bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tolerance of Civil Liberties in a New Democracy
Authors: Marsh Robert 
Published: December 2005

AbstractHow tolerant of the civil liberties of people who advocated various unpopular political stances were the citizens of Taiwan, a new democracy in the late 1980s? Are the reasons some Taiwanese were more tolerant than others the same as in other societies? A 1992 survey of a representative sample of the population of Taiwan (N = 1,408) is used to answer these questions. Of the four political stances studied, communism and Taiwan's independence from China were perceived as "more harmful to Taiwan" than the immediate unification of Taiwan with China and the restoration of martial law.Of the hypotheses tested in multivariate analysis, two were largely confirmed: (1) the more one subscribes to the value of democracy as the correct political system for Taiwan, the more tolerant one is of the civil liberties of the "harmful" target groups, but (2) the greater the perceived threat of the harmful political stance, the more intolerant one is of the civil liberties of those advocating the stance. The remaining hypotheses concern the effects of sex, age, ethnicity, education, occupation and income on tolerance.I contextualize the theoretical causal model by reviewing the political history of Taiwan as it changed from an authoritarian one-party state into a democracy. In conclusion, I suggest that the reason the level of intolerance in Taiwan in 1992 has not lead to a diminution of democracy and civil rights between 1992 and the present may be due to "pluralistic intolerance," i.e., the public does not agree on which group to target for intolerance.
Parish Priest and Community in 18th-century Malta: Patterns of Conflict
Authors: Ciappara Frans 
Published: December 2005

AbstractThis essay explores the relations between parish priests and their parishioners in eighteenth-century Malta. It argues that pastors did not succeed in governing the community and controlling local religious life. Generally, they were outsiders. This was a great liability since rivalry between villages was intense and the inhabitants were reluctant to admit new people, to whom they were often hostile. But the main reason for the rivalry between the faithful and the pastor was that the people themselves took an active role in the parish. They regarded the office of parish priest as a subservient one for which service they paid the priest handsomely, and provided him with a livelihood. Pastors were to concern themselves only with vital religious services and leave the administration of the parish to the parishioners. The essay also emphasizes that in the struggle with their parish priest the people found the support from the assistant clergy.
Biominerals
Authors: Skinner H. C. W. 
Published: December 2005

AbstractBiominerals are a subset of the mineral kingdom, those created by living creatures. In spite of usually fine grain size and intimate association with organic materials, biominerals are readily identified as common mineral species. Iron hydroxides and oxyhydroxides, calcium carbonates and calcium phosphates from uni- and multi-cellular species are presented as examples of biominerals, and biomineralization processes. Their special morphological, and crystal chemical, characteristics provide unique structural contributions to the life forms that create them. Investigations of novel habitats should present opportunities to expand the number of biominerals and their potential for industrial applications.
Simultaneous high throughput and quantitative analysis of MTBE and BTEX by P&T-GCMS using a Precept® autosampler
Authors: Houghton S. L. , Hall S. 
Published: December 2005

AbstractFuel-oil contamination of groundwater and waterways is common throughout the world. The fuel components methyl-tert-butyl ether (MTBE) and benzene, toluene, ethylbenzene and o-, p- and m-xylenes (BTEX) compounds are most likely to reach a borehole after a contamination event, and also those that pose the greatest risk.Various gas chromatography-mass spectrometry (GCMS) methods are available for the analysis of volatile organic compounds (VOCs) but many of these are not suitable for rapid and combined analysis of MTBE and BTEX. Here we describe and validate a simple and reliable method that fulfils these requirements. The method is quick: 48 samples can be analysed in a 24 hour period using the Precept II® autosampler and therefore is suitable for high throughput work. Validation of our experiments is presented in the form of linearity, precision and intra-day repeatability of standards as well as limits of detection and limits of quantification for the range 1—20 μg/l.This MTBE/BTEX analytical method developed was used to study the optimization of a modular post-abstraction remediation system incorporating air-stripping and granular activated carbon (GAC) technologies (Hall, 2004), from which a selection of sample data is presented.
Preliminary observations on the release of arsenic to groundwater in the presence of hydrocarbon contaminants in UK aquifers
Authors: Burgess W. G. , Pinto L. 
Published: December 2005

