bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal diagnosis of cardiac rhabdomyomas: incidence of associated cerebral lesions of tuberous sclerosis complex
Authors: Saada J. , Hadj Rabia S. , Fermont L. , Le Bidois J. , Bernades‐Stein L. , Martinovic J. , Sonigo P. , Dumez Y. , Bonnet D. , Benachi A. 
Published: July 2009

AbstractObjectivesTo determine the prevalence of specific cerebral lesions of tuberous sclerosis complex (TSC) and neurological outcome in cases diagnosed prenatally with cardiac rhabdomyomas.MethodsWe reviewed all fetuses diagnosed prenatally with cardiac rhabdomyomas which had undergone detailed ultrasound evaluation and cerebral magnetic resonance imaging (MRI) and which were recorded in the database of a single institution covering the period January 1992 to December 2005.ResultsFifty‐one fetuses were included in the study. MRI was performed at a mean ± SD gestational age of 30 ± 3 gestational weeks and showed specific lesions of TSC in 49% of cases. Termination of pregnancy was chosen by the parents in 26 cases. Neurological development was studied in 20 cases, follow‐up lasting 4.8 ± 2.9 years. Neurodevelopmental events occurred during the follow‐up period in 45% of cases. Neurological complications occurred in 67% of patients who had cerebral lesions at MRI and in 33% of patients with normal MRI results. There was no significant difference between the two groups of patients (P = 0.2).ConclusionIn fetuses with cardiac rhabdomyomas detailed ultrasound examination and third‐trimester cerebral MRI are able to diagnose most TSC cerebral lesions, but fail to determine neurological outcome. Copyright © 2009 ISUOG. Published by John Wiley & Sons, Ltd.
UV plumage color is an honest signal of quality in male budgerigars
Authors: Griggio Matteo , Zanollo Valeria , Hoi Herbert 
Published: July 2009

AbstractElaborate and colorful feathers are important traits in female mate choice in birds. Plumage coloration can result from pigments deposited in feathers such as carotenoids and melanins, or can be caused by nano‐scale reflective tissues (structurally based coloration), usually producing ultraviolet (UV) coloration. Structural colorations remain the least studied of the three most important feather colorations. Previous studies have found a female preference for UV color in the budgerigar, Melopsittacus undulatus, but it is not clear what information this ornament conveys, nor what is the possible cost associated with its production. We investigated possible correlations between immune response and plumage color of wild‐type (green) male budgerigars. In particular we measured the wing web swelling resulting from injection of phytohaemagglutinin (PHA). We did not detect any correlation between the sedimentation rate and morphological and color variables. We found that UV chroma is the best predictor for the cutaneous immune activity. Indeed, male budgerigars with high UV reflectance in the breast feathers showed stronger immune responses. These results are consistent with the idea that UV colors are special signals conveying information about a bird's condition.
A new genus and species of Ptyctodont (Placodermi) from the Late Devonian Gneudna Formation, Western Australia, and an analysis of Ptyctodont phylogeny
Authors: TRINAJSTIC KATE , LONG JOHN A. 
Published: July 2009

AbstractAn almost complete but predominantly disarticulated ptyctodont fish, Kimbryanodus williamburyensis n. gen., n.sp. from the Late Devonian Gneudna Formation, is described. The fossils occur as three-dimensionally preserved isolated plates, and this has allowed the reconstruction of the fish. A taxonomic revision of the ptyctodonts was undertaken based on recently described Australian taxa and new reconstructions of Australian, American and European specimens. The phylogenetic analysis supports a threefold division of the ptyctodonts, with Rhamphodopsis being the most basal taxon and the other ptyctodonts divided into those possessing a median dorsal spine, spinal plate and simple V-shaped overlap of the anterior lateral and anterior dorsolateral plates and those taxa which do not.
Ultrahigh-temperature metamorphism and decompression history of sapphirine granulites from Rajapalaiyam, southern India: implications for the formation of hot orogens during Gondwana assembly
Authors: TSUNOGAE T. , SANTOSH M. 
Published: July 2009

