bluuebunny/crossref_metadata_2025 huggingface dataset:
Child Neurologists as Health Care Surrogate for Imperiled Children
Authors: Weisleder Pedro , Perkins Elizabeth , McLaughlin Aevan
Published: November 2010

We explored child neurologists’ attitudes toward taking on the role of health care surrogate for terminally ill children. Physician members of the Child Neurology Society were sent a 16-question survey via email. Of the assumed 1050 recipients, 116 (11%) answered the questionnaire. Most individuals who have been in practice less than 11 years indicated having received formal end-of-life decision-making education either during medical school or residency. Conversely, a minority of participants who have been in practice more than 11 years indicated having received such education. Regardless of years in practice, 54% (n = 61 of 112) of participants would feel at least ‘‘somewhat comfortable’’ independently making life-limiting decisions for imperiled patients. The number increased to 80% if the decision were made within the context of a multidisciplinary team. Taking our data and the experience published by others into consideration, we suggest a method for establishing such a team.
Social Security in the 21st Century
Authors: Kilgour John G.
Published: November 2010

The Social Security program is now 75 years old and debate and reform are in the air. Some decry that its benefits are inadequate and should be improved, especially for lifetime low earners, women and minorities. Others, more loudly, proclaim that the system is in financial difficulty and, if nothing is done, will soon go broke. As a result of the last major amendments enacted in 1983, Social Security trust funds now have reserves of $2.5 trillion, at least on paper. However, the trust funds are an accounting device. There is no real money there. It has been spent by the Treasury to fund other government programs and has served to mask a significant portion of the federal deficit for the past 25 years. The Social Security problem is really a federal fiscal problem. The U.S. Treasury owes the Social Security Administration a great deal of money, and the bill is about to become due. In 2010, for the first time in decades, Old Age, Survivor and Disability Insurance expenditures are greater than Federal Insurance Contribution Act tax revenue. This will soon become a permanent condition and a great deal of attention is being directed at solving the funding problem. This article, after examining the Old Age Survivor and Disability Insurance program’s origins, development and current benefit structure, focuses on its funding arrangements. Saving Social Security will be relatively easy. Managing its impact on the federal budget will be daunting.
Within-Patient Atazanavir Trough Concentration Monitoring in HIV-1-Infected Patients
Authors: Crutchley Rustin D. , Ma Qing , Sulaiman Adel , Hochreitter Jill , Morse Gene D.
Published: November 2010

Objective: Protease inhibitors (PIs) exhibit considerable interpatient pharmacokinetic variability in plasma trough concentrations. Therapeutic drug monitoring (TDM) is occasionally used to guide chronic dosing to achieve target trough concentrations, but its clinical success assumes minimal intrasubject variability. Therefore, our primary objective was to evaluate intrapatient variability in atazanavir (ATV) plasma trough concentrations in HIV-1-infected patients. Design/Methods: In a single-site, prospective, cohort study, patients on atazanavir with or without ritonavir (ATV/r or ATV) for 2 clinic visits were enrolled. Adherence and time since last dose (TSLD) were verified at each visit. ATV was assayed with high-performance liquid chromatography. Intra- and interpatient variation was evaluated using the median intraindividual percentage coefficient of variation (ICV). Results: The mean 24-hour ATV trough concentrations for the first and second visit for the ATV/r group (n = 10) was 598 (CV 84%) and 525 ng/mL (CV 66%), respectively ( P = .511), and 300 (CV 81%) and 434 ng/mL (CV 106%) for the ATV group (n = 4), respectively ( P = .369). Median ICV was 43.1% for all patients (range: 0.6%-107.6%), 38.1% (0.6%-107.6%) for the ATV/r group, and 33.1% (2.3%-87.6%) for the ATV group. Conclusions: Potential intrapatient variability in ATV troughs suggests that repeated measurements may be required to ensure that target values are maintained.
Gratifications from New Media
Authors: Krishnatray Pradeep , Singh Pushpendra Pal , Raghavan Srividya , Varma Vinay
Published: November 2010

Several uses and gratification (U&G) studies provide bases for understanding motivations for the uses of traditional mass media such as television and radio. As a new medium, U&G research on Internet has tended to rely on studies of such traditional media. This article assumes that Internet is a unique medium and offers a set of gratifications different from those offered by traditional mass media. This study, therefore, sought to first identify motivations for using the Internet and then extract the structure of gratifications. In addition, it determined the gratifications of male and female respondents separately assuming that access to and use of any new and emergent media tends to favour the male gender. The study identified an eight-factor gratification structure. The study concludes that the underlying motivations for the use of Internet for the entire sample as well as the male and the female sample, separately, varies slightly but is largely stable and consistent.
ILO Convention No. 94 in the aftermath of the Rüffert case
Authors: Bruun Niklas , Jacobs Antoine , Schmidt Marlene
Published: November 2010