AbstractDegradation of contaminant hydrocarbons in groundwater by microbially mediated oxidation, linked to the reduction of electron acceptors, is fundamental to the strategy of ‘monitored natural attenuation’ (MNA) for oxidizable hydrocarbons, which is increasingly being adopted at polluted aquifer sites throughout Europe and North America. Commonly, oxygen is depleted and following the reduction of nitrate, solid-phase Fe oxides become the dominant electron acceptors. Arsenic, associated with Fe and Mn oxides in soils and sediments, may therefore be mobilized to groundwater and pose an additional threat to environmental receptors. In a pilot study of three aquifers in England, we have examined the extent to which arsenic is released to groundwater under Fe(III)-reducing conditions imposed by contaminant hydrocarbons. Results show that arsenic is locally mobilized in the Chalk to <10 μg/1, in Quaternary gravels to 70 μg/1 and in the Triassic sandstones to 160 μg/1. At the Chalk and Quaternary gravels sites arsenic mobilization is demonstrably linked to reduction of Fe- and Mn-oxides. This is not so at the Triassic sandstone site, where release of arsenic is related to elevated bicarbonate alkalinity. Redox-driven arsenic mobilization at other Triassic sandstone locations is possible. Further work is required on the solid-phase sources of arsenic in the aquifers, and to relate the hydrochemical observations to groundwater hydraulic conditions.
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society
Authors: Helmer-Citterich Manuela , Casadio Rita , Guffanti Alessandro , Mauri Giancarlo , Milanesi Luciano , Pesole Graziano , Valle Giorgio , Saccone Cecilia 
Published: December 2005

Abstract
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan. This Editorial provides a brief overview of the Conference topics and introduces the peer-reviewed manuscripts accepted for publication in this Supplement.
Modelling the interaction of steroid receptors with endocrine disrupting chemicals
Authors: D'Ursi Pasqualina , Salvi Erika , Fossa Paola , Milanesi Luciano , Rovida Ermanna 
Published: December 2005

Abstract

Background
The organic polychlorinated compounds like dichlorodiphenyltrichloroethane with its metabolites and polychlorinated biphenyls are a class of highly persistent environmental contaminants. They have been recognized to have detrimental health effects both on wildlife and humans acting as endocrine disrupters due to their ability of mimicking the action of the steroid hormones, and thus interfering with hormone response. There are several experimental evidences that they bind and activate human steroid receptors. However, despite the growing concern about the toxicological activity of endocrine disrupters, molecular data of the interaction of these compounds with biological targets are still lacking.

Results
We have used a flexible docking approach to characterize the molecular interaction of seven endocrine disrupting chemicals with estrogen, progesterone and androgen receptors in the ligand-binding domain. All ligands docked in the buried hydrophobic cavity corresponding to the hormone steroid pocket. The interaction was characterized by multiple hydrophobic contacts involving a different number of residues facing the binding pocket, depending on ligands orientation. The EDC ligands did not display a unique binding mode, probably due to their lipophilicity and flexibility, which conferred them a great adaptability into the hydrophobic and large binding pocket of steroid receptors.

Conclusion
Our results are in agreement with toxicological data on binding and allow to describe a pattern of interactions for a group of ECD to steroid receptors suggesting the requirement of a hydrophobic cavity to accommodate these chlorine carrying compounds. Although the affinity is lower than for hormones, their action can be brought about by a possible synergistic effect.
A quantization method based on threshold optimization for microarray short time series
Authors: Di Camillo Barbara , Sanchez-Cabo Fatima , Toffolo Gianna , Nair Sreekumaran K , Trajanoski Zlatko , Cobelli Claudio 
Published: December 2005

Abstract

Background
Reconstructing regulatory networks from gene expression profiles is a challenging problem of functional genomics. In microarray studies the number of samples is often very limited compared to the number of genes, thus the use of discrete data may help reducing the probability of finding random associations between genes.

Results
A quantization method, based on a model of the experimental error and on a significance level able to compromise between false positive and false negative classifications, is presented, which can be used as a preliminary step in discrete reverse engineering methods. The method is tested on continuous synthetic data with two discrete reverse engineering methods: Reveal and Dynamic Bayesian Networks.

