bluuebunny/crossref_metadata_2025_split huggingface dataset:
Motif discovery in physiological datasets
Authors: Syed Zeeshan , Stultz Collin , Kellis Manolis , Indyk Piotr , Guttag John 
Published: January 2010

In this article, we propose a methodology for identifying predictive physiological patterns in the absence of prior knowledge. We use the principle of conservation to identify activity that consistently precedes an outcome in patients, and describe a two-stage process that allows us to efficiently search for such patterns in large datasets. This involves first transforming continuous physiological signals from patients into symbolic sequences, and then searching for patterns in these reduced representations that are strongly associated with an outcome.
Our strategy of identifying conserved activity that is unlikely to have occurred purely by chance in symbolic data is analogous to the discovery of regulatory motifs in genomic datasets. We build upon existing work in this area, generalizing the notion of a regulatory motif and enhancing current techniques to operate robustly on non-genomic data. We also address two significant considerations associated with motif discovery in general: computational efficiency and robustness in the presence of degeneracy and noise. To deal with these issues, we introduce the concept of active regions and new subset-based techniques such as a two-layer Gibbs sampling algorithm. These extensions allow for a framework for information inference, where precursors are identified as approximately conserved activity of arbitrary complexity preceding multiple occurrences of an event.
We evaluated our solution on a population of patients who experienced sudden cardiac death and attempted to discover electrocardiographic activity that may be associated with the endpoint of death. To assess the predictive patterns discovered, we compared likelihood scores for motifs in the sudden death population against control populations of normal individuals and those with non-fatal supraventricular arrhythmias. Our results suggest that predictive motif discovery may be able to identify clinically relevant information even in the absence of significant prior knowledge.
Five Defining Issues: The International Classical Pentecostal/Roman Catholic Dialogue
Authors: McDonnell Kilian 
Published: January 2010

AbstractIn the previous article on the international Classical Pentecostal/Roman Catholic dialogue I looked at a range of issues affecting the conversations, reserving to this article a more focused look at five theological areas. The range of topics over the first three quinquennia is extensive and merits attention. The fourth is not complete and is at issue here only in an incidental way.1 In a preliminary way the two sides agree of the basic content of the Christian faith: trinity,2 the divinity of Christ, virgin birth, centrality of the death and resurrection of Jesus, Pentecost as constitutive of the church, forgiveness of sins, promise of eternal life. We may look at these areas differently, but there is a measure of agreement on them. Beyond these theological areas of basic Christian faith, a number of issues emerged in the first three quinquennia which define the dialogue and give it an unmistakable profile. In this essay, I treat five of these defining issues: the hermeneutical moment, infant and believers' baptism, baptism in the Holy Spirit, the church as koinonia, and Mary.
The Influence of Dr. J. E. Purdie's Reformed Anglican Theology on the Formation and Development of the Pentecostal Assemblies of Canada
Authors: Althouse Peter 
Published: January 2010

AbstractThe Pentecostal Assemblies of Canada (PAOC) has had many similarities with its United States counterpart, the Assemblies of God. In fact, in its early years the PAOC was affiliated with the Assemblies of God.1 Yet the PAOC was unique in that it had a friendly relationship with the Anglican Church of Canada2 vis-à-vis the Toronto low-church Anglican theological school, Wycliffe College.3 This relationship centered on one man, a Wycliffe College graduate and Anglican priest, who was asked to be principal of the first Canadian Pentecostal Bible school in 1925, a position he held until 1950. This man was James Eustace Purdie, arguably the most influential person in the formation and development of PAOC doctrine through the theological education of Pentecostal ministers.4
Cameroonian light on the propagation of Christianity in Kenjo Jumbam's The white man of God
Authors: Hale F. 
Published: January 2010

AbstractIn this article the author shows how the arrival of Christianity in Cameroon is portrayed in the work of Cameroonian writer KenjoJumbam. Writing some time after independence, Jumbam's work (especially The White man of God) exhibits a balanced valuation of Christian missionary work in contrast to other Cameroonian authors writing around the time of independence who displayed a more negative valuation of Christianity as a result of anti-colonialist feelings. In Jumbam's portrayal of the work of Christian missionaries the issue of inculturation of Christianity in indigenous culture is also raised.
Situating biblical narrative studies in literary theory and literary approaches
Authors: de Klerk Johannes C 
Published: January 2010

