bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment of infantile Pompe disease with alglucosidase alpha: the UK experience
Authors: Chakrapani Anupam , Vellodi Ashok , Robinson Peter , Jones Simon , Wraith J. E. 
Published: September 2010

AbstractTreatment of infantile Pompe disease with recombinant human acid α‐glucosidase has shown substantial improvement in survival, and in cardiac, motor and respiratory functions. We analyzed the outcome of all patients with infantile Pompe disease treated in the United Kingdom since the availability of the enzyme, using a questionnaire‐based survey circulated to all treating centres. A total of 20 infants were treated from 2000 to 2009. Median ages at diagnosis and treatment were 5.75 months (range 0.25–31 months) and 6.5 months (0.5–32 months), respectively. Median duration of treatment was 31 months (1–102 months). Overall ventilator‐free survival was 35% (7/20 infants), while 35% (7/20) died at a median age of 10 months (5.75–15 months) and 30% (6/20) were alive but ventilator‐dependent. Endotracheal intubation for acute deterioration carried a high risk of failure of extubation and progression to long‐term ventilation (LTV), but elective general anaesthesia, in contrast, was well tolerated. Overall outcome was worse than in the pivotal clinical trials; possible causes include later diagnosis and treatment in our patients and a higher incidence of infants at the severe end of the clinical spectrum. Careful consideration must be given to all possible outcomes, including LTV, before commencing enzyme replacement therapy in newly diagnosed infants.
The Future of Rice Genomics: Sequencing the Collective Oryza Genome
Authors: Goicoechea Jose Luis , Ammiraju Jetty Siva S. , Marri Pradeep Reddy , Chen Mingsheng , Jackson Scott , Yu Yeisoo , Rounsley Steve , Wing Rod A. 
Published: September 2010

Abstract
The main objectives of the “Oryza Map Alignment Project” (OMAP) are to characterize the rice genome from a comparative standpoint by establishing a genus-wide and genome-scale comparative framework from representative species. Here, we report our progress in the analyses of these datasets and emerging “comparative phylogenomics” insights into Oryza evolution at two different resolutions—chromosomal and sequence levels. We demonstrate the abundance and impact of structural variations (SV) on genome diversity using African Oryza as a model. The molecular basis of SV was inferred using three genus-wide vertical sequence datasets. Combined, these data demonstrate that a single reference genome sequence for the genus Oryza is insufficient to comprehensively capture the genomic and allelic diversity present within the genus. Towards this end, we present a strategy to generate high-quality and cost-effective de novo reference sequences of collective Oryza. The application and broader scientific impact of the OMAP resources under an international cooperative effort (I-OMAP) are discussed.
Combined diffusion‐ and perfusion‐weighted imaging: a new way for the assessment of hemispheric transient ischemic attack patients
Authors: Tong Tong , Zhenwei Yao , Xiaoyuan Feng 
Published: September 2010

AbstractAbnormalities in diffusion‐weighted and perfusion‐weighted magnetic resonance images not only occur in stroke patients but also in transient ischemic attack patients. We found magnetic resonance images were abnormal in 28 patients (68%): 15 had diffusion‐weighted imaging abnormalities, 7 had both diffusion‐weighted imaging and perfusion‐weighted imaging defects and 6 had an isolated perfusion‐weighted imaging abnormality. Patients with shorter onset to magnetic resonance imaging, large artery atherothrombosis, coronary artery disease, hyperlipidemia and hemiparesis were more likely to show perfusion‐weighted imaging abnormalities. Compared with patients who had a good prognosis, in poor prognosis patients, the relative cerebral blood flow and relative cerebral blood volume was significantly higher. The data suggest that transient ischemic attack patients are more likely to have a poor prognosis when white matter of the symptomatic side shows hyperperfusion within 24 h of symptom onset; however, patients are more likely to have a good prognosis when white matter of the symptomatic side shows hypoperfusion.
More Than a Category: Han Supremacism on the Chinese Internet
Authors: Leibold James 
Published: September 2010