The purpose of this article is to discuss the ILO’s Labour Clauses (Public Contracts) Convention 1949 (Convention No. 94) and, in particular, the legal situation in the aftermath of the decision on 3 April 2008 of the European Court of Justice (ECJ) in the Rüffert case (Case C-346/06). The authors argue that the labour law concerning social clauses in public contracts is an old and well-established institution that still has an important role to play. They analyse the Rüffert case and argue that there is a conflict or contradiction between the ECJ’s judgment and Convention No. 94. The authors propose how the Posted Workers Directive 96/71/EC and the EU public procurement regime should be clarified in order to resolve this contradiction. This issue should be raised and promoted both by the EU Member States, in the aftermath of the discussions in June 2008 at the ILO Labour Conference in Geneva on Convention No. 94, and by the new Barroso Commission, which took office in spring 2010, as well as the European Parliament.
Sectoral social dialogue at EU level - recent results and implementation challenges
Authors: Weber Sabrina
Published: November 2010

This article deals with recent developments in EU social dialogue, namely so-called ‘new generation texts’, which are non-binding legally, but ‘implementation-oriented’. Aspects of their follow-up, implementation and multi-level characteristics are therefore discussed. Findings from two sectoral dialogues indicate that follow-up procedures can vary considerably. Furthermore, the implementation or impact of such ‘new generation texts’ seem hard to prove. It is argued that characteristics of national industrial relations systems are insufficient to explain implementation results, since both the interests and attitudes of the actors involved and the specific topic of a given ‘new generation text’ must be taken into account. The main difficulty is found to be the lack of adequate implementation structures due to missing inter- and intraorganizational ‘level linkage’.
Meeting the Psychosocial Needs of Sibling Survivors
Authors: Buchbinder David , Casillas Jacqueline , Zeltzer Lonnie
Published: November 2010

Although increasing numbers of studies have examined late effects in survivors, there is a paucity of long-term outcome studies in their siblings, so-called sibling survivors. Our aim was to provide a review of publications relevant to survivorship and its impact on the long-term psychosocial health of sibling survivors using a family systems framework. A review of publications identified 19 articles that reported findings suggesting that aspects of psychosocial health may be impaired in sibling survivors. Baseline functioning of sibling survivors may be altered at the start of survivorship secondary to apprehension, memories, and emotions. New demands are placed on sibling survivors, including doubts, questions, and worries due to survivorship. Survivor disfigurement may also place demands on sibling survivors associated with behavioral problems. Associated with these changes, there may be alterations in adaptation, including depression, somatic complaints, and posttraumatic stress symptoms. Sibling survivors may also report health risk behaviors and decreased vitality. Identification of the impact of survivorship on the long-term psychosocial health of sibling survivors may help ensure the long-term psychosocial health of all survivors.
A Review of the Appropriate and Inappropriate Use of Dronedarone: Lessons Learned From Controlled Studies and Regulatory Submission
Authors: Naccarelli Gerald V. , Wolbrette Deborah L. , Samii Soraya , Banchs Javier E. , Penny-Peterson Erica , Gonzalez Mario D.
Published: November 2010

Dronedarone is a multichannel blocker with electrophysiologic effects similar to amiodarone. Dronedarone has been documented to prevent atrial fibrillation recurrences and also has efficacy in slowing the ventricular response during episodes of atrial fibrillation. However, in the ANDROMEDA trial, dronedarone was associated with increased mortality when tested in New York Heart Association (NYHA) III/IV patients with left ventricular ejection fractions of less than 35%, who also had a recent hospitalization for decompensated heart failure. When such high-risk patients with heart failure were excluded in the ATHENA trial, dronedarone treatment resulted in a statistical reduction in the composite primary end point of all-cause mortality or cardiovascular hospitalization. In ATHENA, dronedarone reduced cardiovascular hospitalizations even though in the DIONY-SOS trial dronedarone had less effect than amiodarone on suppressing atrial fibrillation recurrences. The most appropriate patients for treatment with dronedarone would be patients with a recent history of paroxysmal or persistent atrial fibrillation/atrial flutter (AF/AFL) that have associated risk factors per the inclusion criteria of ATHENA. Inappropriate patients would be those with class IV heart failure or recently hospitalized for heart failure within the last month from an acute decompensation, the main inclusion criteria in ANDROMEDA. Dronedarone is a novel, multichannel blocking antiarrhythmic agent that may have some pleiotropic effects in addition to its ability to suppress and maintain sinus rhythm and control the rate during AF/AFL recurrences.
Review Article: Current Status of Myocardial Regeneration: New Cell Sources and New Strategies
Authors: Rangappa Sunil , Makkar Rajendra , Forrester James
Published: November 2010