AbstractIn literary studies of biblical texts one often encounters amazing ignorance of the intricacies of literary theory and the complexity of literary issues. This article addresses this problem from the viewpoint of biblical narrative studies. General trends of these studies are discussed, then biblical narrative studies are situated in the phenomena of 'literature', and consequently in narrative theories and some crucial literary issues. Finally the article focuses on whether biblical narrative studies should persist in an old-fashioned literary approach, and some cardinal pointers ahead are presented.
Proposing the Simplification of the Multilayer Urban Canopy Model: Intercomparison Study of Four Models
Authors: Ikeda Ryosaku , Kusaka Hiroyuki 
Published: January 2010

AbstractThe study proposes the simplification of the multilayer urban canopy model. Four types of multilayer urban canopy models—level 4, level 3, level 2, and level 1—are developed to reduce the computational load of the heat budget calculations at the wall surface. The level 4 model, which accounts for the wall directions and the vertical layer, is simplified in three ways: the level 3 model only accounts for the vertical layers, the level 2 model accounts for the wall directions, and the level 1 model accounts for neither the wall directions nor the vertical layer. From the simplification, compared to the level 4 model, the memory is reduced by 57%, 65%, and 72% for the level 3–level 1 models, respectively, when the vertical canopy layer is seven. At the same time, the CPU time is reduced by 67%, 70%, and 78% for the level 3–level 1 models. Then, each canopy model is compared with observations in Tokyo. The results show that the simulations from the four models are close to the observed ones, and the differences among the four models are very small. An additional model intercomparison study based on idealized simulations indicates that the level 3 model can be used instead of the level 4 model in any condition, whereas the level 2 and level 1 models are proposed to be used under conditions with a large sky view factor.
The Role of Entrainment in the Diurnal Cycle of Continental Convection
Authors: Del Genio Anthony D. , Wu Jingbo 
Published: January 2010

Abstract
In continental convective environments, general circulation models typically produce a diurnal cycle of rainfall that peaks close to the noon maximum of insolation, hours earlier than the observed peak. One possible reason is insufficient sensitivity of their cumulus parameterizations to the state of the environment due to weak entrainment. The Weather Research and Forecasting (WRF) model, run at cloud-resolving (600 and 125 m) resolution, is used to study the diurnal transition from shallow to deep convection during the monsoon break period of the Tropical Warm Pool–International Cloud Experiment. The WRF model develops a transition from shallow to deep convection in isolated events by 1430–1500 local time. The inferred entrainment rate weakens with increasing time of day as convection deepens. Several current cumulus parameterizations are tested for their ability to reproduce the WRF behavior. The Gregory parameterization, in which entrainment rate varies directly with parcel buoyancy and inversely as the square of the updraft speed, is the best predictor of the inferred WRF entrainment profiles. The Gregory scheme depends on a free parameter that represents the fraction of buoyant turbulent kinetic energy generation on the cloud scale that is consumed by the turbulent entrainment process at smaller scales. A single vertical profile of this free parameter, increasing with height above the boundary layer but constant with varying convection depth, produces entrainment rate profiles consistent with those inferred from the WRF over the buoyant depth of the convection. Parameterizations in which entrainment varies inversely with altitude or updraft speed or increases with decreasing tropospheric relative humidity do not perform as well. Entrainment rate at cloud base decreases as convection depth increases; this behavior appears to be related to an increase in vertical velocity at downdraft cold pool edges.
A Nonparametric Postprocessor for Bias Correction of Hydrometeorological and Hydrologic Ensemble Forecasts
Authors: Brown James D. , Seo Dong-Jun 
Published: January 2010