AbstractUsing the October 2008 slapping incident of historian Yan Chongnian 阎崇年 as a case study, this article attempts to contextualize and critically examine the articulation of Han supremacism on the Chinese internet. It demonstrates how an informal group of non-elite, urban youth are mobilizing the ancient Han ethnonym to challenge the Chinese Communist Party's official policy of multiculturalism, while seeking to promote pride and self-identification with the Han race (han minzu汉民族) to the exclusion of the non-Han minorities. In contrast to most of the Anglophone literature on Chinese nationalism, this article seeks to employ “Han” as a “boundary-spanner,” a category that turns our analysis of Chinese national identity formation on its head, side-stepping the “usual suspects” (intellectuals, dissidents and the state itself) and the prominent role of the “foreign other” in Chinese ethnogenesis, and instead probing the unstable plurality of the self/othering process in modern China and the role of the internet in opening up new spaces for non-mainstream identity articulation.
Nanjing's Failed “January Revolution” of 1967: The Inner Politics of a Provincial Power Seizure
Authors: Guoqiang Dong , Walder Andrew G. 
Published: September 2010

AbstractScholarship on factional warfare during the first two years of the Cultural Revolution has long portrayed a struggle between “conservative” factions that sought to preserve the status quo and “radical” factions that sought to transform it. Recent accounts, however, claim that the axis of political conflict was fundamentally transformed after the fall of civilian governments in early 1967, violating the central tenet of this interpretation. A close examination of Nanjing's abortive power seizure of January 1967 addresses this issue in some depth. The power seizure in fact was a crucial turning point: it removed the defenders of local authorities from the political stage and generated a split between two wings of the rebel movement that overthrew them. The political divisions among former rebel allies intensified and hardened in the course of tortuous negotiations in Beijing that were buffeted by confusing political shifts in the capital. This created a contest that was not between “conservatives” and “radicals” over the restoration of the status quo, but about the respective places of the rival radical factions in restored structures of authority.
The African Trading Community in Guangzhou: An Emerging Bridge for Africa–China Relations
Authors: Bodomo Adams 
Published: September 2010

AbstractThis article analyses an emerging African trading community in Guangzhou, China. It is argued that migrant communities such as this one act as linguistic, cultural and economic bridges between their source communities and their host communities, even in the midst of tensions created by incidents such as immigration restrictions and irregularities. Socio-linguistic and socio-cultural profiles of this community are built, through questionnaire surveys and interviews, to address issues such as why Africans go to Guangzhou, which African countries are represented, what languages are spoken there, how communication takes place between Africans and Chinese, what socio-economic contributions Africans in Guangzhou are making to the Chinese economy, and how the state reacts to this African presence. Following from the argument that this community acts as a bridge for Africa–China relations it is suggested that both the Chinese and the African governments should work towards eliminating the harassment of members in this community by many Guangzhou law enforcement officials and instead harness the contributions of this community to promote Africa–China socio-economic relations.
Towards community-based forest management in Southern Africa: do decentralization experiments work for local livelihoods?
Authors: MATOSE FRANK , WATTS SCOTNEY 
Published: September 2010

SUMMARYDifferences are emerging in decentralization of forest and community management in Zimbabwe, Mozambique and South Africa. This paper draws on case studies in each country to examine five aspects of their decentralization experience, namely forest tenure, new organizational structures, accountability and livelihood outcomes. Tenure arrangements developed as a result of decentralization are important for communities, as these determine the nature of access sanctioned by the state and security of the arrangements. The transfer of power to new organizations is proving to be a challenge. Experiences across the three case studies show that new committees were formed for these forestry initiatives by outside agencies and attempts were made to make them relevant to the way local communities managed forests. One of the main tenets of decentralization revolves around accountability of community representatives to their constituents rather than to the state. Although moves have been made to promote the accountability of community representatives, these have produced mixed results in Zimbabwe, Mozambique and South Africa. Only after changes in the approach taken by the state in Zimbabwe did community representatives become more accountable. In Mozambique, because of the special arrangements around the specific case, greater authority was given to community representatives, whereas, in South Africa, the state retained authority over representatives. Decentralization may bring benefits and improve communities' livelihoods from forestry activities, however much more still needs to be done by states in order for forests to take communities out of poverty.
Integrating governance and socioeconomic indicators to assess the performance of community-based natural resources management in Caprivi (Namibia)
Authors: COLLOMB J.G.E. , MUPETA P. , BARNES G. , CHILD B. 
Published: September 2010