AbstractSapphirine-bearing Mg–Al granulites from Rajapalaiyam in the southern part of the Madurai Block provide critical evidence for Late Neoproterozoic–Cambrian ultrahigh-temperature (UHT) metamorphism in southern India. Poikiloblastic garnet in quartzo-feldspathic and pelitic granulites contain inclusions of fine-grained subidioblastic to xenoblastic sapphirine associated with quartz, suggesting that the rocks underwentT> 1000°C peak metamorphism. Quartz inclusions in spinel within garnet are also regarded as clear evidence for a UHT condition. Inclusions of orthopyroxene within porphyroblastic garnet in the sapphirine-bearing rocks show the highest Al2O3content of up to 10.3 wt%, suggestingT= 1050–1070°C andP= 8.5–9.5 kbar. Temperatures estimated from ternary feldspar and other geothermometers (T= 950–1000°C) further support extreme thermal metamorphism in this region. Xenoblastic spinel inclusions in sapphirine coexisting with quartz suggest that the spinel + quartz assemblage pre-dates the sapphirine + quartz assemblage, probably implying a cooling fromT~ 1050°C or an anticlockwiseP–Tpath. The FMAS reaction sapphirine + quartz + garnet → orthopyroxene + sillimanite indicates a cooling from the sapphirine + quartz stability field after the peak metamorphism. Corona textures of orthopyroxene + cordierite (± sapphirine), orthopyroxene + sapphirine + cordierite, and cordierite + spinel around garnet suggest subsequent near-isothermal decompression followed by decompressional cooling towardT= 650–750°C andP= 4.5–5.5 kbar. The sapphirine–quartz association and related textures described in this study have an important bearing on the UHT metamorphism and exhumation history of the Madurai Block, as well as on the tectonic evolution of the continental deep crust in southern India. Our study provides a typical example for extreme metamorphism associated with collisional tectonics during the Late Neoproterozoic–Cambrian assembly of the Gondwana supercontinent.
Support for Free Trade: Self-Interest, Sociotropic Politics, and Out-Group Anxiety
Authors: Mansfield Edward D. , Mutz Diana C. 
Published: July 2009

AbstractAlthough it is widely acknowledged that an understanding of mass attitudes about trade is crucial to the political economy of foreign commerce, only a handful of studies have addressed this topic. These studies have focused largely on testing two models, both of which emphasize that trade preferences are shaped by how trade affects an individual's income. The factor endowments or Heckscher-Ohlin model posits that these preferences are affected primarily by a person's skills. The specific factors or Ricardo-Viner model posits that trade preferences depend on the industry in which a person works. We find little support for either of these models using two representative national surveys of Americans. The only potential exception involves the effects of education. Initial tests indicate that educational attainment and support for open trade are directly related, which is often interpreted as support for the Heckscher-Ohlin model. However, further analysis reveals that education's effects are less representative of skill than of individuals' anxieties about involvement with out-groups in their own country and beyond. Furthermore, we find strong evidence that trade attitudes are guided less by material self-interest than by perceptions of how the U.S. economy as a whole is affected by trade.
Determining Trade Policy: Do Voters Hold Politicians Accountable?
Authors: Guisinger Alexandra 
Published: July 2009

AbstractModels of trade policy often depend on the efficient aggregation of individual preferences. While much of the recent empirical work on trade focuses on whether domestic coalitions form along class or sectoral lines, the process of preference aggregation itself remains understudied. In democratic countries, voting is typically assumed to be an unproblematic mechanism for aggregating preferences, but such an assumption may be misleading when the salience of trade policy is low or heterogeneous throughout the electorate. Using data from a survey of 36,501 potential voters in the 2006 U.S. midterm congressional elections, this article explores the salience of trade policy for voters as a whole and for populations predicted to be most affected by changing trade patterns. The article offers an estimation of trade policy salience based on the degree to which voters held Senate incumbents accountable for their 2005 vote on the Central American Free Trade Agreement, relative to roll call votes on other issues of the day. The article finds trade policy salience to be relatively low in terms of stated importance, in voters' knowledge of their representatives' policy positions, and in its effect on voters' propensity to vote for the incumbent. The low salience of trade policy, particularly among highly affected groups, calls into question voter-driven models of trade policy.
Lone Mothers, Ethnicity and Welfare Dynamics
Authors: MOKHTAR CHRISTINA , PLATT LUCINDA 
Published: July 2009