AbstractThis paper describes a technique for quantifying and removing biases from ensemble forecasts of hydrometeorological and hydrologic variables. The technique makes no a priori assumptions about the distributional form of the variables, which is often unknown or difficult to model parametrically. The aim is to estimate the conditional cumulative distribution function (ccdf) of the observed variable given a (possibly biased) real-time ensemble forecast. This ccdf represents the “true” probability distribution of the forecast variable, subject to sampling uncertainties. In the absence of a known distributional form, the ccdf should be estimated nonparametrically. It is noted that the probability of exceeding a threshold of the observed variable, such as flood stage, is equivalent to the expectation of an indicator variable defined for that threshold. The ccdf is then modeled through a linear combination of the indicator variables of the forecast ensemble members. The technique is based on Bayesian optimal linear estimation of indicator variables and is analogous to indicator cokriging (ICK) in geostatistics. By developing linear estimators for the conditional expectation of the observed variable at many thresholds, ICK provides a discrete approximation of the full ccdf. Since ICK minimizes the conditional error variance of the indicator variable at each threshold, it effectively minimizes the continuous ranked probability score (CRPS) when infinitely many thresholds are employed. The technique is used to bias-correct precipitation ensemble forecasts from the NCEP Global Ensemble Forecast System (GEFS) and streamflow ensemble forecasts from the National Weather Service (NWS) River Forecast Centers (RFCs). Split-sample validation results are presented for several attributes of ensemble forecast quality, including reliability and discrimination. In general, the forecast biases were substantially reduced following ICK. Overall, the technique shows significant potential for bias-correcting ensemble forecasts whose distributional form is unknown or nonparametric.
Error Analysis and Sampling Strategy Design for Using Fixed or Mobile Platforms to Estimate Ocean Flux
Authors: Zhang Yanwu , Bellingham James G. , Chao Yi 
Published: January 2010

Abstract
For estimating lateral flux in the ocean using fixed or mobile platforms, the authors present a method of analyzing the estimation error and designing the sampling strategy. When an array of moorings is used, spatial aliasing leads to an error in flux estimation. When an autonomous underwater vehicle (AUV) is run, measurements along its course are made at different times. Such nonsynopticity in the measurements leads to an error in flux estimation. It is assumed that the temporal–spatial autocovariance function of the flux variable can be estimated from historical data or ocean models (as in this paper). Using the temporal–spatial autocovariance function of the flux variable, the mean-square error of the flux estimate by fixed or mobile platforms is derived. The method is used to understand the relative strengths of moorings and AUVs (assumed here to be able to maintain constant speed) under different scenarios of temporal and spatial variabilities. The flux estimate by moorings through trapezoidal approximation generally carries a bias that drops quadratically with the number of moorings. The authors also show that a larger number of slower AUVs may achieve a more accurate flux estimate than a smaller number of faster AUVs under the same cumulative speed, but the performance margin shrinks with the increase of the cumulative speed. Using the error analysis results, one can choose the type of platforms and optimize the sampling strategy under resource constraints. To verify the theoretical analysis, the authors run simulated surveys in synthesized ocean fields. The flux estimation errors agree very well with the analytical predictions. Using an ocean model dataset, the authors estimate the lateral heat flux across a section in Monterey Bay, California, and also compare the flux estimation errors with the analytical predictions.
Measuring aid governance in developing countries: an application to post-tsunami Aceh, Indonesia
Authors: Brassard Caroline 
Published: January 2010

In contrast to the popular debate on managing international aid to achieve good governance in developing countries, this article focuses on ensuring good governance of aid processes (or good aid governance) between partners in development, to achieve national and local development objectives. Starting with the case of the reconstruction process in Aceh, Indonesia, since the December 2004 tsunami, the article draws conclusions on the aid governance challenges involved when coordinating multiple stakeholders and projects, while taking into consideration the complexities of the local political economy. Taking a critical look at the indicators of aid effectiveness developed from the Paris Declaration in 2005, the article argues for the use of a more relevant, simple and realistic set of locally generated aid governance indicators to achieve the desired development outcomes. Points for practitioners Partners in development need to shift their focus from aid for good governance, to ensuring good governance of aid processes (or good aid governance) in order to achieve national and local development objectives. Despite mixed evidence, current aid effectiveness frameworks such as the Paris Declaration of 2005 still implicitly suggest that good governance is a pre-requisite to development. The concept and measurement of aid governance by donors and country recipients, as partners in the design, delivery, implementation and management of aid, will vary according to local contexts. In a participatory manner, partners must develop a simple, clear and locally generated measurement framework to provide evidence on aid governance. This framework requires focusing on aid processes and outcomes in a collaborative effort between partners involved in the management and administration of aid, as well as with implementers at the local level.
Analysis of novel sph (spherocytosis) alleles in mice reveals allele-specific loss of band 3 and adducin in α-spectrin–deficient red cells
Authors: Robledo Raymond F. , Lambert Amy J. , Birkenmeier Connie S. , Cirlan Marius V. , Cirlan Andreea Flavia M. , Campagna Dean R. , Lux Samuel E. , Peters Luanne L. 
Published: January 2010

