bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Genes Particularly Sensitive to Lipopolysaccharide (LPS) in Human Monocytes Induced by Wild-Type versus LPS-DeficientNeisseria meningitidisStrains
Authors: Øvstebø Reidun , Olstad Ole Kristoffer , Brusletto Berit , Møller Anne Sophie , Aase Audun , Haug Kari Bente Foss , Brandtzaeg Petter , Kierulf Peter 
Published: March 2008

ABSTRACTLipopolysaccharide (LPS) in the outer membrane ofNeisseria meningitidisplays a dominant role as an inflammation-inducing molecule in meningococcal disease. We have used microarray analysis to study the global gene expression after exposure of human monocytes for 3 h to wild-typeN. meningitidis(106), LPS-deficientN. meningitidis(106and 108), and purifiedN. meningitidisLPS (1 ng [33 endotoxin units]/ml) to identify LPS-inducible genes. Wild-typeN. meningitidis(106) induced 4,689 differentially expressed genes, compared with 72 differentially expressed genes induced by 106LPS-deficientN. meningitidisorganisms. However, 108LPS-deficientN. meningitidisorganisms induced 3,905 genes, indicating a dose-response behavior of non-LPS cell wall molecules. A comparison of the gene expression patterns from 106wild-typeN. meningitidisand 108LPS-deficientN. meningitidisorganisms showed that 2,401 genes in human monocytes were not strictly LPS dependent. A list of “particularly LPS-sensitive” genes (2,288), differentially induced by 106wild-typeN. meningitidisbut not by 108LPS-deficientN. meningitidisorganisms, showed an early expression of beta interferon (IFN-β), most likely through the Toll-like receptor-MyD88-independent pathway. Subsequently, IFN-β may activate the type I IFN signaling pathway, and an unknown number of IFN-β-inducible genes, such as those for CXCL9, CXCL10, CXCL11, IFIT1, IFIT2, IFIT3, and IFIT5, are transcribed. Supporting this, human monocytes secreted significantly higher levels of CXCL10 and CXCL11 when stimulated by 106wild-typeN. meningitidisorganisms than when stimulated by 108LPS-deficientN. meningitidisorganisms. Plasma CXCL10, but not CXCL11, was positively correlated (r= 0.67;P< 0.01) to LPS in patients (n= 24) with systemic meningococcal disease. Thus, new circulating biomarkers in meningococcal disease may be suggested through LPS-induced gene expression changes in human monocytes.
Drought Index Mapping at Different Spatial Units
Authors: Rhee Jinyoung , Carbone Gregory J. , Hussey James 
Published: March 2008

AbstractThis paper investigates the influence of spatial interpolation and aggregation of data to depict drought at different spatial units relevant to and often required for drought management. Four different methods for drought index mapping were explored, and comparisons were made between two spatial operation methods (simple unweighted average versus spatial interpolation plus aggregation) and two calculation procedures (whether spatial operations are performed before or after the calculations of drought index values). Deterministic interpolation methods including Thiessen polygons, inverse distance weighted, and thin-plate splines as well as a stochastic and geostatistical interpolation method of ordinary kriging were compared for the two methods that use interpolation. The inverse distance weighted method was chosen based on the cross-validation error. After obtaining drought index values for different spatial units using each method in turn, differences in the empirical binned frequency distributions were tested between the methods and spatial units. The two methods using interpolation and aggregation introduced fewer errors in cross validation than the two simple unweighted average methods. Whereas the method performing spatial interpolation and aggregation before calculating drought index values generally provided consistent drought information between various spatial units, the method performing spatial interpolation and aggregation after calculating drought index values reduced errors related to the calculations of precipitation data.
Sources of Eddy Energy Simulated by a Model of the Northeast Pacific Ocean
Authors: Shore Jennifer , Stacey Michael W. , Wright Daniel G. 
Published: March 2008

Abstract
This paper examines the energy sources for eddy variability in the Gulf of Alaska using a numerical model and a novel form of data assimilation referred to as spectral nudging. Spectral nudging is distinguished from conventional nudging by its ability to operate only on specified frequency and wavenumber bands; in the present case, only the subannual variability is nudged, and only on spatial scales of 100 km or more. By using this approach, the broad-brush aspects of the model’s mean state are constrained to remain near the mean climatological conditions, while the simulated eddy field is determined by the model dynamics. Simulations of the North Pacific Ocean with a 0.25° horizontal resolution and spectral nudging have been previously shown to produce eddy fields that are significantly more energetic and more realistic than those produced by prognostic (i.e., not nudged) simulations. The analysis of the spectrally nudged model results undertaken here reveals the tendency of the circulation to be both baroclinically and barotropically unstable in different regions and to differing degrees. Along the north coast of the Gulf of Alaska, the simulation suggests that barotropic instability is more important overall as an energy source for eddies than is baroclinic instability. Along the east coast of the Gulf of Alaska, the simulation suggests that both baroclinic and barotropic instabilities are important. Although the overall energy transfer is from the mean state to the eddy field, there are regions of the model, particularly along the north coast of the Gulf of Alaska, where the transfer of energy is from the eddy field to the mean flow.
Problems Experienced By Administrators in Conducting Systematic Planning for Social Service Agencies
Authors: Eldridge William D. 
Published: March 2008