Clinical trials of stem cell therapy in cardiology are based upon a reasonably solid foundation in animal laboratory research. The most widely used cell source in clinical trials has been the patient’s own reconstituted bone marrow cell (BMC) aspirate. Cell sources in human bone marrow include hematopoietic stem cells, mesenchymal progenitor cells, and other cell types with many desirable characteristics. In vitro, they can be induced to become typical sarcomeres with centrally positioned nuclei and abundant mitochondria and to express atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and contractile proteins including myosin heavy chain, myosin light chain, and alpha actin. Intracoronary BMC infusion significantly decreases infarct size, increases myocardial perfusion, and improves regional and global cardiac function. Meta-analyses of clinical trials of intracoronary autologous BMC infusion following acute myocardial infarction (MI) report that the mean absolute increase in ejection fraction (EF) is approximately 3% to 4%. This modest improvement in function appears to persist for 1 year. Some trials have shown that clinical events are reduced at 12 months, but others have reported no long-term clinical benefit, and the only 5-year follow-up suggests persistent benefit with decreased mortality, but also little evidence of significant myocardial regeneration in humans. These results have led to efforts to identify better cell sources and to create more conducive myocardial environment for cell proliferation. Among the cell types are skeletal myoblasts, cardiac stem cells, and induced pluripotent stem cells. Environmental modifiers are designed to increase cell survival, persistence, and proliferation.
Augmenting Maintenance of Sinus Rhythm in the Control of Atrial Fibrillation by Antiarrhythmic Drug Combinations
Authors: Singh Bramah N.
Published: November 2010

In recent years, a major development in the treatment of atrial fibrillation (AF) is the use of catheter ablation, and a significant number of patients may benefit from this mode of therapy. On a global scale, it may not be feasible to deal with most patients solely on the basis of ablation. Therefore, it is likely that much of the therapy for AF will continue to rely on antiarrhythmic agents for maintaining sinus rhythm. For many years, amiodarone and sotalol have been the dominant antiarrhythmic agents, with amiodarone being the most effective antiarrhythmic in suppressing AF; however, amiodarone use is limited due to concerns of end-organ toxicity. Upstream therapies, such as statins, fish oil, angiotensin converting enzyme (ACE) inhibitors, and angiotensin receptor blockers may also provide additive efficacy to these and other membrane-active antiarrhythmics. In recent years, a number of new agents are being developed and the first successful congener of amiodarone, dronedarone, has been shown to be effective in controlling AF and reducing cardiovascular hospitalization. This paper explores the possibility of augmenting the extent of controlling AF by combining multiple potent antiarrhythmic agents old and new.
Nonlinear vibration control of long, flexible structures employing inter-modal energy transfer (modal damping)
Authors: May James , Menzemer Craig
Published: November 2010

In the not too distant past, the design philosophy for tall civil structures could be summarized as LARGE MASS-LARGE STIFFNESS. Advances in material science and design technologies provide the means to explore and construct high-reaching, expansive and much lighter-duty geometries requiring not only extensive strength-based engineering but also carefully executed motion-based analysis as such structures are prone to transverse vibrations. Complicating matters, the inherent natural damping properties of such structures are small, leading to drawn out settling times. Motion-based augmentations offer enabling solutions. ‘Modal Damping’ (MD) exploits damping mechanisms inherent in structures by capitalizing on distinctive dynamic properties existing among the structures vibration modes. An automated, nonlinear control scheme was developed to transfer energy from the fundamental vibration mode, where most vibration energy of the structures of interest resides, to higher order modes where vibration impedance was shown to be more effective. To achieve this objective, MD employs motion control forces self-powered by the redistribution of fundamental mode kinetic energy making the strategy highly efficient. The MD conceptual basis, its dynamic simulation implementation, and the simulation results and analysis are presented herein.
Adaptive inverse control of time waveform replication for electrohydraulic shaking table
Authors: Gang Shen  , Zheng Shu-Tao , Ye Zheng-Mao , Huang Qi-Tao , Cong Da-Cheng , Han Jun-Wei
Published: November 2010

A combined control strategy with an adaptive inverse control (AIC) and an inverse frequency response function (IFRF) equalization technique is proposed for the electrohydraulic shaking table (EST) system. The control purpose is to improve the accuracy of time waveform replication. In contrast to the iterative compensation through repetitive excitations control approach of industrial EST controllers, the proposed control strategy utilizes an IFRF of the EST system for extending the EST system frequency bandwidth and obtaining asymptotic reference tracking, and employs a variable tap-length filtered-x least-mean-squares algorithm to adaptively tune the time-domain drive signal and further improve the position and acceleration tracking performance of the EST system. Thus, the proposed combined control strategy is designed to combine the merits of IFRF and AIC. The procedures of the proposed control strategy are programmed in MATLAB/Simulink, and then compiled to a real-time PC with Microsoft Visual Studio.NET for implementation. The simulated and experimental results show that this control strategy achieves satisfactory position and acceleration waveform replication accuracy.
Active vibration control with comparative algorithms of half rail vehicle model under various track irregularities
Authors: Metin Muzaffer , Guclu Rahmi
Published: November 2010

This study represents the comparison of fuzzy logic and PID controlled active suspensions’ performances on an 11 degree-of-freedom rail vehicle model. First, a PID controller and then a fuzzy logic controller (FLC) are designed for the same model separately to obtain a comfortable travel for the users. Since the PID control method can be applied easily and is well known, it has an important place in control applications and a FLC is preferred because of its superior performance in active vibration control. Controllers are used to secondary suspension systems placed between rail vehicle and bogie. This vehicle is modeled as a lumped parameter system which consists of a body, bogie, primary and secondary suspensions and rigid wheels. The model has been designed to take into account the complexity of wheel-rail contact. For the purpose of observing both controllers’ performances, two different track irregularities are considered as disruptive effects of the system. All parameters for both controllers are achieved by the use of genetic algorithm for the same simulation conditions and performance criteria. At the end of the study, time history and frequency response for accelerations and displacements of the rail vehicle are presented for both uncontrolled and controlled systems. Performances of the compared approaches are discussed.
Active control of an unsymmetrical rotor system with tilting pad journal bearings
Authors: Xiaochun Gong  , Dengqing Cao
Published: November 2010

