bluuebunny/crossref_metadata_2025_split huggingface dataset:
DEMOCRATIC LEGITIMATION OF DELEGATED LEGISLATION—A COMPARATIVE VIEW ON THE AMERICAN, BRITISH AND GERMAN LAW
Authors: Pünder Hermann 
Published: April 2009

AbstractThis article addresses the problem of democratic legitimacy posed by the executive branch's use of delegated legislative powers. After some remarks on the need for delegated legislation and the problem of legitimation the study identifies in a comparative perspective three approaches of ensuring that delegated legislation carries sufficient democratic legitimation. A first means of democratic legitimation is parliamentary predetermination of the executive role. German law proves that the proper legislature under the Damocles sword of unconstitutionality is in many cases well able to prescribe for the executive a substantive programme of delegated legislation. A second technique of democratic legitimation is that parliament in some way participates in the rule-making procedure. German and British law show that by means of subsequent approval the proper legislature assumes political responsibility for subordinate legislation beyond the original empowerment. The US Supreme Court, however, considers the legislative veto to be unconstitutional. Therefore, American law developed a third approach to solve the problem of democratic legitimacy. American experience makes clear that the democratic legitimation of secondary legislation can also be secured by means of comprehensively involving the public in the delegated legislative process. The author assesses the different models for legitimation and explains that the different approaches suggest valuable solutions to each country's problems.
Kenya Colony: A Note on the 1958 Report of the Game Policy Committee
Authors: Darling F. Fraser 
Published: April 2009

The Game Policy Committee of Kenya was given the following terms of reference:—1. To consider and make recommendations as to the policy to be adopted for the long-term preservation of game, having regard to the interests of human population in game areas and to the economic development of the country;2. In view of the urgency of a solution of the conflict in the Amboseli National Reserve between game and human interests which is rapidly reducing the value of this area as a game reserve, to make interim recommendations for the preservation of the game interest, having due regard to the considerations in (1) above;
Endemic Birds of the Seychelles
Authors: Penny Malcom 
Published: April 2009

1. The populations of the endemic avifauna of Seychelles have declined in numbers, some very seriously, during the last hundred years. Only those in danger of extinction are discussed here.2. The magpie robin population is reduced to a score of birds; the population will soon be extinct unless drastic action is taken.3. The population of the paradise flycatcher is reduced to about 30 birds; conservation must take the form of propaganda, especially since the population is in danger of being reduced still further by the economic development of La Digue.
The Chinese View of Wildlife
Authors: Shen Susan , Ables Ernest D. , Qian–zhu Xiao 
Published: April 2009

The Chinese regard conservation as important, more for economic than for aesthetic or moral reasons. An economic rationale is a persuasive tool in a developing country such as China. The trade in wild-animal products plus the potential of rare and endemic wildlife species to attract much-needed foreign exchange are important factors. Rational use of wildlife through domestication and sustained-yield harvesting can alleviate pressures on wild populations and help to ensure genetic diversity for the future. Rare and endemic species such as the giant panda attract foreign exchange through tourism and research, and conservation measures preserve a cultural heritage, something of increasing importance to the Chinese.Several questions arise, however. How do economically unimportant species fit into this scheme? How can conflicts of interest created by economic incentives be resolved? Will the shortage of trained manpower undermine the conservation effort? Once these obstacles are resolved, China may become a leader i n wildlife conservation among the developing countries of the world, and show that conservation and development can co-exist.
Construction of a membrane-lytic immunotoxin using melittin and epidermal growth factor
Authors: Mei-Ling Chen , Dong Niu , Hui Ruan , Bing-Qing Pan , Jin-Ling Wang , De Wu , Jia-Jia Zhang , Qi-He Chen , Guo-Qing He 
Published: April 2009

AbstractEpidermal growth factor receptor (EGFR) is becoming a perfect target for killing carcinoma cells, especially because of its overexpression on the surface of these cells. Cationic antimicrobial peptides (CAP) have their own special mechanism of membrane-lytic cytotoxicity. In this study, a membrane-lytic immunotoxin (IT), chimeric protein MEGFMEL, was constructed to kill carcinoma cells with EGFR overexpression. This protein is composed of mouse (Mus musculus) epidermal growth factor (MEGF), as the target part, and melittin (MEL), as the cytotoxic part. Using Escherichia coli BL21 and pET30a as expression strain and vector, respectively, 63.45 μg/ml of MEGFMEL (68% purity) was obtained through low-temperature induction of expression and a thawing-freezing purification procedure (without cytolysis). In vitro activity measurement showed that this MEGFMEL significantly induced a lethal effect on A431 carcinoma cells overexpressing EGFR on the surface, with an LD50 value 52.6 μg/ml. The results suggest that the use of CAP as the toxin in the construction of unique membrane-lytic ITs aimed at EGFR is feasible.
Construction and utilization of plant expression vectors withPMIgene as selection marker to recover transgenic plants ofCitrus sinensisL. Osbeck
Authors: Li-Hui Zeng , Hai-Feng Xu , Hui-Quang Wang , Shao-Hua Wu , Yi-Xuan Zhu 
Published: April 2009