SUMMARYThe achievements of community-based natural resources management (CBNRM) in southern Africa over the past 20 years have been hampered by the struggle to develop institutions of good governance. This paper explores what good governance is, how it can be measured and why it is relevant to communities' socioeconomic development goals. Horizontal accountability, used as a proxy for good governance, and people's perception of CBNRM benefits were documented through 236 individual interviews in five conservancies in the Caprivi Province (Namibia). These complex concepts were captured in order to strengthen performance assessments of CBNRM. Horizontal accountability was weak across the five conservancies studied and conservancy leaders could transfer more information to their constituents. Smaller and older conservancies displayed higher rates of information transfer, but horizontal accountability was not linked to different levels of socioeconomic benefits. In order to properly study the potential connections between good governance and the provision of socioeconomic benefits within CBNRM, the measures used in this study require further refinement.
Formal polytypic programs and proofs
Authors: VERBRUGGEN WENDY , DE VRIES EDSKO , HUGHES ARTHUR 
Published: September 2010

AbstractThe aim of our work is to be able to do fully formal, machine-verified proofs over Generic Haskell-style polytypic programs. In order to achieve this goal, we embed polytypic programming in the proof assistantCoqand provide an infrastructure for polytypic proofs. Polytypic functions are reified within Coq as a datatype and they can then be specialized by applying a dependently typed term specialization function. Polytypic functions are thus first-class citizens and can be passed as arguments or returned as results. Likewise, we reify polytypic proofs as a datatype and provide a lemma that a polytypic proof can be specialized to any datatype in the universe. The correspondence between polytypic functions and their polytypic proofs is very clear: programmers need to give proofs for, and only for, the same cases that they need to give instances for when they define the polytypic function itself. Finally, we discuss how to write (co)recursive functions and do (co)recursive proofs in a similar way that recursion is handled in Generic Haskell.
Polar Airborne Observations Fill Gap in Satellite Data
Authors: Koenig Lora , Martin Seelye , Studinger Michael , Sonntag John 
Published: September 2010

In October 2009, NASA's Ice, Cloud, and land Elevation Satellite (ICESat) stopped collecting science data. However, noting the progressive degradation of ICESat's Geoscience Laser Altimeter System (GLAS), NASA had begun the previous year to plan a series of instrumented aircraft missions to fill the impending gap in satellite observations due to the loss of GLAS. Called Operation IceBridge, the project has been collecting data since March 2009 and will continue until the scheduled launch of ICESat's replacement, ICESat‐2, in about 2015.The primary goal of IceBridge is to use airborne laser altimetry to monitor rapidly changing areas of ice sheets, glaciers, and sea ice; a secondary goal is to acquire ice‐penetrating‐radar data to map the bedrock topography beneath the ice sheets. Data collected by IceBridge will yield a three‐dimensional view of ice sheets and sea ice as they change. IceBridge will improve modeling efforts and knowledge of the contribution of the Greenland and Antarctic ice sheets to sea level rise. The project will also contribute to scientific understanding of changes in the extent and thickness of the sea ice cover as the planet warms. IceBridge flights maintain altimetry time series over outlet glaciers started by NASA in the early 1990s, expand airborne altimeter coverage to new areas, and add grids of ice‐penetrating‐radar data to better resolve bedrock topography.
Functional gene diversity of soil microbial communities from five oil-contaminated fields in China
Authors: Liang Yuting , Van Nostrand Joy D , Deng Ye , He Zhili , Wu Liyou , Zhang Xu , Li Guanghe , Zhou Jizhong 
Published: September 2010

Abstract
To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
Authors: Mariotti M. , Guigó R. 
Published: September 2010