The active hybrid tilting-pad bearing, together with the unsymmetrical flexible rotor and the hydraulic system is modeled and studied in this paper. Then the 8 degrees-of-freedom nonlinear dynamic model of unsymmetrical flexible rotor-bearing system with the effect of gyroscopic moment is formulated. The active lubrications based on injecting pressurized oil into the bearing gap through orifices (machined in the bearing sliding surface) are utilized to suppress the shaft vibrations. A proportional—integral (PI) controller is designed for the active lubricated system and the finite difference method is applied to solve the pressure distribution on each tilting pad surface. Numerical results show that the actively lubricated system presents effective vibration reduction for the unbalance response subjected on the flexible rotor and the proposed PI controller exhibits a commendable performance. The feasibility of putting off rotor-bearing instabilities (phenomena of whirl) by using active lubrication is also investigated, which illustrates clearly one of its most promising applications.
Advancing governmentality studies
Authors: Lippert Randy , Stenson Kevin
Published: November 2010

Criminology has been significantly influenced by governmentality studies and the social constructionist perspective on social problems. Despite emerging in distinctive academic networks, this article elaborates how both programmes similarly focus on the simultaneous governance and constitution of problematized—often moralized or criminalized—conduct; imagine plurality, temporality and continuous failure of their subject matters; and presume language is constitutive. These similarities are discussed in order to show how the governmentality project in relation to criminology can learn from the social constructionist perspective on social problems. Using empirical illustrations, it is shown how governmentality studies can benefit from adopting constructionism’s concept of claims-making activities; attention to context; and earlier acceptance of the futility of cutting the cord with ‘the real’.
Nodal wars and network fallacies
Authors: Shearing Clifford , Johnston Les
Published: November 2010

In this article we examine three prominent discourses of security governance and suggest, through a critical review of organizational network theory, that the nodal model can offer theoretical, methodological and ethical benefits over alternative ones. These benefits, we argue, are especially pertinent to the analysis of contemporary global insecurities. The article closes by reflecting on two issues raised in the earlier analysis: how an awareness of discursive contiguity can help inform our understanding of nodal tendencies in global security governance; and how the methodological fallacy of ‘nodal-network equivalence’ plays out under conditions of the ‘war on terror’.
The passion and melancholia of performing dietitian
Authors: Gingras Jacqui
Published: November 2010

Dietitians provide nutritional care in various contexts and it is expected that dietetic subjectivity shapes and is shaped by health/nutrition discourse, but this has not been sufficiently explored. The purpose of this study was to further understand dietetic subjectivity, dietitians’ experiences of their education and relationships between educational and practice discourses. Twelve dietitians were recruited to participate in semi-structured research interviews. Feminist theoretical perspectives informed the research including the interpretation of data, which was analyzed according to the Listening Guide, a feminist voice-centered relational method. A theory of dietitian performativity informed by Butler (1999) emerged whereby dietitians expressed passion and melancholia for their practice. Also, participants experienced discontinuity between educational and practice contexts, which highlighted the need to integrate embodied epistemic perspectives throughout undergraduate education. These findings support a critical gesture in dietetic educational discourse away from positivism towards embodiment as a means for highlighting and reinforcing the complexity and fluidity of dietetic performativity.
Shokuiku
Authors: Mah Catherine L.
Published: November 2010

This paper examines the issue of public health governance in a globalized context through the lens of nutrition policy in contemporary Japan. I focus upon the case of shokuiku (food education), institutionalized in the 2005 national-level Basic Law on Food Education. First, I consider the emergence of shokuiku within the context of recent public health policy developments, specifically, a shift towards a decentralized and personalized view of public health in Japan. Second, I examine the policy discourses around shokuiku and how they convey the relationships between food and public health. These discourses centre upon the notion of a healthy and traditional Japanese food culture practiced in the home, only recently interrupted by modernity. When presented within a health promotion framework focused upon lifestyle diseases, such ideas can enable and reinforce neoliberal approaches to public health and food security where the locus of governing authority lies largely outside the state.
Creating Images of Old People as Home Care Receivers
Authors: Olaison Anna
Published: November 2010

Central to the assessment process in case management is how older people’s needs are constructed through documentation and case files. This article examines how older people’s needs are categorized in written documentation. Sixteen case files from three social work districts in Sweden were studied using discourse analysis. The results identified two general types of case files; the fact-oriented (using objective language) and event-oriented case file (using more personal language) — which depicted the older individuals quite differently. All case files employed several need categories; though social needs were important in describing living conditions, it was medical and physical needs that impinged on home care decisions. This raises questions about how case documentation depicts older people through society’s eyes and about the discourses prevailing in gerontological social work.
Staff Narratives
Authors: Thaden Emily , Robinson Jill
Published: November 2010