AbstractThe plant expression vectors pCAMBIA1301PMIand pBIPMIwere constructed by substituting theEscherichia coliphosphomannose-isomerase (PMI) gene for thehptgene of pCAMBIA1301 andgusgene of pBI121, respectively. Epicotyl explants of the Xuegan sweet orange (Citrus sinensisL. Osbeck) were inoculated withAgrobacterium tumefaciensEHA105- pCAMBIA1301PMIand EHA105-pBIPMIand subsequently selected in a medium supplemented with a combination of 25 g/l mannose and 5 g/l sucrose as the carbon source. The transformation efficiency rate was 27.7% when transformed by pCAMBIA1301PMIand 12.7% by pBIPMI. Genetic transformation was confirmed by chlorophenol red assay and polymerase chain reaction (PCR). A new method for obtaining transgenic Xuegan sweet orange plants was developed using thePMI/mannose selection system.
UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and computational linguists
Authors: Mellebeek Bart , Rodriguez-Penagos Carlos , Furlong Laura Ines 
Published: April 2009

AbstractAs collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths from Computational Linguistics and Biomedicine to produce a robust Text Mining system to generate data that will help biocurators in their daily work. The first version of this system will focus on the discovery of relationships between genes, SNPs (Single Nucleotide Polymorphisms) and diseases from the literature.A first challenge that we were faced with during the setup of this project is the fact that most current tools that support the curation workflow are complex, ad-hoc built applications which sometimes make difficult the interoperability and results sharing between research groups from different and unrelated expert fields. Often, biologists (even computer-savvy ones) are hard pressed to use and adapt sophisticated Natural Language Processing systems, and computational linguists are challenged by the intricacies of biology in applying their processing pipelines to elicit knowledge from texts. The flow of knowledge (needed to develop a usable, practical tool) to and from the parties involved in the development of such systems is not always easy or straightforward.The modular and versatile architecture of UIMA (Unstructed Information Management Architecture) provides a framework to address these challenges. UIMA is a component architecture and software framework implementation (including a UIMA SDK) to develop applications that analyse large volumes of unstructured information, and has been increasingly adopted by a significant part of the BioNLP community that needs industrial-grade and robust applications to exploit the whole bibliome. The use of UIMA to develop Text Mining applications useful for curation purposes allows the combination of diverse expertises which is beyond the individual know-how of biologists, computer scientists or linguists in isolation. A good synergy and circulation of knowledge between these experts is fundamental to the development of a successful curation tool.
Assistive Technology Toolkit to Increase Access to Early Learning Environments for Young Children With Disabilities
Authors: Sadao Kathleen C. , Brown Jennifer , Grant Debbie 
Published: April 2009

Abstract
The development of assistive technology (AT) and augmentative and alternative communication (AAC) interventions for young children with disabilities is rapidly expanding with a range of no-tech, low-tech, and high-tech approaches to provide access to adapted and augmented tools for participation in inclusive early childhood settings. Discrepancies exist in the legal requirements to consider AT and AAC for all children in the IFSP/IEP planning process. Researchers in the applications of AT and AAC with young children identify the importance of activity-based approaches that infuse AT methods and AAC systems within natural routines for young children. This article focuses on the development of an AT Toolkit Guide for early intervention and early childhood providers. The development of the AT Toolkit concept, content, and applications is based on research-based methods and tools with demonstrated effectiveness to promote language development, emergent literacy skills, play, mobility, and interaction with the environment for young children with disabilities. Suggested items, sources, applications and development guidelines for the SWEET AT Toolkit are provided.
Protein function annotation from sequence: prediction of residues interacting with RNA
Authors: Spriggs R. V. , Murakami Y. , Nakamura H. , Jones S. 
Published: April 2009

Abstract
Motivation: All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein sequence information. A series of sequence properties (position specific scoring matrices, interface propensities, predicted accessibility and hydrophobicity) are used to train a support vector machine. This method is then evaluated for its potential to be applied to RNA-binding function prediction at the level of the complete protein.
Results: The 5-fold cross-validation of PiRaNhA on a dataset of 81 RNA-binding proteins achieves a Matthews Correlation Coefficient (MCC) of 0.50 and accuracy of 87.2%. When used to predict RBRs in 42 proteins not used in training, PiRaNhA achieves an MCC of 0.41 and accuracy of 84.5%. Decision values from the PiRaNhA predictions were used in a second SVM to make predictions of RNA-binding function at the protein level, achieving an MCC of 0.53 and accuracy of 76.1%. The PiRaNhA RBR predictions allow experimentalists to perform more targeted experiments for function annotation; and the prediction of RNA-binding function at the protein level shows promise for proteome-wide annotations.
Availability and Implementation: Freely available on the web at www.bioinformatics.sussex.ac.uk/PIRANHA or http://piranha.protein.osaka-u.ac.jp.
Contact: s.jones@sussex.ac.uk.
Supplementary Information: Supplementary data are available at the Bioinformatics online.
A Bayesian segmentation approach to ascertain copy number variations at the population level
Authors: Wu Long Yang , Chipman Hugh A. , Bull Shelley B. , Briollais Laurent , Wang Kesheng 
Published: April 2009