AbstractThis article investigates the ethnic patterning of exit from means-tested benefits in a UK town. Lone parents in the UK face high risks of poverty and high rates of receipt of means-tested, out-of-work benefits. There has been extensive policy concern with lone parents' poverty and with potential ‘welfare dependency’. Investigation of welfare dynamics has unpacked the notion of welfare dependency, and has stimulated policy to better understand the factors associated with longer rather than shorter durations. However, within this analysis, there has been little attention paid to ethnicity. This is despite the fact that the extensive literature on the UK's minority ethnic groups has emphasised diversity in both rates of lone parenthood and risks of poverty. To date we have little understanding of ethnic variation in lone parents' welfare dynamics. Using a data set drawn from administrative records, this article analyses the chances of leaving means-tested benefit for a set of lone mothers in a single town, exploring whether there is variation by ethnic group. We find that, controlling for basic demographic characteristics, there is little evidence to suggest that ethnicity affects the chances of benefit exit, even between groups where rates of lone parenthood are very different.
Medicine and Management in English Primary Care: A Shifting Balance of Power?
Authors: SHEAFF ROD 
Published: July 2009

AbstractThe English NHS has been repeatedly restructured since 1991. Drawing on multiple case studies in English primary health care from 1998 to 2005 and on (other) published studies, this article uses Therborn's theory of power to make a framework analysis of how these reforms redistributed power between medicine and management in NHS primary care. Legal changes ended the GP monopoly of primary medical care provision and, with greater managerial discretion in NHS spending, allowed more diverse organisational forms of primary care provision to appear, although general practice remained predominant. Changes in managerial and professional ideologies relaxed the restrictions on managerial decisions about general practice. Re-negotiations between the medical profession and the state mostly tended to increase managerial power. Evidence-based medicine has tended to weaken the impersonal sources of medical power. On balance, these events have tended to increase managerial power over medical practice. They also suggest adjustments to Therborn's conceptualisation of power.
ADAN: a database for prediction of protein–protein interaction of modular domains mediated by linear motifs
Authors: Encinar J. A. , Fernandez-Ballester G. , Sánchez I. E. , Hurtado-Gomez E. , Stricher F. , Beltrao P. , Serrano L. 
Published: July 2009

Abstract
Motivation: Most of the structures and functions of proteome globular domains are yet unknown. We can use high-resolution structures from different modular domains in combination with automatic protein design algorithms to predict genome-wide potential interactions of a protein. ADAN database and related web tools are online resources for the predictive analysis of ligand–domain complexes. ADAN database is a collection of different modular protein domains (SH2, SH3, PDZ, WW, etc.). It contains 3505 entries with extensive structural and functional information available, manually integrated, curated and annotated with cross-references to other databases, biochemical and thermodynamical data, simplified coordinate files, sequence files and alignments. Prediadan, a subset of ADAN database, offers position-specific scoring matrices for protein–protein interactions, calculated by FoldX, and predictions of optimum ligands and putative binding partners. Users can also scan a query sequence against selected matrices, or improve a ligand–domain interaction.
Availability: ADAN is accessible at http://adan-embl.ibmc.umh.es/ or http://adan.crg.es/.
Contact: gregorio@umh.es
Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition
Authors: Karpievitch Yuliya V. , Taverner Thomas , Adkins Joshua N. , Callister Stephen J. , Anderson Gordon A. , Smith Richard D. , Dabney Alan R. 
Published: July 2009

