased crackle-count when upright. Two patients had single, weakly positive results with normal pulse oximetry. No association was seen between a positive contrast study and the severity of liver disease. Contrast-enhanced carotid Doppler intensitometry is a relatively simple, non-invasive test that may help identify patients with IVD. Comparison with an established technique will be required in future trials to determine its accuracy and assess whether the crackle-count can reliably quantify the degree of IVD.
Antenatal Screening: How will the UK National Screening Committee (UK NSC) Recommendations Affect Sonographers?
Authors: Armstrong Valerie
Published: May 2005

This article reviews the development and organization of the Down's Syndrome Screening Policy by the National Screening Committee, outlining the implications for sonographer training and practice, and for antenatal ultrasound service provision.
Short-term variability of biomarkers of proteinase activity in patients with emphysema associated with type Z alpha-1-antitrypsin deficiency
Authors: Stolk Jan , Veldhuisen Barbara , Annovazzi Laura , Zanone Chiara , Versteeg Elly M , van Kuppevelt Toine H , Nieuwenhuizen Willem , Iadarola Paolo , Luisetti Maurizio
Published: May 2005

Background

The burden of proteinases from inflammatory cells in the lung of subjects with type Pi ZZ of alpha-1-antitrypsin deficiency is higher than in those without the deficiency. Cross-sectional studies have shown increased levels of biomarkers of extracellular matrix degradation in vivo. Longitudinal variability of these biomarkers is unknown but desirable for clinical studies with proteinase inhibitors.

Methods

We measured three different types of biomarkers, including desmosines, elastase-formed fibrinogen fragments and heparan sulfate epitope JM403, in plasma and urine for a period of 7 weeks in a group of 12 patients who participated in a placebo-controlled study to assess the safety of a single inhalation of hyaluronic acid.

Results

Effect of study medication on any of the biomarkers was not seen. Baseline desmosines in plasma and urine correlated with baseline CO diffusion capacity (R = 0.81, p = 0.01 and R = 0.65, p = 0.05). Mean coefficient of variation within patients (CVi) for plasma and urine desmosines was 18.7 to 13.5%, respectively. Change in urinary desmosine levels correlated significantly with change in plasma desmosine levels (R = 0.84, p < 0.01). Mean CVi for fibrinogen fragments in plasma was 20.5% and for JM403 in urine was 27.8%. No correlations were found between fibrinogen fragments or JM403 epitope and desmosines.

Conclusion

We found acceptable variability in our study parameters, indicating the feasibility of their use in an evaluation of biochemical efficacy of alpha-1-antitrypsin augmentation therapy in Pi Z subjects.
Characterization of the aggregates formed during recombinant protein expression in bacteria
Authors: Schrödel Andrea , de Marco Ario
Published: May 2005

Background

The first aim of the work was to analyze in detail the complexity of the aggregates formed upon overexpression of recombinant proteins in E. coli. A sucrose step gradient succeeded in separating aggregate subclasses of a GFP-GST fusion protein with specific biochemical and biophysical features, providing a novel approach for studying recombinant protein aggregates.

Results

The total lysate separated into 4 different fractions whereas only the one with the lowest density was detected when the supernatant recovered after ultracentrifugation was loaded onto the sucrose gradient. The three further aggregate sub-classes were otherwise indistinctly precipitated in the pellet. The distribution of the recombinant protein among the four subclasses was strongly dependent on the DnaK availability, with larger aggregates formed in Dnak- mutants. The aggregation state of the GFP-GST recovered from each of the four fractions was further characterized by examining three independent biochemical parameters. All of them showed an increased complexity of the recombinant protein aggregates starting from the top of the sucrose gradient (lower mass aggregates) to the bottom (larger mass aggregates). These results were also confirmed by electron microscopy analysis of the macro-structure formed by the different aggregates. Large fibrils were rapidly assembled when the recombinant protein was incubated in the presence of cellular extracts, but the GFP-GST fusion purified soon after lysis failed to undergo amyloidation, indicating that other cell components probably participate in the active formation of large aggregates. Finally, we showed that aggregates of lower complexity are more efficiently disaggregated by a combination of molecular chaperones.

Conclusion

An additional analytical tool is now available to investigate the aggregation process and separate subclasses by their mass. It was possible to demonstrate the complexity of the aggregation pattern of a recombinant protein expressed in bacteria and to characterize biochemically the different aggregate subclasses. Furthermore, we have obtained evidence that the cellular environment plays a role in the development of the aggregates and the problem of the artifact generation of aggregates has been discussed using in vitro models. Finally, the possibility of separating aggregate fractions with different complexities offers new options for biotechnological strategies aimed at improving the yield of folded and active recombinant proteins.
Considerations when using the significance analysis of microarrays (SAM) algorithm
Authors: Larsson Ola , Wahlestedt Claes , Timmons James A
Published: May 2005

Background

Users of microarray technology typically strive to use universally acceptable data analysis strategies to determine significant expression changes in their experiments. One of the most frequently utilised methods for gene expression data analysis is SAM (significance analysis of microarrays). The impact of selection thresholds, on the output from SAM, may critically alter the conclusion of a study, yet this consideration has not been systematically evaluated in any publication.

Results

We have examined the effect of discrete data selection criteria (qualification criteria for inclusion) and response thresholds (out-put filtering) on the number of significant genes reported by SAM. The use of a reduced data set by applying arbitrary restrictions vis-à-vis abundance calls (e.g. from D-chip) or application of the fold change (FC) option within SAM (named the FC hurdle hereafter), can substantially alter the significant gene list when running SAM in Microsoft Excel. We determined that for a given final FC criteria (e.g. 1.5 fold change) the FC hurdle applied within Microsoft Excel SAM alters the number of reported genes above the final FC criteria. The reason is that the FC hurdle changes the composition of the control data set, such that a different significance level (q-value) is obtained for any given gene. This effect can be so large that it changes subsequent post hoc analysis interpretation, such as ontology overrepresentation analysis.