Abstract
Motivation: Efficient and accurate ascertainment of copy number variations (CNVs) at the population level is essential to understand the evolutionary process and population genetics, and to apply CNVs in population-based genome-wide association studies for complex human diseases. We propose a novel Bayesian segmentation approach to identify CNVs in a defined population of any size. It is computationally efficient and provides statistical evidence for the detected CNVs through the Bayes factor. This approach has the unique feature of carrying out segmentation and assigning copy number status simultaneously—a desirable property that current segmentation methods do not share.
Results: In comparisons with popular two-step segmentation methods for a single individual using benchmark simulation studies, we find the new approach to perform competitively with respect to false discovery rate and sensitivity in breakpoint detection. In a simulation study of multiple samples with recurrent copy numbers, the new approach outperforms two leading single sample methods. We further demonstrate the effectiveness of our approach in population-level analysis of previously published HapMap data. We also apply our approach in studying population genetics of CNVs.
Availability: R programs are available at http://www.mshri.on.ca/mitacs/software/SOFTWARE.HTML
Contact: lwu@math.uwaterloo.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction
Authors: Hu Gang-Qing , Guo Jiang-Tao , Liu Yong-Chu , Zhu Huaiqiu 
Published: April 2009

Abstract
Summary: We proposed a tool named MetaTISA with an aim to improve TIS prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict translation initiation sites (TISs) by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.
Availability: The C++ source code is freely available under the GNU GPL license viahttp://mech.ctb.pku.edu.cn/MetaTISA/.
Contact: hqzhu@pku.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Literature-based priors for gene regulatory networks
Authors: Steele E. , Tucker A. , Hoen P.A.C. 't , Schuemie M.J. 
Published: April 2009

Abstract
Motivation: The use of prior knowledge to improve gene regulatory network modelling has often been proposed. In this article we present the first research on the massive incorporation of prior knowledge from literature for Bayesian network learning of gene networks. As the publication rate of scientific papers grows, updating online databases, which have been proposed as potential prior knowledge in past research, becomes increasingly challenging. The novelty of our approach lies in the use of gene-pair association scores that describe the overlap in the contexts in which the genes are mentioned, generated from a large database of scientific literature, harnessing the information contained in a huge number of documents into a simple, clear format.
Results: We present a method to transform such literature-based gene association scores to network prior probabilities, and apply it to learn gene sub-networks for yeast, Escherichia coli and Human organisms. We also investigate the effect of weighting the influence of the prior knowledge. Our findings show that literature-based priors can improve both the number of true regulatory interactions present in the network and the accuracy of expression value prediction on genes, in comparison to a network learnt solely from expression data. Networks learnt with priors also show an improved biological interpretation, with identified subnetworks that coincide with known biological pathways.
Contact: emma.steele@brunel.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences
Authors: Schultheiss Sebastian J. , Busch Wolfgang , Lohmann Jan U. , Kohlbacher Oliver , Rätsch Gunnar 
Published: April 2009

AbstractMotivation: Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor (TF) binding sites in promoter regions of potential TF target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cis-regulatory modules.Results: We propose a new algorithm that combines the benefits of existing motif finding with the ones of support vector machines (SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules. In experiments on microarray data from Arabidopsis thaliana, we were able to show that the newly developed strategy significantly improves the recognition of TF targets.Availability: The python source code (open source-licensed under GPL), the data for the experiments and a Galaxy-based web service are available at http://www.fml.mpg.de/raetsch/suppl/kirmes/Contact: sebi@tuebingen.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online.
HAb18G (CD147), a cancer‐associated biomarker and its role in cancer detection
Authors: Li Yu , Xu Jing , Chen Li , Zhong Wei‐De , Zhang Zheng , Mi Li , Zhang Yang , Liao Cheng‐Gong , Bian Hui‐Jie , Jiang Jian‐Li , Yang Xiang‐Min , Li Xiao‐Yan , Fan Chun‐Mei , Zhu Ping , Fu Li , Chen Zhi‐Nan 
Published: April 2009