Abstract
Motivation: LC-MS allows for the identification and quantification of proteins from biological samples. As with any high-throughput technology, systematic biases are often observed in LC-MS data, making normalization an important preprocessing step. Normalization models need to be flexible enough to capture biases of arbitrary complexity, while avoiding overfitting that would invalidate downstream statistical inference. Careful normalization of MS peak intensities would enable greater accuracy and precision in quantitative comparisons of protein abundance levels.
Results: We propose an algorithm, called EigenMS, that uses singular value decomposition to capture and remove biases from LC-MS peak intensity measurements. EigenMS is an adaptation of the surrogate variable analysis (SVA) algorithm of Leek and Storey, with the adaptations including (i) the handling of the widespread missing measurements that are typical in LC-MS, and (ii) a novel approach to preventing overfitting that facilitates the incorporation of EigenMS into an existing proteomics analysis pipeline. EigenMS is demonstrated using both large-scale calibration measurements and simulations to perform well relative to existing alternatives.
Availability: The software has been made available in the open source proteomics platform DAnTE (Polpitiya et al., 2008)) (http://omics.pnl.gov/software/), as well as in standalone software available at SourceForge (http://sourceforge.net).
Contact: yuliya@stat.tamu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases–schizophrenia as a case
Authors: Sun Jingchun , Jia Peilin , Fanous Ayman H. , Webb Bradley T. , van den Oord Edwin J.C.G. , Chen Xiangning , Bukszar Jozsef , Kendler Kenneth S. , Zhao Zhongming 
Published: July 2009

Abstract
Motivation: During the past decade, we have seen an exponential growth of vast amounts of genetic data generated for complex disease studies. Currently, across a variety of complex biological problems, there is a strong trend towards the integration of data from multiple sources. So far, candidate gene prioritization approaches have been designed for specific purposes, by utilizing only some of the available sources of genetic studies, or by using a simple weight scheme. Specifically to psychiatric disorders, there has been no prioritization approach that fully utilizes all major sources of experimental data.
Results: Here we present a multi-dimensional evidence-based candidate gene prioritization approach for complex diseases and demonstrate it in schizophrenia. In this approach, we first collect and curate genetic studies for schizophrenia from four major categories: association studies, linkage analyses, gene expression and literature search. Genes in these data sets are initially scored by category-specific scoring methods. Then, an optimal weight matrix is searched by a two-step procedure (core genes and unbiased P-values in independent genome-wide association studies). Finally, genes are prioritized by their combined scores using the optimal weight matrix. Our evaluation suggests this approach generates prioritized candidate genes that are promising for further analysis or replication. The approach can be applied to other complex diseases.
Availability: The collected data, prioritized candidate genes, and gene prioritization tools are freely available at http://bioinfo.mc.vanderbilt.edu/SZGR/.
Contact: zhongming.zhao@vanderbilt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Sieve Element Ca2+ Channels as Relay Stations between Remote Stimuli and Sieve Tube Occlusion inVicia faba
Authors: Furch Alexandra C.U. , van Bel Aart J.E. , Fricker Mark D. , Felle Hubert H. , Fuchs Maike , Hafke Jens B. 
Published: July 2009

AbstractDamage induces remote occlusion of sieve tubes in Vicia faba by forisome dispersion, triggered during the passage of an electropotential wave (EPW). This study addresses the role of Ca2+ channels and cytosolic Ca2+ elevation as a link between EPWs and forisome dispersion. Ca2+ channel antagonists affect the initial phase of the EPW as well as the prolonged plateau phase. Resting levels of sieve tube Ca2+ of ∼50 nM were independently estimated using Ca2+-selective electrodes and a Ca2+-sensitive dye. Transient changes in cytosolic Ca2+ were observed in phloem tissue in response to remote stimuli and showed profiles similar to those of EPWs. The measured elevation of Ca2+ in sieve tubes was below the threshold necessary for forisome dispersion. Therefore, forisomes need to be associated with Ca2+ release sites. We found an association between forisomes and endoplasmic reticulum (ER) at sieve plates and pore-plasmodesma units where high-affinity binding of a fluorescent Ca2+ channel blocker mapped an increased density of Ca2+ channels. In conclusion, propagation of EPWs in response to remote stimuli is linked to forisome dispersion through transiently high levels of parietal Ca2+, release of which depends on both plasma membrane and ER Ca2+ channels.
Arabidopsis tRNA Adenosine Deaminase Arginine Edits the Wobble Nucleotide of Chloroplast tRNAArg(ACG) and Is Essential for Efficient Chloroplast Translation
Authors: Delannoy Etienne , Le Ret Monique , Faivre-Nitschke Emmanuelle , Estavillo Gonzalo M. , Bergdoll Marc , Taylor Nicolas L. , Pogson Barry J. , Small Ian , Imbault Patrice , Gualberto José M. 
Published: July 2009