Conclusion

Our results argue for caution when using SAM. All data sets analysed with SAM could be reanalysed taking into account the potential impact of the use of arbitrary thresholds to trim data sets before significance testing.
Vestige: Maximum likelihood phylogenetic footprinting
Authors: Wakefield Matthew J , Maxwell Peter , Huttley Gavin A
Published: May 2005

Background

Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less than neutral DNA. Vestige is a phylogenetic footprinting package built on the PyEvolve toolkit that uses probabilistic molecular evolutionary modelling to represent aspects of sequence evolution, including the conventional divergence measure employed by other footprinting approaches. In addition to measuring the divergence, Vestige allows the expansion of the definition of a phylogenetic footprint to include variation in the distribution of any molecular evolutionary processes. This is achieved by displaying the distribution of model parameters that represent partitions of molecular evolutionary substitutions. Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process.

Results

Vestige was applied to a reference dataset of the SCL locus from four species and provided clear identification of the known conserved regions in this dataset. To demonstrate the flexibility to use diverse models of molecular evolution and dissect the nature of the evolutionary process Vestige was used to footprint the Ka/Ks ratio in primate BRCA1 with a codon model of evolution. Two regions of putative adaptive evolution were identified illustrating the ability of Vestige to represent the spatial distribution of distinct molecular evolutionary processes.

Conclusion

Vestige provides a flexible, open platform for phylogenetic footprinting. Underpinned by the PyEvolve toolkit, Vestige provides a framework for visualising the signatures of evolutionary processes across the genome of numerous organisms simultaneously. By exploiting the maximum-likelihood statistical framework, the complex interplay between mutational processes, DNA repair and selection can be evaluated both spatially (along a sequence alignment) and temporally (for each branch of the tree) providing visual indicators to the attributes and functions of DNA sequences.
Gene finding in the chicken genome
Authors: Eyras Eduardo , Reymond Alexandre , Castelo Robert , Bye Jacqueline M , Camara Francisco , Flicek Paul , Huckle Elizabeth J , Parra Genis , Shteynberg David D , Wyss Carine , Rogers Jane , Antonarakis Stylianos E , Birney Ewan , Guigo Roderic , Brent Michael R
Published: May 2005

Background

Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method.

Results

We performed experimental evaluation by RT-PCR of three different computational gene finders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram was computed and each component of it was evaluated. The results showed that de novo comparative methods can identify up to about 700 chicken genes with no previous evidence of expression, and can correctly extend about 40% of homology-based predictions at the 5' end.

Conclusions

De novo comparative gene prediction followed by experimental verification is effective at enhancing the annotation of the newly sequenced genomes provided by standard homology-based methods.
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
Authors: Peters Bjoern , Sette Alessandro
Published: May 2005

Background

Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC) molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as a sequence motif, a scoring matrix or an artificial neural network. The purpose of these models is two-fold. First, they can provide a summary of experimental results, allowing for a deeper understanding of the mechanisms involved in sequence recognition. Second, such models can be used to predict the experimental outcome for yet untested sequences. In the past we reported the development of a method to generate such models called the Stabilized Matrix Method (SMM). This method has been successfully applied to predicting peptide binding to MHC molecules, peptide transport by the transporter associated with antigen presentation (TAP) and proteasomal cleavage of protein sequences.

Results

Herein we report the implementation of the SMM algorithm as a publicly available software package. Specific features determining the type of problems the method is most appropriate for are discussed. Advantageous features of the package are: (1) the output generated is easy to interpret, (2) input and output are both quantitative, (3) specific computational strategies to handle experimental noise are built in, (4) the algorithm is designed to effectively handle bounded experimental data, (5) experimental data from randomized peptide libraries and conventional peptides can easily be combined, and (6) it is possible to incorporate pair interactions between positions of a sequence.

Conclusion

Making the SMM method publicly available enables bioinformaticians and experimental biologists to easily access it, to compare its performance to other prediction methods, and to extend it to other applications.
Changes in gravitational force affect gene expression in developing organ systems at different developmental times
Authors: Shimada Naoko , Sokunbi Gbolabo , Moorman Stephen J
Published: May 2005

Background

Little is known about the affect of microgravity on gene expression, particularly in vivo during embryonic development. Using transgenic zebrafish that express the gfp gene under the influence of a β-actin promoter, we examined the affect of simulated-microgravity on GFP expression in the heart, notochord, eye, somites, and rohon beard neurons. We exposed transgenic zebrafish to simulated-microgravity for different durations at a variety of developmental times in an attempt to determine periods of susceptibility for the different developing organ systems.

Results

The developing heart had a period of maximum susceptibility between 32 and 56 hours after fertilization when there was an approximately 30% increase in gene expression. The notochord, eye, somites, and rohon beard neurons all showed periods of susceptibility occurring between 24 and 72 hours after fertilization. In addition, the notochord showed a second period of susceptibility between 8 and 32 hours after fertilization. Interestingly, all organs appeared to be recovering by 80 hours after fertilization despite continued exposure to simulated-microgravity.

Conclusion

These results support the idea that exposure to microgravity can cause changes in gene expression in a variety of developing organ systems in live embryos and that there are periods of maximum susceptibility to the effects.