The 1996 welfare reform devolved greater responsibility and flexibility to state welfare organizations; however, most of these organizations have not transformed their organizational cultures towards a vision of client well-being. This study examines dominant and alternative narratives espoused during twenty-two interviews with staff in a welfare organization. The dominant narrative endorsed the welfare program and understood ‘success’ as client compliance, which resulted in regulatory suggestions for change, such as implementing stricter policies. The alternative narrative subverted this dominant narrative by identifying problems with the welfare program, which resulted in suggestions for organizational change that promoted client well-being. Fostering alternative narratives in welfare organizations may prompt liberatory organizational culture shifts that redefine the notion of client ‘success’.
Street to Home
Authors: Jost John J. , Levitt Aaron J. , Porcu Leide
Published: November 2010

This article presents findings from in-depth qualitative interviews conducted with 20 long-term unsheltered homeless adults who had recently been placed into housing by Street to Home (S2H), a housing-focused outreach program in New York City. S2H places individuals directly into transitional and permanent housing, breaking from the prevailing linear treatment and housing models that require a demonstration of ‘housing readiness’ via sobriety and psychiatric stability prior to permanent housing placements. The major themes identified were: (1) negative perceptions of homeless services and service resistance; (2) readiness to leave the street; (3) believable housing options as triggers for change; (4) adapting to new surroundings and discovering benefits; and (5) the importance of knowing supports are in place. Fulfilling promises in the wake of past disappointments and providing an ongoing sense of support appear to be the key elements that have enabled the program to engage and maintain clients.
Student authority: Antidote to alienation
Authors: Goodman Joan
Published: November 2010

The widespread disaffection of students from school is manifested in academic failure, indifference, and defiance. These problems can be alleviated, I argue, when an authority structure is developed that combines three components — freedom, power, and legitimacy. Authority understood as either power or freedom is apt to subvert students’ school attachment even while attempting to strengthen it; authority that combines power and freedom, when perceived by all parties as serving a legitimate mission, is apt to enhance engagement. The bonding potency of authority is augmented when it is joined to strongly marked school purposes and dispersed to students. The three components of authority are interwoven with school visions and student authority into various patterns: some schools lean more towards power, others more towards freedom; some operate under highly moralized and totalizing visions, others under vaguer, less moral, and less encompassing visions. The nature and interdependence of the three components and the trade-offs under various combinations are discussed. While legitimate authority has many faces, if schools are to be engaging places for students it is essential that the norms promoted are welcomed by them; advantageous to that process is ordaining students with authority to advance prevailing norms.
Peptide binding predictions for HLA DR, DP and DQ molecules
Authors: Wang Peng , Sidney John , Kim Yohan , Sette Alessandro , Lund Ole , Nielsen Morten , Peters Bjoern
Published: November 2010

Background

MHC class II binding predictions are widely used to identify epitope candidates in infectious agents, allergens, cancer and autoantigens. The vast majority of prediction algorithms for human MHC class II to date have targeted HLA molecules encoded in the DR locus. This reflects a significant gap in knowledge as HLA DP and DQ molecules are presumably equally important, and have only been studied less because they are more difficult to handle experimentally.

Results

In this study, we aimed to narrow this gap by providing a large scale dataset of over 17,000 HLA-peptide binding affinities for a set of 11 HLA DP and DQ alleles. We also expanded our dataset for HLA DR alleles resulting in a total of 40,000 MHC class II binding affinities covering 26 allelic variants. Utilizing this dataset, we generated prediction tools utilizing several machine learning algorithms and evaluated their performance.

Conclusion

We found that 1) prediction methodologies developed for HLA DR molecules perform equally well for DP or DQ molecules. 2) Prediction performances were significantly increased compared to previous reports due to the larger amounts of training data available. 3) The presence of homologous peptides between training and testing datasets should be avoided to give real-world estimates of prediction performance metrics, but the relative ranking of different predictors is largely unaffected by the presence of homologous peptides, and predictors intended for end-user applications should include all training data for maximum performance. 4) The recently developed NN-align prediction method significantly outperformed all other algorithms, including a naïve consensus based on all prediction methods. A new consensus method dropping the comparably weak ARB prediction method could outperform the NN-align method, but further research into how to best combine MHC class II binding predictions is required.
Reticular alignment: A progressive corner-cutting method for multiple sequence alignment
Authors: Szabó Adrienn , Novák Ádám , Miklós István , Hein Jotun
Published: November 2010

Background

In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table. Instead, it defines a set of optimal and suboptimal alignments at each step during the progressive alignment. The set of alignments are represented with a network to store them and use them during the progressive alignment in an efficient way. The program contains a threshold parameter on which the size of the network depends. The larger the threshold parameter and thus the network, the deeper the search in the alignment space for better scored alignments.