Abstract
RNA editing changes the coding/decoding information relayed by transcripts via nucleotide insertion, deletion, or conversion. Editing of tRNA anticodons by deamination of adenine to inosine is used both by eukaryotes and prokaryotes to expand the decoding capacity of individual tRNAs. This limits the number of tRNA species required for codon-anticodon recognition. We have identified the Arabidopsis thaliana gene that codes for tRNA adenosine deaminase arginine (TADA), a chloroplast tRNA editing protein specifically required for deamination of chloroplast (cp)-tRNAArg(ACG) to cp-tRNAArg(ICG). Land plant TADAs have a C-terminal domain similar in sequence and predicted structure to prokaryotic tRNA deaminases and also have very long N-terminal extensions of unknown origin and function. Biochemical and mutant complementation studies showed that the C-terminal domain is sufficient for cognate tRNA deamination both in vitro and in planta. Disruption of TADA has profound effects on chloroplast translation efficiency, leading to reduced yields of chloroplast-encoded proteins and impaired photosynthetic function. By contrast, chloroplast transcripts accumulate to levels significantly above those of wild-type plants. Nevertheless, absence of cp-tRNAArg(ICG) is compatible with plant survival, implying that two out of three CGN codon recognition occurs in chloroplasts, though this mechanism is less efficient than wobble pairing.
Mycobacterial antigen-induced T helper type 1 (Th1) and Th2 reactivity of peripheral blood mononuclear cells from diabetic and non-diabetic tuberculosis patients andMycobacterium bovisbacilli Calmette–Guérin (BCG)-vaccinated healthy subjects
Authors: Al-Attiyah R J , Mustafa A S 
Published: July 2009

SummaryPatients with diabetes mellitus are more susceptible to tuberculosis (TB), and the clinical conditions of diabetic TB patients deteriorate faster than non-diabetic TB patients, but the immunological basis for this phenomenon is not understood clearly. Given the role of cell-mediated immunity (CMI) in providing protection against TB, we investigated whether CMI responses in diabetic TB patients are compromised. Peripheral blood mononuclear cells (PBMC) obtained from diabetic TB patients, non-diabetic TB patients and Mycobacterium bovis bacilli Calmette–Guérin (BCG)-vaccinated healthy subjects were cultured in the presence of complex mycobacterial antigens and pools of M. tuberculosis regions of difference (RD)1, RD4, RD6 and RD10 peptides. The PBMC were assessed for antigen-induced cell proliferation and secretion of T helper 1 (Th1) [interferon (IFN)-γ, interleukin (IL)-2, tumour necrosis factor (TNF)-β], and Th2 (IL-4, IL-5, IL-10) cytokines as CMI parameters. All the complex mycobacterial antigens and RD1pool stimulated strong proliferation of PBMC of all groups, except moderate responses to RD1pool in healthy subjects. In response to complex mycobacterial antigens, both IFN-γ and TNF-β were secreted by PBMC of all groups whereas diabetic TB patients secreted IL-10 with concentrations higher than the other two groups. Furthermore, in response to RD peptides, IFN-γ and IL-10 were secreted by PBMC of diabetic TB patients only. The analyses of data in relation to relative cytokine concentrations showed that diabetic TB patients had lower Th1 : Th2 cytokines ratios, and a higher Th2 bias. The results demonstrate a shift towards Th2 bias in diabetic TB patients which may explain, at least in part, a faster deterioration in their clinical conditions.
Vitamin D and respiratory health
Authors: Hughes D A , Norton R 
Published: July 2009

Summary
Vitamin D is now known to be of physiological importance outside of bone health and calcium homeostasis, and there is mounting evidence that it plays a beneficial role in the prevention and/or treatment of a wide range of diseases. In this brief review the known effects of vitamin D on immune function are described in relation to respiratory health. Vitamin D appears capable of inhibiting pulmonary inflammatory responses while enhancing innate defence mechanisms against respiratory pathogens. Population-based studies showing an association between circulating vitamin D levels and lung function provide strong justification for randomized controlled clinical trials of vitamin D supplementation in patients with respiratory diseases to assess both efficacy and optimal dosage.