Aims:  To evaluate HAb18G/CD147 as a cancer‐associated biomarker using its monoclonal antibody HAb18.Methods and results:  On immunohistochemical analysis of 28 tissue microarrays and pathological sections of 1117 breast tissue samples, HAb18G/CD147 was expressed in carcinoma with an overall positivity rate of 67.76%, which was significantly higher than that in sarcomas (27.34%, P < 0.0001) and normal epithelial (5.18%, P < 0.0001) and fetal (2.67%, P < 0.0001) tissues. In epithelial tissues from 14 organs, the difference in HAb18G/CD147 expression between normal epithelium and the corresponding carcinoma was also significant (P < 0.05 for each pair). This expression in carcinoma was also found at the mRNA level, suggesting transcriptional level regulation of HAb18G/CD147 expression. In a retrospective study of 106 patients with infiltrating ductal carcinoma of the breast, the level of HAb18G/CD147 expression was positively correlated with tumour recurrence/metastasis (P = 0.0003) and negatively correlated with survival of breast cancer patients (P = 0.002). Multivariable Cox regression analysis showed that HAb18G/CD147 was an independent prognostic factor.Conclusions:  HAb18G/CD147 is significantly expressed in various cancers and appears to have prognostic significance, rendering it a possible cancer‐associated biomarker for pathological diagnosis, prognostic evaluation, targeted therapy and radioimmunoimaging of a broad range of cancer types.
Barrett’s dysplasia and the Vienna classification: reproducibility, prediction of progression and impact of consensus reporting and p53 immunohistochemistry
Authors: Kaye Philip V , Haider Syeda A , Ilyas Mohammed , James Peter D , Soomro Irshad , Faisal Wasek , Catton James , Parsons Simon L , Ragunath Krish 
Published: April 2009

Aims:  The Vienna classification is used to classify dysplasia in Barrett’s oesophagus (BO), but reproducibility and value of diagnosis of lower grades in particular are often questioned. The aim was to test the diagnostic variability and correlation with patient outcome and to attempt to define histological features causing discrepant diagnoses, as well as to test the impact of adding p53 immunohistochemistry on reproducibility and prediction of outcome.Methods and results:  One hundred and forty‐three patients with 154 sets of biopsy specimens originally diagnosed with Barrett’s dysplasia were retrieved from the pathology records of Nottingham University Hospital. Thirty‐two Barrett’s patients without dysplasia were added. Anonymized slides were graded independently by five pathologists without and with p53‐stained slides. Interobserver variation, correlation with outcome and diagnostic accuracy were determined. Weighted κ scores between pairs of pathologists showed substantial agreement and improved after p53 immunohistochemistry. Agreement with the original diagnosis was substantially lower. Fourteen of 34 low‐grade dysplasias (LGD) and 27 of 30 high‐grade dysplasias on consensus progressed within 10 years compared with 18/94 and 28/39 of original diagnoses. Progression correlated with p53 positivity.Conclusion:  The Vienna classification is useful and reproducible in BO. Consensus diagnosis by gastrointestinal pathologists produces high specificity and predictive value, even for LGD. p53 immunohistochemistry assists in diagnosis in difficult cases and predicts progression.
Increased expression of SDF‐1/CXCR4 is associated with lymph node metastasis of invasive micropapillary carcinoma of the breast
Authors: Liu Fangfang , Lang Ronggang , Wei Jia , Fan Yu , Cui Lifang , Gu Feng , Guo Xiaojing , Pringle Gordon A , Zhang Xinmin , Fu Li 
Published: April 2009

Aims:  Stromal cell‐derived factor‐1 (SDF‐1) and its receptor CXCR4 are implicated in tumour chemotaxis and metastasis. The aim was to examine their roles in the metastasis of invasive micropapillary carcinoma (IMPC) of the breast, a tumour with a high propensity for nodal spread.Methods and results:  We compared the expression of SDF‐1 and CXCR4 in 103 cases of breast cancer containing IMPC components with a control group of 96 cases of invasive ductal carcinoma (IDC), not otherwise specified type by immunohistochemistry and chemical in situ hybridization (CISH). The results showed that the predominant cytoplasmic expression of both SDF‐1 and CXCR4 was greater in tumour cells of the IMPC components than in those of the non‐IMPC components and the control IDC cases, and was correlated significantly with the number of positive lymph nodes (P < 0.05). SDF‐1 expression on cell membranes was less frequently identified in IMPC than IDC (P = 0.021). Immunohistochemical detection of SDF‐1 in endothelial cells of lymphatic vessels was more common in IMPC (P = 0.007) and correlated significantly with lymph node status (P = 0.002), although SDF‐1 mRNA was rarely detected by CISH.Conclusions:  This study suggests that up‐regulation of cytoplasmic expression of SDF‐1/CXCR4 might be one of the molecular mechanisms facilitating lymph node metastasis of IMPC.