AbstractFive spontaneous, allelic mutations in the α-spectrin gene, Spna1, have been identified in mice (spherocytosis [sph], sph1J, sph2J, sph2BC, sphDem). All cause severe hemolytic anemia. Here, analysis of 3 new alleles reveals previously unknown consequences of red blood cell (RBC) spectrin deficiency. In sph3J, a missense mutation (H2012Y) in repeat 19 introduces a cryptic splice site resulting in premature termination of translation. In sphIhj, a premature stop codon occurs (Q1853Stop) in repeat 18. Both mutations result in markedly reduced RBC membrane spectrin content, decreased band 3, and absent β-adducin. Reevaluation of available, previously described sph alleles reveals band 3 and adducin deficiency as well. In sph4J, a missense mutation occurs in the C-terminal EF hand domain (C2384Y). Notably, an equally severe hemolytic anemia occurs despite minimally decreased membrane spectrin with normal band 3 levels and present, although reduced, β-adducin. The severity of anemia in sph4J indicates that the highly conserved cysteine residue at the C-terminus of α-spectrin participates in interactions critical to membrane stability. The data reinforce the notion that a membrane bridge in addition to the classic protein 4.1-p55-glycophorin C linkage exists at the RBC junctional complex that involves interactions between spectrin, adducin, and band 3.
A benchmark for statistical microarray data analysis that preserves actual biological and technical variance
Authors: De Hertogh Benoît , De Meulder Bertrand , Berger Fabrice , Pierre Michael , Bareke Eric , Gaigneaux Anthoula , Depiereux Eric 
Published: January 2010

Abstract

Background
Recent reanalysis of spike-in datasets underscored the need for new and more accurate benchmark datasets for statistical microarray analysis. We present here a fresh method using biologically-relevant data to evaluate the performance of statistical methods.

Results
Our novel method ranks the probesets from a dataset composed of publicly-available biological microarray data and extracts subset matrices with precise information/noise ratios. Our method can be used to determine the capability of different methods to better estimate variance for a given number of replicates. The mean-variance and mean-fold change relationships of the matrices revealed a closer approximation of biological reality.

Conclusions
Performance analysis refined the results from benchmarks published previously.
We show that the Shrinkage t test (close to Limma) was the best of the methods tested, except when two replicates were examined, where the Regularized t test and the Window t test performed slightly better.

Availability
The R scripts used for the analysis are available at http://urbm-cluster.urbm.fundp.ac.be/~bdemeulder/.
Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets
Authors: Scharfe Michael , Pielot Rainer , Schreiber Falk 
Published: January 2010

Abstract

Background
Solving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks.

Results
We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de.

Conclusions
The results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics.
Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines
Authors: Gutiérrez Andrés Gonzalo , Carabalí Silvio James , Giraldo Olga Ximena , Martínez César Pompilio , Correa Fernando , Prado Gustavo , Tohme Joe , Lorieux Mathias 
Published: January 2010

Abstract

Background
Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs.

Results
We built a set of 64 chromosome segment substitution lines carrying contiguous chromosomal segments of African rice Oryza glaberrima MG12 (acc. IRGC103544) in the genetic background of Oryza sativa ssp. tropical japonica (cv. Caiapó). Well-distributed simple-sequence repeats markers were used to characterize the introgression events. Average size of the substituted chromosomal segments in the substitution lines was about 10 cM and covered the whole donor genome, except for small regions on chromosome 2 and 4. Proportions of recurrent and donor genome in the substitution lines were 87.59% and 7.64%, respectively. The remaining 4.78% corresponded to heterozygotes and missing data. Strong segregation distortion was found on chromosomes 3 and 6, indicating the presence of interspecific sterility genes. To illustrate the advantages and the power of quantitative trait loci (QTL) detection using substitution lines, a QTL detection was performed for scored traits. Transgressive segregation was observed for several traits measured in the population. Fourteen QTLs for plant height, tiller number per plant, panicle length, sterility percentage, 1000-grain weight and grain yield were located on chromosomes 1, 3, 4, 6 and 9. Furthermore, a highly significant QTL controlling resistance to the Rice stripe necrosis virus was located between SSR markers RM202-RM26406 (44.5-44.8 cM) on chromosome 11.

Conclusions
Development and phenotyping of CSSL libraries with entire genome coverage represents a useful strategy for QTL discovery. Mapping of the RSNV locus represents the first identification of a genetic factor underlying resistance to this virus. This population is a powerful breeding tool. It also helps in overcoming hybrid sterility barriers between species of rice.