Results

We implemented the program in the Java programming language, and tested it on the BAliBASE database. Reticular Alignment can outperform ClustalW even if a very simple scoring scheme (BLOSUM62 and affine gap penalty) is implemented and merely the threshold value is increased. However, this set-up is not sufficient for outperforming other cutting-edge alignment methods. On the other hand, the reticular alignment search strategy together with sophisticated scoring schemes (for example, differentiating gap penalties for hydrophobic and hydrophylic amino acids) overcome FSA and in some accuracy measurement, even MAFFT. The program is available from http://phylogeny-cafe.elte.hu/RetAlign/

Conclusions

Reticular alignment is an efficient search strategy for finding accurate multiple alignments. The highest accuracy achieved when this searching strategy is combined with sophisticated scoring schemes.
Comparative genomic analysis of Atlantic salmon, Salmo salar, from Europe and North America
Authors: Lubieniecki Krzysztof P , Jones Stacy L , Davidson Evelyn A , Park Jay , Koop Ben F , Walker Seumas , Davidson William S
Published: November 2010

Background

Several lines of evidence including allozyme analysis, restriction digest patterns and sequencing of mtDNA as well as mini- and micro-satellite allele frequencies indicate that Atlantic salmon (Salmo salar) from North America and Europe are genetically distinct. These observations are supported by karyotype analysis, which revealed that North American Atlantic salmon have 27 pairs of chromosomes whereas European salmon have 29 pairs. We set out to construct a linkage map for a North American Atlantic salmon family and to compare this map with the well developed map for European Atlantic salmon.

Results

We used microsatellite markers, which had previously been mapped in the two Atlantic salmon SALMAP mapping families from the River Tay, Scotland, to carry out linkage analysis in an Atlantic salmon family (NB1) whose parents were derived from the Saint John River stock in New Brunswick, Canada. As large differences in recombination rates between female and male Atlantic salmon have been noted, separate genetic maps were constructed for each sex. The female linkage map comprises 218 markers in 37 linkage groups while the male map has 226 markers in 28 linkage groups. We combined 280 markers from the female and male maps into 27 composite linkage groups, which correspond to the haploid number of chromosomes in Atlantic salmon from the Western Atlantic.

Conclusions

A comparison of the composite NB1 and SALMAP linkage maps revealed the reason for the difference in the chromosome numbers between European and North American Atlantic salmon: Linkage groups AS-4 and AS-32 in the Scottish salmon, which correspond to chromosomes Ssa-6 and Ssa-22, are combined into a single NB1 linkage group as are linkage groups AS-21 and AS-33 (corresponding to chromosomes Ssa-26 and Ssa-28). The comparison of the linkage maps also suggested some additional chromosomal rearrangements, but it will require finer mapping, potentially using SNPs, to test these predictions. Our results provide the first comparison of the genomic architecture of Atlantic salmon from North America and Europe with respect to chromosome organization.
Identification and analysis of the germin-like gene family in soybean
Authors: Lu Mo , Han Ying-Peng , Gao Ji-Guo , Wang Xiang-Jing , Li Wen-Bin
Published: November 2010

Background

Germin and germin-like proteins constitute a ubiquitous family of plant proteins. A role of some family members in defense against pathogen attack had been proposed based on gene regulation studies and transgenic approaches. Soybean (G. max L. Merr.) germin genes had not been characterized at the molecular and functional levels.

Results

In the present study, twenty-one germin gene members in soybean cultivar 'Maple Arrow' (partial resistance to Sclerotinia stem rot of soybean) were identified by in silico identification and RACE method (GmGER 1 to GmGER 21). A genome-wide analyses of these germin-like protein genes using a bioinformatics approach showed that the genes located on chromosomes 8, 1, 15, 20, 16, 19, 7, 3 and 10, on which more disease-resistant genes were located on. Sequence comparison revealed that the genes encoded three germin-like domains. The phylogenetic relationships and functional diversity of the germin gene family of soybean were analyzed among diverse genera. The expression of the GmGER genes treated with exogenous IAA suggested that GmGER genes might be regulated by auxin. Transgenic tobacco that expressed the GmGER 9 gene exhibited high tolerance to the salt stress. In addition, the GmGER mRNA increased transiently at darkness and peaked at a time that corresponded approximately to the critical night length. The mRNA did not accumulate significantly under the constant light condition, and did not change greatly under the SD and LD treatments.

Conclusions

This study provides a complex overview of the GmGER genes in soybean. Phylogenetic analysis suggested that the germin and germin-like genes of the plant species that had been founded might be evolved by independent gene duplication events. The experiment indicated that germin genes exhibited diverse expression patterns during soybean development. The different time courses of the mRNAs accumulation of GmGER genes in soybean leaves appeared to have a regular photoperiodic reaction in darkness. Also the GmGER genes were proved to response to abiotic stress (such as auxin and salt), suggesting that these paralogous genes were likely involved in complex biological processes in soybean.
Expression of 3-hydroxy-3-methylglutaryl-CoA reductase, p-hydroxybenzoate-m-geranyltransferase and genes of phenylpropanoid pathway exhibits positive correlation with shikonins content in arnebia [Arnebia euchroma (Royle) Johnston]
Authors: Singh Ravi S , Gara Rishi K , Bhardwaj Pardeep K , Kaachra Anish , Malik Sonia , Kumar Ravi , Sharma Madhu , Ahuja Paramvir S , Kumar Sanjay
Published: November 2010

Background

Geranyl pyrophosphate (GPP) and p-hydroxybenzoate (PHB) are the basic precursors involved in shikonins biosynthesis. GPP is derived from mevalonate (MVA) and/or 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway(s), depending upon the metabolite and the plant system under consideration. PHB, however, is synthesized by only phenylpropanoid (PP) pathway. GPP and PHB are central moieties to yield shikonins through the synthesis of m-geranyl-p-hydroxybenzoate (GHB). Enzyme p-hydroxybenzoate-m-geranyltransferase (PGT) catalyses the coupling of GPP and PHB to yield GHB.