At a time in the history of social services where demands for accountability place increasing pressure on agency administrators and planners, a discussion of problems in organizing and conducting effective planning activities may create awareness of typical errors in logical and relevant decision making in establishing goals and objectives for agency programs. This discussion will focus on frequently observed difficulties in seleeting and utilizing planning teams, discovering and properly assessing agency data, and using creative and open-minded perspectives in defining tasks and arenas for flexible program planning. Along with this outline of problem areas, the author will also suggest some simple methods to avoid common roadblocks, and to more effectively utilize staff input, agency information and logical decision making processes to engineer sound programs as a result of good planning.
Conceptual Frame Work On Self-Reliance in Community Development in Zimbabwe
Authors: Agere Samuel Takarinda 
Published: March 2008

[Development theory and policy have been the subject of discussion in both the developed and the under-developed countries. The implementation of these policies have varied from one country to another. The central and critical question that is often raised is whether there is development among and within the poorest sections of society. The new trend in development process particularly in the third world countries, is that, citizens should be involved in decision making, planning and implementation of programmes of action. This paper provides a critical analysis of various theories of development and shows through examples, how they have failed in third world countries. An alternative self-reliant development strategy is examined and recommended within the economic, political and social conditions prevailing in Zimbabwe. Community Development is suggested as an important instrument of facilitating and accelerating the development process. The use of external aid is not encouraged because it does not trickle down to the poor section of society. Further, aid does not help to bring about fundamental structural changes within society. Inequality between regions and more importantly between men and women is not tackled very effectively and meaningfully by external aid. Aid, like technology may not be neutral and may reflect the political ideals and economic interests of the donor countries. Self-reliance inevitably implies the formation of self-help organisations through which development projects can be implemented and realised. For self-help organiza tions to be successful, certain political, economic and social conditions have to be met. Human and financial resources need to be committed by the Central Government to build the social infrastructure that will facilitate the development process. The question of who participates in decision-making is discussed and recommenda tion is made that the beneficiaries or the direct consumers of the service should be involved in the identification of problems and implementation of projects. On the whole, emphasis is placed on qualitative rather than quantitative aspect of development. This is very pertinent in community development which aims at the promotion of the quality of life of the majority of people in the country.]
Maternal Health Care Problems in Rural Communities, Korea
Authors: Suh Edward K. 
Published: March 2008

[In recent years, overall health conditions in Korea seem to be gradually improving along with the relatively rapid growth of the national economy and the continuing efforts of social development. The rural health situation, however, is still far behind that of many other developing nations. The author especially made an attempt not only to describe the maternal health care problems such as mortality, morbidity, and utilization of health care services which exist today in rural communities of South Korea, but also to make suggestions as to the ways of improving the conditions of the health care services.]
Social Workers' Attitudes Towards Public Accountability
Authors: Sung Kyu-taik 
Published: March 2008

The public demand for accountability of human services has been increasing in the United States. Despite the growing importance of public accountability as a special responsibility of social workers, little information is available in U.S. on how these pro fessionals react to the implementation of accountability programs. The survey reported in this paper was made to explore the attitudes of social workers in U.S. hospitals toward PSRO, a nationwide health care service review system. The paper presents a descriptive overview of significant aspects of American social workers' personal attitudes toward various issues of current concern about this accountability system.
Computational evaluation of TIS annotation for prokaryotic genomes
Authors: Hu Gang-Qing , Zheng Xiaobin , Ju Li-Ning , Zhu Huaiqiu , She Zhen-Su 
Published: March 2008

Abstract

Background
Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks.

Results
Based on a homogeneity assumption that gene translation-related signals are uniformly distributed across a genome, we have established a computational method for a large-scale quantitative assessment of the reliability of TIS annotations for any prokaryotic genome. The method consists of modeling a positional weight matrix (PWM) of aligned sequences around predicted TISs in terms of a linear combination of three elementary PWMs, one for true TIS and the two others for false TISs. The three elementary PWMs are obtained using a reference set with highly reliable TIS predictions. A generalized least square estimator determines the weighting of the true TIS in the observed PWM, from which the accuracy of the prediction is derived. The validity of the method and the extent of the limitation of the assumptions are explicitly addressed by testing on experimentally verified TISs with variable accuracy of the reference sets. The method is applied to estimate the accuracy of TIS annotations that are provided on public databases such as RefSeq and ProTISA and by programs such as EasyGene, GeneMarkS, Glimmer 3 and TiCo. It is shown that RefSeq's TIS prediction is significantly less accurate than two recent predictors, Tico and ProTISA. With convincing proofs, we show two general preferential biases in the RefSeq annotation, i.e. over-annotating the longest open reading frame (LORF) and under-annotating ATG start codon. Finally, we have established a new TIS database, SupTISA, based on the best prediction of all the predictors; SupTISA has achieved an average accuracy of 92% over all 532 complete genomes.