Conclusion
The quantization method, evaluated in comparison with two standard methods, 5% threshold based on experimental error and rank sorting, improves the ability of Reveal and Dynamic Bayesian Networks to identify relations among genes.
A neural strategy for the inference of SH3 domain-peptide interaction specificity
Authors: Ferraro Enrico , Via Allegra , Ausiello Gabriele , Helmer-Citterich Manuela 
Published: December 2005

Abstract

Background
The SH3 domain family is one of the most representative and widely studied cases of so-called Peptide Recognition Modules (PRM). The polyproline II motif PxxP that generally characterizes its ligands does not reflect the complex interaction spectrum of the over 1500 different SH3 domains, and the requirement of a more refined knowledge of their specificity implies the setting up of appropriate experimental and theoretical strategies. Due to the limitations of the current technology for peptide synthesis, several experimental high-throughput approaches have been devised to elucidate protein-protein interaction mechanisms. Such approaches can rely on and take advantage of computational techniques, such as regular expressions or position specific scoring matrices (PSSMs) to pre-process entire proteomes in the search for putative SH3 targets.
In this regard, a reliable inference methodology to be used for reducing the sequence space of putative binding peptides represents a valuable support for molecular and cellular biologists.

Results
Using as benchmark the peptide sequences obtained from in vitro binding experiments, we set up a neural network model that performs better than PSSM in the detection of SH3 domain interactors. In particular our model is more precise in its predictions, even if its performance can vary among different SH3 domains and is strongly dependent on the number of binding peptides in the benchmark.

Conclusion
We show that a neural network can be more effective than standard methods in SH3 domain specificity detection. Neural classifiers identify general SH3 domain binders and domain-specific interactors from a PxxP peptide population, provided that there are a sufficient proportion of true positives in the training sets. This capability can also improve peptide selection for library definition in array experiments. Further advances can be achieved, including properly encoded domain sequences and structural information as input for a global neural network.
Browsing Isolated Population Data
Authors: Mancosu Gianmaria , Cosso Massimiliano , Marras Francesca , Borlino Cesare Cappio , Ledda Giuseppe , Manias Teresa , Adamo Mauro , Serra Donatella , Melis Paola , Pirastu Mario 
Published: December 2005

Abstract

Background
In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80–85% of the inhabitants of each village belong to a single huge pedigree with families strictly connected to each other through hundreds of loops. Moreover, intermarriages between villages join pedigrees of different villages through links that make family trees even more complicated. Unfortunately, none of the commonly used pedigree drawing tools are able to draw the complete pedigree, whereas it is commonly accepted that the visual representation of families is very important as it helps researchers in identifying clusters of inherited traits and genotypes. We had a representation issue that compels researchers to work with subsets extracted from the overall genealogy, causing a serious loss of information on familiar relationships.
To visually explore such complex pedigrees, we developed PedNavigator, a browser for genealogical databases properly suited for genetic studies.

Results
The PedNavigator is useful for genealogical research due to its capacity to represent family relations between persons and to make a visual verification of the links during family history reconstruction. As for genetic studies, it is helpful to follow propagation of a specific set of genetic markers (haplotype), or to select people for linkage analysis, showing relations between various branch of a family tree of affected subjects.

Availability
PedNavigator is an application integrated into a Framework designed to handle data for human genetic studies based on the Oracle platform. To allow the use of PedNavigator also to people not owning the same required informatics infrastructure or systems, we developed PedNavigator Lite with mainly the same features of the integrated one, based on MySQL database server. This version is free for academic users, and it is available for download from our site http://www.shardna.com.
Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists
Authors: Masseroli Marco , Galati Osvaldo , Manzotti Mauro , Gibert Karina , Pinciroli Francesco 
Published: December 2005

AbstractBackgroundAnalysis of inherited diseases and their associated phenotypes is of great importance to gain knowledge of underlying genetic interactions and could ultimately give clinically useful insights into disease processes, including complex diseases influenced by multiple genetic loci. Nevertheless, to date few computational contributions have been proposed for this purpose, mainly due to lack of controlled clinical information easily accessible and structured for computational genome-wise analyses. To allow performing phenotype analyses of inherited disorder related genes we implemented new original modules withinGFINDerhttp://www.bioinformatics.polimi.it/GFINDer/, a Web system we previously developed that dynamically aggregates functional annotations of user uploaded gene lists and allows performing their statistical analysis and mining.ResultsNewGFINDermodules allow annotating large numbers of user classified biomolecular sequence identifiers with morbidity and clinical information, classifying them according to genetic disease phenotypes and their locations of occurrence, and statistically analyzing the obtained classifications. To achieve this we exploited, normalized and structured the information present in textual form in the Clinical Synopsis sections of the Online Mendelian Inheritance in Man (OMIM) databank. Such valuable information delineates numerous signs and symptoms accompanying many genetic diseases and it is divided into phenotype location categories, either by organ system or type of finding.ConclusionSupporting phenotype analyses of inherited diseases and biomolecular functional evaluations,GFINDerfacilitates a genomic approach to the understanding of fundamental biological processes and complex cellular mechanisms underlying patho-physiological phenotypes.
Regularized Least Squares Cancer Classifiers from DNA microarray data
Authors: Ancona Nicola , Maglietta Rosalia , D'Addabbo Annarita , Liuni Sabino , Pesole Graziano 
Published: December 2005