The present research was carried out in shikonins yielding plant arnebia [Arnebia euchroma (Royle) Johnston], wherein no molecular work has been reported so far. The objective of the work was to identify the preferred GPP synthesizing pathway for shikonins biosynthesis, and to determine the regulatory genes involved in the biosynthesis of GPP, PHB and GHB.

Results

A cell suspension culture-based, low and high shikonins production systems were developed to facilitate pathway identification and finding the regulatory gene. Studies with mevinolin and fosmidomycin, inhibitors of MVA and MEP pathway, respectively suggested MVA as a preferred route of GPP supply for shikonins biosynthesis in arnebia. Accordingly, genes of MVA pathway (eight genes), PP pathway (three genes), and GHB biosynthesis were cloned. Expression studies showed down-regulation of all the genes in response to mevinolin treatment, whereas gene expression was not influenced by fosmidomycin. Expression of all the twelve genes vis-à-vis shikonins content in low and high shikonins production system, over a period of twelve days at frequent intervals, identified critical genes of shikonins biosynthesis in arnebia.

Conclusion

A positive correlation between shikonins content and expression of 3-hydroxy-3-methylglutaryl-CoA reductase (AeHMGR) and AePGT suggested critical role played by these genes in shikonins biosynthesis. Higher expression of genes of PP pathway was a general feature for higher shikonins biosynthesis.
Subcellular distribution of nuclear import-defective isoforms of the promyelocytic leukemia protein
Authors: Jul-Larsen Åsne , Grudic Amra , Bjerkvig Rolf , Bøe Stig O
Published: November 2010

Background

The promyelocytic leukemia (PML) protein participates in a number of cellular processes, including transcription regulation, apoptosis, differentiation, virus defense and genome maintenance. This protein is structurally organized into a tripartite motif (TRIM) at its N-terminus, a nuclear localization signal (NLS) at its central region and a C-terminus that varies between alternatively spliced isoforms. Most PML splice variants target the nucleus where they define sub-nuclear compartments termed PML nuclear bodies (PML NBs). However, PML variants that lack the NLS are also expressed, suggesting the existence of PML isoforms with cytoplasmic functions. In the present study we expressed PML isoforms with a mutated NLS in U2OS cells to identify potential cytoplasmic compartments targeted by this protein.

Results

Expression of NLS mutated PML isoforms in U2OS cells revealed that PML I targets early endosomes, PML II targets the inner nuclear membrane (partially due to an extra NLS at its C-terminus), and PML III, IV and V target late endosomes/lysosomes. Clustering of PML at all of these subcellular locations depended on a functional TRIM domain.

Conclusions

This study demonstrates the capacity of PML to form macromolecular protein assemblies at several different subcellular sites. Further, it emphasizes a role of the variable C-terminus in subcellular target selection and a general role of the N-terminal TRIM domain in promoting protein clustering.
IP-10 detection in urine is associated with lung diseases
Authors: Cannas Angela , Calvo Ludovica , Chiacchio Teresa , Cuzzi Gilda , Vanini Valentina , Lauria Francesco N , Pucci Luigia , Girardi Enrico , Goletti Delia
Published: November 2010

Background

blood cytokines and chemokines have been proposed as biomarkers for tuberculosis (TB). Recently, some immune mediators found in the urine of patients with renal dysfunctions have also been suggested as potential biomarkers. Finding biomarkers for TB in urine would present several advantages over blood in terms of collection and safety. The objective of this study was to investigate the presence of cytokines and chemokines in the urine of patients with pulmonary TB at the time of diagnosis. In a subgroup, the evaluation was also performed during TB treatment and at therapy completion. Patients with lung diseases other than TB, and healthy subjects were also enrolled.

Methods

urine samples from 138 individuals, after exclusion of renal dysfunctions, were collected during an 18 month-period. Among them, 58 received a diagnosis of pulmonary TB, 28 resulted having lung diseases other than TB, and 34 were healthy subjects. Moreover, 18 TB patients, 9 of whom were tested 2 months after AFB smear sputum reversion and 9 of whom were cured of TB were also included. Cytokines and chemokines in urine were evaluated using a Cytometric-Bead-Array-Flex-Set. IP-10 detection in 49 subjects was also carried out in parallel by using an Enzyme Linked ImmunoSorbent Assay (ELISA).