Abstract
Motivation: Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins, UGA is recoded to Sec in presence of specific features on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks, and even known selenoproteins are often misannotated in genome databases.
Results: We present an homology-based in silico method to scan genomes for members of the known eukaryotic selenoprotein families: selenoprofiles. The core of the method is a set of manually curated highly reliable multiple sequence alignments of selenoprotein families, which are used as queries to scan genomic sequences. Results of the scan are processed through a number of steps, to produce highly accurate predictions of selenoprotein genes with little or no human intervention. Selenoprofiles is a valuable tool for bioinformatic characterization of eukaryotic selenoproteomes, and can complement genome annotation pipelines.
Availability and Implementation: Selenoprofiles is a python-built pipeline that internally runs psitblastn, exonerate, genewise, SECISearch and a number of custom-made scripts and programs. The program is available at http://big.crg.cat/services/selenoprofiles. The predictions presented in this article are available through DAS at http://genome.crg.cat:9000/das/Selenoprofiles_ensembl.
Contact: marco.mariotti@crg.es
Supplementary information: Supplementary data are available at Bioinformatics online.
girafe – an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads
Authors: Toedling Joern , Ciaudo Constance , Voinnet Olivier , Heard Edith , Barillot Emmanuel 
Published: September 2010

Abstract
Summary: The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these intervals. Moreover, the package operates within and extends the ever-growing Bioconductor framework and thus enables users to leverage a multitude of methods for their data in order to answer specific research questions.
Availability and Implementation: The R package girafe is available from the Bioconductor web site: http://www.bioconductor.org/packages/release/bioc/html/girafe.html
An extensive vignette and the Bioconductor mailing lists provide additional documentation and help for using the package.
Contact: joern.toedling@curie.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
Authors: Larget Bret R. , Kotha Satish K. , Dewey Colin N. , Ané Cécile 
Published: September 2010

Abstract
Motivation: BUCKy is a C++ program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors.
Availability: BUCKy is open source and distributed under the GNU general public license at www.stat.wisc.edu/∼ane/bucky/.
Contact: ane@stat.wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The binding site distance test score: a robust method for the assessment of predicted protein binding sites
Authors: Roche Daniel B. , Tetchner Stuart J. , McGuffin Liam J. 
Published: September 2010

Abstract
Motivation: We propose a novel method for scoring the accuracy of protein binding site predictions—the Binding-site Distance Test (BDT) score. Recently, the Matthews Correlation Coefficient (MCC) has been used to evaluate binding site predictions, both by developers of new methods and by the assessors for the community-wide prediction experiment—CASP8. While being a rigorous scoring method, the MCC does not take into account the actual 3D location of the predicted residues from the observed binding site. Thus, an incorrectly predicted site that is nevertheless close to the observed binding site will obtain an identical score to the same number of non-binding residues predicted at random. The MCC is somewhat affected by the subjectivity of determining observed binding residues and the ambiguity of choosing distance cutoffs. By contrast the BDT method produces continuous scores ranging between 0 and 1, relating to the distance between the predicted and observed residues. Residues predicted close to the binding site will score higher than those more distant, providing a better reflection of the true accuracy of predictions. The CASP8 function predictions were evaluated using both the MCC and BDT methods and the scores were compared. The BDT was found to strongly correlate with the MCC scores while also being less susceptible to the subjectivity of defining binding residues. We therefore suggest that this new simple score is a potentially more robust method for future evaluations of protein–ligand binding site predictions.
Availability: http://www.reading.ac.uk/bioinf/downloads/
Contact: l.j.mcguffin@reading.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
1. Regression Analysis of Multivariate Binary Response Variables Using Rasch-Type Models and Finite-Mixture Methods
Authors: Arminger Gerhard , Clogg Clifford C. , Cheng Tzuwei 
Published: September 2010

A model is considered for the regression analysis of multivariate binary data such as repeated-measures data (for example, panel data) or multiple-indicators with measures of some underlying characteristic such as attitude or ability (for example, surveys or tests). The model is related to the usual Rasch model, the usual latent-class model, and other familiar models such as logistic regression. In addition to a regression specification, the model includes parameters that describe heterogeneity not accounted for by the predictors. In contrast to most other approaches, a nonparametric specification of the latent mixing distribution is used, leading to a formulation based on scaled latent classes. We examine the relationship between this model and several other models, give a tractable formulation of the likelihood function and likelihood equations, present an algorithm for maximum-likelihood estimation, and analyze marginal and conditional latent structures. The approach is illustrated with longitudinal data from the German Socioeconomic Panel.