Conclusion
Large-scale computational evaluation of TIS annotation has been achieved. A new TIS database much better than RefSeq has been constructed, and it provides a valuable resource for further TIS studies.
The evolution of core proteins involved in microRNA biogenesis
Authors: Murphy Dennis , Dancis Barry , Brown James R 
Published: March 2008

Abstract

Background
MicroRNAs (miRNAs) are a recently discovered class of non-coding RNAs (ncRNAs) which play important roles in eukaryotic gene regulation. miRNA biogenesis and activation is a complex process involving multiple protein catalysts and involves the large macromolecular RNAi Silencing Complex or RISC. While phylogenetic analyses of miRNA genes have been previously published, the evolution of miRNA biogenesis itself has been little studied. In order to better understand the origin of miRNA processing in animals and plants, we determined the phyletic occurrences and evolutionary relationships of four major miRNA pathway protein components; Dicer, Argonaute, RISC RNA-binding proteins, and Exportin-5.

Results
Phylogenetic analyses show that all four miRNA pathway proteins were derived from large multiple protein families. As an example, vertebrate and invertebrate Argonaute (Ago) proteins diverged from a larger family of PIWI/Argonaute proteins found throughout eukaryotes. Further gene duplications among vertebrates after the evolution of chordates from urochordates but prior to the emergence of fishes lead to the evolution of four Ago paralogues. Invertebrate RISC RNA-binding proteins R2D2 and Loquacious are related to other RNA-binding protein families such as Staufens as well as vertebrate-specific TAR (HIV trans-activator RNA) RNA-binding protein (TRBP) and protein kinase R-activating protein (PACT). Export of small RNAs from the nucleus, including miRNA, is facilitated by three closely related karyopherin-related nuclear transporters, Exportin-5, Exportin-1 and Exportin-T. While all three exportins have direct orthologues in deutrostomes, missing exportins in arthropods (Exportin-T) and nematodes (Exportin-5) are likely compensated by dual specificities of one of the other exportin paralogues.

Conclusion
Co-opting particular isoforms from large, diverse protein families seems to be a common theme in the evolution of miRNA biogenesis. Human miRNA biogenesis proteins have direct, orthologues in cold-blooded fishes and, in some cases, urochordates and deutrostomes. However, lineage specific expansions of Dicer in plants and invertebrates as well as Argonaute and RNA-binding proteins in vertebrates suggests that novel ncRNA regulatory mechanisms can evolve in relatively short evolutionary timeframes. The occurrence of multiple homologues to RNA-binding and Argonaute/PIWI proteins also suggests the possible existence of further pathways for additional types of ncRNAs.
Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer
Authors: Wang Chun Ming , Lo Loong Chueng , Feng Felicia , Gong Ping , Li Jian , Zhu Ze Yuan , Lin Grace , Yue Gen Hua 
Published: March 2008

Abstract

Background
Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for specific traits, genomic large insert libraries are of crucial importance. We reported herein a bacterial artificial chromosome (BAC) library and the mapping of BAC clones to the linkage map.

Results
This BAC library consisted of 49,152 clones with an average insert size of 98 kb, representing 6.9-fold haploid genome coverage. Screening the library with 24 microsatellites and 15 ESTs/genes demonstrated that the library had good genome coverage. In addition, 62 novel microsatellites each isolated from 62 BAC clones were mapped onto the first generation linkage map. A total of 86 BAC clones were anchored on the linkage map with at least one BAC clone on each linkage group.

Conclusion
We have constructed the first BAC library for L. calcarifer and mapped 86 BAC clones to the first generation linkage map. This BAC library and the improved linkage map with 302 DNA markers not only supply an indispensable tool to the integration of physical and linkage maps, the fine mapping of QTL and map based cloning genes located in QTL of commercial importance, but also contribute to comparative genomic studies and eventually whole genome sequencing.
Charge environments around phosphorylation sites in proteins
Authors: Kitchen James , Saunders Rebecca E , Warwicker Jim 
Published: March 2008

Abstract

Background
Phosphorylation is a central feature in many biological processes. Structural analyses have identified the importance of charge-charge interactions, for example mediating phosphorylation-driven allosteric change and protein binding to phosphopeptides. Here, we examine computationally the prevalence of charge stabilisation around phosphorylated sites in the structural database, through comparison with locations that are not phosphorylated in the same structures.