Results

IFN-γ, TNF-α, IL-2, IL-8, MIP-1α, MIP-1β and RANTES were poorly detected in all urine samples. Conversely, IP-10 was consistently detected in urine and its level was significantly increased in patients with lung disease compared to healthy subjects (p < 0.001). Increased IP-10 levels were found in both pulmonary TB and lung diseases other than TB. Moreover lower IP-10 levels were found in cured-TB patients compared to the levels at the time of diagnosis, and this difference was close to significance (p = 0.06). Interestingly, we demonstrated a significant correlation between the data obtained by flow cytometry and ELISA (r20.82, p < 0.0001).

Conclusions

IP-10, in contrast to IFN-γ, TNF-α, IL-2, IL-8, MIP-1α, MIP-1β and RANTES, is detectable in the urine of patients with pulmonary diseases in the absence of renal dysfunctions. Moreover, the IP-10 level in cured-TB patients is comparable to that found in healthy subjects. More studies are needed to further investigate the clinical utility of these findings.
Prevalence and clustering of metabolic risk factors for type 2 diabetes among Chinese adults in Shanghai, China
Authors: Xu He , Song Yiqing , You Nai-Chieh , Zhang Zuo-Feng , Greenland Sander , Ford Earl S , He Lin , Liu Simin
Published: November 2010

Background

Type 2 diabetes is becoming an epidemic in China. To evaluate the prevalence, clustering of metabolic risk factors and their impact on type 2 diabetes, we conducted a population-based study in Shanghai, China's largest metropolitan area.

Methods

From 2006 to 2007, 2,113 type 2 diabetes cases and 2,458 comparable controls of adults aged 40 to 79 years were enrolled. Demographic, lifestyle, and dietary factors were assessed via standardized questionnaires. Plasma, red and white blood cells were collected and stored for future studies. Anthropometric indices and biochemical intermediates (including blood pressure, fasting glucose, glycosylated hemoglobin, and blood lipids) were measured. The prevalence of metabolic syndrome were also compared following two criteria recommended by the Chinese Diabetes Society (CDS, 2004) and the National Cholesterol Education Program's Adult Treatment Panel III (ATP III, 2002).

Results

Prevalence of metabolic syndrome (62% vs. 15% using CDS criteria) and its individual components, including obesity (51% vs. 42%), hypertension (54% vs. 41%), hypertriglyceridemia (42% vs. 32%), and low high-density lipoprotein-cholesterol (HDL) levels (36% vs. 25%) were higher in diabetes cases than controls. Regardless of criteria used, those with impaired fasting glucose (IFG) had similarly high prevalence of metabolic syndrome as did diabetes cases. In a multiple logistic regression model adjusted for demographics and lifestyle risk factors, the odds ratios of diabetes (95% CI) were 1.23 (1.04-1.45) for overweight (28 >= BMI >= 24), 1.81 (1.45-2.25) for obesity (BMI > 28), 1.53 (1.30-1.80) for central obesity (waist circumference > 80 cm for woman or waist circumference > 85 cm for man), 1.36 (1.17-1.59) for hypertension (sbp/dbp >= 140/90 mmHg), 1.55 (1.32-1.82) for high triglycerides (triglycerides > 1.70 mmol/l) and 1.52 (1.23-1.79) for low HDL-C (HDL-C < 1.04 mmol/L).

Conclusions

These data indicate that multiple metabolic risk factors--individually or jointly--were more prevalent in diabetes patients than in controls. Further research will examine hypotheses concerning the high prevalence of IFG, family history, and central obesity, aiding development of multifaceted preventive strategies specific to this population.
Rationale and methods of the cardiometabolic valencian study (escarval-risk) for validation of risk scales in mediterranean patients with hypertension, diabetes or dyslipidemia
Authors: Gil-Guillen Vicente , Orozco-Beltran Domingo , Redon Josep , Pita-Fernandez Salvador , Navarro-Pérez Jorge , Pallares Vicente , Valls Francisco , Fluixa Carlos , Fernandez Antonio , Martin-Moreno Jose M , Pascual-de-la-Torre Manuel , Trillo Jose L , Durazo-Arvizu Ramon , Cooper Richard , Hermenegildo Marta , Rosado Luis
Published: November 2010

Background

The Escarval-Risk study aims to validate cardiovascular risk scales in patients with hypertension, diabetes or dyslipidemia living in the Valencia Community, a European Mediterranean region, based on data from an electronic health recording system comparing predicted events with observed during 5 years follow-up study.

Methods/Design

A cohort prospective 5 years follow-up study has been designed including 25000 patients with hypertension, diabetes and/or dyslipidemia attended in usual clinical practice. All information is registered in a unique electronic health recording system (ABUCASIS) that is the usual way to register clinical practice in the Valencian Health System (primary and secondary care). The system covers about 95% of population (near 5 million people). The system is linked with database of mortality register, hospital withdrawals, prescriptions and assurance databases in which each individual have a unique identification number. Diagnoses in clinical practice are always registered based on IDC-9. Occurrence of CV disease was the main outcomes of interest. Risk survival analysis methods will be applied to estimate the cumulative incidence of developing CV events over time.

Discussion

The Escarval-Risk study will provide information to validate different cardiovascular risk scales in patients with hypertension, diabetes or dyslipidemia from a low risk Mediterranean Region, the Valencia Community.