Abstract

Background
The advent of the technology of DNA microarrays constitutes an epochal change in the classification and discovery of different types of cancer because the information provided by DNA microarrays allows an approach to the problem of cancer analysis from a quantitative rather than qualitative point of view. Cancer classification requires well founded mathematical methods which are able to predict the status of new specimens with high significance levels starting from a limited number of data. In this paper we assess the performances of Regularized Least Squares (RLS) classifiers, originally proposed in regularization theory, by comparing them with Support Vector Machines (SVM), the state-of-the-art supervised learning technique for cancer classification by DNA microarray data. The performances of both approaches have been also investigated with respect to the number of selected genes and different gene selection strategies.

Results
We show that RLS classifiers have performances comparable to those of SVM classifiers as the Leave-One-Out (LOO) error evaluated on three different data sets shows. The main advantage of RLS machines is that for solving a classification problem they use a linear system of order equal to either the number of features or the number of training examples. Moreover, RLS machines allow to get an exact measure of the LOO error with just one training.

Conclusion
RLS classifiers are a valuable alternative to SVM classifiers for the problem of cancer classification by gene expression data, due to their simplicity and low computational complexity. Moreover, RLS classifiers show generalization ability comparable to the ones of SVM classifiers also in the case the classification of new specimens involves very few gene expression levels.
NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae
Authors: Rambaldi Davide , Guffanti Alessandro , Morandi Paolo , Cassata Giuseppe 
Published: December 2005

Abstract

Background
NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications:
a) Automated identification of orthologous gene pairs.
b) Interactive selection of the boundaries of the genes to be compared.
c) Pairwise sequence comparison with a range of different methods.
d) Identification of putative transcription factor binding sites on conserved, non-exonic DNA segments.

Results
Starting from a C. elegans or C. briggsae gene name or identifier, the software identifies the putative ortholog (if any), based on information derived from public nematode genome annotation databases. The investigator can then retrieve the genome DNA sequences of the two orthologous genes; visualize graphically the genes' intron/exon structure and the surrounding DNA regions; select, through an interactive graphical user interface, subsequences of the two gene regions. Using a bioinformatics toolbox (Blast2seq, Dotmatcher, Ssearch and connection to the rVista database) the investigator is able at the end of the procedure to identify and analyze significant sequences similarities, detecting the presence of transcription factor binding sites corresponding to the conserved segments. The software automatically masks exons.

Discussion
This software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae. These sequences may contain regulatory transcriptional elements since they are conserved between two related, but rapidly evolving genomes. This software also highlights the power of genome annotation databases when they are conceived as an open resource and the possibilities offered by seamless integration of different web services via the http protocol.

Availability: the program is freely available at http://bio.ifom-firc.it/NTFootPrinter
Web services and workflow management for biological resources
Authors: Romano Paolo , Marra Domenico , Milanesi Luciano 
Published: December 2005

Abstract

Backgorund
The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for a system that is able to automate accesses to remote sites and to "understand" the information that it is managing in order to link data properly. Workflow management systems combined with Web Services are promising Information and Communication Technologies (ICT) tools. Some have already been proposed and are being increasingly applied to the biomedical domain, especially as many biology-related Web Services are now becoming available. Information on biological resources and on genomic sequences mutations are two examples of very specialized datasets that are useful for specific research domains.

Results
The architecture of a system that is able to access and execute predefined workflows is presented in this paper. Web Services allowing access to the IARC TP53 Mutation Database and CABRI catalogues of biological resources have been implemented and are available on-line. Example workflows which retrieve data from these Web Services have also been created and are available on-line.

Conclusion
We present a general architecture and some building blocks for the implementation of a system that is able to remotely execute workflows of biomedical interest and show how this approach can effectively produce useful outputs. The further development and implementation of Web Services allowing access to an exhaustive set of biomedical databases and the creation of effective and useful workflows will improve the automation of in-silico analysis.