Results
A significant fraction of phosphorylated sites appear to be electrostatically stabilised, largely through interaction with sidechains. Some examples of stabilisation across a subunit interface are evident from calculations with biological units. When considering the immediately surrounding environment, in many cases favourable interactions are only apparent after conformational change that accompanies phosphorylation. A simple calculation of potential interactions at longer-range, applied to non-phosphorylated structures, recovers the separation exhibited by phosphorylated structures. In a study of sites in the Phospho.ELM dataset, for which structural annotation is provided by non-phosphorylated proteins, there is little separation of the known phospho-acceptor sites relative to background, even using the wider interaction radius. However, there are differences in the distributions of patch polarity for acceptor and background sites in the Phospho.ELM dataset.

Conclusion
In this study, an easy to implement procedure is developed that could contribute to the identification of phospho-acceptor sites associated with charge-charge interactions and conformational change. Since the method gives information about potential anchoring interactions subsequent to phosphorylation, it could be combined with simulations that probe conformational change. Our analysis of the Phospho.ELM dataset also shows evidence for mediation of phosphorylation effects through (i) conformational change associated with making a solvent inaccessible phospho-acceptor site accessible, and (ii) modulation of protein-protein interactions.
Moderators of the intention-behaviour and perceived behavioural control-behaviour relationships for leisure-time physical activity
Authors: Amireault Steve , Godin Gaston , Vohl Marie-Claude , Pérusse Louis 
Published: March 2008

Abstract

Background
Intention is a key determinant of action. However, there is a gap between intention and behavioural performance that remains to be explained. Therefore, the aim of this study was to identify moderators of the intention-behaviour and perceived behavioural control (PBC)- behaviour relationships for leisure-time physical activity.

Method
This was tested in reference to Ajzen's Theory of Planned Behaviour. A sample of 300 volunteers, 192 women and 108 men, aged 18 to 55, participated in the study. At baseline, the participants completed a self-administrated psychosocial questionnaire assessing Ajzen's theory variables (i.e., intention and perceived behavioural control). The behavioural measure was obtained by mail three months later.

Results
Multiple hierarchical regression analyses indicated that age and annual income moderated the intention-behaviour and PBC-behaviour relationships. However, in the final model predicting behaviour (R2 = .46), only the interaction term of PBC by annual income (β = .24, p = 0.0003) significantly contributed to the prediction of behaviour along with intention (β = .49, p = 0.0009) and past behaviour (β = .44, p < 0.0001).

Conclusion
Physical activity promotion programs would benefit not only from focusing on increasing the intention of low intenders, but also from targeting factors that moderate the perceived behavioural control-behaviour relationships.
Endogenous retroviruses of the chicken genome
Authors: Huda Ahsan , Polavarapu Nalini , Jordan I King , McDonald John F 
Published: March 2008

Abstract

Abstract
We analyzed the chicken (Gallus gallus) genome sequence to search for previously uncharacterized endogenous retrovirus (ERV) sequences using ab initio and combined evidence approaches. We discovered 11 novel families of ERVs that occupy more than 21 million base pairs, approximately 2%, of the chicken genome. These novel families include a number of recently active full-length elements possessing identical long terminal repeats (LTRs) as well as intact gag and pol open reading frames. The abundance and diversity of chicken ERVs we discovered underscore the utility of an approach that combines multiple methods for the identification of interspersed repeats in vertebrate genomes.

Reviewers
This article was reviewed by Igor Zhulin and Itai Yanai.
A sequence-based survey of the complex structural organization of tumor genomes
Authors: Raphael Benjamin J , Volik Stanislav , Yu Peng , Wu Chunxiao , Huang Guiqing , Linardopoulou Elena V , Trask Barbara J , Waldman Frederic , Costello Joseph , Pienta Kenneth J , Mills Gordon B , Bajsarowicz Krystyna , Kobayashi Yasuko , Sridharan Shivaranjani , Paris Pamela L , Tao Quanzhou , Aerni Sarah J , Brown Raymond P , Bashir Ali , Gray Joe W , Cheng Jan-Fang , de Jong Pieter , Nefedov Mikhail , Ried Thomas , Padilla-Nash Hesed M , Collins Colin C 
Published: March 2008

Abstract
Background
The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes.

Results
In the present study brain, breast, ovary, and prostate tumors, along with three breast cancer cell lines, were surveyed using end sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization confirmed translocations and complex tumor genome structures that include co-amplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms revealed candidate somatic mutations and an elevated rate of novel single nucleotide polymorphisms in an ovarian tumor.

Conclusion
These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than was previously appreciated and that genomic fusions, including fusion transcripts and proteins, may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.